GENERAL INFO

Title: /AB-DB Polymyxin - Soralimixin +5 Polymyxin - Soralimixin +5 opt
Browse item: https://iochem-bd.bsc.es:443/browse/handle/100/500376
Program: xtb 6.7.1 (edcfbbe)
Author: Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia
Formula: C48H85Cl2N16O13
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]
Cl1 C80 1.762317
Cl2 C84 1.752469
O3 C42 1.219685
O4 C44 1.219915
O5 C49 1.217843
O6 C55 1.232214
O7 H144 0.971936
O7 C61 1.414238
O8 C59 1.221837
O9 C62 1.229021
O10 C63 1.234389
O11 C64 1.228005
O12 C71 1.421862
O12 H159 0.963202
O13 C70 1.222991
O14 C74 1.224306
O15 C78 1.227498
N16 C37 1.442566
N16 C44 1.341072
N16 H90 1.007770
N17 C42 1.344356
N17 C43 1.460412
N17 H97 1.010670
N18 C40 1.463418
N18 H98 1.009487
N18 C49 1.343872
N19 H112 1.008636
N19 C41 1.454201
N19 C62 1.328779
N20 C55 1.335108
N20 C50 1.453083
N20 H113 1.019723
N21 C59 1.342099
N21 C53 1.459627
N21 H121 1.008356
N22 C51 1.452192
N22 C63 1.323837
N22 H123 1.011074
N23 C54 1.445845
N23 C64 1.324806
N23 H124 1.016647
N24 H131 1.007963
N24 C58 1.454018
N24 C70 1.331951
N25 H140 1.033097
N25 C57 1.479560
N25 H26 1.025210
N25 H141 1.028064
N27 C74 1.344593
N27 H142 1.020173
N27 C66 1.444139
N28 C67 1.482147
N28 H29 1.024569
N28 H151 1.023918
N28 H150 1.050637
N30 H152 1.021978
N30 H31 1.043537
N30 H153 1.041504
N30 C68 1.476875
N32 C69 1.480750
N32 H155 1.023403
N32 H33 1.022749
N32 H154 1.054917
N34 C78 1.343702
N34 C73 1.458067
N34 H156 1.013638
N35 H160 1.027488
N35 H36 1.026340
N35 C77 1.482177
N35 H161 1.027151
C37 C42 1.541119
C37 H85 1.097936
C37 C38 1.543439
C38 H86 1.091983
C38 C39 1.540001
C38 H87 1.090954
C39 H88 1.097024
C39 C47 1.529197
C39 C48 1.528132
C40 H89 1.094487
C40 C46 1.529237
C40 C44 1.541403
C41 C45 1.530433
C41 C49 1.534452
C41 H91 1.097050
C43 C55 1.528166
C43 H92 1.100758
C43 C52 1.536376
C45 H93 1.091837
C45 H94 1.090705
C45 C51 1.535109
C46 H96 1.087005
C46 H95 1.089329
C46 C57 1.522545
C47 H99 1.087707
C47 H101 1.087018
C47 H100 1.088540
C48 H103 1.086581
C48 H104 1.088122
C48 H102 1.088573
C50 C59 1.536044
C50 H105 1.096202
C50 C56 1.534016
C51 H106 1.089828
C51 H107 1.093273
C52 C65 1.523508
C52 H108 1.092079
C52 H109 1.089661
C53 H110 1.096543
C53 C64 1.543564
C53 C60 1.539409
C54 C61 1.563668
C54 H111 1.092514
C54 C63 1.530163
C56 C67 1.523484
C56 H114 1.089815
C56 H115 1.090862
C57 H116 1.087844
C57 H117 1.089655
C58 C68 1.540484
C58 C62 1.537916
C58 H118 1.092631
C60 H119 1.089885
C60 C69 1.530361
C60 H120 1.089718
C61 H122 1.095342
C61 C72 1.523372
C65 H127 1.084548
C65 H128 1.086162
C65 H126 1.086469
C66 C70 1.525546
C66 H125 1.094783
C66 C71 1.548190
C67 H130 1.090072
C67 H129 1.089518
C68 H132 1.090202
C68 H133 1.091181
C69 H135 1.089593
C69 H134 1.089504
C71 H136 1.098284
C71 C76 1.526779
C72 H138 1.086611
C72 H139 1.082779
C72 H137 1.084912
C73 C75 1.539676
C73 H143 1.099020
C73 C74 1.534339
C75 C77 1.530934
C75 H145 1.091390
C75 H146 1.090068
C76 H149 1.086366
C76 H147 1.082742
C76 H148 1.085667
C77 H157 1.089118
C77 H158 1.088232
C78 C79 1.503092
C79 C80 1.393413
C79 C81 1.397589
C80 C82 1.388222
C81 H162 1.078146
C81 C83 1.383622
C82 C84 1.388067
C82 H163 1.076515
C83 H164 1.076237
C83 C84 1.387634

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 -253.624413131 Eh
SCC Energy -256.5143463051 Eh
Isotropic ES 1.6879123862 Eh
Anisotropic ES -0.2049490359 Eh
Anisotropic XC 0.0541559776 Eh
Dispersion -0.2108339497 Eh
Repulsion Energy 2.8899331742 Eh
Additional Restraining 0 Eh
Property Value Units
Gradient Norm 0.0000381025 Eh/Bohr
HOMO-LUMO Gap 3.165649 eV

Orbital Energies

# Occupation Energy (eV)
1 2.0000 -29.1745

Multipole molecular moments

Dipole moment

Type X Y Z Total (D)
q only 7.617 11.077 4.171 14.075
full 5.612 10.675 3.169 31.694

Quadrupole moment (Traceless)

Type XX XY YY XZ YZ ZZ
q only 86.037 -231.874 121.109 205.891 7.664 -207.146
q+dip 107.743 -267.854 107.202 220.916 -28.554 -214.945
full 106.219 -269.265 108.743 221.743 -27.702 -214.962

Timings

Property Value Units
Wall time 56.599 s
CPU time 56.553 s
End time 2026-02-09T16:58:53.501


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