GENERAL INFO

Title: /AB-DB Lipo-glyco-peptides - Chloroeremomycin +2 Lipo-glyco-peptides - Chloroeremomycin +2 opt
Browse item: https://iochem-bd.bsc.es:443/browse/handle/100/500224
Program: xtb 6.7.1 (edcfbbe)
Author: Hospital Gasch, Adam: Malloci, Giuliano: Gervasoni, Silvia
Formula: C73H90Cl2N10O26
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 C78 1.746917
Cl2 C95 1.722239
O3 C46 1.439662
O3 C45 1.388897
O4 C47 1.399810
O4 C45 1.437651
O5 C52 1.398661
O5 C53 1.433501
O6 H138 0.967655
O6 C43 1.396209
O7 C57 1.436120
O7 C58 1.394324
O8 C52 1.419006
O8 C64 1.384094
O9 H149 0.972666
O9 C48 1.400879
O10 C58 1.423222
O10 C62 1.410550
O11 H150 0.966468
O11 C51 1.406056
O12 C54 1.408139
O12 H152 0.962275
O13 H154 0.969258
O13 C60 1.404769
O14 C66 1.362936
O14 C74 1.380434
O15 C67 1.373115
O15 C84 1.385462
O16 C68 1.225179
O17 C76 1.219540
O18 C81 1.221793
O19 C89 1.238224
O20 C89 1.239831
O21 C90 1.224220
O22 C93 1.353878
O22 H182 0.967999
O23 C97 1.361772
O23 H183 0.970348
O24 H187 0.966007
O24 C99 1.408641
O25 C101 1.355313
O25 H188 0.968985
O26 C106 1.222134
O27 C108 1.227920
O28 C109 1.227332
N29 C42 1.492176
N29 H130 1.026193
N29 H129 1.026049
N29 H30 1.041908
N31 C50 1.492742
N31 H145 1.025191
N31 H144 1.034458
N31 H32 1.025740
N33 C76 1.346570
N33 H155 1.010448
N33 C63 1.453829
N34 H163 1.011600
N34 C68 1.341169
N34 C80 1.444835
N35 C77 1.444724
N35 H165 1.014881
N35 C81 1.332698
N36 C90 1.338639
N36 C75 1.446814
N36 H166 1.012480
N37 C106 1.338540
N37 H179 1.011454
N37 C91 1.446230
N38 C100 1.445998
N38 C109 1.329888
N38 H181 1.016659
N39 C114 1.471507
N39 H40 1.046377
N39 H190 1.024304
N39 C107 1.482945
N41 C108 1.329591
N41 H192 1.005534
N41 H191 1.008783
C42 C44 1.535287
C42 C43 1.557108
C42 C49 1.526125
C43 C46 1.541161
C43 H115 1.095181
C44 H116 1.089285
C44 C45 1.531414
C44 H117 1.088252
C45 H118 1.097903
C46 C56 1.523172
C46 H119 1.100934
C47 C52 1.533288
C47 H120 1.097489
C47 C48 1.550109
C48 H121 1.094971
C48 C51 1.541052
C49 H123 1.085639
C49 H124 1.086248
C49 H122 1.085831
C50 C54 1.550422
C50 C55 1.537501
C50 C59 1.523408
C51 H125 1.099152
C51 C53 1.541948
C52 H126 1.096636
C53 H127 1.099140
C53 C60 1.536489
C54 C57 1.544275
C54 H128 1.097644
C55 H132 1.088521
C55 H131 1.087723
C55 C58 1.531428
C56 H134 1.084311
C56 H133 1.086732
C56 H135 1.084555
C57 C61 1.532491
C57 H136 1.099019
C58 H137 1.102037
C59 H140 1.085467
C59 H141 1.084025
C59 H139 1.085360
C60 H142 1.097578
C60 H143 1.090370
C61 H147 1.085686
C61 H148 1.085265
C61 H146 1.086937
C62 C63 1.557534
C62 H151 1.098561
C62 C65 1.505679
C63 C68 1.548344
C63 H153 1.094395
C64 C66 1.401015
C64 C67 1.393705
C65 C70 1.387025
C65 C69 1.388048
C66 C72 1.391609
C67 C73 1.386793
C69 H156 1.079891
C69 C78 1.380947
C70 C79 1.382216
C70 H157 1.076725
C71 C75 1.526813
C71 C73 1.382492
C71 C72 1.385478
C72 H158 1.078153
C73 H159 1.074728
C74 C78 1.394998
C74 C79 1.387732
C75 H160 1.096314
C75 C81 1.531898
C76 C77 1.550629
C77 H161 1.093452
C77 C82 1.510079
C79 H162 1.077683
C80 H164 1.096360
C80 C83 1.502790
C80 C89 1.602530
C82 C88 1.390902
C82 C86 1.387657
C83 C92 1.393449
C83 C85 1.405487
C84 C96 1.390786
C84 C95 1.392662
C85 C87 1.483695
C85 C97 1.406937
C86 C87 1.391765
C86 H167 1.078935
C87 C93 1.405592
C88 C94 1.380922
C88 H168 1.077851
C90 C91 1.544873
C91 C104 1.536549
C91 H169 1.098374
C92 C101 1.386398
C92 H170 1.080947
C93 C94 1.395234
C94 H171 1.077348
C95 C102 1.385507
C96 C103 1.379790
C96 H172 1.079335
C97 C105 1.384259
C98 C103 1.389571
C98 C99 1.512505
C98 C102 1.390821
C99 C100 1.562094
C99 H173 1.098361
C100 H174 1.097460
C100 C106 1.532703
C101 C105 1.387156
C102 H177 1.077843
C103 H178 1.078225
C104 C108 1.525924
C104 H176 1.086899
C104 H175 1.092215
C105 H180 1.076539
C107 C109 1.537318
C107 C110 1.535090
C107 H184 1.092729
C110 C111 1.539175
C110 H186 1.090695
C110 H185 1.091414
C111 C112 1.529383
C111 H189 1.095863
C111 C113 1.528803
C112 H195 1.087916
C112 H194 1.086707
C112 H193 1.087005
C113 H197 1.088224
C113 H198 1.086738
C113 H196 1.087261
C114 H200 1.087010
C114 H201 1.086288
C114 H199 1.087078

