# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:35:02 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5-chloro-N-{[(4S)-4-(1-methyl-1H-imidazol-2-yl)-2,5-dioxoimidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccnc1[C@]2(CNC(=O)c3oc4ccc(Cl)cc4c3)NC(=O)NC2=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
 3PW  3PW  5-chloro-N-{[(4S)-4-(1-methyl-1H-imidazol-2-yl)-2,5-dioxoimidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide  ligand  41  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3PW
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
 3PW  C4   C   CR15  0  -0.217   6.0929   1.5740   1.1146
 3PW  C5   C   CR15  0  -0.106   6.5237   0.4137   0.5404
 3PW  C6   C   CR16  0  -0.292  -5.0840   0.2182  -0.9002
 3PW  C7   C   CR15  0  -0.352  -2.6258   1.0764  -1.0580
 3PW  C8   C   CH2   0  -0.276   1.9910   1.2798   0.8020
 3PW  C10  C   CR56  0   0.388  -3.2909  -0.2235   0.6561
 3PW  C13  C   CR5   0   0.573   4.3462   0.5387   0.4659
 3PW  C15  C   CR5   0   0.659   1.8583  -1.8005  -0.3555
 3PW  C17  C   CR5   0  -0.154   2.9166   0.2034   0.1791
 3PW  C2   C   CR16  0  -0.223  -5.4073  -1.1562   1.0889
 3PW  C3   C   CR16  0  -0.338  -4.0903  -0.9976   1.4788
 3PW  C9   C   CR6   0  -0.043  -5.8838  -0.5528  -0.0829
 3PW  C11  C   CR56  0   0.054  -3.7529   0.3829  -0.5139
 3PW  C12  C   CR5   0   0.257  -1.6048   0.8437  -0.2033
 3PW  C14  C   CR5   0   0.556   2.6519   0.1165  -1.3315
 3PW  C16  C   C     0   0.496  -0.2060   1.3039  -0.2847
 3PW  N18  N   N     0  -0.451   4.7339   1.6381   1.0611
 3PW  N19  N   NR15  0  -0.690   1.9586  -1.0369  -1.5184
 3PW  N20  N   NR15  0  -0.645   2.5336  -1.1215   0.6028
 3PW  N21  N   NH1   0  -0.658   0.6038   0.9114   0.7163
 3PW  N22  N   NR5   0  -0.450   5.4010  -0.2416   0.1245
 3PW  O23  O   O     0  -0.398   3.0052   0.9128  -2.1614
 3PW  O24  O   O     0  -0.456   1.2962  -2.8655  -0.2645
 3PW  O25  O   O     0  -0.462   0.1525   1.9905  -1.2270
 3PW  O26  O   O     0  -0.463  -1.9861   0.0591   0.8406
 3PW  H1   H   HCR5  0   0.254   6.6863   2.3570   1.5596
 3PW  H2   H   HCR5  0   0.294   7.5082   0.0023   0.3932
 3PW  H3   H   HCR6  0   0.288  -5.4693   0.6751  -1.8012
 3PW  H4   H   HCR5  0   0.282  -2.5866   1.6647  -1.9600
 3PW  H5   H   HCH2  0   0.296   2.2510   1.3837   1.8539
 3PW  H6   H   HCH2  0   0.285   2.1649   2.2418   0.3245
 3PW  H7   H   HCH3  0   0.260   4.8378  -1.5013  -1.4653
 3PW  H8   H   HCH3  0   0.279   6.4199  -1.8045  -0.7678
 3PW  H9   H   HCH3  0   0.269   4.9738  -2.2998   0.1151
 3PW  H10  H   HCR6  0   0.289  -6.0750  -1.7532   1.6940
 3PW  H11  H   HCR6  0   0.288  -3.7138  -1.4591   2.3812
 3PW  H12  H   HNR5  0   0.433   1.6254  -1.3651  -2.4145
 3PW  H13  H   HNR5  0   0.419   2.4599  -1.3792   1.5756
 3PW  H14  H   HNH1  0   0.419   0.2194   0.3861   1.4855
