GENERAL INFO
| Title: | /AB-DB Lipo-glyco-peptides - Ramoplanin A3 +2 Lipo-glyco-peptides - Ramoplanin A3 +2 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/499987 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C120H158ClN21O40 |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| Cl1 | C171 | 1.763590 |
| O2 | C67 | 1.398236 |
| O2 | C65 | 1.426836 |
| O3 | C74 | 1.430704 |
| O3 | C67 | 1.404085 |
| O4 | C71 | 1.387527 |
| O4 | C72 | 1.431656 |
| O5 | H199 | 0.971580 |
| O5 | C66 | 1.401460 |
| O6 | C77 | 1.392859 |
| O6 | C71 | 1.412558 |
| O7 | H200 | 0.969095 |
| O7 | C68 | 1.407598 |
| O8 | H201 | 0.965487 |
| O8 | C69 | 1.406442 |
| O9 | C70 | 1.401788 |
| O9 | H202 | 0.970552 |
| O10 | C73 | 1.411318 |
| O10 | H203 | 0.968303 |
| O11 | C75 | 1.405632 |
| O11 | H204 | 0.968458 |
| O12 | C76 | 1.406830 |
| O12 | H205 | 0.968249 |
| O13 | C84 | 1.218676 |
| O14 | C85 | 1.224377 |
| O15 | C89 | 1.402588 |
| O15 | H228 | 0.974030 |
| O16 | C91 | 1.232646 |
| O17 | C93 | 1.226999 |
| O18 | C99 | 1.229750 |
| O19 | C101 | 1.224743 |
| O20 | H254 | 0.965786 |
| O20 | C105 | 1.415837 |
| O21 | C113 | 1.355010 |
| O21 | H260 | 0.968827 |
| O22 | C116 | 1.229246 |
| O23 | C117 | 1.220950 |
| O24 | C123 | 1.228261 |
| O25 | C124 | 1.223445 |
| O26 | C136 | 1.422199 |
| O26 | H302 | 0.963047 |
| O27 | C155 | 1.331065 |
| O27 | C150 | 1.419399 |
| O28 | C135 | 1.228901 |
| O29 | C139 | 1.227313 |
| O30 | C141 | 1.357143 |
| O30 | H307 | 0.969507 |
| O31 | C143 | 1.228241 |
| O32 | C145 | 1.225875 |
| O33 | C153 | 1.222937 |
| O34 | C155 | 1.206785 |
| O35 | C159 | 1.355803 |
| O35 | H321 | 0.967194 |
| O36 | C160 | 1.229525 |
| O37 | C163 | 1.224035 |
| O38 | C170 | 1.358761 |
| O38 | H322 | 0.969471 |
| O39 | C173 | 1.339410 |
| O39 | H326 | 0.970068 |
| O40 | C174 | 1.228000 |
| O41 | C175 | 1.234248 |
| N42 | C83 | 1.447049 |
| N42 | C85 | 1.339547 |
| N42 | H211 | 1.009816 |
| N43 | H212 | 1.012527 |
| N43 | C84 | 1.340152 |
| N43 | C87 | 1.448099 |
| N44 | H218 | 1.009441 |
| N44 | C93 | 1.335733 |
| N44 | C86 | 1.451855 |
| N45 | H226 | 1.008445 |
| N45 | C96 | 1.461363 |
| N45 | C91 | 1.330818 |
| N46 | C95 | 1.445346 |
| N46 | H232 | 1.015757 |
| N46 | C101 | 1.333262 |
| N47 | H234 | 1.035442 |
| N47 | H48 | 1.036216 |
| N47 | H233 | 1.022194 |
| N47 | C94 | 1.480332 |
| N49 | H238 | 1.021663 |
| N49 | C108 | 1.448346 |
| N49 | C99 | 1.333401 |
| N50 | H242 | 1.010524 |
| N50 | C116 | 1.333071 |
| N50 | C102 | 1.456835 |
| N51 | C117 | 1.341719 |
| N51 | H256 | 1.016163 |
| N51 | C119 | 1.450364 |
| N52 | C118 | 1.450653 |
| N52 | H261 | 1.015947 |
| N52 | C124 | 1.337428 |
| N53 | C123 | 1.337006 |
| N53 | H271 | 1.009211 |
| N53 | C131 | 1.453566 |
| N54 | H275 | 1.014033 |
| N54 | C125 | 1.443067 |
| N54 | C135 | 1.322775 |
| N55 | H279 | 1.013712 |
| N55 | C139 | 1.332946 |
| N55 | C130 | 1.446827 |
| N56 | C132 | 1.458644 |
| N56 | H284 | 1.007514 |
| N56 | C145 | 1.332673 |
| N57 | C151 | 1.449454 |
| N57 | H300 | 1.011641 |
