# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 21:04:01 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3S)-1-cyclohexyl-N-(3,5-dichlorophenyl)-5-oxopyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(NC(=O)[C@@H]2CN(C3CCCCC3)C(=O)C2)c1
#
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
 641  641  (3S)-1-cyclohexyl-N-(3,5-dichlorophenyl)-5-oxopyrrolidine-3-carboxamide  ligand  43  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_641
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
 641  C1    C   CH2   0  -0.435  -1.7169  1.5646  -2.3796
 641  C2    C   CH2   0  -0.440  -0.9793  2.3301  -3.4744
 641  C3    C   CH1   0  -0.075   0.5326  2.1854  -3.3118
 641  C4    C   CH2   0  -0.419   0.9844  2.6410  -1.9232
 641  C5    C   CH2   0  -0.438   0.2389  1.8788  -0.8317
 641  C6    C   CH2   0  -0.432  -1.2719  2.0107  -0.9908
 641  C7    C   CR5   0   0.532   2.2498  2.3362  -5.0739
 641  C8    C   CH2   0  -0.569   2.7433  3.3748  -6.0592
 641  C9    C   CR15  0  -0.464   2.2031  4.6989  -5.4997
 641  C10   C   CH2   0  -0.254   0.9676  4.2585  -4.7130
 641  N11   N   NR5   0  -0.449   1.2523  2.8825  -4.3593
 641  C12   C   C     0   0.584   3.2532  5.3201  -4.5980
 641  N13   N   NH1   0  -0.756   4.0853  6.1745  -5.2548
 641  O14   O   O     0  -0.441   3.3568  5.0393  -3.4207
 641  O15   O   O     0  -0.504   2.6710  1.1941  -4.9726
 641  C15   C   CR6   0   0.388   5.2081  6.8476  -4.7826
 641  C20   C   CR16  0  -0.277   5.6574  6.7842  -3.4630
 641  C19   C   CR6   0  -0.026   6.7901  7.5020  -3.1145
 641  CL2   CL  CL    0  -0.109   7.3425  7.4213  -1.4761
 641  C18   C   CR16  0  -0.204   7.4983  8.2797  -4.0135
 641  C17   C   CR6   0  -0.027   7.0259  8.3223  -5.3160
 641  C16   C   CR16  0  -0.308   5.9025  7.6255  -5.7129
 641  CL1   CL  CL    0  -0.108   7.8733  9.2787  -6.4806
 641  HN13  H   HNH1  0   0.426   3.8749  6.3345  -6.2287
 641  H9    H   HCR5  0   0.303   1.9326  5.3902  -6.2987
 641  H101  H   HCH2  0   0.262   0.7936  4.8663  -3.8252
 641  H102  H   HCH2  0   0.261   0.0757  4.3260  -5.3421
 641  H81   H   HCH2  0   0.284   3.8271  3.3371  -6.1710
 641  H82   H   HCH2  0   0.297   2.3107  3.1623  -7.0402
 641  H3    H   HCH1  0   0.241   0.7854  1.1270  -3.4218
 641  H41   H   HCH2  0   0.214   0.8015  3.7149  -1.8117
 641  H42   H   HCH2  0   0.236   2.0625  2.4951  -1.8266
 641  H51   H   HCH2  0   0.232   0.5526  2.2380   0.1508
 641  H52   H   HCH2  0   0.213   0.5154  0.8196  -0.8772
 641  H61   H   HCH2  0   0.230  -1.7852  1.4262  -0.2237
 641  H62   H   HCH2  0   0.211  -1.5642  3.0547  -0.8341
 641  H4    H   HCH2  0   0.215  -1.5284  0.4917  -2.4944
 641  H1    H   HCH2  0   0.233  -2.7942  1.7025  -2.4971
 641  H2    H   HCH2  0   0.240  -1.2813  1.9699  -4.4611
 641  H5    H   HCH2  0   0.222  -1.2620  3.3876  -3.4205
 641  H16   H   HCR6  0   0.300   5.5642  7.6784  -6.7397
 641  H18   H   HCR6  0   0.301   8.3806  8.8268  -3.7148
 641  H20   H   HCR6  0   0.308   5.1458  6.1920  -2.7237

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
 641  C1   C6    single    1.525  0.020  1.525
 641  C1   H4    single    0.970  0.020  1.090
 641  C1   H1    single    0.970  0.020  1.090
 641  C1   C2    single    1.526  0.020  1.526
 641  C2   C3    single    1.527  0.020  1.527
 641  C2   H2    single    0.970  0.020  1.090
 641  C2   H5    single    0.970  0.020  1.090
 641  C3   N11   single    1.450  0.020  1.450
 641  C3   H3    single    0.970  0.020  1.090
 641  C3   C4    single    1.530  0.020  1.530
 641  C4   H41   single    0.970  0.020  1.090
