# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:57:20 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3~{R},4~{R},5~{S})-4-acetamido-5-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]-3-pentan-3-yloxy-cyclohexene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1C=C(C[C@@H]([C@H]1NC(C)=O)n2cc(CO)nn2)C(O)=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
 GJT  GJT  '(3~{R},4~{R},5~{S})-4-acetamido-5-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]-3-pentan-3-yloxy-cyclohexene-1-carboxylic acid'  ligand  51  26  .  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_GJT
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
 GJT  N1   N  NH1    0  -0.632  -0.2326  -1.6923  -0.3899
 GJT  N3   N  N      0  -0.327  -4.1291  -0.6808  -1.1975
 GJT  C4   C  CH2    0  -0.431   4.6150  -0.4444   1.0927
 GJT  C5   C  CH3    0  -0.668   4.4471   0.9601   1.6531
 GJT  C6   C  CH1    0   0.060   1.4845   0.0547  -0.5342
 GJT  C7   C  C1     0  -0.256   1.6958   1.5408  -0.4919
 GJT  C8   C  C      0  -0.107   0.7256   2.4510  -0.4245
 GJT  C10  C  CH1    0  -0.101  -0.9177   0.6199  -0.8350
 GJT  C15  C  CR5    0   0.107  -4.1772  -0.4595   0.1322
 GJT  C17  C  C      0   0.397   1.0570   3.9361  -0.3436
 GJT  C1   C  CH3    0  -0.678   3.1599  -2.5882  -1.8262
 GJT  C2   C  CH2    0  -0.411   3.9789  -2.1748  -0.6115
 GJT  O1   O  O2     0  -0.503   2.3545  -0.6349   0.3329
 GJT  C9   C  CH2    0  -0.483  -0.7239   2.0627  -0.3902
 GJT  C11  C  CH1    0  -0.123   0.0621  -0.3117  -0.1168
 GJT  C12  C  C      0   0.531  -0.4200  -2.6293   0.5606
 GJT  O2   O  O      0  -0.499  -0.4067  -2.3834   1.7573
 GJT  N2   N  NR5    0  -0.259  -2.2828   0.1734  -0.6351
 GJT  C14  C  CR15   0  -0.080  -2.9827   0.0936   0.5122
 GJT  O3   O  OH1    0  -0.666  -5.0962  -0.3892   2.2824
 GJT  N4   N  N      0  -0.104  -2.9817  -0.3022  -1.6478
 GJT  O4   O  O      0  -0.591   2.2509   4.2692  -0.4639
 GJT  O5   O  OC    -1  -0.596   0.0857   4.6950  -0.1499
 GJT  H1   H  HNH1   0   0.398  -0.2566  -1.9813  -1.3556
 GJT  H2   H  HCH2   0   0.220   5.6490  -0.5855   0.7669
 GJT  H3   H  HCH2   0   0.216   4.4440  -1.1823   1.8835
 GJT  H4   H  HCH3   0   0.229   5.1578   1.1415   2.4600
 GJT  H5   H  HCH3   0   0.217   4.6197   1.7191   0.8872
 GJT  H6   H  HCH3   0   0.224   3.4454   1.1167   2.0524
 GJT  H7   H  HCH1   0   0.224   1.6379  -0.2859  -1.5704
 GJT  H9   H  H      0   0.247   2.7219   1.8885  -0.5325
 GJT  H11  H  HCH1   0   0.289  -0.7530   0.5522  -1.9140
 GJT  H12  H  HCH3   0   0.269   0.2442  -4.6312   0.2540
 GJT  H13  H  HCH3   0   0.266  -1.4782  -4.4845   0.5635
 GJT  H14  H  HCH3   0   0.249  -0.8285  -4.0728  -1.0303
 GJT  H15  H  HCH3   0   0.218   3.2760  -1.8806  -2.6497
 GJT  H16  H  HCH3   0   0.234   3.4789  -3.5663  -2.1882