 3PW  C1   C   CH3   0  -0.541   5.3952  -1.5339  -0.5311
 3PW  CL2  CL  CL    0  -0.124  -7.5475  -0.7922  -0.5122

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
 3PW  CL2  C9   single    1.735  0.020  1.735
 3PW  C2   C3   aromatic  1.383  0.020  1.383
 3PW  C2   C9   aromatic  1.402  0.020  1.402
 3PW  C3   C10  aromatic  1.384  0.020  1.384
 3PW  C9   C6   aromatic  1.379  0.020  1.379
 3PW  C10  C11  aromatic  1.396  0.020  1.396
 3PW  C10  O26  aromatic  1.348  0.020  1.348
 3PW  C6   C11  aromatic  1.396  0.020  1.396
 3PW  C11  C7   aromatic  1.431  0.020  1.431
 3PW  O26  C12  aromatic  1.360  0.020  1.360
 3PW  C12  C7   aromatic  1.352  0.020  1.352
 3PW  C12  C16  single    1.475  0.020  1.475
 3PW  O23  C14  double    1.203  0.020  1.203
 3PW  N21  C16  single    1.346  0.020  1.346
 3PW  N21  C8   single    1.438  0.020  1.438
 3PW  C16  O25  double    1.220  0.020  1.220
 3PW  C8   C17  single    1.550  0.020  1.550
 3PW  C14  N19  single    1.359  0.020  1.359
 3PW  C14  C17  single    1.536  0.020  1.536
 3PW  N19  C15  single    1.395  0.020  1.395
 3PW  C17  C13  single    1.496  0.020  1.496
 3PW  C17  N20  single    1.443  0.020  1.443
 3PW  C15  N20  single    1.355  0.020  1.355
 3PW  C15  O24  double    1.208  0.020  1.208
 3PW  N18  C13  aromatic  1.309  0.020  1.309
 3PW  N18  C4   aromatic  1.361  0.020  1.361
 3PW  C13  N22  aromatic  1.356  0.020  1.356
 3PW  C4   C5   aromatic  1.364  0.020  1.364
 3PW  N22  C1   single    1.449  0.020  1.449
 3PW  N22  C5   aromatic  1.365  0.020  1.365
 3PW  C4   H1   single    0.930  0.020  1.080
 3PW  C5   H2   single    0.930  0.020  1.080
 3PW  C6   H3   single    0.930  0.020  1.080
 3PW  C7   H4   single    0.930  0.020  1.080
 3PW  C8   H5   single    0.970  0.020  1.090
 3PW  C8   H6   single    0.970  0.020  1.090
 3PW  C1   H7   single    0.970  0.020  1.090
 3PW  C1   H8   single    0.970  0.020  1.090
 3PW  C1   H9   single    0.970  0.020  1.090
 3PW  C2   H10  single    0.930  0.020  1.080
 3PW  C3   H11  single    0.930  0.020  1.080
 3PW  N19  H12  single    0.860  0.020  1.020
 3PW  N20  H13  single    0.890  0.020  1.040
 3PW  N21  H14  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
 3PW  H1   C4   N18  122.09  3.000
 3PW  H1   C4   C5   128.12  3.000
 3PW  N18  C4   C5   109.80  3.000
 3PW  H2   C5   N22  121.79  3.000
 3PW  H2   C5   C4   132.14  3.000
 3PW  N22  C5   C4   106.07  3.000
 3PW  H3   C6   C11  121.37  3.000
 3PW  H3   C6   C9   121.56  3.000
 3PW  C11  C6   C9   117.07  3.000
 3PW  H4   C7   C12  126.57  3.000
 3PW  H4   C7   C11  127.70  3.000
 3PW  C12  C7   C11  105.73  3.000
 3PW  H6   C8   H5   107.55  3.000
 3PW  H6   C8   N21  110.77  3.000
 3PW  H5   C8   N21  108.21  3.000
 3PW  H6   C8   C17  110.01  3.000
 3PW  H5   C8   C17  108.18  3.000
 3PW  N21  C8   C17  111.97  3.000
 3PW  O26  C10  C11  110.11  3.000