 641  C4   H42   single    0.970  0.020  1.090
 641  C4   C5    single    1.526  0.020  1.526
 641  C5   H51   single    0.970  0.020  1.090
 641  C5   H52   single    0.970  0.020  1.090
 641  C5   C6    single    1.525  0.020  1.525
 641  C6   H61   single    0.970  0.020  1.090
 641  C6   H62   single    0.970  0.020  1.090
 641  C7   N11   single    1.343  0.020  1.343
 641  C7   O15   double    1.222  0.020  1.222
 641  C7   C8    single    1.514  0.020  1.514
 641  C8   C9    single    1.536  0.020  1.536
 641  C8   H81   single    0.970  0.020  1.090
 641  C8   H82   single    0.970  0.020  1.090
 641  C9   C12   single    1.517  0.020  1.517
 641  C9   H9    single    0.970  0.020  1.090
 641  C9   C10   single    1.529  0.020  1.529
 641  C10  H101  single    0.970  0.020  1.090
 641  C10  H102  single    0.970  0.020  1.090
 641  C10  N11   single    1.449  0.020  1.449
 641  C12  N13   single    1.361  0.020  1.361
 641  C12  O14   double    1.215  0.020  1.215
 641  N13  HN13  single    0.860  0.020  1.020
 641  N13  C15   single    1.392  0.020  1.392
 641  C15  C16   aromatic  1.397  0.020  1.397
 641  C15  C20   aromatic  1.395  0.020  1.395
 641  C20  C19   aromatic  1.386  0.020  1.386
 641  C20  H20   single    0.930  0.020  1.080
 641  C19  C18   aromatic  1.384  0.020  1.384
 641  C19  CL2   single    1.731  0.020  1.731
 641  C18  C17   aromatic  1.386  0.020  1.386
 641  C18  H18   single    0.930  0.020  1.080
 641  C17  C16   aromatic  1.380  0.020  1.380
 641  C17  CL1   single    1.729  0.020  1.729
 641  C16  H16   single    0.930  0.020  1.080

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
 641  H1    C1   H4    106.39  3.000
 641  H1    C1   C6    110.42  3.000
 641  H4    C1   C6    109.37  3.000
 641  H1    C1   C2    109.64  3.000
 641  H4    C1   C2    109.45  3.000
 641  C6    C1   C2    111.44  3.000
 641  H5    C2   H2    106.93  3.000
 641  H5    C2   C3    109.97  3.000
 641  H2    C2   C3    109.78  3.000
 641  H5    C2   C1    108.91  3.000
 641  H2    C2   C1    110.41  3.000
 641  C3    C2   C1    110.76  3.000
 641  H3    C3   N11   106.14  3.000
 641  H3    C3   C4    108.13  3.000
 641  N11   C3   C4    111.47  3.000
 641  C4    C3   C2    111.15  3.000
 641  H3    C3   C2    108.05  3.000
 641  N11   C3   C2    111.66  3.000
 641  H42   C4   H41   106.67  3.000
 641  H42   C4   C5    110.63  3.000
 641  H41   C4   C5    109.60  3.000
 641  C5    C4   C3    110.87  3.000
 641  H42   C4   C3    109.40  3.000
 641  H41   C4   C3    109.58  3.000
 641  H52   C5   H51   106.42  3.000
 641  H52   C5   C6    109.22  3.000
 641  H51   C5   C6    110.49  3.000
 641  C6    C5   C4    111.49  3.000
 641  H52   C5   C4    109.27  3.000
 641  H51   C5   C4    109.81  3.000
 641  H62   C6   H61   106.50  3.000
 641  H62   C6   C5    109.39  3.000
 641  H61   C6   C5    110.24  3.000
 641  H62   C6   C1    109.34  3.000
 641  H61   C6   C1    110.23  3.000
 641  C5    C6   C1    111.03  3.000
 641  O15   C7   N11   126.31  3.000
 641  O15   C7   C8    125.65  3.000
 641  N11   C7   C8    108.02  3.000
 641  H82   C8   H81   107.14  3.000
 641  H82   C8   C9    110.81  3.000
 641  H81   C8   C9    114.64  3.000
 641  H82   C8   C7    108.76  3.000
 641  H81   C8   C7    111.54  3.000
 641  C9    C8   C7    103.87  3.000
 641  H9    C9   C12   110.34  3.000
 641  H9    C9   C10   111.04  3.000
 641  C12   C9   C10   111.79  3.000
 641  C10   C9   C8    102.90  3.000
 641  H9    C9   C8    111.53  3.000
 641  C12   C9   C8    109.03  3.000
 641  H102  C10  H101  107.69  3.000
 641  H102  C10  N11   111.06  3.000