 GJT  H17  H  HCH3   0   0.217   2.0986  -2.6628  -1.5908
 GJT  H18  H  HCH2   0   0.216   3.8185  -2.8914   0.2004
 GJT  H19  H  HCH2   0   0.216   5.0421  -2.2315  -0.8618
 GJT  H20  H  HCH1   0   0.204   3.9154  -0.0476  -0.8953
 GJT  H21  H  HCH2   0   0.251  -1.1177   2.2064   0.6213
 GJT  H22  H  HCH2   0   0.262  -1.3076   2.7196  -1.0366
 GJT  H23  H  HCH1   0   0.272  -0.0283  -0.1623   0.9620
 GJT  H24  H  HCR5   0   0.313  -2.5979   0.4168   1.4635
 GJT  H25  H  HCH2   0   0.222  -6.2505  -0.2899   0.5513
 GJT  H26  H  HCH2   0   0.224  -5.5638  -1.8701   0.8966
 GJT  H27  H  HOH1   0   0.464  -5.8277  -0.6701   2.8390
 GJT  C3   C  CH1    0   0.049   3.7054  -0.7670  -0.0892
 GJT  C13  C  CH3    0  -0.784  -0.6394  -4.0278   0.0407
 GJT  C16  C  CH2    0  -0.204  -5.3666  -0.7927   0.9645

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
 GJT  O4   C17  deloc     1.245  0.020  1.245
 GJT  O5   C17  deloc     1.248  0.020  1.248
 GJT  C17  C8   single    1.524  0.020  1.524
 GJT  C8   C9   single    1.501  0.020  1.501
 GJT  C8   C7   double    1.332  0.020  1.332
 GJT  C9   C10  single    1.522  0.020  1.522
 GJT  C7   C6   single    1.502  0.020  1.502
 GJT  N4   N2   aromatic  1.319  0.020  1.319
 GJT  N4   N3   aromatic  1.289  0.020  1.289
 GJT  C10  N2   single    1.450  0.020  1.450
 GJT  C10  C11  single    1.531  0.020  1.531
 GJT  N2   C14  aromatic  1.346  0.020  1.346
 GJT  N3   C15  aromatic  1.349  0.020  1.349
 GJT  C14  C15  aromatic  1.370  0.020  1.370
 GJT  C6   C11  single    1.527  0.020  1.527
 GJT  C6   O1   single    1.409  0.020  1.409
 GJT  C15  C16  single    1.489  0.020  1.489
 GJT  C11  N1   single    1.438  0.020  1.438
 GJT  C16  O3   single    1.405  0.020  1.405
 GJT  O1   C3   single    1.421  0.020  1.421
 GJT  C1   C2   single    1.522  0.020  1.522
 GJT  N1   C12  single    1.348  0.020  1.348
 GJT  C2   C3   single    1.526  0.020  1.526
 GJT  C3   C4   single    1.526  0.020  1.526
 GJT  O2   C12  double    1.222  0.020  1.222
 GJT  C12  C13  single    1.508  0.020  1.508
 GJT  C4   C5   single    1.521  0.020  1.521
 GJT  N1   H1   single    0.860  0.020  1.020
 GJT  C4   H2   single    0.970  0.020  1.090
 GJT  C4   H3   single    0.970  0.020  1.090
 GJT  C5   H4   single    0.970  0.020  1.090
 GJT  C5   H5   single    0.970  0.020  1.090
 GJT  C5   H6   single    0.970  0.020  1.090
 GJT  C6   H7   single    0.970  0.020  1.090
 GJT  C7   H9   single    0.930  0.020  1.080
 GJT  C10  H11  single    0.970  0.020  1.090
 GJT  C13  H12  single    0.970  0.020  1.090
 GJT  C13  H13  single    0.970  0.020  1.090
 GJT  C13  H14  single    0.970  0.020  1.090
 GJT  C1   H15  single    0.970  0.020  1.090
 GJT  C1   H16  single    0.970  0.020  1.090
 GJT  C1   H17  single    0.970  0.020  1.090
 GJT  C2   H18  single    0.970  0.020  1.090