| N57 | C143 | 1.332609 |
| N58 | H299 | 1.010529 |
| N58 | C153 | 1.337486 |
| N58 | C142 | 1.452820 |
| N59 | H301 | 1.023265 |
| N59 | C163 | 1.343666 |
| N59 | C146 | 1.450061 |
| N60 | C152 | 1.487609 |
| N60 | H310 | 1.034726 |
| N60 | H309 | 1.019703 |
| N60 | H61 | 1.038584 |
| N62 | C175 | 1.350311 |
| N62 | H317 | 1.010343 |
| N62 | C164 | 1.441008 |
| N63 | C160 | 1.324868 |
| N63 | H319 | 1.013869 |
| N63 | H318 | 1.010070 |
| N64 | H323 | 1.007576 |
| N64 | H324 | 1.005281 |
| N64 | C174 | 1.335342 |
| C65 | C71 | 1.543159 |
| C65 | H185 | 1.095670 |
| C65 | C66 | 1.540366 |
| C66 | H186 | 1.094708 |
| C66 | C68 | 1.536903 |
| C67 | C69 | 1.534256 |
| C67 | H187 | 1.107016 |
| C68 | H188 | 1.094407 |
| C68 | C72 | 1.535688 |
| C69 | H189 | 1.097697 |
| C69 | C70 | 1.543203 |
| C70 | C73 | 1.555280 |
| C70 | H190 | 1.097755 |
| C71 | H191 | 1.098773 |
| C72 | C75 | 1.537587 |
| C72 | H192 | 1.096304 |
| C73 | H193 | 1.096966 |
| C73 | C74 | 1.533958 |
| C74 | C76 | 1.533598 |
| C74 | H194 | 1.098781 |
| C75 | H196 | 1.095758 |
| C75 | H195 | 1.091034 |
| C76 | H197 | 1.097416 |
| C76 | H198 | 1.094906 |
| C77 | C78 | 1.389793 |
| C77 | C79 | 1.386919 |
| C78 | C81 | 1.379434 |
| C78 | H206 | 1.079018 |
| C79 | C82 | 1.383002 |
| C79 | H207 | 1.078395 |
| C80 | C81 | 1.389750 |
| C80 | C83 | 1.511992 |
| C80 | C82 | 1.385664 |
| C81 | H208 | 1.079218 |
| C82 | H209 | 1.079022 |
| C83 | H210 | 1.096505 |
| C83 | C84 | 1.549170 |
| C85 | C86 | 1.536233 |
| C86 | H213 | 1.093879 |
| C86 | C88 | 1.533792 |
| C87 | H214 | 1.092411 |
| C87 | C89 | 1.558941 |
| C87 | C91 | 1.519146 |
| C88 | H216 | 1.088799 |
| C88 | H215 | 1.089498 |
| C88 | C90 | 1.531530 |
| C89 | C92 | 1.528273 |
| C89 | H217 | 1.095686 |
| C90 | H220 | 1.088336 |
| C90 | C94 | 1.530206 |
| C90 | H219 | 1.084995 |
| C92 | H223 | 1.085496 |
| C92 | H221 | 1.086190 |
| C92 | H222 | 1.087774 |
| C93 | C95 | 1.536120 |
| C94 | H224 | 1.090186 |
| C94 | H225 | 1.087573 |
| C95 | C97 | 1.537077 |
| C95 | H227 | 1.096416 |
| C96 | H229 | 1.095007 |
| C96 | C98 | 1.519775 |
| C96 | C99 | 1.537584 |
| C97 | H231 | 1.091138 |
| C97 | H230 | 1.088701 |
| C97 | C100 | 1.504714 |
| C98 | C104 | 1.389596 |
| C98 | C103 | 1.389210 |
| C100 | C106 | 1.389531 |
| C100 | C107 | 1.389256 |
| C101 | C102 | 1.537580 |
| C102 | H235 | 1.093100 |
| C102 | C105 | 1.539751 |
| C103 | C109 | 1.380224 |
| C103 | H236 | 1.078543 |
| C104 | H237 | 1.079410 |
| C104 | C110 | 1.381500 |
| C105 | H239 | 1.099095 |
| C105 | C114 | 1.526317 |
| C106 | H240 | 1.079317 |
| C106 | C111 | 1.383150 |
| C107 | C112 | 1.384289 |
| C107 | H241 | 1.081194 |
| C108 | H243 | 1.092782 |
| C108 | C117 | 1.530612 |
| C108 | H244 | 1.088522 |
| C109 | C113 | 1.392510 |
| C109 | H245 | 1.078052 |
| C110 | H246 | 1.079889 |
| C110 | C113 | 1.391279 |
| C111 | C115 | 1.384940 |
| C111 | H247 | 1.079857 |
| C112 | C115 | 1.384671 |
| C112 | H248 | 1.080431 |
| C114 | H249 | 1.086740 |
| C114 | H251 | 1.087493 |
