GENERAL INFO
| Title: | /AB-DB Polymyxin - Colistin +5 Polymyxin - Colistin +5 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/499922 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C52H103N16O13 |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| O1 | C41 | 1.226592 |
| O2 | C43 | 1.223664 |
| O3 | C45 | 1.226742 |
| O4 | C54 | 1.222768 |
| O5 | C57 | 1.228946 |
| O6 | C63 | 1.224485 |
| O7 | H177 | 0.963908 |
| O7 | C71 | 1.425412 |
| O8 | C69 | 1.219542 |
| O9 | H182 | 0.964340 |
| O9 | C76 | 1.414947 |
| O10 | C73 | 1.224064 |
| O11 | C75 | 1.222793 |
| O12 | C80 | 1.229838 |
| O13 | C82 | 1.230519 |
| N14 | C36 | 1.447273 |
| N14 | H95 | 1.008709 |
| N14 | C41 | 1.332129 |
| N15 | H97 | 1.008481 |
| N15 | C45 | 1.333535 |
| N15 | C35 | 1.449294 |
| N16 | H106 | 1.013562 |
| N16 | C44 | 1.446287 |
| N16 | C43 | 1.339784 |
| N17 | C42 | 1.457138 |
| N17 | H117 | 1.010139 |
| N17 | C54 | 1.336511 |
| N18 | C63 | 1.339400 |
| N18 | H125 | 1.012432 |
| N18 | C46 | 1.448070 |
| N19 | H131 | 1.014412 |
| N19 | C57 | 1.339274 |
| N19 | C55 | 1.455976 |
| N20 | H143 | 1.012931 |
| N20 | C58 | 1.449980 |
| N20 | C73 | 1.335005 |
| N21 | H144 | 1.016658 |
| N21 | C56 | 1.462007 |
| N21 | C75 | 1.342084 |
| N22 | H146 | 1.009219 |
| N22 | C61 | 1.453809 |
| N22 | C69 | 1.338825 |
| N23 | H154 | 1.008741 |
| N23 | C66 | 1.450787 |
| N23 | C80 | 1.337813 |
| N24 | H161 | 1.007843 |
| N24 | C72 | 1.445083 |
| N24 | C82 | 1.347502 |
| N25 | C62 | 1.478433 |
| N25 | H165 | 1.032333 |
| N25 | H166 | 1.044020 |
| N25 | H26 | 1.021218 |
| N27 | H28 | 1.039765 |
| N27 | C68 | 1.481439 |
| N27 | H174 | 1.023803 |
| N27 | H173 | 1.023822 |
| N29 | H178 | 1.037168 |
| N29 | C78 | 1.477489 |
| N29 | H30 | 1.021584 |
| N29 | H179 | 1.053094 |
| N31 | H32 | 1.048785 |
| N31 | H180 | 1.022334 |
| N31 | H181 | 1.023730 |
| N31 | C81 | 1.484169 |
| N33 | H184 | 1.025003 |
| N33 | H34 | 1.051100 |
| N33 | H183 | 1.024381 |
| N33 | C86 | 1.481047 |
| C35 | H87 | 1.097158 |
| C35 | C37 | 1.534765 |
| C35 | C41 | 1.533253 |
| C36 | C43 | 1.547204 |
| C36 | C38 | 1.526408 |
| C36 | H88 | 1.096250 |
| C37 | H90 | 1.092107 |
| C37 | H89 | 1.091413 |
| C37 | C39 | 1.537441 |
| C38 | H92 | 1.092946 |
| C38 | C40 | 1.537344 |
| C38 | H91 | 1.092058 |
| C39 | C48 | 1.528236 |
| C39 | C47 | 1.527356 |
| C39 | H93 | 1.096100 |
| C40 | C51 | 1.528345 |
| C40 | H94 | 1.096686 |
| C40 | C50 | 1.529236 |
| C42 | C49 | 1.547532 |
| C42 | H96 | 1.093534 |
| C42 | C45 | 1.538882 |
| C44 | H98 | 1.094715 |
| C44 | C57 | 1.531748 |
| C44 | C53 | 1.530705 |
| C46 | C54 | 1.534181 |
| C46 | H99 | 1.097337 |
| C46 | C52 | 1.533268 |
| C47 | H101 | 1.087823 |
| C47 | H100 | 1.084071 |
| C47 | H102 | 1.087815 |
| C48 | H104 | 1.088564 |
| C48 | H103 | 1.087996 |
| C48 | H105 | 1.088674 |
| C49 | H107 | 1.089694 |
| C49 | H108 | 1.089597 |
| C49 | C62 | 1.525299 |
| C50 | H111 | 1.088036 |
| C50 | H109 | 1.085079 |
| C50 | H110 | 1.088593 |
| C51 | H113 | 1.087189 |
| C51 | H112 | 1.086904 |
| C51 | H114 | 1.088023 |
| C52 | H116 | 1.088434 |
| C52 | C58 | 1.536021 |
