# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:48:10 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: [[(3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-ylidene]amino] N-(4-chlorophenyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1N\C(=N/OC(=O)Nc2ccc(Cl)cc2)[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
 GHR  GHR  '[[(3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)piperidin-2-ylidene]amino] N-(4-chlorophenyl)carbamate'  ligand  39  23  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GHR
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
 GHR  C1    C   C     0   0.456   2.4127  -0.6177  -0.3886
 GHR  N5    N   NH1   0  -0.665   2.7314   0.6722  -0.1916
 GHR  C5    C   CH1   0  -0.117   3.9679   1.1231   0.4283
 GHR  C6    C   CH2   0  -0.142   4.2345   2.5560   0.0007
 GHR  O6    O   OH1   0  -0.672   3.1302   3.3369   0.3998
 GHR  C4    C   CH1   0   0.032   5.1176   0.1995   0.0489
 GHR  O4    O   OH1   0  -0.668   6.2295   0.5806   0.8133
 GHR  C3    C   CH1   0   0.002   4.7239  -1.2474   0.3178
 GHR  O3    O   OH1   0  -0.672   5.8432  -2.0463   0.0297
 GHR  C2    C   CH1   0  -0.026   3.5393  -1.6170  -0.5621
 GHR  O2    O   OH1   0  -0.664   3.1434  -2.9231  -0.2637
 GHR  N1    N   N     0  -0.249   1.2426  -1.1191  -0.5580
 GHR  C12   C   CR6   0  -0.058  -5.9811   0.5416   0.1999
 GHR  C11   C   CR16  0  -0.201  -5.2937  -0.6006   0.5709
 GHR  C10   C   CR16  0  -0.316  -3.9171  -0.6714   0.4139
 GHR  C13   C   CR16  0  -0.202  -5.3009   1.6263  -0.3306
 GHR  C14   C   CR16  0  -0.344  -3.9295   1.5542  -0.4913
 GHR  C9    C   CR6   0   0.382  -3.2188   0.4088  -0.1261
 GHR  N9    N   NH1   0  -0.777  -1.8366   0.4416  -0.3104
 GHR  C8    C   C     0   0.752  -0.9660  -0.5986  -0.2461
 GHR  O8    O   O     0  -0.468  -1.2305  -1.7505  -0.0190
 GHR  O7    O   O2    0  -0.423   0.2697  -0.1225  -0.4782
 GHR  H5    H   HCH1  0   0.257   3.8622   1.0955   1.5216
 GHR  H6    H   HCH2  0   0.218   5.1627   2.9017   0.4664
 GHR  H6A   H   HCH2  0   0.207   4.3770   2.5805  -1.0869
 GHR  HO6   H   HOH1  0   0.463   3.2007   4.2001  -0.0175
 GHR  H4    H   HCH1  0   0.220   5.3192   0.3107  -1.0292
 GHR  HO4   H   HOH1  0   0.455   6.9419  -0.0425   0.6323
 GHR  H3    H   HCH1  0   0.234   4.4283  -1.3439   1.3737
 GHR  HO3   H   HOH1  0   0.463   5.7348  -2.9043   0.4510
 GHR  H2    H   HCH1  0   0.246   3.8602  -1.5286  -1.6129
 GHR  HO2   H   HOH1  0   0.456   2.2599  -3.0613  -0.6273
 GHR  H10   H   HCR6  0   0.288  -3.4091  -1.5701   0.7222
 GHR  H13   H   HCR6  0   0.283  -5.8291   2.5227  -0.6247
 GHR  H14   H   HCR6  0   0.282  -3.4062   2.4042  -0.9114
 GHR  HN9   H   HNH1  0   0.420  -1.4537   1.3351  -0.5839
 GHR  H16   H   HNH1  0   0.400   1.9662   1.3261  -0.1153
 GHR  H11   H   HCR6  0   0.282  -5.8209  -1.4466   0.9904
 GHR  CL12  CL  CL    0  -0.135  -7.7017   0.6188   0.4014

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
 GHR  C1   N1    double    1.284  0.020  1.284
 GHR  N5   C1    single    1.343  0.020  1.343
 GHR  C5   N5    single    1.455  0.020  1.455
 GHR  C5   H5    single    0.970  0.020  1.090
 GHR  C6   C5    single    1.519  0.020  1.519