 3PW  O26  C10  C3   126.53  3.000
 3PW  C11  C10  C3   123.36  3.000
 3PW  N22  C13  N18  111.57  3.000
 3PW  N22  C13  C17  124.48  3.000
 3PW  N18  C13  C17  123.95  3.000
 3PW  O24  C15  N20  128.36  3.000
 3PW  O24  C15  N19  125.39  3.000
 3PW  N20  C15  N19  106.23  3.000
 3PW  N20  C17  C14  101.02  3.000
 3PW  N20  C17  C13  113.77  3.000
 3PW  C14  C17  C13  111.46  3.000
 3PW  N20  C17  C8   111.17  3.000
 3PW  C13  C17  C8   109.75  3.000
 3PW  C14  C17  C8   109.36  3.000
 3PW  H10  C2   C9   119.72  3.000
 3PW  H10  C2   C3   119.60  3.000
 3PW  C9   C2   C3   120.68  3.000
 3PW  H11  C3   C2   121.21  3.000
 3PW  H11  C3   C10  122.25  3.000
 3PW  C2   C3   C10  116.54  3.000
 3PW  CL2  C9   C2   118.27  3.000
 3PW  C2   C9   C6   122.61  3.000
 3PW  CL2  C9   C6   119.12  3.000
 3PW  C10  C11  C7   105.58  3.000
 3PW  C7   C11  C6   134.68  3.000
 3PW  C10  C11  C6   119.74  3.000
 3PW  O26  C12  C16  119.22  3.000
 3PW  C16  C12  C7   128.89  3.000
 3PW  O26  C12  C7   111.89  3.000
 3PW  O23  C14  N19  128.08  3.000
 3PW  N19  C14  C17  105.74  3.000
 3PW  O23  C14  C17  126.18  3.000
 3PW  O25  C16  N21  124.18  3.000
 3PW  O25  C16  C12  119.80  3.000
 3PW  N21  C16  C12  116.01  3.000
 3PW  C13  N18  C4   105.90  3.000
 3PW  H12  N19  C14  124.46  3.000
 3PW  H12  N19  C15  122.52  3.000
 3PW  C14  N19  C15  112.75  3.000
 3PW  H13  N20  C17  122.48  3.000
 3PW  H13  N20  C15  121.17  3.000
 3PW  C17  N20  C15  112.63  3.000
 3PW  H14  N21  C16  119.36  3.000
 3PW  H14  N21  C8   117.13  3.000
 3PW  C16  N21  C8   123.37  3.000
 3PW  C1   N22  C13  128.62  3.000
 3PW  C1   N22  C5   124.70  3.000
 3PW  C13  N22  C5   106.67  3.000
 3PW  C12  O26  C10  106.69  3.000
 3PW  H9   C1   H8   108.65  3.000
 3PW  H9   C1   H7   109.43  3.000
 3PW  H8   C1   H7   107.68  3.000
 3PW  H9   C1   N22  111.15  3.000
 3PW  H8   C1   N22  108.49  3.000
 3PW  H7   C1   N22  111.33  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
 3PW  CONST_01  N22  C13  N18  C4      0.00   0.0  0
 3PW  CONST_02  C13  N22  C5   C4      0.00   0.0  0
 3PW  CONST_03  C13  N18  C4   C5      0.00   0.0  0
 3PW  CONST_04  N18  C13  N22  C5      0.00   0.0  0
 3PW  CONST_05  C3   C2   C9   C6      0.00   0.0  0
 3PW  CONST_06  C3   C10  C11  C6      0.00   0.0  0
 3PW  CONST_07  O26  C10  C11  C6    180.00   0.0  0
 3PW  CONST_08  C12  C7   C11  C6    180.00   0.0  0
 3PW  CONST_09  C3   C10  C11  C7    180.00   0.0  0
 3PW  CONST_10  O26  C10  C11  C7      0.00   0.0  0
 3PW  CONST_11  C9   C6   C11  C7    180.00   0.0  0
 3PW  CONST_12  C10  O26  C12  C7      0.00   0.0  0
 3PW  CONST_13  C9   C2   C3   C10     0.00   0.0  0
 3PW  CONST_14  C9   C6   C11  C10     0.00   0.0  0
 3PW  CONST_15  C12  C7   C11  C10     0.00   0.0  0
 3PW  CONST_16  C11  C10  C3   C2      0.00   0.0  0
 3PW  CONST_17  O26  C10  C3   C2    180.00   0.0  0
