# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:29:52 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3sc(Cl)cc3
#
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
 OQZ  OQZ  (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide  ligand  48  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OQZ
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
 OQZ  C12  C   CH2   0  -0.517  77.9408  14.4040  90.1427
 OQZ  C13  C   CR6   0   0.102  76.5315  14.0318  89.7769
 OQZ  C14  C   CR16  0  -0.302  76.1961  13.7507  88.4541
 OQZ  C15  C   CR16  0  -0.240  74.9127  13.3459  88.1130
 OQZ  C16  C   CR16  0  -0.268  73.9398  13.2168  89.0958
 OQZ  C17  C   CR16  0  -0.241  74.2587  13.5046  90.4164
 OQZ  C18  C   CR16  0  -0.290  75.5432  13.9099  90.7523
 OQZ  N    N   NH2   0  -0.795  80.1650  13.6367  90.7703
 OQZ  C    C   CH1   0  -0.188  78.8119  13.1838  90.4919
 OQZ  O    O   O     0  -0.488  79.0634  10.0597  93.6263
 OQZ  C1   C   C     0   0.560  78.2395  12.5325  91.7493
 OQZ  C10  C   CH2   0  -0.473  76.0167   9.8337  90.8082
 OQZ  C11  C   CH2   0  -0.280  77.2394  10.6432  90.4027
 OQZ  C2   C   CR15  0  -0.163  76.9331  10.8036  92.7977
 OQZ  C3   C   C     0   0.570  77.9498  10.4915  93.8840
 OQZ  C4   C   CH2   0  -0.378  78.3137  10.2877  96.2829
 OQZ  C5   C   CR5   0  -0.143  78.3206   8.8196  96.5771
 OQZ  C6   C   CR15  0  -0.226  77.7890   8.1922  97.6617
 OQZ  C7   C   CR15  0  -0.133  77.9656   6.7812  97.6515
 OQZ  C8   C   CR5   0  -0.257  78.6364   6.3775  96.5430
 OQZ  C9   C   CH2   0  -0.477  76.2852   9.5150  92.2731
 OQZ  N1   N   NR5   0  -0.476  77.5590  11.3816  91.6227
 OQZ  N2   N   NH1   0  -0.623  77.5057  10.6467  95.1391
 OQZ  O1   O   O     0  -0.493  78.3681  13.0683  92.8435
 OQZ  S    S   S2    0   0.272  79.0587   7.6833  95.5040
 OQZ  CL   CL  CL    0  -0.086  79.0543   4.7729  96.1240
 OQZ  H1   H   HCH2  0   0.258  78.4135  14.9231  89.3046
 OQZ  H2   H   HCH2  0   0.253  77.9528  15.0893  90.9927
 OQZ  H3   H   HCR6  0   0.247  76.9515  13.8462  87.6823
 OQZ  H4   H   HCR6  0   0.252  74.6721  13.1326  87.0793
 OQZ  H5   H   HCR6  0   0.253  72.9383  12.9012  88.8332
 OQZ  H6   H   HCR6  0   0.252  73.5046  13.4156  91.1881
 OQZ  H7   H   HCR6  0   0.248  75.7791  14.1335  91.7864
 OQZ  H8   H   HNH2  0   0.350  80.7656  12.8382  90.9370
 OQZ  H9   H   HNH2  0   0.352  80.5310  14.0824  89.9375
 OQZ  H11  H   HCH1  0   0.249  78.7731  12.4868  89.6471
 OQZ  H12  H   HCH2  0   0.244  75.1184  10.4466  90.7115
 OQZ  H13  H   HCH2  0   0.257  75.8881   8.9437  90.1940
 OQZ  H14  H   HCH2  0   0.246  78.0700   9.9920  90.1162
 OQZ  H15  H   HCH2  0   0.263  77.0256  11.3096  89.5703
 OQZ  H16  H   HCR5  0   0.274  76.1647  11.4833  93.1822
 OQZ  H17  H   HCH2  0   0.273  79.3291  10.6583  96.1364
 OQZ  H18  H   HCH2  0   0.286  77.9106  10.8046  97.1526
 OQZ  H19  H   HCR5  0   0.272  77.2830   8.7252  98.4553