 GHR  C6   O6    single    1.410  0.020  1.410
 GHR  C6   H6    single    0.970  0.020  1.090
 GHR  C6   H6A   single    0.970  0.020  1.090
 GHR  O6   HO6   single    0.850  0.020  0.980
 GHR  C4   C5    single    1.523  0.020  1.523
 GHR  C4   C3    single    1.524  0.020  1.524
 GHR  C4   H4    single    0.970  0.020  1.090
 GHR  O4   C4    single    1.402  0.020  1.402
 GHR  O4   HO4   single    0.850  0.020  0.980
 GHR  C3   C2    single    1.521  0.020  1.521
 GHR  C3   H3    single    0.970  0.020  1.090
 GHR  O3   C3    single    1.405  0.020  1.405
 GHR  O3   HO3   single    0.850  0.020  0.980
 GHR  C2   C1    single    1.516  0.020  1.516
 GHR  C2   O2    single    1.397  0.020  1.397
 GHR  C2   H2    single    0.970  0.020  1.090
 GHR  O2   HO2   single    0.850  0.020  0.980
 GHR  N1   O7    single    1.395  0.020  1.395
 GHR  C12  CL12  single    1.734  0.020  1.734
 GHR  C11  C12   aromatic  1.384  0.020  1.384
 GHR  C11  H11   single    0.930  0.020  1.080
 GHR  C10  C11   aromatic  1.387  0.020  1.387
 GHR  C10  H10   single    0.930  0.020  1.080
 GHR  C13  C12   aromatic  1.386  0.020  1.386
 GHR  C13  H13   single    0.930  0.020  1.080
 GHR  C14  C13   aromatic  1.383  0.020  1.383
 GHR  C14  H14   single    0.930  0.020  1.080
 GHR  C9   C10   aromatic  1.395  0.020  1.395
 GHR  C9   C14   aromatic  1.397  0.020  1.397
 GHR  N9   C9    single    1.395  0.020  1.395
 GHR  N9   HN9   single    0.860  0.020  1.020
 GHR  C8   N9    single    1.358  0.020  1.358
 GHR  C8   O7    single    1.344  0.020  1.344
 GHR  O8   C8    double    1.203  0.020  1.203
 GHR  N5   H16   single    0.890  0.020  1.040

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
 GHR  N1   C1   C2    113.87  3.000
 GHR  C2   C1   N5    118.27  3.000
 GHR  N1   C1   N5    127.62  3.000
 GHR  H16  N5   C5    114.28  3.000
 GHR  H16  N5   C1    116.96  3.000
 GHR  C5   N5   C1    124.17  3.000
 GHR  H5   C5   C4    107.78  3.000
 GHR  C4   C5   C6    111.69  3.000
 GHR  H5   C5   C6    108.70  3.000
 GHR  C4   C5   N5    110.34  3.000
 GHR  C6   C5   N5    108.76  3.000
 GHR  H5   C5   N5    109.54  3.000
 GHR  H6A  C6   H6    107.73  3.000
 GHR  H6A  C6   O6    111.71  3.000
 GHR  H6   C6   O6    111.64  3.000
 GHR  H6A  C6   C5    108.84  3.000
 GHR  H6   C6   C5    109.09  3.000
 GHR  O6   C6   C5    107.78  3.000
 GHR  HO6  O6   C6    108.48  3.000
 GHR  H4   C4   C3    108.40  3.000
 GHR  H4   C4   O4    111.15  3.000
 GHR  C3   C4   O4    111.52  3.000
 GHR  O4   C4   C5    107.35  3.000
 GHR  H4   C4   C5    108.69  3.000
 GHR  C3   C4   C5    109.69  3.000
 GHR  HO4  O4   C4    107.95  3.000
 GHR  H3   C3   C2    108.93  3.000
 GHR  H3   C3   O3    111.15  3.000
 GHR  C2   C3   O3    111.32  3.000
 GHR  O3   C3   C4    107.33  3.000
 GHR  H3   C3   C4    108.78  3.000
 GHR  C2   C3   C4    109.26  3.000
 GHR  HO3  O3   C3    109.12  3.000
 GHR  H2   C2   O2    111.17  3.000
 GHR  H2   C2   C3    107.77  3.000
 GHR  O2   C2   C3    108.92  3.000
 GHR  H2   C2   C1    105.82  3.000
 GHR  O2   C2   C1    112.41  3.000
 GHR  C3   C2   C1    110.63  3.000
 GHR  HO2  O2   C2    108.23  3.000