 3PW  CONST_18  C11  C6   C9   C2      0.00   0.0  0
 3PW  CONST_19  C12  O26  C10  C3    180.00   0.0  0
 3PW  CONST_20  C12  O26  C10  C11     0.00   0.0  0
 3PW  CONST_21  O26  C12  C7   C11     0.00   0.0  0
 3PW  CONST_22  N22  C5   C4   N18     0.00   0.0  0
 3PW  CONST_23  C17  C13  N18  C4    180.00   0.0  0
 3PW  CONST_24  C17  C13  N22  C5    180.00   0.0  0
 3PW  CONST_25  C17  C14  N19  C15     0.00   0.0  0
 3PW  CONST_26  N19  C15  N20  C17     0.00   0.0  0
 3PW  CONST_27  N20  C15  N19  C14     0.00   0.0  0
 3PW  CONST_28  C1   N22  C5   C4    180.00   0.0  0
 3PW  CONST_29  C16  C12  O26  C10   180.00   0.0  0
 3PW  CONST_30  C1   N22  C13  C17     0.00   0.0  0
 3PW  CONST_31  N18  C13  N22  C1    180.00   0.0  0
 3PW  CONST_32  CL2  C9   C2   C3    180.00   0.0  0
 3PW  CONST_33  CL2  C9   C6   C11   180.00   0.0  0
 3PW  CONST_34  C16  C12  C7   C11   180.00   0.0  0
 3PW  CONST_35  O24  C15  N20  C17   180.00   0.0  0
 3PW  CONST_36  O24  C15  N19  C14   180.00   0.0  0
 3PW  CONST_37  H10  C2   C9   C6    180.00   0.0  0
 3PW  CONST_38  H4   C7   C11  C6      0.00   0.0  0
 3PW  CONST_39  H3   C6   C11  C7      0.00   0.0  0
 3PW  CONST_40  H1   C4   N18  C13   180.00   0.0  0
 3PW  CONST_41  H2   C5   N22  C13   180.00   0.0  0
 3PW  CONST_42  H11  C3   C2   C9    180.00   0.0  0
 3PW  CONST_43  H12  N19  C14  C17   180.00   0.0  0
 3PW  CONST_44  H13  N20  C15  N19   180.00   0.0  0
 3PW  CONST_45  C12  C16  N21  C8    180.00   0.0  0
 3PW  CONST_46  H14  N21  C16  C12     0.00   0.0  0
 3PW  CONST_47  O25  C16  N21  C8      0.00   0.0  0
 3PW  Var_01    N21  C16  C12  C7   -179.74  30.0  2
 3PW  Var_02    H7   C1   N22  C5   -127.05  30.0  2
 3PW  Var_03    C16  N21  C8   C17   -94.22  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
 3PW  chir_01  C17  C14  C13  N20  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
 3PW  plan-1  C4   0.020
 3PW  plan-1  C5   0.020
 3PW  plan-1  C13  0.020
 3PW  plan-1  C17  0.020
 3PW  plan-1  N18  0.020
 3PW  plan-1  N22  0.020
 3PW  plan-1  H1   0.020
 3PW  plan-1  H2   0.020
 3PW  plan-1  C1   0.020
 3PW  plan-2  C6   0.020
 3PW  plan-2  C7   0.020
 3PW  plan-2  C10  0.020
 3PW  plan-2  C2   0.020
 3PW  plan-2  C3   0.020
 3PW  plan-2  C9   0.020
 3PW  plan-2  C11  0.020
 3PW  plan-2  C12  0.020
 3PW  plan-2  C16  0.020
 3PW  plan-2  O26  0.020
 3PW  plan-2  H3   0.020
 3PW  plan-2  H4   0.020
 3PW  plan-2  H10  0.020
 3PW  plan-2  H11  0.020
 3PW  plan-2  CL2  0.020
 3PW  plan-3  C15  0.020
 3PW  plan-3  C17  0.020
 3PW  plan-3  C14  0.020
 3PW  plan-3  N19  0.020
 3PW  plan-3  N20  0.020
 3PW  plan-3  O23  0.020
 3PW  plan-3  O24  0.020
 3PW  plan-3  H12  0.020
 3PW  plan-3  H13  0.020
 3PW  plan-4  C8   0.020
 3PW  plan-4  C12  0.020
 3PW  plan-4  C16  0.020
 3PW  plan-4  N21  0.020
 3PW  plan-4  O25  0.020
 3PW  plan-4  H14  0.020

