# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:02:29 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  52  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  -0.634  -0.2221  -1.6745  -0.3709
 GJT  N3   N  N     0  -0.323  -4.1220  -0.6682  -1.1885
 GJT  C4   C  CH2   0  -0.430   4.6263  -0.4166   1.1004
 GJT  C5   C  CH3   0  -0.674   4.4594   0.9865   1.6649
 GJT  C6   C  CH1   0   0.050   1.4874   0.0755  -0.5133
 GJT  C7   C  C1    0  -0.209   1.6969   1.5611  -0.4651
 GJT  C8   C  C     0  -0.080   0.7152   2.4603  -0.3938
 GJT  C10  C  CH1   0  -0.101  -0.9181   0.6341  -0.8125
 GJT  C15  C  CR5   0   0.109  -4.1758  -0.4520   0.1424
 GJT  C17  C  C     0   0.531   1.0976   3.8951  -0.3134
 GJT  C1   C  CH3   0  -0.680   3.1656  -2.5470  -1.8269
 GJT  C2   C  CH2   0  -0.411   3.9832  -2.1417  -0.6086
 GJT  O1   O  O2    0  -0.498   2.3644  -0.6009   0.3480
 GJT  C9   C  CH2   0  -0.483  -0.7374   2.0791  -0.3645
 GJT  C11  C  CH1   0  -0.127   0.0658  -0.2952  -0.0946
 GJT  C12  C  C     0   0.532  -0.4234  -2.6090   0.5822
 GJT  O2   O  O     0  -0.494  -0.4186  -2.3564   1.7766
 GJT  N2   N  NR5   0  -0.264  -2.2802   0.1863  -0.6157
 GJT  C14  C  CR15  0  -0.081  -2.9840   0.1008   0.5296
 GJT  O3   O  OH1   0  -0.665  -5.0934  -0.4165   2.2932
 GJT  N4   N  N     0  -0.100  -2.9752  -0.2862  -1.6338
 GJT  O4   O  O     0  -0.437   2.2266   4.3127  -0.4120
 GJT  O5   O  OH1   0  -0.592   0.0489   4.6797  -0.1061
 GJT  H1   H  HNH1  0   0.401  -0.2453  -1.9637  -1.3366
 GJT  H2   H  HCH2  0   0.224   5.6595  -0.5562   0.7721
 GJT  H3   H  HCH2  0   0.220   4.4562  -1.1567   1.8891
 GJT  H4   H  HCH3  0   0.234   5.1724   1.1658   2.4698
 GJT  H5   H  HCH3  0   0.217   4.6338   1.7477   0.9011
 GJT  H6   H  HCH3  0   0.225   3.4598   1.1426   2.0703
 GJT  H7   H  HCH1  0   0.244   1.6399  -0.2460  -1.5553
 GJT  H9   H  H     0   0.275   2.7239   1.9061  -0.5000
 GJT  H11  H  HCH1  0   0.302  -0.7511   0.5732  -1.8913
 GJT  H12  H  HCH3  0   0.271   0.2433  -4.6088   0.2738
 GJT  H13  H  HCH3  0   0.268  -1.4783  -4.4653   0.5907
 GJT  H14  H  HCH3  0   0.251  -0.8359  -4.0525  -1.0059
 GJT  H15  H  HCH3  0   0.220   3.2789  -1.8323  -2.6445
 GJT  H16  H  HCH3  0   0.237   3.4892  -3.5203  -2.1971
 GJT  H17  H  HCH3  0   0.215   2.1045  -2.6307  -1.5933
 GJT  H18  H  HCH2  0   0.219   3.8194  -2.8605   0.2005
 GJT  H19  H  HCH2  0   0.220   5.0465  -2.2003  -0.8572
 GJT  H20  H  HCH1  0   0.210   3.9233  -0.0138  -0.8860
 GJT  H21  H  HCH2  0   0.276  -1.1335   2.2209   0.6456
 GJT  H22  H  HCH2  0   0.284  -1.3219   2.7249  -1.0215
 GJT  H23  H  HCH1  0   0.283  -0.0229  -0.1480   0.9848
 GJT  H24  H  HCR5  0   0.317  -2.6038   0.4212   1.4838
 GJT  H25  H  HCH2  0   0.223  -6.2451  -0.2629   0.5646
 GJT  H26  H  HCH2  0   0.225  -5.5813  -1.8605   0.8751
