GENERAL INFO
| Title: | /AB-DB Phospho-glyco-lipids - Moenomycin -2 Phospho-glyco-lipids - Moenomycin -2 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/500373 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C69H106N5O34P |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| P1 | O27 | 1.491502 |
| P1 | O24 | 1.622177 |
| P1 | O26 | 1.487611 |
| P1 | O13 | 1.657108 |
| O2 | C47 | 1.405910 |
| O2 | C41 | 1.404706 |
| O3 | C44 | 1.425857 |
| O3 | C45 | 1.420242 |
| O4 | C45 | 1.393907 |
| O4 | C46 | 1.419237 |
| O5 | C47 | 1.393049 |
| O5 | C53 | 1.435832 |
| O6 | C54 | 1.385166 |
| O6 | C56 | 1.420923 |
| O7 | C52 | 1.416900 |
| O7 | C58 | 1.405661 |
| O8 | H131 | 0.963525 |
| O8 | C42 | 1.403608 |
| O9 | C61 | 1.404774 |
| O9 | C55 | 1.422604 |
| O10 | C72 | 1.357404 |
| O10 | C49 | 1.415386 |
| O11 | C50 | 1.402704 |
| O11 | H138 | 0.968970 |
| O12 | H139 | 0.975463 |
| O12 | C51 | 1.405777 |
| O13 | C54 | 1.385899 |
| O14 | C67 | 1.424292 |
| O14 | C58 | 1.405096 |
| O15 | C70 | 1.432380 |
| O15 | C61 | 1.396593 |
| O16 | H154 | 0.967274 |
| O16 | C60 | 1.403961 |
| O17 | C63 | 1.405234 |
| O17 | H158 | 0.966915 |
| O18 | C64 | 1.405486 |
| O18 | H159 | 0.978900 |
| O19 | H160 | 0.985799 |
| O19 | C65 | 1.396588 |
| O20 | C62 | 1.221100 |
| O21 | C68 | 1.403392 |
| O21 | H161 | 0.973556 |
| O22 | C69 | 1.408301 |
| O22 | H162 | 0.969515 |
| O23 | C66 | 1.221889 |
| O24 | C77 | 1.412511 |
| O25 | C71 | 1.228558 |
| O28 | C72 | 1.217414 |
| O29 | H168 | 0.986032 |
| O29 | C74 | 1.401763 |
| O30 | C75 | 1.219996 |
| O31 | C85 | 1.436789 |
| O31 | C79 | 1.413718 |
| O32 | C80 | 1.321807 |
| O32 | H174 | 0.971112 |
| O33 | C81 | 1.228897 |
| O34 | C84 | 1.236635 |
| O35 | C84 | 1.254226 |
| N36 | C66 | 1.354535 |
| N36 | C43 | 1.441612 |
| N36 | H126 | 1.010478 |
| N37 | H130 | 1.017431 |
| N37 | C48 | 1.441641 |
| N37 | C71 | 1.349864 |
| N38 | H151 | 1.008356 |
| N38 | C62 | 1.328980 |
| N38 | H150 | 1.008175 |
| N39 | H164 | 1.009433 |
| N39 | H163 | 1.005389 |
| N39 | C72 | 1.341258 |
| N40 | H165 | 1.018835 |
| N40 | C78 | 1.418388 |
| N40 | C75 | 1.354710 |
| C41 | H110 | 1.098940 |
| C41 | C42 | 1.542282 |
| C41 | C44 | 1.560119 |
| C42 | H111 | 1.096243 |
| C42 | C43 | 1.540267 |
| C43 | H112 | 1.095118 |
| C43 | C45 | 1.536503 |
| C44 | H113 | 1.097260 |
| C44 | C55 | 1.543023 |
| C45 | H114 | 1.103287 |
| C46 | C49 | 1.535353 |
| C46 | C54 | 1.539100 |
| C46 | H115 | 1.098582 |
| C47 | C48 | 1.560158 |
| C47 | H116 | 1.099363 |
| C48 | H117 | 1.095421 |
| C48 | C50 | 1.535664 |
| C49 | C51 | 1.554686 |
| C49 | H118 | 1.095264 |
| C50 | C52 | 1.547072 |
| C50 | H119 | 1.094548 |
| C51 | C56 | 1.546787 |
| C51 | C57 | 1.528043 |
| C52 | H120 | 1.099707 |
| C52 | C53 | 1.547924 |
| C53 | C59 | 1.520832 |
| C53 | H121 | 1.097967 |
| C54 | H122 | 1.108987 |
| C55 | H124 | 1.092033 |
| C55 | H123 | 1.096758 |
| C56 | H125 | 1.098675 |
| C56 | C62 | 1.534339 |
| C57 | H128 | 1.084624 |
| C57 | H129 | 1.085053 |
| C57 | H127 | 1.084877 |
| C58 | C60 | 1.552266 |
| C58 | H132 | 1.097429 |
| C59 | H135 | 1.084149 |
| C59 | H133 | 1.085800 |
| C59 | H134 | 1.085332 |
| C60 | C63 | 1.535822 |
| C60 | H136 | 1.097339 |
| C61 | H137 | 1.115209 |
| C61 | C64 | 1.552856 |
| C63 | H140 | 1.102466 |
| C63 | C65 | 1.530067 |
| C64 | H141 | 1.096570 |
| C64 | C68 | 1.537811 |
| C65 | H142 | 1.097854 |
| C65 | C67 | 1.559571 |
| C66 | C73 | 1.502506 |
| C67 | H143 | 1.096000 |
| C67 | C75 | 1.537883 |
| C68 | C69 | 1.540439 |
| C68 | H144 | 1.097264 |
| C69 | C70 | 1.547118 |
| C69 | H145 | 1.097215 |
