# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:12:17 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (1R,2R,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl (1Z)-2-phenyl-N-(sulfooxy)ethanimidothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@@H](S\C(Cc2ccccc2)=N/O[S](O)(=O)=O)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 CGT  CGT  '(1R,2R,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl (1Z)-2-phenyl-N-(sulfooxy)ethanimidothioate'  ligand  47  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CGT
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
 CGT  C1    C  CH1   0  -0.446   1.6780  -0.1549  -0.5460
 CGT  S1    S  S2    0   0.054   0.4839  -0.1348  -1.9390
 CGT  C2    C  CH1   0   0.103   1.8507  -1.5657  -0.0129
 CGT  O2    O  OH1   0  -0.659   0.6157  -2.0086   0.4936
 CGT  C3    C  CH1   0  -0.009   2.9263  -1.5671   1.0743
 CGT  O3    O  OH1   0  -0.679   3.1522  -2.8778   1.5522
 CGT  C4    C  CH1   0   0.075   4.2527  -1.0350   0.5406
 CGT  O4    O  OH1   0  -0.676   5.2286  -1.0292   1.5545
 CGT  C5    C  CH1   0  -0.326   4.0783   0.3826   0.0052
 CGT  C7    C  CH2   0  -0.416   2.9963   0.3937  -1.0773
 CGT  C6    C  CH2   0  -0.125   5.3953   0.9274  -0.5296
 CGT  O6    O  OH1   0  -0.673   5.1960   2.2493  -0.9793
 CGT  CB    C  CH2   0  -0.562  -1.9176  -1.4741  -1.4900
 CGT  CG    C  CR6   0   0.127  -3.2083  -1.5816  -0.7284
 CGT  CD1   C  CR16  0  -0.310  -4.4269  -1.3481  -1.3527
 CGT  CD2   C  CR16  0  -0.278  -3.1970  -1.9125   0.6256
 CGT  CE1   C  CR16  0  -0.241  -5.6177  -1.4426  -0.6415
 CGT  CE2   C  CR16  0  -0.244  -4.3818  -2.0056   1.3388
 CGT  CZ    C  CR16  0  -0.268  -5.5979  -1.7697   0.7062
 CGT  C13   C  C     0   0.128  -1.0862  -0.2763  -1.1325
 CGT  N17   N  N     0  -0.116  -1.5957   0.5774  -0.3482
 CGT  O18   O  OC2   0  -0.472  -0.7677   1.6802  -0.1282
 CGT  S19   S  S     0   1.666  -1.5020   2.6841   0.9099
 CGT  O20   O  OS    0  -0.612  -2.7663   3.0955   0.3680
 CGT  O21   O  OS    0  -0.610  -0.4785   3.6223   1.2593
 CGT  O22   O  OS    0  -0.693  -1.7132   1.7624   2.1741
 CGT  H1    H  HCH1  0   0.293   1.3075   0.5003   0.2443
 CGT  H2    H  HCH1  0   0.220   2.1896  -2.2063  -0.8401
 CGT  HA    H  HOH1  0   0.458   0.6250  -2.9692   0.5376
 CGT  H3    H  HCH1  0   0.223   2.5970  -0.9088   1.8923
 CGT  HB    H  HOH1  0   0.462   2.5750  -3.0413   2.3028
 CGT  H4    H  HCH1  0   0.199   4.5711  -1.6804  -0.2970
 CGT  HC    H  HOH1  0   0.447   5.2524  -1.9118   1.9405
 CGT  H5    H  HCH1  0   0.241   3.7479   1.0201   0.8360
 CGT  H7C1  H  HCH2  0   0.272   2.8454   1.4090  -1.4420
 CGT  H7C2  H  HCH2  0   0.238   3.3326  -0.2079  -1.9302
 CGT  H6C1  H  HCH2  0   0.185   5.7432   0.2739  -1.3433
 CGT  H6C2  H  HCH2  0   0.215   6.1534   0.8909   0.2588
 CGT  H6    H  HOH1  0   0.456   6.0452   2.5998  -1.2617
 CGT  HBC1  H  HCH2  0   0.294  -2.1082  -1.4293  -2.5667
 CGT  HBC2  H  HCH2  0   0.287  -1.2939  -2.3557  -1.3335
 CGT  HD1   H  HCR6  0   0.250  -4.4493  -1.0934  -2.4059
 CGT  HD2   H  HCR6  0   0.249  -2.2518  -2.0948   1.1236
 CGT  HE1   H  HCR6  0   0.255  -6.5594  -1.2593  -1.1429
 CGT  HE2   H  HCR6  0   0.255  -4.3586  -2.2626   2.3901
 CGT  HZ    H  HCR6  0   0.255  -6.5233  -1.8458   1.2625
 CGT  H22   H  H     0   0.509  -2.4695   1.1564   2.0780

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
 CGT  C1   S1    single    1.835  0.020  1.835
 CGT  C1   C2    single    1.518  0.020  1.518