| C114 | H250 | 1.086230 |
| C115 | H252 | 1.080128 |
| C116 | C118 | 1.535335 |
| C118 | H253 | 1.098259 |
| C118 | C122 | 1.509919 |
| C119 | C123 | 1.527472 |
| C119 | H255 | 1.100553 |
| C119 | C120 | 1.532419 |
| C120 | H258 | 1.090518 |
| C120 | C121 | 1.537128 |
| C120 | H257 | 1.092246 |
| C121 | C126 | 1.527777 |
| C121 | H259 | 1.093806 |
| C121 | C127 | 1.528875 |
| C122 | C129 | 1.392808 |
| C122 | C128 | 1.387476 |
| C124 | C125 | 1.533789 |
| C125 | H262 | 1.094196 |
| C125 | C134 | 1.517663 |
| C126 | H265 | 1.088275 |
| C126 | H263 | 1.086966 |
| C126 | H264 | 1.087451 |
| C127 | H267 | 1.087215 |
| C127 | H266 | 1.087757 |
| C127 | H268 | 1.087756 |
| C128 | H269 | 1.078352 |
| C128 | C137 | 1.383365 |
| C129 | H270 | 1.080150 |
| C129 | C138 | 1.378750 |
| C130 | C135 | 1.526479 |
| C130 | H272 | 1.097593 |
| C130 | C136 | 1.554168 |
| C131 | H274 | 1.095623 |
| C131 | C144 | 1.519013 |
| C131 | C143 | 1.534283 |
| C132 | C139 | 1.544356 |
| C132 | C133 | 1.543727 |
| C132 | H273 | 1.096548 |
| C133 | C140 | 1.537772 |
| C133 | H277 | 1.088915 |
| C133 | H276 | 1.090221 |
| C134 | C148 | 1.390310 |
| C134 | C147 | 1.388958 |
| C136 | H278 | 1.096318 |
| C136 | C149 | 1.527434 |
| C137 | C141 | 1.389790 |
| C137 | H280 | 1.079427 |
| C138 | C141 | 1.394445 |
| C138 | H281 | 1.078296 |
| C140 | C152 | 1.525127 |
| C140 | H283 | 1.088766 |
| C140 | H282 | 1.088334 |
| C142 | H285 | 1.096708 |
| C142 | C154 | 1.514718 |
| C142 | C145 | 1.522500 |
| C144 | H288 | 1.086750 |
| C144 | H287 | 1.085976 |
| C144 | H286 | 1.086010 |
| C146 | C150 | 1.544416 |
| C146 | H289 | 1.099335 |
| C146 | C153 | 1.534344 |
| C147 | C156 | 1.383009 |
| C147 | H293 | 1.078433 |
| C148 | C157 | 1.382661 |
| C148 | H294 | 1.079037 |
| C149 | H291 | 1.087374 |
| C149 | H290 | 1.085291 |
| C149 | H292 | 1.083952 |
| C150 | C160 | 1.544665 |
| C150 | H295 | 1.096468 |
| C151 | H298 | 1.097841 |
| C151 | C158 | 1.504489 |
| C151 | C155 | 1.526356 |
| C152 | H297 | 1.087955 |
| C152 | H296 | 1.088616 |
| C154 | C161 | 1.390079 |
| C154 | C162 | 1.388759 |
| C156 | H303 | 1.079779 |
| C156 | C159 | 1.391509 |
| C157 | H304 | 1.078380 |
| C157 | C159 | 1.394893 |
| C158 | C166 | 1.390387 |
| C158 | C165 | 1.387848 |
| C161 | H305 | 1.079870 |
| C161 | C168 | 1.378149 |
| C162 | H306 | 1.080341 |
| C162 | C169 | 1.382484 |
| C163 | C164 | 1.532672 |
| C164 | H308 | 1.097168 |
| C164 | C167 | 1.535980 |
| C165 | C171 | 1.381257 |
| C165 | H311 | 1.079952 |
| C166 | C172 | 1.379193 |
| C166 | H312 | 1.077695 |
| C167 | H313 | 1.091076 |
| C167 | C174 | 1.519908 |
| C167 | H314 | 1.089874 |
| C168 | C170 | 1.393064 |
| C168 | H315 | 1.078690 |
| C169 | C170 | 1.389745 |
| C169 | H316 | 1.080003 |
| C171 | C173 | 1.396426 |
| C172 | C173 | 1.396056 |
| C172 | H320 | 1.076884 |
| C175 | C176 | 1.470002 |
| C176 | H325 | 1.081406 |
| C176 | C177 | 1.342948 |
| C177 | C181 | 1.441179 |
| C177 | H327 | 1.083406 |
| C178 | H328 | 1.095416 |
| C178 | C183 | 1.528784 |