| C70 | H146 | 1.102504 |
| C70 | C74 | 1.543235 |
| C71 | C76 | 1.505696 |
| C73 | H147 | 1.084959 |
| C73 | H148 | 1.085490 |
| C73 | H149 | 1.090818 |
| C74 | H153 | 1.091829 |
| C74 | H152 | 1.096759 |
| C76 | H155 | 1.085269 |
| C76 | H156 | 1.087669 |
| C76 | H157 | 1.085605 |
| C77 | H167 | 1.094416 |
| C77 | H166 | 1.093519 |
| C77 | C79 | 1.526361 |
| C78 | C80 | 1.358057 |
| C78 | C81 | 1.446227 |
| C79 | C84 | 1.556816 |
| C79 | H169 | 1.097720 |
| C80 | C82 | 1.496009 |
| C81 | C83 | 1.506991 |
| C82 | H171 | 1.089773 |
| C82 | C83 | 1.528860 |
| C82 | H170 | 1.091866 |
| C83 | H172 | 1.089150 |
| C83 | H173 | 1.089034 |
| C85 | C86 | 1.502765 |
| C85 | H175 | 1.094080 |
| C85 | H176 | 1.097259 |
| C86 | H177 | 1.083476 |
| C86 | C87 | 1.330581 |
| C87 | C89 | 1.497999 |
| C87 | C88 | 1.502455 |
| C88 | H178 | 1.090990 |
| C88 | H179 | 1.092571 |
| C88 | C90 | 1.541185 |
| C89 | H180 | 1.091149 |
| C89 | H182 | 1.086178 |
| C89 | H181 | 1.086810 |
| C90 | H183 | 1.087592 |
| C90 | H184 | 1.092406 |
| C90 | C93 | 1.496839 |
| C91 | C96 | 1.534004 |
| C91 | C95 | 1.534777 |
| C91 | C92 | 1.543105 |
| C91 | C94 | 1.515644 |
| C92 | C97 | 1.532329 |
| C92 | H186 | 1.092925 |
| C92 | H185 | 1.092701 |
| C93 | C94 | 1.326657 |
| C93 | H187 | 1.084604 |
| C94 | H188 | 1.083697 |
| C95 | H189 | 1.085232 |
| C95 | H191 | 1.086320 |
| C95 | H190 | 1.087439 |
| C96 | H193 | 1.084716 |
| C96 | H192 | 1.090117 |
| C96 | H194 | 1.087198 |
| C97 | C98 | 1.505753 |
| C97 | H195 | 1.090337 |
| C97 | H196 | 1.088991 |
| C98 | C99 | 1.507659 |
| C98 | C100 | 1.323751 |
| C99 | H198 | 1.090729 |
| C99 | H197 | 1.092445 |
| C99 | C101 | 1.500432 |
| C100 | H199 | 1.078367 |
| C100 | H200 | 1.077521 |
| C101 | C102 | 1.328268 |
| C101 | H201 | 1.083514 |
| C102 | C104 | 1.499523 |
| C102 | C103 | 1.506636 |
| C103 | H202 | 1.092025 |
| C103 | C105 | 1.542094 |
| C103 | H203 | 1.092399 |
| C104 | H205 | 1.090340 |
| C104 | H204 | 1.088427 |
| C104 | H206 | 1.085479 |
| C105 | H207 | 1.093041 |
| C105 | C106 | 1.495893 |
| C105 | H208 | 1.089278 |
| C106 | H209 | 1.083627 |
| C106 | C107 | 1.327753 |
| C107 | C108 | 1.499853 |
| C107 | C109 | 1.503458 |
| C108 | H210 | 1.089556 |
| C108 | H212 | 1.089388 |
| C108 | H211 | 1.087040 |
| C109 | H213 | 1.088706 |
| C109 | H215 | 1.086370 |
| C109 | H214 | 1.087707 |
MOLECULAR INFO
| Charge: | -2 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb moenomycin.xyz --opt extreme --cycles 10000 --charge -2 --uhf 1 --alpb water |
| coordinate file | moenomycin.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 | -358.3106528571 | Eh |
| SCC Energy | -361.837123285 | Eh |
| Isotropic ES | 1.4251607969 | Eh |
| Anisotropic ES | -0.1380009243 | Eh |
| Anisotropic XC | 0.0260523592 | Eh |
| Dispersion | -0.2969145792 | Eh |
| Repulsion Energy | 3.5264704279 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.0000679907 | Eh/Bohr |
| HOMO-LUMO Gap | 2.544692 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -20.7270 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | 10.360 | 3.718 | -1.444 | 11.101 |
| full | 9.270 | 3.724 | -0.346 | 25.407 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -75.950 | 25.844 | 29.501 | 46.154 | 42.671 | 46.450 |
| q+dip | -49.582 | 13.531 | 8.542 | 59.380 | 31.822 | 41.040 |
| full | -50.412 | 14.444 | 7.059 | 60.674 | 32.875 | 43.353 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 349.343 | s |
| CPU time | 348.993 | s |
| End time | 2026-02-09T15:51:32.395 |
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