MOLECULAR INFO

Charge: 2
Spin polarization: 1
Multiplicity: 2

JOB |

Calculation Setup

Parameter Value
program call xtb chloroeremomycin.xyz --opt extreme --cycles 10000 --charge +2 --uhf 1 --alpb water
coordinate file chloroeremomycin.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 -346.0312097168 Eh
SCC Energy -349.8441952509 Eh
Isotropic ES 1.2620407979 Eh
Anisotropic ES -0.1367447465 Eh
Anisotropic XC 0.0453905711 Eh
Dispersion -0.2962502564 Eh
Repulsion Energy 3.8129855341 Eh
Additional Restraining 0 Eh
Property Value Units
Gradient Norm 0.0001132932 Eh/Bohr
HOMO-LUMO Gap 2.885493 eV

Orbital Energies

# Occupation Energy (eV)
1 2.0000 -29.3497

Multipole molecular moments

Dipole moment

Type X Y Z Total (D)
q only 13.286 -15.451 -24.250 31.675
full 12.674 -13.020 -21.805 72.143

Quadrupole moment (Traceless)

Type XX XY YY XZ YZ ZZ
q only 547.304 -315.413 -294.837 398.832 -163.206 -252.467
q+dip 524.223 -285.236 -285.799 398.702 -141.903 -238.424
full 526.484 -283.857 -285.717 398.591 -145.145 -240.767

Timings

Property Value Units
Wall time 215.627 s
CPU time 214.280 s
End time 2026-02-06T11:14:20.363


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