 GJT  C2   H19  single    0.970  0.020  1.090
 GJT  C3   H20  single    0.970  0.020  1.090
 GJT  C9   H21  single    0.970  0.020  1.090
 GJT  C9   H22  single    0.970  0.020  1.090
 GJT  C11  H23  single    0.970  0.020  1.090
 GJT  C14  H24  single    0.930  0.020  1.080
 GJT  C16  H25  single    0.970  0.020  1.090
 GJT  C16  H26  single    0.970  0.020  1.090
 GJT  O3   H27  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
 GJT  H1   N1   C12  118.22  3.000
 GJT  H1   N1   C11  117.51  3.000
 GJT  C12  N1   C11  124.20  3.000
 GJT  N4   N3   C15  109.13  3.000
 GJT  H3   C4   H2   106.01  3.000
 GJT  H3   C4   C3   108.90  3.000
 GJT  H2   C4   C3   107.80  3.000
 GJT  H3   C4   C5   109.80  3.000
 GJT  H2   C4   C5   109.47  3.000
 GJT  C3   C4   C5   114.50  3.000
 GJT  H6   C5   H5   107.60  3.000
 GJT  H6   C5   H4   107.71  3.000
 GJT  H5   C5   H4   107.48  3.000
 GJT  H6   C5   C4   111.66  3.000
 GJT  H5   C5   C4   111.45  3.000
 GJT  H4   C5   C4   110.75  3.000
 GJT  H7   C6   C11  108.22  3.000
 GJT  H7   C6   O1   109.97  3.000
 GJT  C11  C6   O1   106.83  3.000
 GJT  H7   C6   C7   108.24  3.000
 GJT  O1   C6   C7   112.34  3.000
 GJT  C11  C6   C7   111.16  3.000
 GJT  H9   C7   C8   118.17  3.000
 GJT  H9   C7   C6   116.72  3.000
 GJT  C8   C7   C6   125.11  3.000
 GJT  C9   C8   C17  117.44  3.000
 GJT  C9   C8   C7   121.86  3.000
 GJT  C17  C8   C7   120.68  3.000
 GJT  H11  C10  N2   104.99  3.000
 GJT  H11  C10  C11  109.20  3.000
 GJT  N2   C10  C11  110.52  3.000
 GJT  H11  C10  C9   109.13  3.000
 GJT  C11  C10  C9   110.99  3.000
 GJT  N2   C10  C9   111.80  3.000
 GJT  C16  C15  C14  129.17  3.000
 GJT  C16  C15  N3   122.86  3.000
 GJT  C14  C15  N3   107.97  3.000
 GJT  O5   C17  O4   126.77  3.000
 GJT  O5   C17  C8   115.58  3.000
 GJT  O4   C17  C8   117.65  3.000
 GJT  H17  C1   H16  107.17  3.000
 GJT  H17  C1   H15  108.11  3.000
 GJT  H16  C1   H15  107.45  3.000
 GJT  H17  C1   C2   111.73  3.000
 GJT  H16  C1   C2   110.55  3.000
 GJT  H15  C1   C2   111.63  3.000
 GJT  H19  C2   H18  106.15  3.000
 GJT  H19  C2   C3   107.48  3.000
 GJT  H18  C2   C3   108.89  3.000
 GJT  H19  C2   C1   109.05  3.000
 GJT  H18  C2   C1   109.59  3.000
 GJT  C3   C2   C1   115.29  3.000
 GJT  C3   O1   C6   116.73  3.000
 GJT  H22  C9   H21  106.02  3.000
 GJT  H22  C9   C10  109.24  3.000
 GJT  H21  C9   C10  110.40  3.000
 GJT  H22  C9   C8   110.33  3.000
 GJT  H21  C9   C8   109.54  3.000
 GJT  C10  C9   C8   111.19  3.000
 GJT  H23  C11  C10  109.08  3.000
 GJT  H23  C11  C6   108.30  3.000
 GJT  C10  C11  C6   108.78  3.000
 GJT  H23  C11  N1   107.56  3.000
 GJT  C6   C11  N1   111.68  3.000
 GJT  C10  C11  N1   111.35  3.000
 GJT  O2   C12  C13  121.73  3.000
 GJT  C13  C12  N1   114.95  3.000
 GJT  O2   C12  N1   123.32  3.000
 GJT  N4   N2   C14  110.94  3.000
