# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:01:38 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1c[nH]c(CCCCNC(=O)C=C)n1
#
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
 OJP  OJP  N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}prop-2-enamide  ligand  33  16  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OJP
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
 OJP  CB   C  CR15  0  -0.127   4.2506   0.3023  -1.0019
 OJP  CA   C  CR5   0   0.086   4.4170  -0.2888   0.2163
 OJP  C1   C  CR5   0   0.434   2.4614   0.5887   0.2498
 OJP  C2   C  C2    0  -0.474  -7.3804  -0.1215  -0.0707
 OJP  C3   C  C1    0  -0.329  -6.1749   0.3121   0.2773
 OJP  C4   C  C     0   0.539  -4.9393  -0.2243  -0.3541
 OJP  C    C  CH2   0  -0.224   5.5944  -1.0419   0.7334
 OJP  C5   C  CH2   0  -0.524   1.0899   1.0116   0.6471
 OJP  C6   C  CH2   0  -0.426  -0.0112   0.2377  -0.0813
 OJP  C7   C  CH2   0  -0.481  -1.3994   0.6610   0.3780
 OJP  C8   C  CH2   0  -0.233  -2.4918  -0.1077  -0.3462
 OJP  N9   N  NR15  0  -0.603   2.9982   0.8549  -0.9591
 OJP  N    N  N     0  -0.475   3.2995  -0.1047   0.9837
 OJP  N10  N  NH1   0  -0.655  -3.8001   0.3028   0.1181
 OJP  O11  O  O     0  -0.504  -4.9583  -1.0785  -1.2331
 OJP  O    O  OH1   0  -0.669   6.6082  -1.0140  -0.2410
 OJP  H1   H  HCR5  0   0.278   4.8839   0.3846  -1.8679
 OJP  H2   H  H     0   0.256  -7.5144  -0.8811  -0.8302
 OJP  H3   H  H     0   0.260  -8.2734   0.2701   0.3962
 OJP  H4   H  H     0   0.268  -6.0672   1.0733   1.0424
 OJP  H5   H  HCH2  0   0.208   5.9229  -0.5914   1.6801
 OJP  H6   H  HCH2  0   0.209   5.2906  -2.0696   0.9758
 OJP  H7   H  HCH2  0   0.254   0.9942   0.8608   1.7237
 OJP  H8   H  HCH2  0   0.252   0.9629   2.0829   0.4651
 OJP  H9   H  HCH2  0   0.229   0.0794   0.3927  -1.1603
 OJP  H10  H  HCH2  0   0.236   0.1239  -0.8335   0.0921
 OJP  H11  H  HCH2  0   0.236  -1.4911   0.4992   1.4567
 OJP  H12  H  HCH2  0   0.236  -1.5296   1.7341   0.2074
 OJP  H13  H  HCH2  0   0.234  -2.4112   0.0598  -1.4240
 OJP  H14  H  HCH2  0   0.233  -2.3605  -1.1817  -0.1838
 OJP  H15  H  HNR5  0   0.413   2.5650   1.3808  -1.7013
 OJP  H17  H  HNH1  0   0.404  -3.8491   0.9880   0.8546
 OJP  H18  H  HOH1  0   0.460   7.3510  -1.5294   0.0842

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
 OJP  N9   CB   aromatic  1.370  0.020  1.370
 OJP  N9   C1   aromatic  1.349  0.020  1.349
 OJP  CB   CA   aromatic  1.364  0.020  1.364
 OJP  C6   C7   single    1.522  0.020  1.522
 OJP  C6   C5   single    1.530  0.020  1.530
 OJP  C7   C8   single    1.520  0.020  1.520
 OJP  C1   C5   single    1.489  0.020  1.489
 OJP  C1   N    aromatic  1.312  0.020  1.312
 OJP  CA   N    aromatic  1.368  0.020  1.368
 OJP  CA   C    single    1.490  0.020  1.490
 OJP  O    C    single    1.406  0.020  1.406
 OJP  N10  C8   single    1.448  0.020  1.448
 OJP  N10  C4   single    1.341  0.020  1.341
 OJP  C3   C4   single    1.488  0.020  1.488
 OJP  C3   C2   double    1.328  0.020  1.328
 OJP  C4   O11  double    1.226  0.020  1.226
 OJP  CB   H1   single    0.930  0.020  1.080
 OJP  C2   H2   single    0.930  0.020  1.080
 OJP  C2   H3   single    0.930  0.020  1.080
 OJP  C3   H4   single    0.930  0.020  1.080
 OJP  C    H5   single    0.970  0.020  1.090
 OJP  C    H6   single    0.970  0.020  1.090
 OJP  C5   H7   single    0.970  0.020  1.090
 OJP  C5   H8   single    0.970  0.020  1.090
 OJP  C6   H9   single    0.970  0.020  1.090
 OJP  C6   H10  single    0.970  0.020  1.090
 OJP  C7   H11  single    0.970  0.020  1.090
 OJP  C7   H12  single    0.970  0.020  1.090
 OJP  C8   H13  single    0.970  0.020  1.090
 OJP  C8   H14  single    0.970  0.020  1.090
 OJP  N9   H15  single    0.860  0.020  1.020
 OJP  N10  H17  single    0.860  0.020  1.020
