GENERAL INFO
| Title: | /AB-DB Polymyxin - Polymyxin B +5 Polymyxin - Polymyxin B +5 freq |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/500588 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C56H103N16O13 |
| Calculation type: | Geometry optimization Frequency calculation |
| Method: | GFN2-xTB |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| C1 | C2 | 1.535558 |
| C1 | C6 | 1.526979 |
| C1 | C5 | 1.534853 |
| C1 | H11 | 1.098683 |
| C2 | C3 | 1.528282 |
| C2 | H12 | 1.092066 |
| C2 | H13 | 1.090622 |
| C3 | C4 | 1.528158 |
| C3 | H14 | 1.091370 |
| C3 | H15 | 1.096780 |
| C4 | H16 | 1.091248 |
| C4 | H17 | 1.089516 |
| C4 | C7 | 1.536066 |
| C5 | H18 | 1.092127 |
| C5 | H19 | 1.090702 |
| C5 | C8 | 1.527940 |
| C6 | H21 | 1.085764 |
| C6 | H22 | 1.086798 |
| C6 | H20 | 1.087168 |
| C7 | H24 | 1.089885 |
| C7 | C9 | 1.502162 |
| C7 | H23 | 1.091650 |
| C8 | H26 | 1.090142 |
| C8 | H27 | 1.087463 |
| C8 | H25 | 1.090700 |
| C9 | N33 | 1.359761 |
| C9 | O10 | 1.221146 |
| C28 | C29 | 1.545471 |
| C28 | H35 | 1.094222 |
| C28 | C30 | 1.547708 |
| C28 | N33 | 1.455451 |
| C29 | H37 | 1.091307 |
| C29 | H36 | 1.091210 |
| C29 | C31 | 1.527072 |
| C30 | N44 | 1.321392 |
| C30 | O34 | 1.235556 |
| C31 | H39 | 1.091873 |
| C31 | H38 | 1.091744 |
| C31 | N32 | 1.492020 |
| N32 | H40 | 1.030277 |
| N32 | H41 | 1.029937 |
| N32 | H42 | 1.030436 |
| N33 | H43 | 1.007678 |
| N44 | C45 | 1.448978 |
| N44 | H51 | 1.031179 |
| C45 | C49 | 1.521652 |
| C45 | H52 | 1.100400 |
| C45 | C46 | 1.547218 |
| C46 | C47 | 1.526868 |
| C46 | H53 | 1.099253 |
| C46 | O48 | 1.410204 |
| C47 | H56 | 1.087767 |
| C47 | H55 | 1.086671 |
| C47 | H54 | 1.087258 |
| O48 | H57 | 0.963609 |
| C49 | O50 | 1.209971 |
| C49 | N63 | 1.366132 |
| C58 | C60 | 1.545833 |
| C58 | N63 | 1.454446 |
| C58 | H65 | 1.095713 |
| C58 | C59 | 1.549948 |
| C59 | N79 | 1.352628 |
| C59 | O64 | 1.209820 |
| C60 | H67 | 1.090365 |
| C60 | C61 | 1.529837 |
| C60 | H66 | 1.091390 |
| C61 | H68 | 1.089324 |
| C61 | H69 | 1.091982 |
| C61 | N62 | 1.485415 |
| N62 | H72 | 1.023607 |
| N62 | H70 | 1.025196 |
| N62 | H71 | 1.075017 |
| N63 | H73 | 1.009262 |
| C74 | C75 | 1.547532 |
| C74 | H81 | 1.099703 |
| C74 | N79 | 1.446956 |
| C74 | C76 | 1.518029 |
| C75 | H82 | 1.091911 |
| C75 | H83 | 1.090723 |
| C75 | C77 | 1.530708 |
| C76 | N93 | 1.332341 |
| C76 | O80 | 1.235960 |
| C77 | H84 | 1.094516 |
| C77 | H85 | 1.094159 |
| C77 | N78 | 1.454905 |
| N78 | C180 | 1.325939 |
| N78 | H86 | 1.008643 |
| N79 | H87 | 1.007114 |
| C88 | N93 | 1.456436 |
| C88 | C89 | 1.536612 |
| C88 | H95 | 1.098611 |
| C88 | C90 | 1.562315 |
| C89 | C91 | 1.527405 |
| C89 | H96 | 1.090949 |
| C89 | H97 | 1.088423 |
| C90 | N113 | 1.329916 |
| C90 | O94 | 1.217465 |
| C91 | H98 | 1.091970 |
| C91 | N92 | 1.485297 |
| C91 | H99 | 1.091705 |
| N92 | H102 | 1.027544 |
| N92 | H101 | 1.089436 |
| N92 | H100 | 1.024135 |
| N93 | H103 | 1.017634 |
| C104 | H115 | 1.098325 |
| C104 | N113 | 1.455818 |
| C104 | C106 | 1.546566 |
| C104 | C105 | 1.535801 |
| C105 | O114 | 1.225716 |
| C105 | N124 | 1.332240 |
| C106 | H117 | 1.090376 |
| C106 | H116 | 1.091581 |
| C106 | C107 | 1.505145 |
| C107 | C108 | 1.389661 |