 OQZ  H20  H   HCR5  0   0.283  77.6116   6.1136  98.4232
 OQZ  H21  H   HCH2  0   0.265  75.3881   9.2575  92.8337
 OQZ  H22  H   HCH2  0   0.249  76.9826   8.6779  92.3532
 OQZ  H23  H   HNH1  0   0.407  76.5606  10.9545  95.3036

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
 OQZ  C15  C14  aromatic  1.388  0.020  1.388
 OQZ  C15  C16  aromatic  1.389  0.020  1.389
 OQZ  C14  C13  aromatic  1.393  0.020  1.393
 OQZ  C16  C17  aromatic  1.389  0.020  1.389
 OQZ  C11  C10  single    1.521  0.020  1.521
 OQZ  C11  N1   single    1.461  0.020  1.461
 OQZ  C10  C9   single    1.523  0.020  1.523
 OQZ  C13  C12  single    1.503  0.020  1.503
 OQZ  C13  C18  aromatic  1.394  0.020  1.394
 OQZ  C12  C    single    1.539  0.020  1.539
 OQZ  C    N    single    1.454  0.020  1.454
 OQZ  C    C1   single    1.527  0.020  1.527
 OQZ  C17  C18  aromatic  1.388  0.020  1.388
 OQZ  N1   C1   single    1.343  0.020  1.343
 OQZ  N1   C2   single    1.451  0.020  1.451
 OQZ  C9   C2   single    1.535  0.020  1.535
 OQZ  C1   O1   double    1.225  0.020  1.225
 OQZ  C2   C3   single    1.520  0.020  1.520
 OQZ  O    C3   double    1.222  0.020  1.222
 OQZ  C3   N2   single    1.340  0.020  1.340
 OQZ  N2   C4   single    1.446  0.020  1.446
 OQZ  C4   C5   single    1.497  0.020  1.497
 OQZ  C5   S    aromatic  1.728  0.020  1.728
 OQZ  C5   C6   aromatic  1.361  0.020  1.361
 OQZ  S    C8   aromatic  1.721  0.020  1.721
 OQZ  C6   C7   aromatic  1.422  0.020  1.422
 OQZ  C8   C7   aromatic  1.357  0.020  1.357
 OQZ  C8   CL   single    1.710  0.020  1.710
 OQZ  C12  H1   single    0.970  0.020  1.090
 OQZ  C12  H2   single    0.970  0.020  1.090
 OQZ  C14  H3   single    0.930  0.020  1.080
 OQZ  C15  H4   single    0.930  0.020  1.080
 OQZ  C16  H5   single    0.930  0.020  1.080
 OQZ  C17  H6   single    0.930  0.020  1.080
 OQZ  C18  H7   single    0.930  0.020  1.080
 OQZ  N    H8   single    0.890  0.020  1.040
 OQZ  N    H9   single    0.890  0.020  1.040
 OQZ  C    H11  single    0.970  0.020  1.090
 OQZ  C10  H12  single    0.970  0.020  1.090
 OQZ  C10  H13  single    0.970  0.020  1.090
 OQZ  C11  H14  single    0.970  0.020  1.090
 OQZ  C11  H15  single    0.970  0.020  1.090
 OQZ  C2   H16  single    0.970  0.020  1.090
 OQZ  C4   H17  single    0.970  0.020  1.090
 OQZ  C4   H18  single    0.970  0.020  1.090
 OQZ  C6   H19  single    0.930  0.020  1.080
 OQZ  C7   H20  single    0.930  0.020  1.080
 OQZ  C9   H21  single    0.970  0.020  1.090
 OQZ  C9   H22  single    0.970  0.020  1.090
 OQZ  N2   H23  single    0.860  0.020  1.020

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
 OQZ  H2   C12  H1   107.10  3.000
 OQZ  H2   C12  C    108.35  3.000
 OQZ  H1   C12  C    107.79  3.000
 OQZ  H2   C12  C13  110.80  3.000
 OQZ  H1   C12  C13  109.65  3.000
 OQZ  C    C12  C13  112.93  3.000
 OQZ  C18  C13  C14  118.42  3.000
 OQZ  C18  C13  C12  121.08  3.000