 OJP  O    H18  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
 OJP  H1   CB   N9   122.18  3.000
 OJP  H1   CB   CA   132.84  3.000
 OJP  N9   CB   CA   104.98  3.000
 OJP  N    CA   C    121.25  3.000
 OJP  C    CA   CB   128.70  3.000
 OJP  N    CA   CB   110.06  3.000
 OJP  N    C1   N9   110.57  3.000
 OJP  N    C1   C5   126.09  3.000
 OJP  N9   C1   C5   123.33  3.000
 OJP  H3   C2   H2   117.06  3.000
 OJP  H3   C2   C3   121.24  3.000
 OJP  H2   C2   C3   121.70  3.000
 OJP  H4   C3   C4   118.03  3.000
 OJP  H4   C3   C2   120.28  3.000
 OJP  C4   C3   C2   121.68  3.000
 OJP  O11  C4   N10  122.65  3.000
 OJP  O11  C4   C3   122.87  3.000
 OJP  N10  C4   C3   114.48  3.000
 OJP  H6   C    H5   106.03  3.000
 OJP  H6   C    O    111.76  3.000
 OJP  H5   C    O    111.92  3.000
 OJP  H6   C    CA   109.31  3.000
 OJP  H5   C    CA   109.14  3.000
 OJP  O    C    CA   108.61  3.000
 OJP  H8   C5   H7   106.81  3.000
 OJP  H8   C5   C6   109.42  3.000
 OJP  H7   C5   C6   109.67  3.000
 OJP  H8   C5   C1   109.91  3.000
 OJP  H7   C5   C1   107.74  3.000
 OJP  C6   C5   C1   113.08  3.000
 OJP  H10  C6   H9   106.55  3.000
 OJP  H10  C6   C7   109.70  3.000
 OJP  H9   C6   C7   109.50  3.000
 OJP  H10  C6   C5   109.34  3.000
 OJP  H9   C6   C5   109.78  3.000
 OJP  C7   C6   C5   111.83  3.000
 OJP  H12  C7   H11  106.78  3.000
 OJP  H12  C7   C8   109.65  3.000
 OJP  H11  C7   C8   109.55  3.000
 OJP  H12  C7   C6   109.52  3.000
 OJP  H11  C7   C6   109.43  3.000
 OJP  C8   C7   C6   111.79  3.000
 OJP  H14  C8   H13  106.72  3.000
 OJP  H14  C8   N10  109.83  3.000
 OJP  H13  C8   N10  109.83  3.000
 OJP  H14  C8   C7   109.85  3.000
 OJP  H13  C8   C7   109.83  3.000
 OJP  N10  C8   C7   110.70  3.000
 OJP  H15  N9   C1   126.30  3.000
 OJP  H15  N9   CB   125.50  3.000
 OJP  C1   N9   CB   108.19  3.000
 OJP  C1   N    CA   106.21  3.000
 OJP  H17  N10  C8   118.13  3.000
 OJP  H17  N10  C4   118.91  3.000
 OJP  C8   N10  C4   122.91  3.000
 OJP  H18  O    C    108.19  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
 OJP  CONST_01  N    C1   N9   CB     0.00   0.0  0
 OJP  CONST_02  C1   N    CA   CB     0.00   0.0  0
 OJP  CONST_03  C1   N9   CB   CA     0.00   0.0  0
 OJP  CONST_04  N9   C1   N    CA     0.00   0.0  0
 OJP  CONST_05  N    CA   CB   N9     0.00   0.0  0
 OJP  CONST_06  C5   C1   N9   CB   180.00   0.0  0
 OJP  CONST_07  C5   C1   N    CA   180.00   0.0  0
 OJP  CONST_08  C    CA   N    C1   180.00   0.0  0
 OJP  CONST_09  N9   CB   CA   C    180.00   0.0  0
 OJP  CONST_10  H15  N9   CB   CA   180.00   0.0  0
 OJP  CONST_11  H1   CB   N9   C1   180.00   0.0  0
 OJP  CONST_12  C8   N10  C4   C3   180.00   0.0  0
 OJP  CONST_13  O11  C4   N10  C8     0.00   0.0  0
 OJP  CONST_14  H17  N10  C4   C3     0.00   0.0  0
 OJP  Var_01    O    C    CA   CB     2.76  30.0  2
 OJP  Var_02    N9   C1   C5   C6    70.56  30.0  1
 OJP  Var_03    C7   C6   C5   C1   178.18  30.0  1
 OJP  Var_04    N10  C4   C3   C2  -179.17  30.0  2
 OJP  Var_05    C7   C8   N10  C4  -179.70  30.0  3
 OJP  Var_06    C8   C7   C6   C5   179.98  30.0  3
 OJP  Var_07    N10  C8   C7   C6   179.40  30.0  3
 OJP  Var_08    H2   C2   C3   C4    -0.18   0.0  2

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
 OJP  plan-1  CB   0.020
 OJP  plan-1  CA   0.020
 OJP  plan-1  C1   0.020
 OJP  plan-1  C    0.020
 OJP  plan-1  C5   0.020
 OJP  plan-1  N9   0.020
 OJP  plan-1  N    0.020
 OJP  plan-1  H1   0.020
 OJP  plan-1  H15  0.020
 OJP  plan-2  C3   0.020
 OJP  plan-2  C4   0.020
 OJP  plan-2  C8   0.020
 OJP  plan-2  N10  0.020
 OJP  plan-2  O11  0.020
 OJP  plan-2  H17  0.020
 OJP  plan-3  C2   0.020
 OJP  plan-3  C3   0.020
 OJP  plan-3  C4   0.020
 OJP  plan-3  H2   0.020
 OJP  plan-3  H3   0.020
 OJP  plan-3  H4   0.020