 641  H101  C10  N11   111.23  3.000
 641  N11   C10  C9    103.91  3.000
 641  H102  C10  C9    110.19  3.000
 641  H101  C10  C9    112.79  3.000
 641  C10   N11  C7    113.71  3.000
 641  C10   N11  C3    122.38  3.000
 641  C7    N11  C3    123.90  3.000
 641  O14   C12  N13   124.09  3.000
 641  O14   C12  C9    122.71  3.000
 641  N13   C12  C9    113.15  3.000
 641  HN13  N13  C15   114.77  3.000
 641  C15   N13  C12   129.26  3.000
 641  HN13  N13  C12   115.95  3.000
 641  C16   C15  C20   119.66  3.000
 641  C20   C15  N13   123.97  3.000
 641  C16   C15  N13   116.37  3.000
 641  H20   C20  C19   120.05  3.000
 641  H20   C20  C15   121.42  3.000
 641  C19   C20  C15   118.53  3.000
 641  C18   C19  CL2   118.55  3.000
 641  CL2   C19  C20   118.35  3.000
 641  C18   C19  C20   123.10  3.000
 641  H18   C18  C17   121.50  3.000
 641  H18   C18  C19   121.54  3.000
 641  C17   C18  C19   116.96  3.000
 641  CL1   C17  C16   118.98  3.000
 641  CL1   C17  C18   118.88  3.000
 641  C16   C17  C18   122.14  3.000
 641  H16   C16  C17   120.17  3.000
 641  H16   C16  C15   120.23  3.000
 641  C17   C16  C15   119.60  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
 641  CONST_01  C18   C17  C16  C15    0.00   0.0  0
 641  CONST_02  C18   C19  C20  C15    0.00   0.0  0
 641  CONST_03  C17   C16  C15  C20    0.00   0.0  0
 641  CONST_04  C17   C18  C19  C20    0.00   0.0  0
 641  CONST_05  C16   C15  C20  C19    0.00   0.0  0
 641  CONST_06  C16   C17  C18  C19    0.00   0.0  0
 641  CONST_07  C8    C7   N11  C3   180.00   0.0  0
 641  CONST_08  C10   N11  C7   C8     0.00   0.0  0
 641  CONST_09  C17   C16  C15  N13  180.00   0.0  0
 641  CONST_10  C19   C20  C15  N13  180.00   0.0  0
 641  CONST_11  CL1   C17  C16  C15  180.00   0.0  0
 641  CONST_12  CL2   C19  C20  C15  180.00   0.0  0
 641  CONST_13  CL1   C17  C18  C19  180.00   0.0  0
 641  CONST_14  C17   C18  C19  CL2  180.00   0.0  0
 641  CONST_15  O15   C7   N11  C3     0.00   0.0  0
 641  CONST_16  O15   C7   N11  C10  180.00   0.0  0
 641  CONST_17  H16   C16  C15  C20  180.00   0.0  0
 641  CONST_18  H18   C18  C19  C20  180.00   0.0  0
 641  CONST_19  H20   C20  C19  C18  180.00   0.0  0
 641  CONST_20  C15   N13  C12  C9   180.00   0.0  0
 641  CONST_21  C16   C15  N13  C12  180.00   0.0  0
 641  CONST_22  C20   C15  N13  C12    0.00   0.0  0
 641  CONST_23  HN13  N13  C15  C20  180.00   0.0  0
 641  CONST_24  C15   N13  C12  O14    0.00   0.0  0
 641  Var_01    C4    C5   C6   C1    55.32  30.0  1
 641  Var_02    C5    C6   C1   C2   -55.52  30.0  1
 641  Var_03    C6    C1   C2   C3    55.92  30.0  1
 641  Var_04    C9    C10  N11  C3   162.68  30.0  1
 641  Var_05    C6    C5   C4   C3   -55.53  30.0  1
 641  Var_06    N11   C7   C8   C9    17.62  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
 641  chir_01  C3  C2  N11  C4   negativ
 641  chir_02  C9  C8  C12  C10  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
 641  plan-1  C9    0.020
 641  plan-1  C12   0.020
 641  plan-1  N13   0.020
 641  plan-1  O14   0.020
 641  plan-1  C15   0.020
 641  plan-1  HN13  0.020
 641  plan-2  N13   0.020
 641  plan-2  C15   0.020
 641  plan-2  C20   0.020
 641  plan-2  C19   0.020
 641  plan-2  CL2   0.020
 641  plan-2  C18   0.020
 641  plan-2  C17   0.020
 641  plan-2  C16   0.020
 641  plan-2  CL1   0.020
 641  plan-2  H16   0.020
 641  plan-2  H18   0.020
 641  plan-2  H20   0.020
 641  plan-3  C3    0.020
 641  plan-3  C7    0.020
 641  plan-3  C8    0.020
 641  plan-3  C10   0.020
 641  plan-3  N11   0.020
 641  plan-3  O15   0.020