 GHR  O7   N1   C1    110.43  3.000
 GHR  C13  C12  C11   120.32  3.000
 GHR  C13  C12  CL12  119.78  3.000
 GHR  C11  C12  CL12  119.90  3.000
 GHR  H11  C11  C10   119.19  3.000
 GHR  C10  C11  C12   120.31  3.000
 GHR  H11  C11  C12   120.50  3.000
 GHR  H10  C10  C9    121.38  3.000
 GHR  C9   C10  C11   120.07  3.000
 GHR  H10  C10  C11   118.55  3.000
 GHR  H13  C13  C14   119.74  3.000
 GHR  C14  C13  C12   119.37  3.000
 GHR  H13  C13  C12   120.88  3.000
 GHR  H14  C14  C9    119.95  3.000
 GHR  C9   C14  C13   121.14  3.000
 GHR  H14  C14  C13   118.91  3.000
 GHR  N9   C9   C14   116.77  3.000
 GHR  N9   C9   C10   124.43  3.000
 GHR  C14  C9   C10   118.78  3.000
 GHR  HN9  N9   C8    116.58  3.000
 GHR  C8   N9   C9    127.66  3.000
 GHR  HN9  N9   C9    115.62  3.000
 GHR  O7   C8   O8    125.00  3.000
 GHR  O8   C8   N9    126.95  3.000
 GHR  O7   C8   N9    108.05  3.000
 GHR  C8   O7   N1    113.45  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
 GHR  CONST_01  C9   C10  C11  C12      0.00   0.0  0
 GHR  CONST_02  C9   C14  C13  C12      0.00   0.0  0
 GHR  CONST_03  C14  C13  C12  C11      0.00   0.0  0
 GHR  CONST_04  C14  C9   C10  C11      0.00   0.0  0
 GHR  CONST_05  C13  C12  C11  C10      0.00   0.0  0
 GHR  CONST_06  C13  C14  C9   C10      0.00   0.0  0
 GHR  CONST_08  C10  C11  C12  CL12   180.00   0.0  0
 GHR  CONST_09  C14  C13  C12  CL12   180.00   0.0  0
 GHR  CONST_10  N9   C9   C10  C11    180.00   0.0  0
 GHR  CONST_11  N9   C9   C14  C13    180.00   0.0  0
 GHR  CONST_13  H10  C10  C11  C12    180.00   0.0  0
 GHR  CONST_14  H14  C14  C13  C12    180.00   0.0  0
 GHR  CONST_15  H13  C13  C12  C11    180.00   0.0  0
 GHR  CONST_16  H11  C11  C12  C13    180.00   0.0  0
 GHR  CONST_17  H16  N5   C1   C2     180.00   0.0  0
 GHR  CONST_18  C8   N9   C9   C10      0.00   0.0  0
 GHR  CONST_19  C8   N9   C9   C14    180.00   0.0  0
 GHR  CONST_20  O7   N1   C1   N5       0.00   0.0  0
 GHR  CONST_21  O7   N1   C1   C2     180.00   0.0  0
 GHR  CONST_22  HN9  N9   C9   C10    180.00   0.0  0
 GHR  CONST_23  O7   C8   N9   C9     180.00   0.0  0
 GHR  CONST_24  O8   C8   N9   C9       0.00   0.0  0
 GHR  Var_01    N9   C8   O7   N1    -174.55  30.0  1

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
 GHR  chir_01  C5  N5  C6  C4  positiv
 GHR  chir_02  C4  O4  C5  C3  positiv
 GHR  chir_03  C3  O3  C4  C2  negativ
 GHR  chir_04  C2  O2  C3  C1  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
 GHR  plan-1  C12   0.020
 GHR  plan-1  C11   0.020
 GHR  plan-1  C10   0.020
 GHR  plan-1  C13   0.020
 GHR  plan-1  C14   0.020
 GHR  plan-1  C9    0.020
 GHR  plan-1  N9    0.020
 GHR  plan-1  H10   0.020
 GHR  plan-1  H13   0.020
 GHR  plan-1  H14   0.020
 GHR  plan-1  H11   0.020
 GHR  plan-1  CL12  0.020
 GHR  plan-2  C9    0.020
 GHR  plan-2  N9    0.020
 GHR  plan-2  C8    0.020
 GHR  plan-2  HN9   0.020
 GHR  plan-3  C1    0.020
 GHR  plan-3  N5    0.020
 GHR  plan-3  C5    0.020
 GHR  plan-3  C2    0.020
 GHR  plan-3  N1    0.020
 GHR  plan-3  O7    0.020
 GHR  plan-3  H16   0.020
 GHR  plan-4  N9    0.020
 GHR  plan-4  C8    0.020
 GHR  plan-4  O8    0.020
 GHR  plan-4  O7    0.020

