GENERAL INFO
| Title: | /AB-DB Lipo-glyco-peptides - Telavancin +1 Lipo-glyco-peptides - Telavancin +1 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/499935 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C80H107Cl2N11O27P |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| Cl1 | C79 | 1.736520 |
| Cl2 | C81 | 1.733805 |
| P3 | O28 | 1.496255 |
| P3 | O30 | 1.496230 |
| P3 | C124 | 1.883749 |
| P3 | O29 | 1.619752 |
| O4 | C48 | 1.379949 |
| O4 | C49 | 1.430669 |
| O5 | C51 | 1.402047 |
| O5 | C48 | 1.440917 |
| O6 | C46 | 1.409927 |
| O6 | H144 | 0.965650 |
| O7 | C57 | 1.421175 |
| O7 | C54 | 1.394863 |
| O8 | H149 | 0.969572 |
| O8 | C52 | 1.404079 |
| O9 | C60 | 1.382212 |
| O9 | C54 | 1.406350 |
| O10 | C55 | 1.402203 |
| O10 | H150 | 0.971912 |
| O11 | C59 | 1.407490 |
| O11 | H154 | 0.967818 |
| O12 | C63 | 1.368652 |
| O12 | C73 | 1.383542 |
| O13 | C74 | 1.392027 |
| O13 | C64 | 1.376001 |
| O14 | C75 | 1.228512 |
| O15 | C78 | 1.226852 |
| O16 | C92 | 1.402699 |
| O16 | H198 | 0.968763 |
| O17 | H199 | 0.965262 |
| O17 | C93 | 1.415492 |
| O18 | C97 | 1.221236 |
| O19 | C99 | 1.221930 |
| O20 | C101 | 1.226359 |
| O21 | C104 | 1.236419 |
| O22 | C107 | 1.226493 |
| O23 | H219 | 0.969615 |
| O23 | C112 | 1.352908 |
| O24 | H223 | 0.968780 |
| O24 | C115 | 1.362716 |
| O25 | C118 | 1.242166 |
| O26 | H225 | 0.968221 |
| O26 | C119 | 1.350379 |
| O27 | C118 | 1.230921 |
| O29 | H228 | 0.962440 |
| N31 | C45 | 1.454443 |
| N31 | C56 | 1.454119 |
| N31 | H133 | 1.010630 |
| N32 | C61 | 1.476296 |
| N32 | H151 | 1.006151 |
| N32 | H33 | 1.004905 |
| N32 | C58 | 1.479137 |
| N34 | C78 | 1.336592 |
| N34 | C70 | 1.447588 |
| N34 | H168 | 1.023252 |
| N35 | C84 | 1.444127 |
| N35 | H173 | 1.011300 |
| N35 | C75 | 1.335728 |
| N36 | H190 | 1.011140 |
| N36 | C99 | 1.338818 |
| N36 | C83 | 1.448201 |
| N37 | C94 | 1.450574 |
| N37 | H191 | 1.018813 |
| N37 | C97 | 1.339234 |
| N38 | C95 | 1.449074 |
| N38 | H195 | 1.015639 |
| N38 | C107 | 1.326765 |
| N39 | C106 | 1.444628 |
| N39 | H200 | 1.013190 |
| N39 | C101 | 1.348525 |
| N40 | C104 | 1.325139 |
| N40 | H208 | 1.008688 |
| N40 | H209 | 1.007012 |
| N41 | C109 | 1.490126 |
| N41 | C123 | 1.475997 |
| N41 | H210 | 1.023873 |
| N41 | H42 | 1.038617 |
| N43 | C124 | 1.463306 |
| N43 | H224 | 1.005172 |
| N43 | H44 | 1.005720 |
| N43 | C122 | 1.482264 |
| C45 | C50 | 1.539635 |
| C45 | C47 | 1.534498 |
| C45 | C46 | 1.562331 |
| C46 | H125 | 1.098129 |
| C46 | C49 | 1.558571 |
| C47 | H126 | 1.089520 |
| C47 | H127 | 1.091301 |
| C47 | C48 | 1.540029 |