 GJT  H27  H  HOH1  0   0.464  -5.8337  -0.6893   2.8422
 GJT  H28  H  HOH1  0   0.487   0.3320   5.6049  -0.0522
 GJT  C3   C  CH1   0   0.040   3.7165  -0.7355  -0.0813
 GJT  C16  C  CH2   0  -0.204  -5.3694  -0.7877   0.9674
 GJT  C13  C  CH3   0  -0.784  -0.6426  -4.0074   0.0642

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  double    1.208  0.020  1.208
 GJT  O5   C17  single    1.326  0.020  1.326
 GJT  C17  C8   single    1.487  0.020  1.487
 GJT  C8   C9   single    1.502  0.020  1.502
 GJT  C8   C7   double    1.333  0.020  1.333
 GJT  C9   C10  single    1.524  0.020  1.524
 GJT  C7   C6   single    1.501  0.020  1.501
 GJT  N4   N2   aromatic  1.320  0.020  1.320
 GJT  N4   N3   aromatic  1.288  0.020  1.288
 GJT  C10  N2   single    1.447  0.020  1.447
 GJT  C10  C11  single    1.532  0.020  1.532
 GJT  N2   C14  aromatic  1.347  0.020  1.347
 GJT  N3   C15  aromatic  1.349  0.020  1.349
 GJT  C14  C15  aromatic  1.370  0.020  1.370
 GJT  C6   C11  single    1.528  0.020  1.528
 GJT  C6   O1   single    1.403  0.020  1.403
 GJT  C15  C16  single    1.489  0.020  1.489
 GJT  C11  N1   single    1.436  0.020  1.436
 GJT  C16  O3   single    1.404  0.020  1.404
 GJT  O1   C3   single    1.425  0.020  1.425
 GJT  C1   C2   single    1.522  0.020  1.522
 GJT  N1   C12  single    1.350  0.020  1.350
 GJT  C2   C3   single    1.525  0.020  1.525
 GJT  C3   C4   single    1.525  0.020  1.525
 GJT  O2   C12  double    1.221  0.020  1.221
 GJT  C12  C13  single    1.507  0.020  1.507
 GJT  C4   C5   single    1.522  0.020  1.522
 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
 GJT  O5   H28  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  118.30  3.000
 GJT  H1   N1   C11  117.68  3.000
 GJT  C12  N1   C11  123.99  3.000
 GJT  N4   N3   C15  109.20  3.000
 GJT  H3   C4   H2   106.07  3.000
 GJT  H3   C4   C3   108.92  3.000
 GJT  H2   C4   C3   107.72  3.000
 GJT  H3   C4   C5   109.82  3.000
 GJT  H2   C4   C5   109.44  3.000
 GJT  C3   C4   C5   114.51  3.000
 GJT  H6   C5   H5   107.86  3.000
 GJT  H6   C5   H4   107.56  3.000
 GJT  H5   C5   H4   107.30  3.000
 GJT  H6   C5   C4   111.75  3.000
 GJT  H5   C5   C4   111.45  3.000
 GJT  H4   C5   C4   110.72  3.000
 GJT  H7   C6   C11  108.50  3.000
 GJT  H7   C6   O1   110.71  3.000
 GJT  C11  C6   O1   107.24  3.000
 GJT  H7   C6   C7   107.46  3.000
 GJT  O1   C6   C7   111.73  3.000
 GJT  C11  C6   C7   111.18  3.000
 GJT  H9   C7   C8   119.00  3.000
 GJT  H9   C7   C6   116.49  3.000
 GJT  C8   C7   C6   124.51  3.000
 GJT  C9   C8   C17  119.50  3.000
 GJT  C9   C8   C7   122.82  3.000
 GJT  C17  C8   C7   117.67  3.000
 GJT  H11  C10  N2   105.11  3.000
 GJT  H11  C10  C11  109.30  3.000
 GJT  N2   C10  C11  110.67  3.000
 GJT  H11  C10  C9   108.96  3.000
 GJT  C11  C10  C9   111.18  3.000
 GJT  N2   C10  C9   111.41  3.000
 GJT  C16  C15  C14  129.19  3.000