 OQZ  C14  C13  C12  120.45  3.000
 OQZ  H3   C14  C15  119.67  3.000
 OQZ  H3   C14  C13  119.36  3.000
 OQZ  C15  C14  C13  120.97  3.000
 OQZ  H4   C15  C16  120.11  3.000
 OQZ  H4   C15  C14  119.83  3.000
 OQZ  C16  C15  C14  120.06  3.000
 OQZ  H5   C16  C17  120.24  3.000
 OQZ  H5   C16  C15  120.24  3.000
 OQZ  C17  C16  C15  119.53  3.000
 OQZ  H6   C17  C18  119.74  3.000
 OQZ  H6   C17  C16  120.06  3.000
 OQZ  C18  C17  C16  120.20  3.000
 OQZ  H7   C18  C17  119.50  3.000
 OQZ  H7   C18  C13  119.68  3.000
 OQZ  C17  C18  C13  120.82  3.000
 OQZ  H9   N    H8   105.53  3.000
 OQZ  H9   N    C    108.42  3.000
 OQZ  H8   N    C    109.75  3.000
 OQZ  H11  C    C1   110.49  3.000
 OQZ  H11  C    N    112.26  3.000
 OQZ  C1   C    N    108.90  3.000
 OQZ  H11  C    C12  108.01  3.000
 OQZ  C1   C    C12  108.22  3.000
 OQZ  N    C    C12  108.86  3.000
 OQZ  O1   C1   N1   120.81  3.000
 OQZ  O1   C1   C    120.63  3.000
 OQZ  N1   C1   C    118.54  3.000
 OQZ  H13  C10  H12  108.16  3.000
 OQZ  H13  C10  C9   113.10  3.000
 OQZ  H12  C10  C9   110.35  3.000
 OQZ  H13  C10  C11  112.30  3.000
 OQZ  H12  C10  C11  109.81  3.000
 OQZ  C9   C10  C11  103.06  3.000
 OQZ  H15  C11  H14  108.28  3.000
 OQZ  H15  C11  N1   111.86  3.000
 OQZ  H14  C11  N1   110.70  3.000
 OQZ  H15  C11  C10  111.84  3.000
 OQZ  H14  C11  C10  111.31  3.000
 OQZ  N1   C11  C10  102.83  3.000
 OQZ  H16  C2   N1   109.85  3.000
 OQZ  H16  C2   C9   110.17  3.000
 OQZ  N1   C2   C9   103.87  3.000
 OQZ  H16  C2   C3   110.22  3.000
 OQZ  C9   C2   C3   110.74  3.000
 OQZ  N1   C2   C3   111.83  3.000
 OQZ  N2   C3   C2   115.07  3.000
 OQZ  N2   C3   O    122.71  3.000
 OQZ  C2   C3   O    122.10  3.000
 OQZ  H18  C4   H17  106.89  3.000
 OQZ  H18  C4   N2   107.88  3.000
 OQZ  H17  C4   N2   109.24  3.000
 OQZ  H18  C4   C5   108.07  3.000
 OQZ  H17  C4   C5   110.81  3.000
 OQZ  N2   C4   C5   113.68  3.000
 OQZ  S    C5   C6   111.00  3.000
 OQZ  C6   C5   C4   127.35  3.000
 OQZ  S    C5   C4   121.64  3.000
 OQZ  H19  C6   C7   123.53  3.000
 OQZ  H19  C6   C5   122.70  3.000
 OQZ  C7   C6   C5   113.78  3.000
 OQZ  H20  C7   C8   124.18  3.000
 OQZ  H20  C7   C6   124.58  3.000
 OQZ  C8   C7   C6   111.25  3.000
 OQZ  CL   C8   S    120.26  3.000
 OQZ  CL   C8   C7   126.87  3.000
 OQZ  S    C8   C7   112.87  3.000
 OQZ  H22  C9   H21  107.88  3.000
 OQZ  H22  C9   C2   110.41  3.000
 OQZ  H21  C9   C2   111.74  3.000
 OQZ  H22  C9   C10  110.08  3.000
 OQZ  H21  C9   C10  113.54  3.000
 OQZ  C2   C9   C10  103.15  3.000
 OQZ  C2   N1   C11  112.35  3.000
 OQZ  C2   N1   C1   118.91  3.000
 OQZ  C11  N1   C1   128.50  3.000
 OQZ  H23  N2   C4   118.09  3.000
 OQZ  H23  N2   C3   119.94  3.000
 OQZ  C4   N2   C3   121.80  3.000
 OQZ  C8   S    C5    91.10  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
