GENERAL INFO

Title: /AB-DB Polymyxin - SPR-741 +3 Polymyxin - SPR-741 +3 opt
Browse item: https://iochem-bd.bsc.es:443/browse/handle/100/500582
Program: xtb 6.7.1 (edcfbbe)
Author: Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia
Formula: C44H76N13O13
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]
O1 C35 1.229416
O2 C37 1.228468
O3 C45 1.222273
O4 C48 1.225256
O5 H131 0.965468
O5 C53 1.416453
O6 C50 1.222783
O7 C52 1.219527
O8 C56 1.223233
O9 C60 1.225859
O10 C64 1.408791
O10 H142 0.965407
O11 C69 1.405623
O11 H143 0.978800
O12 C66 1.222507
O13 C72 1.227010
N14 C30 1.457548
N14 C37 1.328715
N14 H80 1.011703
N15 C34 1.467567
N15 H82 1.007308
N15 C35 1.338191
N16 C48 1.337522
N16 H97 1.007019
N16 C33 1.444845
N17 C45 1.348109
N17 C39 1.451799
N17 H101 1.019183
N18 C36 1.456379
N18 C50 1.338098
N18 H102 1.009809
N19 H108 1.011101
N19 C46 1.454237
N19 C52 1.344382
N20 H111 1.019316
N20 C38 1.447754
N20 C60 1.335188
N21 H112 1.007873
N21 C56 1.339807
N21 C49 1.451474
N22 C66 1.344385
N22 H123 1.010198
N22 C59 1.457057
N23 C54 1.481422
N23 H24 1.023680
N23 H124 1.022900
N23 H125 1.039025
N25 C57 1.482326
N25 H26 1.026463
N25 H130 1.026828
N25 H129 1.027495
N27 H28 1.025878
N27 H133 1.024574
N27 H132 1.038231
N27 C58 1.486030
N29 C72 1.350563
N29 C65 1.456981
N29 H138 1.011491
C30 H74 1.094243
C30 C31 1.530490
C30 C35 1.534741
C31 H75 1.090931
C31 H76 1.091097
C31 C32 1.536363
C32 C41 1.526798
C32 H77 1.095204
C32 C42 1.528934
C33 H78 1.096461
C33 C37 1.531078
C33 C43 1.538826
C34 H79 1.093245
C34 C40 1.535370
C34 C45 1.541810
C36 C47 1.540557
C36 H81 1.096385
C36 C48 1.540330
C38 C44 1.536995
C38 H83 1.096961
C38 C50 1.536206
C39 H84 1.091505
C39 C52 1.539796
C39 C51 1.543995
C40 C54 1.524479
C40 H85 1.087712
C40 H86 1.088518
C41 H91 1.088450
C41 H90 1.088190
C41 H89 1.086163
C42 H93 1.087696
C42 H92 1.088133
C42 H94 1.087979
C43 C55 1.502229
C43 H88 1.089283
C43 H87 1.089150
C44 H96 1.090422
C44 H95 1.090538
C44 C49 1.534184
C46 H98 1.096307
C46 C56 1.536632
C46 C53 1.539324
C47 H100 1.091193
C47 C57 1.532641
C47 H99 1.089822
C49 H104 1.088217
C49 H103 1.092779
C51 H106 1.088543
C51 H105 1.089033
C51 C58 1.529456
C53 H107 1.096934
C53 C61 1.519858
C54 H110 1.090335
C54 H109 1.089418
C55 C62 1.388810
C55 C63 1.388870
C57 H114 1.089860
C57 H113 1.090692
C58 H115 1.089224
C58 H116 1.089480
C59 C60 1.538502
C59 H117 1.099405
C59 C64 1.544407
C61 H120 1.087254
C61 H118 1.088493
C61 H119 1.086675
C62 H121 1.080890
C62 C67 1.383175
C63 H122 1.078785
C63 C68 1.383709
C64 H126 1.093073
C64 H127 1.091882
C65 C66 1.523787
C65 C69 1.562840
C65 H128 1.099520
C67 C70 1.385407
C67 H134 1.081105
C68 C70 1.384123
C68 H135 1.079591
C69 H136 1.097549
C69 C71 1.528318
C70 H137 1.080546
C71 H141 1.086976
C71 H139 1.086355
C71 H140 1.082993
C72 C73 1.505200
C73 H144 1.085662
C73 H146 1.086073
C73 H145 1.088216

MOLECULAR INFO

Charge: 3
Spin polarization: 1
Multiplicity: 2

JOB |

Calculation Setup

Parameter Value
program call xtb SPR-741.xyz --opt extreme --cycles 10000 --charge +3 --uhf 1 --alpb water
coordinate file SPR-741.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 -223.1627525558 Eh
SCC Energy -225.7791797696 Eh
Isotropic ES 1.1458739817 Eh
Anisotropic ES -0.1037485366 Eh
Anisotropic XC 0.0725172219 Eh
Dispersion -0.1690308978 Eh
Repulsion Energy 2.6164272138 Eh
Additional Restraining 0 Eh
Property Value Units
Gradient Norm 0.0000418597 Eh/Bohr
HOMO-LUMO Gap 3.859244 eV

Orbital Energies

# Occupation Energy (eV)
1 2.0000 -19.8504

Multipole molecular moments

Dipole moment

Type X Y Z Total (D)
q only 12.928 21.605 2.518 25.303
full 12.105 19.074 2.403 57.744

Quadrupole moment (Traceless)

Type XX XY YY XZ YZ ZZ
q only -3.454 58.565 23.579 105.843 -37.570 -20.125
q+dip 7.329 58.140 13.100 107.563 -37.993 -20.429
full 4.169 58.713 14.709 109.446 -39.564 -18.878

Timings

Property Value Units
Wall time 40.643 s
CPU time 40.405 s
End time 2026-02-09T17:24:40.336


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