| C48 | H128 | 1.094786 |
| C49 | H129 | 1.098276 |
| C49 | C53 | 1.523021 |
| C50 | H132 | 1.085423 |
| C50 | H130 | 1.087108 |
| C50 | H131 | 1.086547 |
| C51 | H134 | 1.097311 |
| C51 | C52 | 1.536991 |
| C51 | C54 | 1.555470 |
| C52 | H135 | 1.098567 |
| C52 | C55 | 1.545271 |
| C53 | H137 | 1.086178 |
| C53 | H138 | 1.086076 |
| C53 | H136 | 1.084087 |
| C54 | H139 | 1.099398 |
| C55 | C57 | 1.537482 |
| C55 | H140 | 1.103181 |
| C56 | H141 | 1.088117 |
| C56 | H142 | 1.095877 |
| C56 | C58 | 1.529817 |
| C57 | C59 | 1.527331 |
| C57 | H143 | 1.098349 |
| C58 | H145 | 1.089990 |
| C58 | H146 | 1.089300 |
| C59 | H148 | 1.096183 |
| C59 | H147 | 1.097658 |
| C60 | C64 | 1.396937 |
| C60 | C63 | 1.401593 |
| C61 | H153 | 1.089418 |
| C61 | H152 | 1.090381 |
| C61 | C62 | 1.524703 |
| C62 | H156 | 1.090456 |
| C62 | H155 | 1.091007 |
| C62 | C65 | 1.528895 |
| C63 | C66 | 1.390515 |
| C64 | C67 | 1.387906 |
| C65 | C69 | 1.528095 |
| C65 | H158 | 1.091500 |
| C65 | H157 | 1.088787 |
| C66 | H159 | 1.080725 |
| C66 | C68 | 1.382812 |
| C67 | H160 | 1.078241 |
| C67 | C68 | 1.382242 |
| C68 | C70 | 1.517992 |
| C69 | H161 | 1.092111 |
| C69 | H162 | 1.093066 |
| C69 | C71 | 1.529494 |
| C70 | H163 | 1.099547 |
| C70 | C75 | 1.526089 |
| C71 | H165 | 1.091373 |
| C71 | H164 | 1.092661 |
| C71 | C72 | 1.527754 |
| C72 | H166 | 1.092139 |
| C72 | C76 | 1.529704 |
| C72 | H167 | 1.089948 |
| C73 | C79 | 1.395310 |
| C73 | C80 | 1.388566 |
| C74 | C81 | 1.393674 |
| C74 | C82 | 1.387949 |
| C76 | H170 | 1.093009 |
| C76 | C77 | 1.528016 |
| C76 | H169 | 1.091238 |
| C77 | H172 | 1.093013 |
| C77 | H171 | 1.091523 |
| C77 | C91 | 1.529368 |
| C78 | C83 | 1.536333 |
| C79 | C87 | 1.381852 |
| C80 | H174 | 1.077694 |
| C80 | C88 | 1.381733 |
| C81 | C89 | 1.383631 |
| C82 | C90 | 1.383329 |
| C82 | H175 | 1.078390 |
| C83 | H176 | 1.098265 |
| C83 | C96 | 1.539359 |
| C84 | C98 | 1.505696 |
| C84 | H177 | 1.094458 |
| C84 | C97 | 1.546931 |
| C85 | C88 | 1.387998 |
| C85 | C87 | 1.386643 |
| C85 | C92 | 1.506427 |
| C86 | C89 | 1.390785 |
| C86 | C93 | 1.518271 |
| C86 | C90 | 1.390025 |
| C87 | H178 | 1.077241 |
| C88 | H179 | 1.077696 |
| C89 | H180 | 1.075841 |
| C90 | H181 | 1.078466 |
| C91 | H182 | 1.092566 |
| C91 | H183 | 1.092909 |
| C91 | C100 | 1.524945 |
| C92 | C94 | 1.559538 |
| C92 | H184 | 1.101237 |
| C93 | C95 | 1.552743 |
| C93 | H185 | 1.097462 |
| C94 | C101 | 1.536680 |
| C94 | H186 | 1.096936 |
| C95 | H187 | 1.100048 |
| C95 | C99 | 1.532624 |
| C96 | C104 | 1.518516 |
| C96 | H188 | 1.091248 |