 GJT  C14  N2   C10  128.69  3.000
 GJT  N4   N2   C10  120.26  3.000
 GJT  H24  C14  N2   123.35  3.000
 GJT  H24  C14  C15  132.71  3.000
 GJT  N2   C14  C15  103.94  3.000
 GJT  H27  O3   C16  108.23  3.000
 GJT  N2   N4   N3   108.02  3.000
 GJT  H20  C3   O1   109.76  3.000
 GJT  H20  C3   C2   108.54  3.000
 GJT  O1   C3   C2   110.95  3.000
 GJT  H20  C3   C4   108.38  3.000
 GJT  C2   C3   C4   110.69  3.000
 GJT  O1   C3   C4   108.48  3.000
 GJT  H14  C13  H13  108.74  3.000
 GJT  H14  C13  H12  108.07  3.000
 GJT  H13  C13  H12  107.34  3.000
 GJT  H14  C13  C12  113.76  3.000
 GJT  H13  C13  C12  109.60  3.000
 GJT  H12  C13  C12  109.13  3.000
 GJT  H26  C16  H25  106.36  3.000
 GJT  H26  C16  O3   112.00  3.000
 GJT  H25  C16  O3   112.13  3.000
 GJT  H26  C16  C15  109.18  3.000
 GJT  H25  C16  C15  109.29  3.000
 GJT  O3   C16  C15  107.84  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
 GJT  CONST_01  C14  N2   N4   N3      0.00   0.0  0
 GJT  CONST_02  N2   C14  C15  N3      0.00   0.0  0
 GJT  CONST_03  N2   N4   N3   C15     0.00   0.0  0
 GJT  CONST_04  N4   N2   C14  C15     0.00   0.0  0
 GJT  CONST_05  N4   N3   C15  C14     0.00   0.0  0
 GJT  CONST_06  C10  N2   N4   N3    180.00   0.0  0
 GJT  CONST_07  C15  C14  N2   C10   180.00   0.0  0
 GJT  CONST_08  C16  C15  C14  N2    180.00   0.0  0
 GJT  CONST_09  N4   N3   C15  C16   180.00   0.0  0
 GJT  CONST_10  H24  C14  C15  N3    180.00   0.0  0
 GJT  CONST_11  C11  N1   C12  C13   180.00   0.0  0
 GJT  CONST_12  O2   C12  N1   C11     0.00   0.0  0
 GJT  CONST_13  H1   N1   C12  C13     0.00   0.0  0
 GJT  Var_01    C9   C8   C7   C6     -0.32  30.0  1
 GJT  Var_02    C10  C9   C8   C7    -16.21  30.0  1
 GJT  Var_03    O3   C16  C15  N3   -177.86  30.0  2
 GJT  Var_04    O4   C17  C8   C7      6.31  30.0  2
 GJT  Var_05    C2   C3   O1   C6   -103.22  30.0  3
 GJT  Var_06    C1   C2   C3   C4   -177.94  30.0  2
 GJT  Var_07    O1   C3   C4   C5    -60.01  30.0  2
 GJT  Var_08    H12  C13  C12  N1    108.49  30.0  3
 GJT  Var_09    H15  C1   C2   C3     55.34  30.0  3
 GJT  Var_10    H4   C5   C4   C3   -177.20  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
 GJT  chir_01  C6   C7  C11  O1   positiv
 GJT  chir_02  C10  N2  C9   C11  negativ
 GJT  chir_03  C11  N1  C6   C10  negativ

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
 GJT  plan-1  N3   0.020
 GJT  plan-1  C10  0.020
 GJT  plan-1  C15  0.020
 GJT  plan-1  N2   0.020
 GJT  plan-1  C14  0.020
 GJT  plan-1  N4   0.020
 GJT  plan-1  H24  0.020
 GJT  plan-1  C16  0.020
 GJT  plan-2  N1   0.020
 GJT  plan-2  C11  0.020
 GJT  plan-2  C12  0.020
 GJT  plan-2  O2   0.020
 GJT  plan-2  H1   0.020
 GJT  plan-2  C13  0.020
 GJT  plan-3  C8   0.020
 GJT  plan-3  C17  0.020
 GJT  plan-3  O4   0.020
 GJT  plan-3  O5   0.020