 CGT  C1   C7    single    1.524  0.020  1.524
 CGT  C1   H1    single    0.970  0.020  1.090
 CGT  S1   C13   single    1.771  0.020  1.771
 CGT  C2   O2    single    1.406  0.020  1.406
 CGT  C2   C3    single    1.529  0.020  1.529
 CGT  C2   H2    single    0.970  0.020  1.090
 CGT  O2   HA    single    0.850  0.020  0.980
 CGT  C3   O3    single    1.413  0.020  1.413
 CGT  C3   C4    single    1.526  0.020  1.526
 CGT  C3   H3    single    0.970  0.020  1.090
 CGT  O3   HB    single    0.850  0.020  0.980
 CGT  C4   O4    single    1.407  0.020  1.407
 CGT  C4   C5    single    1.525  0.020  1.525
 CGT  C4   H4    single    0.970  0.020  1.090
 CGT  O4   HC    single    0.850  0.020  0.980
 CGT  C5   C7    single    1.531  0.020  1.531
 CGT  C5   C6    single    1.522  0.020  1.522
 CGT  C5   H5    single    0.970  0.020  1.090
 CGT  C7   H7C1  single    0.970  0.020  1.090
 CGT  C7   H7C2  single    0.970  0.020  1.090
 CGT  C6   O6    single    1.410  0.020  1.410
 CGT  C6   H6C1  single    0.970  0.020  1.090
 CGT  C6   H6C2  single    0.970  0.020  1.090
 CGT  O6   H6    single    0.850  0.020  0.980
 CGT  CB   CG    single    1.503  0.020  1.503
 CGT  CB   C13   single    1.501  0.020  1.501
 CGT  CB   HBC1  single    0.970  0.020  1.090
 CGT  CB   HBC2  single    0.970  0.020  1.090
 CGT  CG   CD1   aromatic  1.389  0.020  1.389
 CGT  CG   CD2   aromatic  1.394  0.020  1.394
 CGT  CD1  CE1   aromatic  1.390  0.020  1.390
 CGT  CD1  HD1   single    0.930  0.020  1.080
 CGT  CD2  CE2   aromatic  1.386  0.020  1.386
 CGT  CD2  HD2   single    0.930  0.020  1.080
 CGT  CE1  CZ    aromatic  1.387  0.020  1.387
 CGT  CE1  HE1   single    0.930  0.020  1.080
 CGT  CE2  CZ    aromatic  1.391  0.020  1.391
 CGT  CE2  HE2   single    0.930  0.020  1.080
 CGT  CZ   HZ    single    0.930  0.020  1.080
 CGT  C13  N17   double    1.266  0.020  1.266
 CGT  N17  O18   single    1.396  0.020  1.396
 CGT  O18  S19   single    1.620  0.020  1.620
 CGT  S19  O20   double    1.436  0.020  1.436
 CGT  S19  O21   double    1.432  0.020  1.432
 CGT  S19  O22   single    1.579  0.020  1.579
 CGT  O22  H22   single    0.850  0.020  0.980

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
 CGT  H1    C1   C7    109.28  3.000
 CGT  H1    C1   C2    110.02  3.000
 CGT  C7    C1   C2    111.02  3.000
 CGT  H1    C1   S1    108.80  3.000
 CGT  C7    C1   S1    107.12  3.000
 CGT  C2    C1   S1    110.54  3.000
 CGT  C13   S1   C1    103.32  3.000
 CGT  H2    C2   C3    108.51  3.000
 CGT  H2    C2   O2    110.98  3.000
 CGT  C3    C2   O2    111.18  3.000
 CGT  H2    C2   C1    108.20  3.000
 CGT  C3    C2   C1    109.30  3.000
 CGT  O2    C2   C1    108.62  3.000
 CGT  HA    O2   C2    108.82  3.000
 CGT  H3    C3   C4    108.16  3.000
 CGT  H3    C3   O3    110.57  3.000
 CGT  C4    C3   O3    107.62  3.000
 CGT  H3    C3   C2    108.50  3.000
 CGT  C4    C3   C2    111.25  3.000
 CGT  O3    C3   C2    110.71  3.000
 CGT  HB    O3   C3    109.02  3.000
 CGT  H4    C4   C5    108.05  3.000
 CGT  H4    C4   O4    110.42  3.000
 CGT  C5    C4   O4    109.16  3.000
 CGT  H4    C4   C3    108.20  3.000
 CGT  C5    C4   C3    110.34  3.000
 CGT  O4    C4   C3    110.63  3.000
 CGT  HC    O4   C4    107.57  3.000
 CGT  H5    C5   C6    108.57  3.000
 CGT  H5    C5   C7    108.56  3.000
 CGT  C6    C5   C7    111.13  3.000
 CGT  H5    C5   C4    107.96  3.000
 CGT  C6    C5   C4    110.92  3.000
 CGT  C7    C5   C4    109.62  3.000
 CGT  H7C2  C7   H7C1  107.06  3.000
