GENERAL INFO
| Title: | /AB-DB Lipo-glyco-peptides - Ramoplanin A2 +2 Lipo-glyco-peptides - Ramoplanin A2 +2 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/500737 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C119H156ClN21O40 |
| Calculation type: | Geometry optimization |
| Method: | GFN2-xTB |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| Cl1 | C171 | 1.743361 |
| O2 | C65 | 1.425021 |
| O2 | C67 | 1.387360 |
| O3 | C74 | 1.419153 |
| O3 | C67 | 1.416239 |
| O4 | C72 | 1.424369 |
| O4 | C71 | 1.398394 |
| O5 | H198 | 0.976984 |
| O5 | C66 | 1.402910 |
| O6 | C77 | 1.370235 |
| O6 | C71 | 1.403997 |
| O7 | H199 | 0.966924 |
| O7 | C68 | 1.408780 |
| O8 | H200 | 0.975411 |
| O8 | C69 | 1.402150 |
| O9 | C70 | 1.404289 |
| O9 | H201 | 0.972346 |
| O10 | H202 | 0.967862 |
| O10 | C73 | 1.408111 |
| O11 | H203 | 0.966282 |
| O11 | C75 | 1.406016 |
| O12 | C76 | 1.407937 |
| O12 | H204 | 0.967353 |
| O13 | C84 | 1.219170 |
| O14 | C85 | 1.228296 |
| O15 | C89 | 1.416769 |
| O15 | H227 | 0.966376 |
| O16 | C91 | 1.223170 |
| O17 | C93 | 1.226778 |
| O18 | C99 | 1.224169 |
| O19 | C101 | 1.225785 |
| O20 | H253 | 0.966826 |
| O20 | C105 | 1.413984 |
| O21 | H260 | 0.969464 |
| O21 | C113 | 1.357889 |
| O22 | C116 | 1.230828 |
| O23 | C117 | 1.226312 |
| O24 | C123 | 1.225668 |
| O25 | C124 | 1.227360 |
| O26 | C136 | 1.405722 |
| O26 | H301 | 0.967741 |
| O27 | C155 | 1.323560 |
| O27 | C148 | 1.439095 |
| O28 | C135 | 1.223267 |
| O29 | C137 | 1.226595 |
| O30 | C142 | 1.357369 |
| O30 | H307 | 0.968934 |
| O31 | C143 | 1.221336 |
| O32 | C145 | 1.222321 |
| O33 | C153 | 1.224204 |
| O34 | C155 | 1.211575 |
| O35 | C159 | 1.353297 |
| O35 | H320 | 0.969157 |
| O36 | C160 | 1.222341 |
| O37 | C163 | 1.223547 |
| O38 | H321 | 0.974342 |
| O38 | C170 | 1.350299 |
| O39 | H325 | 0.973640 |
| O39 | C173 | 1.346419 |
| O40 | C174 | 1.228632 |
| O41 | C175 | 1.240555 |
| N42 | C83 | 1.442092 |
| N42 | H210 | 1.022239 |
| N42 | C85 | 1.332551 |
| N43 | C87 | 1.449385 |
| N43 | H211 | 1.008561 |
| N43 | C84 | 1.346531 |
| N44 | C86 | 1.463043 |
| N44 | H217 | 1.010517 |
| N44 | C93 | 1.336979 |
| N45 | C96 | 1.445659 |
| N45 | C91 | 1.341406 |
| N45 | H225 | 1.008807 |
| N46 | H231 | 1.024213 |
| N46 | C95 | 1.446865 |
| N46 | C101 | 1.333973 |
| N47 | H232 | 1.025717 |
| N47 | H48 | 1.024388 |
| N47 | H233 | 1.043882 |
| N47 | C94 | 1.478578 |
| N49 | C108 | 1.443306 |
| N49 | C99 | 1.333315 |
| N49 | H237 | 1.015046 |
| N50 | C116 | 1.330920 |
| N50 | H241 | 1.019333 |
| N50 | C102 | 1.454439 |
| N51 | C117 | 1.336212 |
| N51 | C119 | 1.449630 |
| N51 | H255 | 1.008702 |
| N52 | C124 | 1.333433 |
| N52 | C118 | 1.462551 |
| N52 | H259 | 1.012486 |
