# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 22:47:42 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 11-[(sulfanylcarbonyl)oxy]undecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCCCCOC(S)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VZZ  VZZ  '11-[(sulfanylcarbonyl)oxy]undecanoic acid'  ligand  39  17  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VZZ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VZZ  O3    O  O     0  -0.446   8.3348  -1.2209  -0.0433
 VZZ  C12   C  C     0   0.549   8.2010  -0.0226  -0.0159
 VZZ  O4    O  OH1   0  -0.599   9.2323   0.8183   0.0084
 VZZ  C11   C  CH2   0  -0.580   6.8866   0.7066  -0.0077
 VZZ  C10   C  CH2   0  -0.418   5.6711  -0.2061  -0.0056
 VZZ  C9    C  CH2   0  -0.415   4.3712   0.5885  -0.0005
 VZZ  C8    C  CH2   0  -0.413   3.1317  -0.2974   0.0008
 VZZ  C7    C  CH2   0  -0.413   1.8322   0.4971   0.0056
 VZZ  C6    C  CH2   0  -0.413   0.5871  -0.3813   0.0030
 VZZ  C5    C  CH2   0  -0.413  -0.7073   0.4216   0.0072
 VZZ  C4    C  CH2   0  -0.429  -1.9553  -0.4526   0.0014
 VZZ  C3    C  CH2   0  -0.467  -3.2404   0.3680   0.0065
 VZZ  C2    C  CH2   0  -0.165  -4.4595  -0.5264  -0.0057
 VZZ  O2    O  O2    0  -0.444  -5.6258   0.3228   0.0030
 VZZ  C1    C  C     0   0.435  -6.8091  -0.2538  -0.0214
 VZZ  O1    O  O     0  -0.422  -7.0296  -1.4315  -0.0501
 VZZ  S1    S  S2    0  -0.175  -8.0342   1.0278  -0.0045
 VZZ  HO4   H  HOH1  0   0.478  10.0639   0.3215  -0.0048
 VZZ  H111  H  HCH2  0   0.274   6.8700   1.3702   0.8629
 VZZ  H112  H  HCH2  0   0.275   6.8640   1.3709  -0.8778
 VZZ  H101  H  HCH2  0   0.225   5.6950  -0.8587  -0.8827
 VZZ  H102  H  HCH2  0   0.225   5.7002  -0.8621   0.8689
 VZZ  H91   H  HCH2  0   0.212   4.3476   1.2454   0.8762
 VZZ  H92   H  HCH2  0   0.212   4.3435   1.2490  -0.8744
 VZZ  H81   H  HCH2  0   0.209   3.1541  -0.9544  -0.8759
 VZZ  H82   H  HCH2  0   0.209   3.1586  -0.9576   0.8749
 VZZ  H71   H  HCH2  0   0.208   1.8110   1.1523   0.8838
 VZZ  H72   H  HCH2  0   0.208   1.8092   1.1601  -0.8668
 VZZ  H61   H  HCH2  0   0.209   0.6064  -1.0365  -0.8751
 VZZ  H62   H  HCH2  0   0.209   0.6075  -1.0433   0.8759
 VZZ  H51   H  HCH2  0   0.212  -0.7271   1.0746   0.8869
 VZZ  H52   H  HCH2  0   0.212  -0.7264   1.0854  -0.8642
 VZZ  H41   H  HCH2  0   0.219  -1.9382  -1.1039  -0.8790
 VZZ  H42   H  HCH2  0   0.219  -1.9387  -1.1154   0.8732
 VZZ  H31   H  HCH2  0   0.235  -3.2627   1.0090   0.8927
 VZZ  H32   H  HCH2  0   0.234  -3.2586   1.0259  -0.8672
 VZZ  H21   H  HCH2  0   0.242  -4.4739  -1.1550  -0.8989
 VZZ  H22   H  HCH2  0   0.242  -4.4771  -1.1766   0.8718
