GENERAL INFO
| Title: | /AB-DB Lipo-glyco-peptides - Vancomycin +1 Lipo-glyco-peptides - Vancomycin +1 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/500231 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C66H76Cl2N9O24 |
| Calculation type: | Geometry optimization |
| Method: | GFN2-xTB |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| Cl1 | C64 | 1.729400 |
| Cl2 | C66 | 1.708060 |
| O3 | C41 | 1.416204 |
| O3 | C42 | 1.427151 |
| O4 | C43 | 1.408028 |
| O4 | C41 | 1.396874 |
| O5 | C47 | 1.409953 |
| O5 | C48 | 1.415856 |
| O6 | C39 | 1.407231 |
| O6 | H122 | 0.962869 |
| O7 | H125 | 0.970220 |
| O7 | C44 | 1.399473 |
| O8 | C51 | 1.385123 |
| O8 | C47 | 1.394789 |
| O9 | C46 | 1.405498 |
| O9 | H126 | 0.968506 |
| O10 | H127 | 0.967695 |
| O10 | C50 | 1.406882 |
| O11 | C59 | 1.381979 |
| O11 | C52 | 1.364675 |
| O12 | C60 | 1.389655 |
| O12 | C53 | 1.378212 |
| O13 | C58 | 1.217629 |
| O14 | C61 | 1.222457 |
| O15 | C68 | 1.410563 |
| O15 | H158 | 0.965567 |
| O16 | H159 | 0.983708 |
| O16 | C71 | 1.406425 |
| O17 | C79 | 1.216779 |
| O18 | C81 | 1.218618 |
| O19 | C83 | 1.225555 |
| O20 | C86 | 1.227935 |
| O21 | C94 | 1.355892 |
| O21 | H175 | 0.968597 |
| O22 | C93 | 1.231531 |
| O23 | H176 | 0.970678 |
| O23 | C98 | 1.356708 |
| O24 | C100 | 1.250673 |
| O25 | C100 | 1.237703 |
| O26 | H177 | 0.968765 |
| O26 | C102 | 1.355625 |
| N27 | H117 | 1.025573 |
| N27 | H28 | 1.032012 |
| N27 | H118 | 1.030868 |
| N27 | C38 | 1.492704 |
| N29 | H131 | 1.022589 |
| N29 | C61 | 1.342250 |
| N29 | C57 | 1.450463 |
| N30 | H132 | 1.010121 |
| N30 | C62 | 1.450793 |
| N30 | C58 | 1.344565 |
| N31 | H145 | 1.010585 |
| N31 | C63 | 1.448282 |
| N31 | C81 | 1.343595 |
| N32 | C79 | 1.348583 |
| N32 | H148 | 1.012909 |
| N32 | C73 | 1.462740 |
| N33 | C86 | 1.326953 |
| N33 | C69 | 1.447309 |
| N33 | H149 | 1.014706 |
| N34 | H157 | 1.014519 |
| N34 | C83 | 1.342918 |
| N34 | C90 | 1.449659 |
| N35 | C101 | 1.470087 |
| N35 | H36 | 1.026649 |
| N35 | C82 | 1.483159 |
| N35 | H161 | 1.044299 |
| N37 | H172 | 1.008335 |
| N37 | H173 | 1.005935 |
| N37 | C93 | 1.330761 |
| C38 | C45 | 1.523965 |
| C38 | C40 | 1.531927 |
| C38 | C39 | 1.544395 |
| C39 | H104 | 1.099649 |
| C39 | C42 | 1.546690 |
| C40 | H105 | 1.088636 |
| C40 | C41 | 1.537016 |
| C40 | H106 | 1.087749 |
| C41 | H107 | 1.100017 |
| C42 | C49 | 1.530654 |
| C42 | H108 | 1.095209 |
| C43 | C44 | 1.536198 |
| C43 | H109 | 1.099125 |
| C43 | C47 | 1.550672 |
| C44 | C46 | 1.548783 |
| C44 | H110 | 1.094469 |
| C45 | H113 | 1.085251 |
| C45 | H112 | 1.085862 |
| C45 | H111 | 1.085543 |
| C46 | C48 | 1.540877 |
| C46 | H114 | 1.098040 |
| C47 | H115 | 1.108964 |
| C48 | H116 | 1.101012 |
| C48 | C50 | 1.530780 |
| C49 | H120 | 1.088546 |
| C49 | H121 | 1.085570 |
| C49 | H119 | 1.086575 |
| C50 | H124 | 1.097699 |
| C50 | H123 | 1.095440 |
| C51 | C53 | 1.399147 |
| C51 | C52 | 1.392787 |
| C52 | C54 | 1.386456 |
| C53 | C55 | 1.391593 |
| C54 | C56 | 1.382450 |
| C54 | H128 | 1.073951 |
| C55 | C56 | 1.388928 |
| C55 | H129 | 1.080406 |
| C56 | C57 | 1.523023 |
| C57 | C58 | 1.538025 |
| C57 | H130 | 1.099864 |
| C59 | C64 | 1.392454 |