| N53 | C123 | 1.338685 |
| N53 | H270 | 1.010547 |
| N53 | C132 | 1.445803 |
| N54 | C125 | 1.449735 |
| N54 | H274 | 1.009398 |
| N54 | C135 | 1.340441 |
| N55 | C137 | 1.337517 |
| N55 | H278 | 1.011431 |
| N55 | C130 | 1.441122 |
| N56 | C145 | 1.339617 |
| N56 | H283 | 1.011824 |
| N56 | C131 | 1.443179 |
| N57 | H298 | 1.009223 |
| N57 | C153 | 1.331659 |
| N57 | C141 | 1.457930 |
| N58 | H299 | 1.011163 |
| N58 | C152 | 1.439472 |
| N58 | C143 | 1.341163 |
| N59 | C163 | 1.336436 |
| N59 | C146 | 1.438949 |
| N59 | H300 | 1.020277 |
| N60 | H61 | 1.040552 |
| N60 | C151 | 1.478328 |
| N60 | H309 | 1.023047 |
| N60 | H308 | 1.022281 |
| N62 | H316 | 1.008293 |
| N62 | C164 | 1.451695 |
| N62 | C175 | 1.347068 |
| N63 | C160 | 1.324412 |
| N63 | H317 | 1.011915 |
| N63 | H318 | 1.009265 |
| N64 | H322 | 1.005019 |
| N64 | C174 | 1.336214 |
| N64 | H323 | 1.007655 |
| C65 | H184 | 1.089497 |
| C65 | C66 | 1.536820 |
| C65 | C71 | 1.545521 |
| C66 | C68 | 1.550771 |
| C66 | H185 | 1.098631 |
| C67 | C69 | 1.564408 |
| C67 | H186 | 1.101935 |
| C68 | C72 | 1.544584 |
| C68 | H187 | 1.094727 |
| C69 | H188 | 1.094578 |
| C69 | C70 | 1.544277 |
| C70 | H189 | 1.094190 |
| C70 | C73 | 1.537300 |
| C71 | H190 | 1.096964 |
| C72 | H191 | 1.097878 |
| C72 | C75 | 1.531666 |
| C73 | C74 | 1.550390 |
| C73 | H192 | 1.096171 |
| C74 | H193 | 1.101448 |
| C74 | C76 | 1.530312 |
| C75 | H195 | 1.093170 |
| C75 | H194 | 1.089543 |
| C76 | H197 | 1.097042 |
| C76 | H196 | 1.095892 |
| C77 | C79 | 1.394462 |
| C77 | C78 | 1.390815 |
| C78 | H205 | 1.077031 |
| C78 | C81 | 1.386620 |
| C79 | H206 | 1.077936 |
| C79 | C82 | 1.380086 |
| C80 | C83 | 1.513756 |
| C80 | C82 | 1.389913 |
| C80 | C81 | 1.388497 |
| C81 | H207 | 1.079319 |
| C82 | H208 | 1.078824 |
| C83 | H209 | 1.094715 |
| C83 | C84 | 1.534432 |
| C85 | C86 | 1.531774 |
| C86 | H212 | 1.094439 |
| C86 | C88 | 1.544741 |
| C87 | C91 | 1.532467 |
| C87 | C89 | 1.543962 |
| C87 | H213 | 1.095049 |
| C88 | H214 | 1.090263 |
| C88 | H215 | 1.091907 |
| C88 | C90 | 1.534546 |
| C89 | H216 | 1.100598 |
| C89 | C92 | 1.524081 |
| C90 | C94 | 1.526871 |
| C90 | H218 | 1.090958 |
| C90 | H219 | 1.087753 |
| C92 | H220 | 1.087477 |
| C92 | H221 | 1.086593 |
| C92 | H222 | 1.085711 |
| C93 | C95 | 1.534187 |
| C94 | H224 | 1.089532 |
| C94 | H223 | 1.090028 |
| C95 | C97 | 1.540404 |
| C95 | H226 | 1.097960 |
| C96 | H228 | 1.094335 |
| C96 | C98 | 1.504929 |
| C96 | C99 | 1.544590 |
| C97 | C100 | 1.505543 |
| C97 | H229 | 1.093767 |
| C97 | H230 | 1.091025 |
| C98 | C104 | 1.389474 |
| C98 | C103 | 1.390912 |
| C100 | C107 | 1.390059 |
| C100 | C106 | 1.390165 |
| C101 | C102 | 1.534349 |