 OQZ  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 OQZ  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 OQZ  CONST_03  C17  C16  C15  C14     0.00   0.0  0
 OQZ  CONST_04  C17  C18  C13  C14     0.00   0.0  0
 OQZ  CONST_05  C18  C13  C14  C15     0.00   0.0  0
 OQZ  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 OQZ  CONST_07  C7   C8   S    C5      0.00   0.0  0
 OQZ  CONST_08  C8   C7   C6   C5      0.00   0.0  0
 OQZ  CONST_09  C8   S    C5   C6      0.00   0.0  0
 OQZ  CONST_10  S    C8   C7   C6      0.00   0.0  0
 OQZ  CONST_11  S    C5   C6   C7      0.00   0.0  0
 OQZ  CONST_12  C15  C14  C13  C12   180.00   0.0  0
 OQZ  CONST_13  C17  C18  C13  C12   180.00   0.0  0
 OQZ  CONST_14  C8   S    C5   C4    180.00   0.0  0
 OQZ  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 OQZ  CONST_16  CL   C8   S    C5    180.00   0.0  0
 OQZ  CONST_17  CL   C8   C7   C6    180.00   0.0  0
 OQZ  CONST_18  H4   C15  C14  C13   180.00   0.0  0
 OQZ  CONST_19  H6   C17  C18  C13   180.00   0.0  0
 OQZ  CONST_20  H5   C16  C15  C14   180.00   0.0  0
 OQZ  CONST_21  H7   C18  C13  C14   180.00   0.0  0
 OQZ  CONST_22  H3   C14  C15  C16   180.00   0.0  0
 OQZ  CONST_23  H20  C7   C6   C5    180.00   0.0  0
 OQZ  CONST_24  H19  C6   C7   C8    180.00   0.0  0
 OQZ  CONST_25  C11  N1   C1   C       0.00   0.0  0
 OQZ  CONST_26  C2   N1   C1   C     180.00   0.0  0
 OQZ  CONST_27  O1   C1   N1   C11   180.00   0.0  0
 OQZ  CONST_28  O1   C1   N1   C2      0.00   0.0  0
 OQZ  CONST_29  C4   N2   C3   C2    180.00   0.0  0
 OQZ  CONST_30  H23  N2   C3   C2      0.00   0.0  0
 OQZ  CONST_31  C4   N2   C3   O       0.00   0.0  0
 OQZ  Var_01    C2   N1   C11  C10    17.77  30.0  1
 OQZ  Var_02    C2   C9   C10  C11    38.12  30.0  1
 OQZ  Var_03    N1   C11  C10  C9    -34.15  30.0  1
 OQZ  Var_04    C    C12  C13  C14   -89.58  30.0  2
 OQZ  Var_05    N2   C4   C5   C6   -112.88  30.0  1
 OQZ  Var_06    C5   C4   N2   C3    -79.44  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
 OQZ  chir_01  C   C12  N   C1  negativ
 OQZ  chir_02  C2  N1   C9  C3  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
 OQZ  plan-1  C4   0.020
 OQZ  plan-1  C5   0.020
 OQZ  plan-1  C6   0.020
 OQZ  plan-1  C7   0.020
 OQZ  plan-1  C8   0.020
 OQZ  plan-1  S    0.020
 OQZ  plan-1  CL   0.020
 OQZ  plan-1  H19  0.020
 OQZ  plan-1  H20  0.020
 OQZ  plan-2  C12  0.020
 OQZ  plan-2  C13  0.020
 OQZ  plan-2  C14  0.020
 OQZ  plan-2  C15  0.020
 OQZ  plan-2  C16  0.020
 OQZ  plan-2  C17  0.020
 OQZ  plan-2  C18  0.020
 OQZ  plan-2  H3   0.020
 OQZ  plan-2  H4   0.020
 OQZ  plan-2  H5   0.020
 OQZ  plan-2  H6   0.020
 OQZ  plan-2  H7   0.020
 OQZ  plan-3  O    0.020
 OQZ  plan-3  C2   0.020
 OQZ  plan-3  C3   0.020
 OQZ  plan-3  C4   0.020
 OQZ  plan-3  N2   0.020
 OQZ  plan-3  H23  0.020
 OQZ  plan-4  C    0.020
 OQZ  plan-4  C1   0.020
 OQZ  plan-4  C11  0.020
 OQZ  plan-4  C2   0.020
 OQZ  plan-4  N1   0.020
 OQZ  plan-4  O1   0.020