 VZZ  HS1   H  HSH1  0   0.259  -9.0893   0.2075  -0.0405

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VZZ  O3   C12   double  1.206  0.020  1.206
 VZZ  C12  O4    single  1.331  0.020  1.331
 VZZ  C12  C11   single  1.503  0.020  1.503
 VZZ  O4   HO4   single  0.850  0.020  0.980
 VZZ  C11  C10   single  1.520  0.020  1.520
 VZZ  C11  H111  single  0.970  0.020  1.090
 VZZ  C11  H112  single  0.970  0.020  1.090
 VZZ  C10  C9    single  1.524  0.020  1.524
 VZZ  C10  H101  single  0.970  0.020  1.090
 VZZ  C10  H102  single  0.970  0.020  1.090
 VZZ  C9   C8    single  1.524  0.020  1.524
 VZZ  C9   H91   single  0.970  0.020  1.090
 VZZ  C9   H92   single  0.970  0.020  1.090
 VZZ  C8   C7    single  1.523  0.020  1.523
 VZZ  C8   H81   single  0.970  0.020  1.090
 VZZ  C8   H82   single  0.970  0.020  1.090
 VZZ  C7   C6    single  1.524  0.020  1.524
 VZZ  C7   H71   single  0.970  0.020  1.090
 VZZ  C7   H72   single  0.970  0.020  1.090
 VZZ  C6   C5    single  1.523  0.020  1.523
 VZZ  C6   H61   single  0.970  0.020  1.090
 VZZ  C6   H62   single  0.970  0.020  1.090
 VZZ  C5   C4    single  1.524  0.020  1.524
 VZZ  C5   H51   single  0.970  0.020  1.090
 VZZ  C5   H52   single  0.970  0.020  1.090
 VZZ  C4   C3    single  1.525  0.020  1.525
 VZZ  C4   H41   single  0.970  0.020  1.090
 VZZ  C4   H42   single  0.970  0.020  1.090
 VZZ  C3   C2    single  1.512  0.020  1.512
 VZZ  C3   H31   single  0.970  0.020  1.090
 VZZ  C3   H32   single  0.970  0.020  1.090
 VZZ  C2   O2    single  1.443  0.020  1.443
 VZZ  C2   H21   single  0.970  0.020  1.090
 VZZ  C2   H22   single  0.970  0.020  1.090
 VZZ  O2   C1    single  1.317  0.020  1.317
 VZZ  C1   O1    double  1.198  0.020  1.198
 VZZ  C1   S1    single  1.773  0.020  1.773
 VZZ  S1   HS1   single  1.200  0.020  1.300

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VZZ  C11   C12  O4    111.78  3.000
 VZZ  C11   C12  O3    125.38  3.000
 VZZ  O4    C12  O3    122.84  3.000
 VZZ  HO4   O4   C12   109.94  3.000
 VZZ  H112  C11  H111  105.30  3.000
 VZZ  H112  C11  C10   110.42  3.000
 VZZ  H111  C11  C10   110.53  3.000
 VZZ  H112  C11  C12   107.94  3.000
 VZZ  H111  C11  C12   108.16  3.000
 VZZ  C10   C11  C12   114.08  3.000
 VZZ  H102  C10  H101  106.43  3.000
 VZZ  H102  C10  C9    109.44  3.000
 VZZ  H101  C10  C9    109.42  3.000
 VZZ  H102  C10  C11   109.88  3.000
 VZZ  H101  C10  C11   109.87  3.000
 VZZ  C9    C10  C11   111.66  3.000
 VZZ  H92   C9   H91   106.03  3.000
 VZZ  H92   C9   C8    109.31  3.000
 VZZ  H91   C9   C8    109.29  3.000
 VZZ  H92   C9   C10   109.47  3.000
 VZZ  H91   C9   C10   109.50  3.000
 VZZ  C8    C9   C10   113.01  3.000
