GENERAL INFO
| Title: | /AB-DB Polymyxin - Polymyxin B +5 Polymyxin - Polymyxin B +5 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/500587 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C56H103N16O13 |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| C1 | C6 | 1.527474 |
| C1 | H11 | 1.094492 |
| C1 | C2 | 1.535487 |
| C1 | C5 | 1.534796 |
| C2 | H13 | 1.093238 |
| C2 | H12 | 1.093337 |
| C2 | C3 | 1.529267 |
| C3 | H14 | 1.090781 |
| C3 | H15 | 1.091780 |
| C3 | C4 | 1.527704 |
| C4 | C7 | 1.537052 |
| C4 | H16 | 1.092874 |
| C4 | H17 | 1.091851 |
| C5 | C8 | 1.525359 |
| C5 | H18 | 1.092347 |
| C5 | H19 | 1.093248 |
| C6 | H21 | 1.086587 |
| C6 | H22 | 1.089062 |
| C6 | H20 | 1.086178 |
| C7 | H23 | 1.091303 |
| C7 | C9 | 1.510605 |
| C7 | H24 | 1.089280 |
| C8 | H26 | 1.085671 |
| C8 | H25 | 1.086441 |
| C8 | H27 | 1.086506 |
| C9 | O10 | 1.230841 |
| C9 | N33 | 1.343134 |
| C28 | C29 | 1.535504 |
| C28 | H35 | 1.093576 |
| C28 | N33 | 1.460304 |
| C28 | C30 | 1.538657 |
| C29 | H37 | 1.090305 |
| C29 | H36 | 1.090564 |
| C29 | C31 | 1.526169 |
| C30 | N44 | 1.328133 |
| C30 | O34 | 1.228090 |
| C31 | H39 | 1.090481 |
| C31 | H38 | 1.090390 |
| C31 | N32 | 1.480820 |
| N32 | H40 | 1.026496 |
| N32 | H41 | 1.027353 |
| N32 | H42 | 1.027292 |
| N33 | H43 | 1.008635 |
| N44 | C45 | 1.445452 |
| N44 | H51 | 1.020149 |
| C45 | C49 | 1.530515 |
| C45 | H52 | 1.099771 |
| C45 | C46 | 1.540257 |
| C46 | C47 | 1.528686 |
| C46 | O48 | 1.414374 |
| C46 | H53 | 1.100613 |
| C47 | H54 | 1.087608 |
| C47 | H56 | 1.088035 |
| C47 | H55 | 1.087620 |
| O48 | H57 | 0.964306 |
| C49 | O50 | 1.222079 |
| C49 | N63 | 1.341988 |
| C58 | H65 | 1.093170 |
| C58 | C60 | 1.544154 |
| C58 | C59 | 1.544614 |
| C58 | N63 | 1.449951 |
| C59 | N79 | 1.331093 |
| C59 | O64 | 1.225367 |
| C60 | H67 | 1.089247 |
| C60 | C61 | 1.526804 |
| C60 | H66 | 1.088765 |
| C61 | H68 | 1.088983 |
| C61 | H69 | 1.089751 |
| C61 | N62 | 1.481260 |
| N62 | H72 | 1.024188 |
| N62 | H71 | 1.036089 |
| N62 | H70 | 1.024445 |
| N63 | H73 | 1.008086 |
| C74 | N79 | 1.443740 |
| C74 | H81 | 1.096255 |
| C74 | C76 | 1.524055 |
| C74 | C75 | 1.541334 |
| C75 | C77 | 1.536706 |
| C75 | H83 | 1.089343 |
| C75 | H82 | 1.090314 |
| C76 | O80 | 1.228604 |
| C76 | N93 | 1.327952 |
| C77 | N78 | 1.448809 |
| C77 | H85 | 1.092200 |
| C77 | H84 | 1.092542 |
| N78 | C180 | 1.328374 |
| N78 | H86 | 1.007168 |
| N79 | H87 | 1.016103 |
| C88 | H95 | 1.096126 |
| C88 | C89 | 1.549032 |
| C88 | N93 | 1.454065 |
| C88 | C90 | 1.531893 |
| C89 | H96 | 1.089482 |
| C89 | H97 | 1.089766 |
| C89 | C91 | 1.526001 |
| C90 | N113 | 1.342222 |
| C90 | O94 | 1.217475 |
| C91 | N92 | 1.480877 |
| C91 | H98 | 1.089830 |
| C91 | H99 | 1.088822 |
| N92 | H101 | 1.052232 |
| N92 | H100 | 1.023824 |
| N92 | H102 | 1.023798 |
| N93 | H103 | 1.009866 |
| C104 | H115 | 1.097829 |
| C104 | C106 | 1.538952 |
| C104 | N113 | 1.444053 |
| C104 | C105 | 1.530540 |
| C105 | N124 | 1.334761 |
| C105 | O114 | 1.227736 |
| C106 | H116 | 1.091822 |
| C106 | H117 | 1.089517 |
| C106 | C107 | 1.506170 |
| C107 | C109 | 1.391330 |
| C107 | C108 | 1.389993 |
| C108 | H118 | 1.080020 |