| C59 | C65 | 1.391087 |
| C60 | C67 | 1.386325 |
| C60 | C66 | 1.390682 |
| C61 | C63 | 1.541210 |
| C62 | C79 | 1.547224 |
| C62 | H133 | 1.092067 |
| C62 | C78 | 1.516504 |
| C63 | C80 | 1.534537 |
| C63 | H134 | 1.094395 |
| C64 | C74 | 1.385452 |
| C65 | H135 | 1.078451 |
| C65 | C75 | 1.379605 |
| C66 | C76 | 1.381965 |
| C67 | H136 | 1.078222 |
| C67 | C77 | 1.380262 |
| C68 | C70 | 1.515100 |
| C68 | H138 | 1.097062 |
| C68 | C69 | 1.552496 |
| C69 | C81 | 1.538091 |
| C69 | H137 | 1.099115 |
| C70 | C75 | 1.389660 |
| C70 | C74 | 1.390145 |
| C71 | C73 | 1.562861 |
| C71 | H139 | 1.102079 |
| C71 | C72 | 1.514713 |
| C72 | C77 | 1.390576 |
| C72 | C76 | 1.389031 |
| C73 | C83 | 1.539913 |
| C73 | H140 | 1.095758 |
| C74 | H141 | 1.076747 |
| C75 | H142 | 1.077948 |
| C76 | H143 | 1.077335 |
| C77 | H144 | 1.076736 |
| C78 | C88 | 1.390637 |
| C78 | C85 | 1.387220 |
| C80 | H146 | 1.091517 |
| C80 | C93 | 1.518618 |
| C80 | H147 | 1.092382 |
| C82 | H150 | 1.094406 |
| C82 | C84 | 1.535416 |
| C82 | C86 | 1.542033 |
| C84 | C87 | 1.538120 |
| C84 | H152 | 1.091176 |
| C84 | H151 | 1.090161 |
| C85 | C89 | 1.386281 |
| C85 | H153 | 1.079509 |
| C87 | H154 | 1.094891 |
| C87 | C96 | 1.528760 |
| C87 | C97 | 1.528284 |
| C88 | H155 | 1.078283 |
| C88 | C95 | 1.380275 |
| C89 | C91 | 1.487200 |
| C89 | C94 | 1.398265 |
| C90 | H156 | 1.098685 |
| C90 | C92 | 1.510902 |
| C90 | C100 | 1.580079 |
| C91 | C92 | 1.399204 |
| C91 | C98 | 1.400647 |
| C92 | C99 | 1.386290 |
| C94 | C95 | 1.393706 |
| C95 | H160 | 1.077603 |
| C96 | H164 | 1.087167 |
| C96 | H163 | 1.087604 |
| C96 | H162 | 1.087033 |
| C97 | H167 | 1.087500 |
| C97 | H165 | 1.086254 |
| C97 | H166 | 1.087192 |
| C98 | C103 | 1.386446 |
| C99 | C102 | 1.390748 |
| C99 | H168 | 1.079913 |
| C101 | H170 | 1.086065 |
| C101 | H171 | 1.087233 |
| C101 | H169 | 1.086569 |
| C102 | C103 | 1.386597 |
| C103 | H174 | 1.076700 |
MOLECULAR INFO
| Charge: | 1 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb vancomycin.xyz --opt extreme --cycles 10000 --charge +1 --uhf 1 --alpb water |
| coordinate file | vancomycin.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 | -313.1030712964 | Eh |
| SCC Energy | -316.5634865463 | Eh |
| Isotropic ES | 1.0788462729 | Eh |
| Anisotropic ES | -0.0924803994 | Eh |
| Anisotropic XC | 0.0285599258 | Eh |
| Dispersion | -0.2613618008 | Eh |
| Repulsion Energy | 3.4604152499 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.0000399277 | Eh/Bohr |
| HOMO-LUMO Gap | 3.103399 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -29.3868 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | -20.412 | 17.999 | -15.949 | 31.543 |
| full | -18.680 | 16.296 | -15.659 | 74.524 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -106.749 | 157.420 | 325.792 | -250.629 | -71.403 | -219.043 |
| q+dip | -123.689 | 135.627 | 325.207 | -237.218 | -66.031 | -201.518 |
| full | -125.865 | 137.967 | 326.514 | -236.463 | -65.318 | -200.649 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 139.088 | s |
| CPU time | 138.928 | s |
| End time | 2026-03-04T11:05:54.513 |
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