| C178 | C184 | 1.528001 |
| C178 | C179 | 1.533249 |
| C179 | H330 | 1.092401 |
| C179 | H329 | 1.092523 |
| C179 | C180 | 1.532450 |
| C180 | H332 | 1.094869 |
| C180 | C182 | 1.488781 |
| C180 | H331 | 1.090576 |
| C181 | C182 | 1.336102 |
| C181 | H333 | 1.081748 |
| C182 | H334 | 1.082477 |
| C183 | H337 | 1.087789 |
| C183 | H336 | 1.088684 |
| C183 | H335 | 1.087064 |
| C184 | H338 | 1.088948 |
| C184 | H339 | 1.088085 |
| C184 | H340 | 1.088881 |
MOLECULAR INFO
| Charge: | 2 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb ramoplanin_A3.xyz --opt extreme --cycles 10000 --charge +2 --uhf 1 --alpb water |
| coordinate file | ramoplanin_A3.xyz |
| omp threads | 1 |
xTB Model Parameters
Hamiltonian
| Parameter | Value |
|---|---|
| H0-scaling (s, p, d) | 1.850000 2.230000 2.230000 |
| zeta-weighting | 0.500000 |
Dispersion
| Parameter | Value |
|---|---|
| s8 | 2.700000 |
| a1 | 0.520000 |
| a2 | 5.000000 |
| s9 | 5.000000 |
Repulsion
| Parameter | Value |
|---|---|
| kExp | 1.500000 1.000000 |
| rExp | 1.000000 |
Coulomb
| Parameter | Value |
|---|---|
| alpha | 2.000000 |
| third order | shell-resolved |
| anisotropic | true |
| a3 | 3.000000 |
| a5 | 4.000000 |
| cn-shift | 1.200000 |
| cn-exp | 4.000000 |
| max-rad | 5.000000 |
Solvation model
| Parameter | Value |
|---|---|
| Solvent | water |
| Parameter file | internal GFN2-xTB/ALPB |
| Dielectric constant | 8.0200E+01 |
| Reference state | gsolv [1 M gas/solution] |
| Free energy shift | 1.0808E-03 Eh 6.7819E-01 kcal/mol |
| Temperature | 2.9815E+02 K |
| Density | 1.0000E+00 kg/L |
| Solvent mass | 1.8000E+01 g/mol |
| Interaction kernel | P16 |
| Born radius scaling (c1) | 1.4744E+00 |
| Born radii integrator | GBOBC |
| Born offset | 0.0000E+00 a0 0.0000E+00 AA |
| H-bond correction | true |
| Ion screening | false |
| Surface tension | 1.0000E-05 Eh 1.5569E+01 dyn/cm |
| Grid points | 230 per atom |
| Solvation model | ALPB |
Energy Breakdown
| Energy Component | Value | Units |
|---|---|---|
| Total Energy | -566.1774744258 | Eh |
| SCC Energy | -572.8232876863 | Eh |
| Isotropic ES | 1.7956041969 | Eh |
| Anisotropic ES | -0.1785252206 | Eh |
| Anisotropic XC | 0.1105264759 | Eh |
| Dispersion | -0.4667442019 | Eh |
| Repulsion Energy | 6.6458132606 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.000076507 | Eh/Bohr |
| HOMO-LUMO Gap | 2.863676 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -28.9934 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | 2.656 | 5.366 | 2.686 | 6.562 |
| full | 1.700 | 5.159 | 2.204 | 14.900 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -204.523 | 1.009 | 117.997 | 62.560 | -59.180 | 86.526 |
| q+dip | -136.755 | 24.456 | 60.746 | 70.247 | -40.685 | 76.009 |
| full | -139.516 | 25.253 | 64.587 | 70.630 | -40.951 | 74.929 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 1151.199 | s |
| CPU time | 1150.460 | s |
| End time | 2026-02-09T11:34:50.250 |
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