| C108 | C110 | 1.384442 |
| C109 | H119 | 1.080685 |
| C109 | C111 | 1.385891 |
| C110 | H120 | 1.079583 |
| C110 | C112 | 1.386158 |
| C111 | C112 | 1.384644 |
| C111 | H121 | 1.079689 |
| C112 | H122 | 1.079256 |
| N113 | H123 | 1.009731 |
| N124 | C125 | 1.457823 |
| N124 | H132 | 1.007909 |
| C125 | C126 | 1.536864 |
| C125 | H133 | 1.091749 |
| C125 | C130 | 1.537932 |
| C126 | H134 | 1.092095 |
| C126 | C127 | 1.536690 |
| C126 | H135 | 1.089589 |
| C127 | C128 | 1.528030 |
| C127 | C129 | 1.527085 |
| C127 | H136 | 1.096214 |
| C128 | H139 | 1.087899 |
| C128 | H138 | 1.087665 |
| C128 | H137 | 1.087837 |
| C129 | H141 | 1.086375 |
| C129 | H142 | 1.087618 |
| C129 | H140 | 1.086735 |
| C130 | N148 | 1.334212 |
| C130 | O131 | 1.227558 |
| C143 | C145 | 1.534049 |
| C143 | H150 | 1.097798 |
| C143 | C144 | 1.538623 |
| C143 | N148 | 1.445057 |
| C144 | H152 | 1.089981 |
| C144 | H151 | 1.089379 |
| C144 | C146 | 1.527495 |
| C145 | N164 | 1.324589 |
| C145 | O149 | 1.235840 |
| C146 | H154 | 1.089519 |
| C146 | H153 | 1.088462 |
| C146 | N147 | 1.480799 |
| N147 | H156 | 1.023930 |
| N147 | H155 | 1.024505 |
| N147 | H157 | 1.045225 |
| N148 | H158 | 1.019017 |
| C159 | N164 | 1.451120 |
| C159 | C161 | 1.532440 |
| C159 | H166 | 1.099393 |
| C159 | C160 | 1.543636 |
| C160 | H168 | 1.089937 |
| C160 | C162 | 1.532119 |
| C160 | H167 | 1.088025 |
| C161 | N175 | 1.343294 |
| C161 | O165 | 1.222668 |
| C162 | H170 | 1.091675 |
| C162 | N163 | 1.480459 |
| C162 | H169 | 1.089606 |
| N163 | H172 | 1.023521 |
| N163 | H171 | 1.023329 |
| N163 | H173 | 1.048313 |
| N164 | H174 | 1.015902 |
| N175 | H182 | 1.013686 |
| N175 | C176 | 1.448913 |
| C176 | C177 | 1.560808 |
| C176 | H183 | 1.096701 |
| C176 | C180 | 1.529930 |
| C177 | O179 | 1.411087 |
| C177 | C178 | 1.522505 |
| C177 | H184 | 1.095533 |
| C178 | H187 | 1.084624 |
| C178 | H186 | 1.088696 |
| C178 | H185 | 1.087854 |
| O179 | H188 | 0.965455 |
| C180 | O181 | 1.227830 |
MOLECULAR INFO
| Charge: | 5 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb xtbhess1.xyz --opt extreme --cycles 50000 --charge +5 --uhf 1 --alpb water |
| 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 | -270.7965169987 | Eh |
| SCC Energy | -274.069347586 | Eh |
| Isotropic ES | 1.4489395607 | Eh |
| Anisotropic ES | -0.1062394489 | Eh |
| Anisotropic XC | 0.1003113366 | Eh |
| Dispersion | -0.2151661064 | Eh |
| Repulsion Energy | 3.2728305873 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.1236684587 | Eh/Bohr |
| HOMO-LUMO Gap | 3.938076 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -19.8826 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | -29.064 | 3.827 | 14.506 | 32.708 |
| full | -26.723 | 1.352 | 13.943 | 76.689 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -232.121 | 323.940 | 602.179 | -226.605 | -368.801 | -370.058 |
| q+dip | -227.015 | 346.489 | 598.586 | -218.265 | -372.551 | -371.571 |
| full | -227.611 | 346.861 | 598.667 | -220.099 | -373.290 | -371.056 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 304.197 | s |
| CPU time | 304.138 | s |
| End time | 2026-02-09T16:40:41.950 |
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