GENERAL INFO

Title: /AB-DB Phospho-glyco-lipids - Flavomycin -3 Phospho-glyco-lipids - Flavomycin -3 opt
Browse item: https://iochem-bd.bsc.es:443/browse/handle/100/499870
Program: xtb 6.7.1 (edcfbbe)
Author: Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia
Formula: C69H104N4O35P
Calculation type: Geometry optimization (Solvation)
Method: GFN2-xTB
Solvation model: water

ATOM INFO

Atomic coordinates [Å]

Atom x y z

Bond distances

Atom1 Atom2 Distance [Å]
P1 O28 1.488461
P1 O27 1.479392
P1 O13 1.664641
P1 O25 1.645474
O2 C46 1.423583
O2 C41 1.412896
O3 C45 1.397376
O3 C44 1.431456
O4 C45 1.411557
O4 C48 1.411898
O5 C53 1.434264
O5 C46 1.380369
O6 C54 1.393735
O6 C56 1.431803
O7 C50 1.418932
O7 C58 1.401968
O8 C42 1.403434
O8 H132 0.964000
O9 C55 1.414306
O9 C61 1.400627
O10 C51 1.409604
O10 C72 1.365447
O11 H138 0.968466
O11 C49 1.403786
O12 H140 0.985645
O12 C52 1.414243
O13 C54 1.389327
O14 C67 1.425323
O14 C58 1.411092
O15 C61 1.400165
O15 C70 1.429738
O16 C60 1.402744
O16 H152 0.968881
O17 H156 0.968508
O17 C62 1.400019
O18 H157 0.976471
O18 C63 1.406909
O19 C64 1.243643
O20 C65 1.406282
O20 H158 0.970952
O21 H159 0.964916
O21 C68 1.416608
O22 C64 1.236396
O23 C69 1.405895
O23 H160 0.970481
O24 C66 1.224236
O25 C77 1.419568
O26 C71 1.224352
O29 C72 1.218840
O30 H164 0.973100
O30 C74 1.403432
O31 C75 1.226822
O32 C79 1.405968
O32 C85 1.434515
O33 H172 0.978513
O33 C80 1.318597
O34 C81 1.225876
O35 C84 1.247467
O36 C84 1.241032
N37 C66 1.351097
N37 C43 1.445238
N37 H126 1.009317
N38 H127 1.012612
N38 C71 1.350896
N38 C47 1.449079
N39 C75 1.341952
N39 H161 1.020031
N39 C78 1.415396
N40 C72 1.331896
N40 H162 1.006614
N40 H163 1.006408
C41 H110 1.096052
C41 C44 1.546297
C41 C42 1.557511
C42 C43 1.549269
C42 H111 1.092740
C43 H112 1.098940
C43 C45 1.553667
C44 H113 1.097257
C44 C55 1.550866
C45 H114 1.100308
C46 H115 1.102598
C46 C47 1.535356
C47 H116 1.099301
C47 C49 1.542660
C48 H117 1.102189
C48 C51 1.532656
C48 C54 1.544710
C49 H118 1.094457
C49 C50 1.552165
C50 C53 1.538568
C50 H119 1.102195
C51 H120 1.099579
C51 C52 1.554515
C52 C57 1.533296
C52 C56 1.539258
C53 H121 1.097076
C53 C59 1.519330
C54 H122 1.102320
C55 H124 1.094700
C55 H123 1.094148
C56 H125 1.095921
C56 C64 1.571884
C57 H129 1.084670
C57 H128 1.087308
C57 H130 1.083220
C58 C60 1.541827
C58 H131 1.097034
C59 H134 1.085241
C59 H135 1.084167
C59 H133 1.085374
C60 C62 1.543576
C60 H136 1.094784
C61 C63 1.529864
C61 H137 1.098047
C62 C65 1.548532
C62 H139 1.097537
C63 H141 1.101518
C63 C68 1.532074
C65 H142 1.101799
C65 C67 1.544504
C66 C73 1.501221
C67 C75 1.544351
C67 H143 1.097598
C68 C69 1.535638
C68 H144 1.101533
C69 C70 1.547339
C69 H145 1.096871
C70 C74 1.541522
C70 H146 1.097266
C71 C76 1.507641
C73 H148 1.085235
C73 H149 1.086410
C73 H147 1.085894
C74 H150 1.092934
C74 H151 1.097007
C76 H154 1.090148
C76 H155 1.085374
C76 H153 1.085102
C77 H166 1.092300
C77 H165 1.093872
C77 C79 1.529506
C78 C81 1.447976
C78 C80 1.359219
C79 H167 1.104003
C79 C84 1.563663
C80 C82 1.496736
C81 C83 1.514773
C82 H168 1.091895
C82 C83 1.527789
C82 H169 1.088996
C83 H171 1.092272
C83 H170 1.087888
C85 C86 1.496109
C85 H173 1.099956
C85 H174 1.098552
C86 C87 1.329329
C86 H175 1.082346
C87 C88 1.508604
C87 C89 1.497250
C88 H176 1.090591
C88 C90 1.541085
C88 H177 1.090223
C89 H178 1.085147
C89 H180 1.088778
C89 H179 1.088290
C90 H181 1.093838
C90 H182 1.087376
C90 C93 1.495430
C91 C96 1.536744
C91 C94 1.513191
C91 C95 1.534711
C91 C92 1.541585
C92 H183 1.092009
C92 H184 1.089441
C92 C97 1.532794
C93 H185 1.085935
C93 C94 1.326301
C94 H186 1.084062
C95 H188 1.086623
C95 H189 1.088050
C95 H187 1.087451
C96 H190 1.087663
C96 H192 1.085181
C96 H191 1.088061
C97 H194 1.091704
C97 C98 1.505001
C97 H193 1.089113
C98 C99 1.507857
C98 C100 1.323736
C99 H195 1.091194
C99 C101 1.500313
C99 H196 1.092798
C100 H197 1.077522
C100 H198 1.076989
C101 C102 1.328227
C101 H199 1.083333
C102 C103 1.506472
C102 C104 1.499007
C103 H200 1.092184
C103 C105 1.542259
C103 H201 1.092192
C104 H204 1.085504
C104 H202 1.088461
C104 H203 1.090319
C105 C106 1.495814
C105 H205 1.089444
C105 H206 1.092902
C106 H207 1.083554
C106 C107 1.327819
C107 C108 1.500519
C107 C109 1.501799
C108 H210 1.089377
C108 H209 1.086807
C108 H208 1.089470
C109 H212 1.087125
C109 H211 1.086522
C109 H213 1.089410