| C107 | C109 | 1.388707 |
| C108 | H118 | 1.079392 |
| C108 | C110 | 1.382422 |
| C109 | H119 | 1.080460 |
| C109 | C111 | 1.385943 |
| C110 | H120 | 1.079665 |
| C110 | C112 | 1.386744 |
| C111 | C112 | 1.385628 |
| C111 | H121 | 1.080494 |
| C112 | H122 | 1.080099 |
| N113 | H123 | 1.007516 |
| N124 | C125 | 1.461146 |
| N124 | H132 | 1.007008 |
| C125 | C130 | 1.529155 |
| C125 | H133 | 1.092190 |
| C125 | C126 | 1.537326 |
| C126 | H134 | 1.091579 |
| C126 | H135 | 1.091066 |
| C126 | C127 | 1.538507 |
| C127 | C128 | 1.526112 |
| C127 | H136 | 1.095163 |
| C127 | C129 | 1.527239 |
| C128 | H139 | 1.086474 |
| C128 | H138 | 1.087304 |
| C128 | H137 | 1.086057 |
| C129 | H141 | 1.087813 |
| C129 | H140 | 1.089955 |
| C129 | H142 | 1.086372 |
| C130 | O131 | 1.208208 |
| C130 | N148 | 1.361936 |
| C143 | N148 | 1.439648 |
| C143 | C144 | 1.547438 |
| C143 | H150 | 1.105563 |
| C143 | C145 | 1.523049 |
| C144 | C146 | 1.530506 |
| C144 | H151 | 1.091297 |
| C144 | H152 | 1.090999 |
| C145 | O149 | 1.234826 |
| C145 | N164 | 1.331502 |
| C146 | N147 | 1.484457 |
| C146 | H153 | 1.091239 |
| C146 | H154 | 1.090993 |
| N147 | H155 | 1.024618 |
| N147 | H156 | 1.025156 |
| N147 | H157 | 1.079364 |
| N148 | H158 | 1.014554 |
| C159 | N164 | 1.450725 |
| C159 | H166 | 1.098691 |
| C159 | C161 | 1.535664 |
| C159 | C160 | 1.541400 |
| C160 | C162 | 1.528458 |
| C160 | H168 | 1.090617 |
| C160 | H167 | 1.090334 |
| C161 | O165 | 1.213283 |
| C161 | N175 | 1.343815 |
| C162 | H169 | 1.091568 |
| C162 | H170 | 1.091080 |
| C162 | N163 | 1.488474 |
| N163 | H173 | 1.098166 |
| N163 | H172 | 1.024698 |
| N163 | H171 | 1.024138 |
| N164 | H174 | 1.017330 |
| N175 | C176 | 1.447620 |
| N175 | H182 | 1.017955 |
| C176 | C177 | 1.574981 |
| C176 | C180 | 1.523332 |
| C176 | H183 | 1.096357 |
| C177 | C178 | 1.519103 |
| C177 | O179 | 1.402299 |
| C177 | H184 | 1.098199 |
| C178 | H186 | 1.088747 |
| C178 | H185 | 1.087693 |
| C178 | H187 | 1.085750 |
| O179 | H188 | 0.965754 |
| C180 | O181 | 1.236515 |
MOLECULAR INFO
| Charge: | 5 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb xtbopt.xyz --ohess --charge +5 --uhf 1 |
| coordinate file | xtbopt.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 | -269.7700210452 | Eh |
| SCC Energy | -273.0691958312 | Eh |
| Isotropic ES | 1.447798151 | Eh |
| Anisotropic ES | -0.0849530987 | Eh |
| Anisotropic XC | 0.0967191535 | Eh |
| Dispersion | -0.2227507848 | Eh |
| Repulsion Energy | 3.299174786 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.1134404244 | Eh/Bohr |
| HOMO-LUMO Gap | 1.165833 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -29.1658 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | -15.523 | 0.034 | 11.299 | 19.200 |
| full | -15.450 | -1.298 | 11.016 | 48.343 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -307.361 | 705.174 | 782.900 | -211.826 | -325.622 | -475.539 |
| q+dip | -297.752 | 713.830 | 776.484 | -206.168 | -328.316 | -478.733 |
| full | -298.041 | 713.622 | 777.993 | -206.908 | -329.309 | -479.952 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 453.193 | s |
| CPU time | 453.114 | s |
| End time | 2026-02-09T16:48:15.147 |
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