 CGT  H7C2  C7   C5    109.22  3.000
 CGT  H7C1  C7   C5    109.97  3.000
 CGT  H7C2  C7   C1    109.82  3.000
 CGT  H7C1  C7   C1    109.42  3.000
 CGT  C5    C7   C1    111.25  3.000
 CGT  H6C2  C6   H6C1  107.09  3.000
 CGT  H6C2  C6   O6    111.03  3.000
 CGT  H6C1  C6   O6    111.45  3.000
 CGT  H6C2  C6   C5    109.53  3.000
 CGT  H6C1  C6   C5    108.72  3.000
 CGT  O6    C6   C5    108.98  3.000
 CGT  H6    O6   C6    108.09  3.000
 CGT  HBC2  CB   HBC1  105.89  3.000
 CGT  HBC2  CB   C13   107.09  3.000
 CGT  HBC1  CB   C13   107.34  3.000
 CGT  HBC2  CB   CG    111.13  3.000
 CGT  HBC1  CB   CG    110.61  3.000
 CGT  C13   CB   CG    114.34  3.000
 CGT  CD2   CG   CD1   118.93  3.000
 CGT  CD2   CG   CB    120.16  3.000
 CGT  CD1   CG   CB    120.91  3.000
 CGT  HD1   CD1  CE1   119.69  3.000
 CGT  HD1   CD1  CG    119.64  3.000
 CGT  CE1   CD1  CG    120.67  3.000
 CGT  HD2   CD2  CE2   119.85  3.000
 CGT  HD2   CD2  CG    119.56  3.000
 CGT  CE2   CD2  CG    120.59  3.000
 CGT  HE1   CE1  CZ    120.17  3.000
 CGT  HE1   CE1  CD1   119.78  3.000
 CGT  CZ    CE1  CD1   120.06  3.000
 CGT  HE2   CE2  CZ    120.04  3.000
 CGT  HE2   CE2  CD2   119.83  3.000
 CGT  CZ    CE2  CD2   120.13  3.000
 CGT  HZ    CZ   CE2   120.12  3.000
 CGT  HZ    CZ   CE1   120.24  3.000
 CGT  CE2   CZ   CE1   119.63  3.000
 CGT  N17   C13  CB    117.55  3.000
 CGT  N17   C13  S1    125.80  3.000
 CGT  CB    C13  S1    116.51  3.000
 CGT  O18   N17  C13   113.04  3.000
 CGT  S19   O18  N17   108.76  3.000
 CGT  O22   S19  O21   106.42  3.000
 CGT  O22   S19  O20   110.59  3.000
 CGT  O21   S19  O20   122.26  3.000
 CGT  O22   S19  O18   102.24  3.000
 CGT  O21   S19  O18   103.79  3.000
 CGT  O20   S19  O18   109.56  3.000
 CGT  H22   O22  S19   112.84  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
 CGT  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 CGT  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 CGT  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 CGT  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 CGT  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 CGT  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 CGT  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 CGT  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 CGT  CONST_09  HE1  CE1  CD1  CG    180.00   0.0  0
 CGT  CONST_10  HE2  CE2  CD2  CG    180.00   0.0  0
 CGT  CONST_11  HD2  CD2  CG   CD1   180.00   0.0  0
 CGT  CONST_12  HZ   CZ   CE1  CD1   180.00   0.0  0
 CGT  CONST_13  HD1  CD1  CG   CD2   180.00   0.0  0
 CGT  Var_01    C13  CB   CG   CD1   108.42  30.0  2
 CGT  Var_02    CB   C13  S1   C1   -119.56  30.0  3
 CGT  Var_03    CG   CB   C13  S1    177.13  30.0  3
 CGT  Var_04    O20  S19  O18  N17   -58.75  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CGT  chir_01  C1  S1  C2  C7  negativ
 CGT  chir_02  C2  O2  C1  C3  negativ
 CGT  chir_03  C3  O3  C2  C4  positiv
 CGT  chir_04  C4  O4  C3  C5  negativ
 CGT  chir_05  C5  C4  C7  C6  positiv

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
 CGT  plan-1  CB   0.020
 CGT  plan-1  CG   0.020
 CGT  plan-1  CD1  0.020
 CGT  plan-1  CD2  0.020
 CGT  plan-1  CE1  0.020
 CGT  plan-1  CE2  0.020
 CGT  plan-1  CZ   0.020
 CGT  plan-1  HD1  0.020
 CGT  plan-1  HD2  0.020
 CGT  plan-1  HE1  0.020
 CGT  plan-1  HE2  0.020
 CGT  plan-1  HZ   0.020
 CGT  plan-2  S1   0.020
 CGT  plan-2  CB   0.020
 CGT  plan-2  C13  0.020
 CGT  plan-2  N17  0.020
 CGT  plan-2  O18  0.020

