# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:44:04 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-chloro-4-[(7R,7aS)-7-hydroxy-1,3-dioxotetrahydro-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl]-3-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Cl)c(ccc1N2C(=O)[C@@H]3[C@H](O)CCN3C2=O)C#N
#
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
 8NH  8NH  2-chloro-4-[(7R,7aS)-7-hydroxy-1,3-dioxotetrahydro-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl]-3-methylbenzonitrile  ligand  33  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8NH
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
 8NH  CL1   CL  CL    0  -0.072  7.7800   2.6220   4.9445
 8NH  C2    C   CR6   0  -0.141  6.3441   3.3809   4.3746
 8NH  C3    C   CR6   0   0.201  5.3887   2.6293   3.6935
 8NH  C4    C   CR6   0   0.279  4.2705   3.3243   3.2243
 8NH  C5    C   CR16  0  -0.236  4.0851   4.6797   3.4580
 8NH  C7    C   CR16  0  -0.292  5.0317   5.3953   4.1606
 8NH  C9    C   CR6   0   0.115  6.1746   4.7445   4.6147
 8NH  C10   C   CSP   0   0.058  7.1673   5.4837   5.3229
 8NH  N11   N   NS    0  -0.229  7.9473   6.1037   5.8999
 8NH  N12   N   NR5   0  -0.678  3.2794   2.6437   2.4836
 8NH  C13   C   CR5   0   0.715  3.4683   2.2275   1.1541
 8NH  N14   N   NR5   0  -0.490  2.2852   1.7354   0.7186
 8NH  C15   C   CR15  0  -0.254  1.3412   1.6102   1.8142
 8NH  C17   C   CH1   0   0.053  1.1408   0.1018   1.9246
 8NH  C19   C   CH2   0  -0.535  1.1151  -0.2823   0.4449
 8NH  C22   C   CH2   0  -0.271  2.1933   0.6001  -0.2024
 8NH  O25   O   OH1   0  -0.661  2.2726  -0.4024   2.5906
 8NH  C27   C   CR5   0   0.555  2.0454   2.2813   2.9675
 8NH  O28   O   O     0  -0.410  1.6315   2.4859   4.0784
 8NH  O29   O   O     0  -0.454  4.5133   2.3113   0.5569
 8NH  C30   C   CH3   0  -0.744  5.5704   1.1597   3.4814
 8NH  H5    H   HCR6  0   0.291  3.2041   5.1760   3.0753
 8NH  H7    H   HCR6  0   0.297  4.8987   6.4510   4.3489
 8NH  H15   H   HCR5  0   0.328  0.3931   2.1136   1.6060
 8NH  H17   H   HCH1  0   0.255  0.2093  -0.1542   2.4382
 8NH  H191  H   HCH2  0   0.261  0.1324  -0.0477   0.0324
 8NH  H192  H   HCH2  0   0.278  1.2928  -1.3458   0.2841
 8NH  H221  H   HCH2  0   0.255  3.1559   0.0926  -0.2670
 8NH  H222  H   HCH2  0   0.263  1.9113   0.9238  -1.2026
 8NH  HO25  H   HOH1  0   0.465  2.2820  -1.3621   2.5122
 8NH  H301  H   HCH3  0   0.265  5.8996   0.6735   4.3984
 8NH  H302  H   HCH3  0   0.261  4.6495   0.6747   3.1703
 8NH  H303  H   HCH3  0   0.272  6.3262   0.9680   2.7188

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
 8NH  CL1  C2    single    1.721  0.020  1.721
 8NH  C2   C9    aromatic  1.395  0.020  1.395
 8NH  C2   C3    aromatic  1.393  0.020  1.393
 8NH  C3   C4    aromatic  1.398  0.020  1.398
 8NH  C3   C30   single    1.496  0.020  1.496
 8NH  C4   C5    aromatic  1.388  0.020  1.388
 8NH  C4   N12   single    1.412  0.020  1.412
 8NH  C5   C7    aromatic  1.379  0.020  1.379