MOLECULAR INFO

Charge: -3
Spin polarization: 1
Multiplicity: 2

JOB |

Calculation Setup

Parameter Value
program call xtb flavomycin.xyz --opt extreme --cycles 10000 --charge -3 --uhf 1 --alpb water
coordinate file flavomycin.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 -358.7760981491 Eh
SCC Energy -362.2628826551 Eh
Isotropic ES 1.8262490987 Eh
Anisotropic ES -0.18790528 Eh
Anisotropic XC 0.0186207033 Eh
Dispersion -0.2861724954 Eh
Repulsion Energy 3.486784506 Eh
Additional Restraining 0 Eh
Property Value Units
Gradient Norm 0.0000437095 Eh/Bohr
HOMO-LUMO Gap 2.769814 eV

Orbital Energies

# Occupation Energy (eV)
1 2.0000 -20.7426

Multipole molecular moments

Dipole moment

Type X Y Z Total (D)
q only -13.230 -12.956 10.509 21.292
full -11.876 -12.291 7.899 47.857

Quadrupole moment (Traceless)

Type XX XY YY XZ YZ ZZ
q only -202.870 -1.356 107.094 60.417 270.218 95.776
q+dip -179.031 -0.863 93.728 55.463 218.294 85.303
full -180.128 0.945 94.313 59.630 218.896 85.815

Timings

Property Value Units
Wall time 224.766 s
CPU time 222.365 s
End time 2026-02-09T15:26:58.397


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