GENERAL INFO
| Title: | /AB-DB Lipo-glyco-peptides - Dalbavancin +1 Lipo-glyco-peptides - Dalbavancin +1 opt |
| Browse item: | https://iochem-bd.bsc.es:443/browse/handle/100/499975 |
| Program: | xtb 6.7.1 (edcfbbe) |
| Author: | Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia |
| Formula: | C88H101Cl2N10O28 |
| Calculation type: | Geometry optimization (Solvation) |
| Method: | GFN2-xTB |
| Solvation model: | water |
ATOM INFO
Bond distances
| Atom1 | Atom2 | Distance [Å] |
|---|---|---|
| Cl1 | C101 | 1.740235 |
| Cl2 | C116 | 1.748015 |
| O3 | C46 | 1.392630 |
| O3 | C47 | 1.432187 |
| O4 | C46 | 1.422125 |
| O4 | C57 | 1.388050 |
| O5 | C44 | 1.400681 |
| O5 | H142 | 0.986884 |
| O6 | C51 | 1.430140 |
| O6 | C52 | 1.396560 |
| O7 | H143 | 0.975148 |
| O7 | C45 | 1.398051 |
| O8 | C52 | 1.401333 |
| O8 | C61 | 1.380227 |
| O9 | H152 | 0.978708 |
| O9 | C48 | 1.405943 |
| O10 | C49 | 1.408927 |
| O10 | H153 | 0.970225 |
| O11 | H154 | 0.973451 |
| O11 | C50 | 1.401694 |
| O12 | C53 | 1.252896 |
| O13 | C53 | 1.242753 |
| O14 | C55 | 1.411286 |
| O14 | H167 | 0.968189 |
| O15 | C54 | 1.230986 |
| O16 | C92 | 1.395750 |
| O16 | C62 | 1.373818 |
| O17 | C63 | 1.368290 |
| O17 | C94 | 1.397892 |
| O18 | C82 | 1.351737 |
| O18 | H196 | 0.968814 |
| O19 | C85 | 1.402167 |
| O19 | H198 | 0.967557 |
| O20 | C87 | 1.356275 |
| O20 | H204 | 0.969622 |
| O21 | C84 | 1.228719 |
| O22 | C86 | 1.219655 |
| O23 | C88 | 1.220629 |
| O24 | C89 | 1.225474 |
| O25 | C97 | 1.222297 |
| O26 | C111 | 1.223687 |
| O27 | C118 | 1.364510 |
| O27 | C125 | 1.384651 |
| O28 | H224 | 0.974895 |
| O28 | C120 | 1.341623 |
| O29 | C117 | 1.225849 |
| O30 | C128 | 1.350293 |
| O30 | H229 | 0.970674 |
| N31 | H136 | 1.013414 |
| N31 | C54 | 1.342470 |
| N31 | C43 | 1.444856 |
| N32 | C72 | 1.454479 |
| N32 | H176 | 1.008004 |
| N32 | C86 | 1.340388 |
| N33 | H178 | 1.018721 |
| N33 | C76 | 1.456386 |
| N33 | C84 | 1.335388 |
| N34 | C70 | 1.451328 |
| N34 | C97 | 1.337569 |
| N34 | H179 | 1.018609 |
| N35 | C88 | 1.342563 |
| N35 | C78 | 1.442926 |
| N35 | H180 | 1.020049 |
| N36 | H193 | 1.011154 |
| N36 | C103 | 1.449691 |
| N36 | C89 | 1.333012 |
| N37 | C111 | 1.343070 |
| N37 | H203 | 1.011648 |
| N37 | C98 | 1.444843 |
| N38 | C117 | 1.332075 |
| N38 | C104 | 1.448973 |
| N38 | H211 | 1.015231 |
| N39 | C123 | 1.470478 |
| N39 | H40 | 1.025183 |
| N39 | C114 | 1.484916 |
| N39 | C124 | 1.473111 |
| N41 | H221 | 1.045229 |
| N41 | H42 | 1.025461 |
| N41 | C130 | 1.472493 |
| N41 | C119 | 1.490013 |
| C43 | C44 | 1.533980 |
| C43 | H131 | 1.096800 |
| C43 | C46 | 1.533180 |
| C44 | C45 | 1.543415 |
| C44 | H132 | 1.101931 |
| C45 | H133 | 1.097654 |
| C45 | C47 | 1.549151 |
| C46 | H134 | 1.100184 |