 8NH  C5   H5    single    0.930  0.020  1.080
 8NH  C7   C9    aromatic  1.391  0.020  1.391
 8NH  C7   H7    single    0.930  0.020  1.080
 8NH  C9   C10   single    1.426  0.020  1.426
 8NH  C10  N11   triple    1.151  0.020  1.151
 8NH  N12  C13   single    1.406  0.020  1.406
 8NH  N12  C27   single    1.374  0.020  1.374
 8NH  C13  O29   double    1.207  0.020  1.207
 8NH  C13  N14   single    1.353  0.020  1.353
 8NH  N14  C22   single    1.465  0.020  1.465
 8NH  N14  C15   single    1.452  0.020  1.452
 8NH  C15  C17   single    1.526  0.020  1.526
 8NH  C15  C27   single    1.509  0.020  1.509
 8NH  C15  H15   single    0.970  0.020  1.090
 8NH  C17  C19   single    1.529  0.020  1.529
 8NH  C17  O25   single    1.407  0.020  1.407
 8NH  C17  H17   single    0.970  0.020  1.090
 8NH  C19  C22   single    1.536  0.020  1.536
 8NH  C19  H191  single    0.970  0.020  1.090
 8NH  C19  H192  single    0.970  0.020  1.090
 8NH  C22  H221  single    0.970  0.020  1.090
 8NH  C22  H222  single    0.970  0.020  1.090
 8NH  O25  HO25  single    0.850  0.020  0.980
 8NH  C27  O28   double    1.203  0.020  1.203
 8NH  C30  H301  single    0.970  0.020  1.090
 8NH  C30  H302  single    0.970  0.020  1.090
 8NH  C30  H303  single    0.970  0.020  1.090

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
 8NH  C9    C2   C3    121.88  3.000
 8NH  C3    C2   CL1   119.74  3.000
 8NH  C9    C2   CL1   118.38  3.000
 8NH  C30   C3   C4    122.55  3.000
 8NH  C30   C3   C2    121.06  3.000
 8NH  C4    C3   C2    116.38  3.000
 8NH  N12   C4   C5    117.73  3.000
 8NH  N12   C4   C3    119.86  3.000
 8NH  C5    C4   C3    122.41  3.000
 8NH  H5    C5   C7    120.10  3.000
 8NH  H5    C5   C4    119.84  3.000
 8NH  C7    C5   C4    120.06  3.000
 8NH  H7    C7   C9    120.08  3.000
 8NH  H7    C7   C5    120.75  3.000
 8NH  C9    C7   C5    119.17  3.000
 8NH  C10   C9   C7    119.44  3.000
 8NH  C10   C9   C2    120.50  3.000
 8NH  C7    C9   C2    120.06  3.000
 8NH  N11   C10  C9    180.00  3.000
 8NH  C27   N12  C13   112.06  3.000
 8NH  C27   N12  C4    124.93  3.000
 8NH  C13   N12  C4    122.99  3.000
 8NH  O29   C13  N14   128.55  3.000
 8NH  N14   C13  N12   107.13  3.000
 8NH  O29   C13  N12   124.32  3.000
 8NH  C22   N14  C15   111.53  3.000
 8NH  C15   N14  C13   110.91  3.000
 8NH  C22   N14  C13   122.61  3.000
 8NH  H15   C15  C27   110.21  3.000
 8NH  H15   C15  C17   110.79  3.000
 8NH  C27   C15  C17   116.47  3.000
 8NH  H15   C15  N14   112.36  3.000
 8NH  C27   C15  N14   103.60  3.000
 8NH  C17   C15  N14   103.02  3.000
 8NH  H17   C17  O25   112.26  3.000
 8NH  H17   C17  C19   112.41  3.000
 8NH  O25   C17  C19   112.44  3.000
 8NH  H17   C17  C15   112.16  3.000
 8NH  O25   C17  C15   106.44  3.000
 8NH  C19   C17  C15   100.40  3.000
 8NH  H192  C19  H191  107.49  3.000
 8NH  H192  C19  C22   112.57  3.000
 8NH  H191  C19  C22   110.44  3.000
 8NH  H192  C19  C17   112.65  3.000