| C102 | H234 | 1.093032 |
| C102 | C105 | 1.546972 |
| C103 | C109 | 1.380504 |
| C103 | H235 | 1.079260 |
| C104 | C110 | 1.382333 |
| C104 | H236 | 1.078823 |
| C105 | C114 | 1.525991 |
| C105 | H238 | 1.100194 |
| C106 | H239 | 1.076944 |
| C106 | C111 | 1.383086 |
| C107 | C112 | 1.385876 |
| C107 | H240 | 1.081164 |
| C108 | H242 | 1.094823 |
| C108 | H243 | 1.095101 |
| C108 | C117 | 1.523972 |
| C109 | H244 | 1.078222 |
| C109 | C113 | 1.393322 |
| C110 | H245 | 1.079503 |
| C110 | C113 | 1.390805 |
| C111 | H246 | 1.078413 |
| C111 | C115 | 1.384356 |
| C112 | C115 | 1.386522 |
| C112 | H247 | 1.081017 |
| C114 | H248 | 1.086885 |
| C114 | H249 | 1.086234 |
| C114 | H250 | 1.087182 |
| C115 | H251 | 1.079683 |
| C116 | C118 | 1.530951 |
| C118 | C122 | 1.515812 |
| C118 | H252 | 1.095605 |
| C119 | C123 | 1.533929 |
| C119 | C120 | 1.536648 |
| C119 | H254 | 1.097581 |
| C120 | H256 | 1.090513 |
| C120 | C121 | 1.539729 |
| C120 | H257 | 1.091487 |
| C121 | C126 | 1.527679 |
| C121 | H258 | 1.096644 |
| C121 | C127 | 1.527655 |
| C122 | C128 | 1.386473 |
| C122 | C129 | 1.392645 |
| C124 | C125 | 1.536011 |
| C125 | H261 | 1.095302 |
| C125 | C134 | 1.508123 |
| C126 | H264 | 1.087719 |
| C126 | H262 | 1.086753 |
| C126 | H263 | 1.086173 |
| C127 | H267 | 1.087683 |
| C127 | H265 | 1.087957 |
| C127 | H266 | 1.088507 |
| C128 | H268 | 1.078359 |
| C128 | C138 | 1.384149 |
| C129 | H269 | 1.079673 |
| C129 | C139 | 1.377956 |
| C130 | H271 | 1.096585 |
| C130 | C135 | 1.521198 |
| C130 | C136 | 1.563106 |
| C131 | H272 | 1.096689 |
| C131 | C133 | 1.535296 |
| C131 | C137 | 1.531069 |
| C132 | C144 | 1.532050 |
| C132 | H273 | 1.094613 |
| C132 | C143 | 1.530723 |
| C133 | H276 | 1.089852 |
| C133 | H275 | 1.090223 |
| C133 | C140 | 1.536935 |
| C134 | C149 | 1.389761 |
| C134 | C150 | 1.389603 |
| C136 | H277 | 1.101747 |
| C136 | C147 | 1.525042 |
| C138 | C142 | 1.389075 |
| C138 | H279 | 1.079746 |
| C139 | H280 | 1.078305 |
| C139 | C142 | 1.393430 |
| C140 | H281 | 1.089674 |
| C140 | C151 | 1.524314 |
| C140 | H282 | 1.088143 |
| C141 | C154 | 1.510161 |
| C141 | H284 | 1.097195 |
| C141 | C145 | 1.550317 |
| C144 | H286 | 1.087178 |
| C144 | H285 | 1.086005 |
| C144 | H287 | 1.085213 |
| C146 | H288 | 1.098381 |
| C146 | C153 | 1.535214 |
| C146 | C148 | 1.541106 |
| C147 | H291 | 1.085898 |
| C147 | H289 | 1.085921 |
| C147 | H290 | 1.086025 |
| C148 | C160 | 1.540192 |
| C148 | H292 | 1.100931 |
| C149 | C156 | 1.381579 |
| C149 | H295 | 1.080364 |
| C150 | C157 | 1.379621 |
| C150 | H296 | 1.079306 |
| C151 | H293 | 1.089828 |
| C151 | H294 | 1.090185 |
| C152 | C158 | 1.525599 |
| C152 | C155 | 1.513355 |
| C152 | H297 | 1.092107 |