 VZZ  H82   C8   H81   106.06  3.000
 VZZ  H82   C8   C7    109.43  3.000
 VZZ  H81   C8   C7    109.43  3.000
 VZZ  H82   C8   C9    109.34  3.000
 VZZ  H81   C8   C9    109.35  3.000
 VZZ  C7    C8   C9    113.00  3.000
 VZZ  H72   C7   H71   106.01  3.000
 VZZ  H72   C7   C6    109.28  3.000
 VZZ  H71   C7   C6    109.27  3.000
 VZZ  H72   C7   C8    109.33  3.000
 VZZ  H71   C7   C8    109.33  3.000
 VZZ  C6    C7   C8    113.35  3.000
 VZZ  H62   C6   H61   106.07  3.000
 VZZ  H62   C6   C5    109.39  3.000
 VZZ  H61   C6   C5    109.41  3.000
 VZZ  H62   C6   C7    109.37  3.000
 VZZ  H61   C6   C7    109.37  3.000
 VZZ  C5    C6   C7    112.99  3.000
 VZZ  H52   C5   H51   106.10  3.000
 VZZ  H52   C5   C4    109.29  3.000
 VZZ  H51   C5   C4    109.28  3.000
 VZZ  H52   C5   C6    109.39  3.000
 VZZ  H51   C5   C6    109.37  3.000
 VZZ  C4    C5   C6    113.18  3.000
 VZZ  H42   C4   H41   106.25  3.000
 VZZ  H42   C4   C3    109.62  3.000
 VZZ  H41   C4   C3    109.63  3.000
 VZZ  H42   C4   C5    109.37  3.000
 VZZ  H41   C4   C5    109.36  3.000
 VZZ  C3    C4   C5    112.42  3.000
 VZZ  H32   C3   H31   107.12  3.000
 VZZ  H32   C3   C2    109.62  3.000
 VZZ  H31   C3   C2    109.68  3.000
 VZZ  H32   C3   C4    109.58  3.000
 VZZ  H31   C3   C4    109.59  3.000
 VZZ  C2    C3   C4    111.17  3.000
 VZZ  H22   C2   H21   108.31  3.000
 VZZ  H22   C2   O2    109.42  3.000
 VZZ  H21   C2   O2    109.45  3.000
 VZZ  H22   C2   C3    111.01  3.000
 VZZ  H21   C2   C3    110.96  3.000
 VZZ  O2    C2   C3    107.67  3.000
 VZZ  C1    O2   C2    117.95  3.000
 VZZ  S1    C1   O1    125.69  3.000
 VZZ  S1    C1   O2    107.71  3.000
 VZZ  O1    C1   O2    126.60  3.000
 VZZ  HS1   S1   C1     95.83  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VZZ  CONST_01  HO4  O4   C12  O3      0.00   0.0  0
 VZZ  Var_01    C10  C11  C12  O3      1.32  30.0  3
 VZZ  Var_02    C9   C10  C11  C12  -179.87  30.0  3
 VZZ  Var_03    C8   C9   C10  C11   179.96  30.0  3
 VZZ  Var_04    C7   C8   C9   C10  -179.99  30.0  3
 VZZ  Var_05    C6   C7   C8   C9    179.84  30.0  3
 VZZ  Var_06    C5   C6   C7   C8   -179.98  30.0  3
 VZZ  Var_07    C4   C5   C6   C7    179.87  30.0  3
 VZZ  Var_08    C3   C4   C5   C6    179.97  30.0  3
 VZZ  Var_09    C2   C3   C4   C5    179.74  30.0  3
 VZZ  Var_10    O2   C2   C3   C4    179.87  30.0  3
 VZZ  Var_11    O1   C1   O2   C2      0.04  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VZZ  plan-1  O3   0.020
 VZZ  plan-1  C12  0.020
 VZZ  plan-1  O4   0.020
 VZZ  plan-1  C11  0.020
 VZZ  plan-1  HO4  0.020
 VZZ  plan-2  O2   0.020
 VZZ  plan-2  C1   0.020
 VZZ  plan-2  O1   0.020
 VZZ  plan-2  S1   0.020