| C96 | H189 | 1.090018 |
| C98 | C103 | 1.392224 |
| C98 | C102 | 1.389691 |
| C100 | H194 | 1.088043 |
| C100 | H192 | 1.086565 |
| C100 | H193 | 1.087679 |
| C102 | C105 | 1.392182 |
| C102 | H196 | 1.081220 |
| C103 | C111 | 1.379245 |
| C103 | H197 | 1.077725 |
| C105 | C112 | 1.404485 |
| C105 | C108 | 1.485746 |
| C106 | H201 | 1.093536 |
| C106 | C118 | 1.614556 |
| C106 | C110 | 1.491165 |
| C107 | C109 | 1.551169 |
| C108 | C115 | 1.401842 |
| C108 | C110 | 1.403114 |
| C109 | H202 | 1.096645 |
| C109 | C113 | 1.529375 |
| C110 | C116 | 1.392631 |
| C111 | C112 | 1.392789 |
| C111 | H203 | 1.077039 |
| C113 | H204 | 1.088387 |
| C113 | C114 | 1.538866 |
| C113 | H205 | 1.087769 |
| C114 | H206 | 1.095142 |
| C114 | C121 | 1.528434 |
| C114 | C120 | 1.528883 |
| C115 | C117 | 1.393904 |
| C116 | H207 | 1.079102 |
| C116 | C119 | 1.386207 |
| C117 | C122 | 1.502889 |
| C117 | C119 | 1.394926 |
| C120 | H211 | 1.087325 |
| C120 | H212 | 1.087177 |
| C120 | H213 | 1.087654 |
| C121 | H214 | 1.086380 |
| C121 | H216 | 1.087955 |
| C121 | H215 | 1.086559 |
| C122 | H218 | 1.089516 |
| C122 | H217 | 1.091953 |
| C123 | H222 | 1.086298 |
| C123 | H221 | 1.086493 |
| C123 | H220 | 1.085105 |
| C124 | H227 | 1.087062 |
| C124 | H226 | 1.088927 |
MOLECULAR INFO
| Charge: | 1 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb xtbhess1.xyz --opt extreme --cycles 50000 --charge +1 --uhf 1 --alpb water --input constraints.inp |
| coordinate file | xtbhess1.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 | -379.6570096505 | Eh |
| SCC Energy | -383.910581061 | Eh |
| Isotropic ES | 1.2241865221 | Eh |
| Anisotropic ES | -0.1047375283 | Eh |
| Anisotropic XC | 0.0602586814 | Eh |
| Dispersion | -0.3184271354 | Eh |
| Repulsion Energy | 4.2531380075 | Eh |
| Additional Restraining | 0.0004334029 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.0001497032 | Eh/Bohr |
| HOMO-LUMO Gap | 2.545523 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -29.1260 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | 23.817 | -5.788 | 11.541 | 27.091 |
| full | 23.533 | -6.440 | 12.006 | 69.115 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -268.934 | 209.665 | -8.073 | 218.321 | 145.749 | 277.006 |
| q+dip | -252.517 | 201.375 | -8.490 | 216.815 | 125.867 | 261.008 |
| full | -252.529 | 202.686 | -6.605 | 214.493 | 127.188 | 259.134 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 270.683 | s |
| CPU time | 270.628 | s |
| End time | 2026-03-06T16:01:42.259 |
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