| C154 | C161 | 1.391091 |
| C154 | C162 | 1.392205 |
| C156 | H302 | 1.079814 |
| C156 | C159 | 1.392101 |
| C157 | C159 | 1.393990 |
| C157 | H303 | 1.077995 |
| C158 | C166 | 1.387832 |
| C158 | C167 | 1.388837 |
| C161 | H304 | 1.080217 |
| C161 | C168 | 1.381216 |
| C162 | C169 | 1.380822 |
| C162 | H305 | 1.078207 |
| C163 | C164 | 1.534221 |
| C164 | C165 | 1.546868 |
| C164 | H306 | 1.093896 |
| C165 | H310 | 1.092917 |
| C165 | H311 | 1.089130 |
| C165 | C174 | 1.521075 |
| C166 | H312 | 1.078046 |
| C166 | C171 | 1.379564 |
| C167 | H313 | 1.077922 |
| C167 | C172 | 1.378811 |
| C168 | C170 | 1.393097 |
| C168 | H314 | 1.079530 |
| C169 | H315 | 1.077462 |
| C169 | C170 | 1.394196 |
| C171 | C173 | 1.395155 |
| C172 | C173 | 1.393107 |
| C172 | H319 | 1.077456 |
| C175 | C176 | 1.464976 |
| C176 | H324 | 1.080901 |
| C176 | C177 | 1.343335 |
| C177 | H326 | 1.082004 |
| C177 | C178 | 1.436443 |
| C178 | C181 | 1.337609 |
| C178 | H327 | 1.081087 |
| C179 | C181 | 1.486089 |
| C179 | C180 | 1.539313 |
| C179 | H328 | 1.094023 |
| C179 | H329 | 1.091208 |
| C180 | H330 | 1.095587 |
| C180 | C183 | 1.526269 |
| C180 | C182 | 1.526222 |
| C181 | H331 | 1.082744 |
| C182 | H333 | 1.087631 |
| C182 | H332 | 1.088056 |
| C182 | H334 | 1.088107 |
| C183 | H335 | 1.085704 |
| C183 | H337 | 1.087391 |
| C183 | H336 | 1.087027 |
MOLECULAR INFO
| Charge: | 2 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb ramoplanin_A2.xyz --opt extreme --cycles 10000 --charge +2 --uhf 1 --alpb water |
| coordinate file | ramoplanin_A2.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 |
Energy Breakdown
| Energy Component | Value | Units |
|---|---|---|
| Total Energy | -562.9725823246 | Eh |
| SCC Energy | -569.5687526505 | Eh |
| Isotropic ES | 1.6386825564 | Eh |
| Anisotropic ES | -0.0954695087 | Eh |
| Anisotropic XC | 0.1167907561 | Eh |
| Dispersion | -0.4595369855 | Eh |
| Repulsion Energy | 6.5961703258 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.000066488 | Eh/Bohr |
| HOMO-LUMO Gap | 2.647092 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -29.1604 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | 0.449 | -9.016 | -3.280 | 9.605 |
| full | 0.063 | -8.244 | -2.355 | 21.792 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | 270.906 | -265.732 | -129.869 | 391.605 | 16.583 | -141.036 |
| q+dip | 255.498 | -276.813 | -127.760 | 381.879 | 25.086 | -127.738 |
| full | 255.197 | -280.505 | -123.866 | 385.541 | 28.352 | -131.330 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 1185.217 | s |
| CPU time | 1183.919 | s |
| End time | 2026-03-04T11:20:53.721 |
Report data
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