| C47 | C53 | 1.566087 |
| C47 | H135 | 1.097515 |
| C48 | C49 | 1.532179 |
| C48 | H137 | 1.097930 |
| C48 | C50 | 1.541172 |
| C49 | C51 | 1.552421 |
| C49 | H138 | 1.096950 |
| C50 | C52 | 1.547480 |
| C50 | H139 | 1.092762 |
| C51 | C55 | 1.536408 |
| C51 | H140 | 1.097914 |
| C52 | H141 | 1.098768 |
| C54 | C56 | 1.509267 |
| C55 | H144 | 1.092601 |
| C55 | H145 | 1.090785 |
| C56 | H147 | 1.089527 |
| C56 | H146 | 1.089938 |
| C56 | C58 | 1.540058 |
| C57 | C63 | 1.404815 |
| C57 | C62 | 1.399681 |
| C58 | C59 | 1.530558 |
| C58 | H148 | 1.090570 |
| C58 | H149 | 1.092255 |
| C59 | H150 | 1.091149 |
| C59 | H151 | 1.090223 |
| C59 | C60 | 1.527534 |
| C60 | C64 | 1.528356 |
| C60 | H156 | 1.092878 |
| C60 | H155 | 1.091718 |
| C61 | C65 | 1.397894 |
| C61 | C75 | 1.386608 |
| C62 | C69 | 1.388120 |
| C63 | C71 | 1.386759 |
| C64 | H157 | 1.091035 |
| C64 | C68 | 1.530586 |
| C64 | H158 | 1.091847 |
| C65 | C67 | 1.396762 |
| C65 | C74 | 1.483865 |
| C66 | C69 | 1.379313 |
| C66 | C71 | 1.381534 |
| C66 | C70 | 1.506051 |
| C67 | C80 | 1.381422 |
| C67 | C72 | 1.522274 |
| C68 | H159 | 1.091536 |
| C68 | C73 | 1.532054 |
| C68 | H160 | 1.092529 |
| C69 | H162 | 1.076240 |
| C70 | H161 | 1.097779 |
| C70 | C84 | 1.533910 |
| C71 | H163 | 1.075996 |
| C72 | H164 | 1.094378 |
| C72 | C89 | 1.543792 |
| C73 | H165 | 1.090725 |
| C73 | C77 | 1.528255 |
| C73 | H166 | 1.090944 |
| C74 | C81 | 1.384017 |
| C74 | C87 | 1.398707 |
| C75 | H168 | 1.078178 |
| C75 | C82 | 1.389565 |
| C76 | C79 | 1.523978 |
| C76 | C88 | 1.541532 |
| C76 | H169 | 1.094810 |
| C77 | H170 | 1.092316 |
| C77 | H171 | 1.090991 |
| C77 | C83 | 1.535883 |
| C78 | C86 | 1.537928 |
| C78 | H172 | 1.093851 |
| C78 | C85 | 1.565446 |
| C79 | C81 | 1.390872 |
| C79 | C90 | 1.386935 |
| C80 | H173 | 1.074549 |
| C80 | C82 | 1.389725 |
| C81 | H174 | 1.079858 |
| C83 | C96 | 1.527411 |
| C83 | C95 | 1.527650 |
| C83 | H175 | 1.096611 |
| C85 | H177 | 1.094722 |
| C85 | C91 | 1.513109 |
| C87 | C93 | 1.389325 |
| C90 | H181 | 1.078717 |
| C90 | C93 | 1.381495 |
| C91 | C100 | 1.389403 |
| C91 | C99 | 1.389626 |
| C92 | C102 | 1.388885 |
| C92 | C101 | 1.393982 |
| C93 | H182 | 1.079459 |
| C94 | C107 | 1.390415 |
| C94 | C106 | 1.388291 |
| C95 | H184 | 1.087026 |
| C95 | H183 | 1.086697 |
| C95 | H185 | 1.086685 |
| C96 | H188 | 1.087557 |
| C96 | H186 | 1.087304 |
| C96 | H187 | 1.087381 |
| C97 | C98 | 1.531479 |
| C98 | H189 | 1.096093 |
| C98 | C109 | 1.517916 |
| C99 | H190 | 1.076929 |
| C99 | C101 | 1.381540 |
| C100 | C102 | 1.383071 |
| C100 | H191 | 1.078312 |
| C102 | H192 | 1.078422 |
| C103 | C110 | 1.534480 |
| C103 | H194 | 1.088885 |
| C103 | H195 | 1.092072 |
| C104 | C111 | 1.529481 |