 8NH  H191  C19  C17   109.08  3.000
 8NH  C22   C19  C17   104.58  3.000
 8NH  H222  C22  H221  108.22  3.000
 8NH  H222  C22  C19   112.10  3.000
 8NH  H221  C22  C19   112.17  3.000
 8NH  H222  C22  N14   111.32  3.000
 8NH  H221  C22  N14   110.04  3.000
 8NH  C19   C22  N14   102.96  3.000
 8NH  HO25  O25  C17   109.06  3.000
 8NH  O28   C27  C15   128.38  3.000
 8NH  O28   C27  N12   126.11  3.000
 8NH  C15   C27  N12   105.50  3.000
 8NH  H303  C30  H302  107.98  3.000
 8NH  H303  C30  H301  107.51  3.000
 8NH  H302  C30  H301  107.35  3.000
 8NH  H303  C30  C3    110.85  3.000
 8NH  H302  C30  C3    112.10  3.000
 8NH  H301  C30  C3    110.85  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
 8NH  CONST_01  C5    C7   C9   C2     0.00   0.0  0
 8NH  CONST_02  C5    C4   C3   C2     0.00   0.0  0
 8NH  CONST_03  C7    C9   C2   C3     0.00   0.0  0
 8NH  CONST_04  C7    C5   C4   C3     0.00   0.0  0
 8NH  CONST_05  C9    C2   C3   C4     0.00   0.0  0
 8NH  CONST_06  C9    C7   C5   C4     0.00   0.0  0
 8NH  CONST_07  N12   C4   C3   C2   180.00   0.0  0
 8NH  CONST_08  N12   C4   C5   C7   180.00   0.0  0
 8NH  CONST_09  N14   C13  N12  C4   180.00   0.0  0
 8NH  CONST_10  C15   C27  N12  C4   180.00   0.0  0
 8NH  CONST_12  C15   N14  C13  N12    0.00   0.0  0
 8NH  CONST_13  C15   C27  N12  C13    0.00   0.0  0
 8NH  CONST_14  C27   N12  C13  N14    0.00   0.0  0
 8NH  CONST_15  C7    C9   C2   CL1  180.00   0.0  0
 8NH  CONST_16  C4    C3   C2   CL1  180.00   0.0  0
 8NH  CONST_17  C10   C9   C2   C3   180.00   0.0  0
 8NH  CONST_18  C30   C3   C4   C5   180.00   0.0  0
 8NH  CONST_19  C10   C9   C7   C5   180.00   0.0  0
 8NH  CONST_20  C30   C3   C2   C9   180.00   0.0  0
 8NH  CONST_21  C30   C3   C4   N12    0.00   0.0  0
 8NH  CONST_22  O29   C13  N12  C4     0.00   0.0  0
 8NH  CONST_23  O29   C13  N14  C15  180.00   0.0  0
 8NH  CONST_25  O29   C13  N12  C27  180.00   0.0  0
 8NH  CONST_26  H7    C7   C9   C2   180.00   0.0  0
 8NH  CONST_27  H5    C5   C4   C3   180.00   0.0  0
 8NH  Var_01    C13   N12  C4   C3   -73.36  30.0  2
 8NH  Var_02    C19   C22  N14  C13  133.58  30.0  1
 8NH  Var_03    C17   C19  C22  N14  -24.14  30.0  1
 8NH  Var_04    H301  C30  C3   C2    45.43  30.0  2

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
 8NH  chir_01  C15  N14  C17  C27  negativ
 8NH  chir_02  C17  O25  C15  C19  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
 8NH  plan-1  CL1  0.020
 8NH  plan-1  C2   0.020
 8NH  plan-1  C3   0.020
 8NH  plan-1  C4   0.020
 8NH  plan-1  C5   0.020
 8NH  plan-1  C7   0.020
 8NH  plan-1  C9   0.020
 8NH  plan-1  C10  0.020
 8NH  plan-1  N11  0.020
 8NH  plan-1  N12  0.020
 8NH  plan-1  C30  0.020
 8NH  plan-1  H5   0.020
 8NH  plan-1  H7   0.020
 8NH  plan-2  C4   0.020
 8NH  plan-2  N12  0.020
 8NH  plan-2  C13  0.020
 8NH  plan-2  N14  0.020
 8NH  plan-2  C15  0.020
 8NH  plan-2  C22  0.020
 8NH  plan-2  C27  0.020
 8NH  plan-2  O28  0.020
 8NH  plan-2  O29  0.020