| C52 | H115 | 1.088655 |
| C53 | C68 | 1.524942 |
| C53 | H119 | 1.089275 |
| C53 | H118 | 1.090598 |
| C55 | C65 | 1.539982 |
| C55 | H120 | 1.096334 |
| C55 | C69 | 1.549249 |
| C56 | C67 | 1.550838 |
| C56 | C63 | 1.533761 |
| C56 | H121 | 1.096889 |
| C58 | H122 | 1.091254 |
| C58 | H123 | 1.091573 |
| C59 | C77 | 1.530389 |
| C59 | H124 | 1.095455 |
| C59 | C60 | 1.534249 |
| C59 | C70 | 1.536193 |
| C60 | H127 | 1.091499 |
| C60 | H126 | 1.094938 |
| C60 | C64 | 1.531703 |
| C61 | H128 | 1.094949 |
| C61 | C71 | 1.544212 |
| C61 | C73 | 1.538911 |
| C62 | H130 | 1.089710 |
| C62 | H129 | 1.089746 |
| C64 | C74 | 1.541129 |
| C64 | H132 | 1.091250 |
| C64 | H133 | 1.089681 |
| C65 | H134 | 1.089245 |
| C65 | H135 | 1.090551 |
| C65 | C78 | 1.524827 |
| C66 | C76 | 1.540729 |
| C66 | C75 | 1.537989 |
| C66 | H136 | 1.100885 |
| C67 | H138 | 1.088909 |
| C67 | H137 | 1.087172 |
| C67 | C81 | 1.525833 |
| C68 | H139 | 1.089779 |
| C68 | H140 | 1.088726 |
| C70 | C83 | 1.526157 |
| C70 | H142 | 1.092408 |
| C70 | H141 | 1.087454 |
| C71 | C84 | 1.518826 |
| C71 | H145 | 1.099562 |
| C72 | H147 | 1.099447 |
| C72 | C79 | 1.540770 |
| C72 | C80 | 1.523408 |
| C74 | H149 | 1.089668 |
| C74 | C82 | 1.501637 |
| C74 | H148 | 1.092632 |
| C76 | H150 | 1.104761 |
| C76 | C85 | 1.527361 |
| C77 | H152 | 1.089348 |
| C77 | H153 | 1.087385 |
| C77 | H151 | 1.086526 |
| C78 | H157 | 1.091184 |
| C78 | H158 | 1.090467 |
| C79 | H155 | 1.090208 |
| C79 | C86 | 1.526847 |
| C79 | H156 | 1.090553 |
| C81 | H160 | 1.090063 |
| C81 | H159 | 1.089462 |
| C83 | H163 | 1.085428 |
| C83 | H162 | 1.086226 |
| C83 | H164 | 1.084740 |
| C84 | H168 | 1.086217 |
| C84 | H167 | 1.087883 |
| C84 | H169 | 1.088721 |
| C85 | H172 | 1.087814 |
| C85 | H170 | 1.085316 |
| C85 | H171 | 1.085379 |
| C86 | H175 | 1.090520 |
| C86 | H176 | 1.089788 |
MOLECULAR INFO
| Charge: | 5 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb colistin.xyz --opt extreme --cycles 10000 --charge +5 --uhf 1 --alpb water |
| coordinate file | colistin.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 | -262.298604231 | Eh |
| SCC Energy | -265.3903769386 | Eh |
| Isotropic ES | 1.7139317041 | Eh |
| Anisotropic ES | -0.1630734725 | Eh |
| Anisotropic XC | 0.0942017271 | Eh |
| Dispersion | -0.2208744659 | Eh |
| Repulsion Energy | 3.0917727076 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.0001515457 | Eh/Bohr |
| HOMO-LUMO Gap | 3.941583 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -19.9343 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | -0.485 | 4.335 | 0.769 | 4.429 |
| full | 0.887 | 4.809 | 1.003 | 12.688 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | 17.866 | -24.945 | -70.600 | -14.035 | 71.522 | 52.734 |
| q+dip | -14.220 | -13.432 | -51.246 | -6.389 | 95.103 | 65.465 |
| full | -15.702 | -13.847 | -49.372 | -7.257 | 96.337 | 65.075 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 381.725 | s |
| CPU time | 381.284 | s |
| End time | 2026-02-09T16:14:12.751 |
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