 GJT  C16  C15  N3   122.83  3.000
 GJT  C14  C15  N3   107.98  3.000
 GJT  O5   C17  O4   123.19  3.000
 GJT  O5   C17  C8   112.08  3.000
 GJT  O4   C17  C8   124.72  3.000
 GJT  H17  C1   H16  107.05  3.000
 GJT  H17  C1   H15  108.17  3.000
 GJT  H16  C1   H15  107.41  3.000
 GJT  H17  C1   C2   111.83  3.000
 GJT  H16  C1   C2   110.48  3.000
 GJT  H15  C1   C2   111.67  3.000
 GJT  H19  C2   H18  106.16  3.000
 GJT  H19  C2   C3   107.34  3.000
 GJT  H18  C2   C3   108.88  3.000
 GJT  H19  C2   C1   109.03  3.000
 GJT  H18  C2   C1   109.66  3.000
 GJT  C3   C2   C1   115.36  3.000
 GJT  C3   O1   C6   116.98  3.000
 GJT  H22  C9   H21  106.57  3.000
 GJT  H22  C9   C10  108.71  3.000
 GJT  H21  C9   C10  110.58  3.000
 GJT  H22  C9   C8   110.86  3.000
 GJT  H21  C9   C8   109.58  3.000
 GJT  C10  C9   C8   110.46  3.000
 GJT  H23  C11  C10  109.21  3.000
 GJT  H23  C11  C6   108.27  3.000
 GJT  C10  C11  C6   108.78  3.000
 GJT  H23  C11  N1   107.65  3.000
 GJT  C6   C11  N1   111.53  3.000
 GJT  C10  C11  N1   111.33  3.000
 GJT  O2   C12  C13  121.92  3.000
 GJT  C13  C12  N1   114.92  3.000
 GJT  O2   C12  N1   123.16  3.000
 GJT  N4   N2   C14  110.97  3.000
 GJT  C14  N2   C10  128.83  3.000
 GJT  N4   N2   C10  120.09  3.000
 GJT  H24  C14  N2   123.40  3.000
 GJT  H24  C14  C15  132.71  3.000
 GJT  N2   C14  C15  103.88  3.000
 GJT  H27  O3   C16  108.23  3.000
 GJT  N2   N4   N3   107.96  3.000
 GJT  H28  O5   C17  110.03  3.000
 GJT  H20  C3   O1   109.67  3.000
 GJT  H20  C3   C2   108.60  3.000
 GJT  O1   C3   C2   110.93  3.000
 GJT  H20  C3   C4   108.50  3.000
 GJT  C2   C3   C4   110.88  3.000
 GJT  O1   C3   C4   108.23  3.000
 GJT  H26  C16  H25  106.42  3.000
 GJT  H26  C16  O3   112.07  3.000
 GJT  H25  C16  O3   112.14  3.000
 GJT  H26  C16  C15  109.18  3.000
 GJT  H25  C16  C15  109.17  3.000
 GJT  O3   C16  C15  107.81  3.000
 GJT  H14  C13  H13  108.77  3.000
 GJT  H14  C13  H12  108.08  3.000
 GJT  H13  C13  H12  107.37  3.000
 GJT  H14  C13  C12  113.71  3.000
 GJT  H13  C13  C12  109.61  3.000
 GJT  H12  C13  C12  109.10  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  H28  O5   C17  C8    180.00   0.0  0
 GJT  CONST_14  H1   N1   C12  C13     0.00   0.0  0
 GJT  Var_01    C9   C8   C7   C6     -0.52  30.0  1
 GJT  Var_02    C10  C9   C8   C7    -15.81  30.0  1
 GJT  Var_03    O3   C16  C15  N3   -179.12  30.0  2
 GJT  Var_04    O4   C17  C8   C7      6.03  30.0  2
 GJT  Var_05    C2   C3   O1   C6   -102.45  30.0  3
 GJT  Var_06    C1   C2   C3   C4   -177.72  30.0  2
 GJT  Var_07    O1   C3   C4   C5    -59.95  30.0  2
 GJT  Var_08    H12  C13  C12  N1    107.54  30.0  3
 GJT  Var_09    H15  C1   C2   C3     54.76  30.0  3
 GJT  Var_10    H4   C5   C4   C3   -177.05  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
 GJT  plan-3  H28  0.020