| C104 | H197 | 1.097414 |
| C104 | C105 | 1.547813 |
| C105 | H200 | 1.089912 |
| C105 | H199 | 1.089186 |
| C105 | C108 | 1.498363 |
| C106 | H201 | 1.076675 |
| C106 | C112 | 1.380155 |
| C107 | H202 | 1.079620 |
| C107 | C113 | 1.384506 |
| C108 | C113 | 1.388290 |
| C108 | C112 | 1.389942 |
| C109 | C116 | 1.386782 |
| C109 | C115 | 1.387398 |
| C110 | H206 | 1.088502 |
| C110 | C114 | 1.528745 |
| C110 | H205 | 1.089015 |
| C112 | H207 | 1.078735 |
| C113 | H208 | 1.080217 |
| C114 | H209 | 1.091176 |
| C114 | H210 | 1.090949 |
| C115 | C118 | 1.388046 |
| C115 | H212 | 1.077494 |
| C116 | C120 | 1.401429 |
| C117 | C119 | 1.542353 |
| C118 | C121 | 1.388603 |
| C119 | H213 | 1.093843 |
| C119 | C122 | 1.514474 |
| C120 | C121 | 1.388185 |
| C121 | H214 | 1.076852 |
| C122 | C126 | 1.387651 |
| C122 | C127 | 1.391381 |
| C123 | H215 | 1.086891 |
| C123 | H217 | 1.086275 |
| C123 | H216 | 1.086942 |
| C124 | H219 | 1.086068 |
| C124 | H218 | 1.086346 |
| C124 | H220 | 1.088384 |
| C125 | C126 | 1.387046 |
| C125 | C128 | 1.402941 |
| C126 | H222 | 1.079400 |
| C127 | C129 | 1.379639 |
| C127 | H223 | 1.077787 |
| C128 | C129 | 1.389380 |
| C129 | H225 | 1.077696 |
| C130 | H227 | 1.086898 |
| C130 | H228 | 1.086578 |
| C130 | H226 | 1.086058 |
MOLECULAR INFO
| Charge: | 1 |
| Spin polarization: | 1 |
| Multiplicity: | 2 |
JOB |
Calculation Setup
| Parameter | Value |
|---|---|
| program call | xtb xtbhess1.xyz --opt extreme --cycles 50000 --charge +1 --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 | -392.2869928471 | Eh |
| SCC Energy | -396.827646964 | Eh |
| Isotropic ES | 1.0406535833 | Eh |
| Anisotropic ES | -0.0972600556 | Eh |
| Anisotropic XC | 0.055690864 | Eh |
| Dispersion | -0.3661947187 | Eh |
| Repulsion Energy | 4.5406541169 | Eh |
| Additional Restraining | 0 | Eh |
| Property | Value | Units |
|---|---|---|
| Gradient Norm | 0.0000502158 | Eh/Bohr |
| HOMO-LUMO Gap | 3.108741 | eV |
Orbital Energies
| # | Occupation | Energy (eV) |
|---|---|---|
| 1 | 2.0000 | -29.2978 |
Multipole molecular moments
Dipole moment
| Type | X | Y | Z | Total (D) |
|---|---|---|---|---|
| q only | -8.245 | -0.718 | 9.365 | 12.498 |
| full | -7.070 | -0.727 | 7.312 | 25.918 |
Quadrupole moment (Traceless)
| Type | XX | XY | YY | XZ | YZ | ZZ |
|---|---|---|---|---|---|---|
| q only | -181.325 | 138.477 | 59.028 | -171.730 | -311.601 | 122.298 |
| q+dip | -148.136 | 126.747 | 40.178 | -155.157 | -273.234 | 107.958 |
| full | -151.120 | 124.541 | 45.033 | -156.495 | -272.781 | 106.088 |
Timings
| Property | Value | Units |
|---|---|---|
| Wall time | 155.129 | s |
| CPU time | 153.876 | s |
| End time | 2026-02-06T12:16:32.418 |
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