# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:46:13 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Cl)ccc2c(c[nH]c12)\C=C3/NC(=O)N(Cc4ccc(F)c(F)c4)C3=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
 03M  03M  (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione  ligand  42  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_03M
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
 03M  C4    C   CR16  0  -0.403  -3.7074   1.3184   0.9443
 03M  C6    C   CR15  0  -0.073  -2.5779  -1.7960  -0.5346
 03M  C7    C   CR5   0   0.058  -2.2206  -0.6905   0.2098
 03M  C8    C   CR56  0   0.052  -3.4162   0.1035   0.3224
 03M  C10   C   C1    0  -0.391  -0.9594  -0.3497   0.8033
 03M  N12   N   NR15  0  -0.766   0.6296  -1.9927  -0.1587
 03M  C13   C   CR5   0   0.700   1.9624  -2.2496  -0.0355
 03M  C15   C   CR5   0   0.536   1.4607  -0.5068   1.3549
 03M  C20   C   CR16  0  -0.289   5.3645  -0.9881  -0.6342
 03M  C21   C   CR16  0  -0.394   6.1162  -0.1836  -1.4803
 03M  C22   C   CR6   0   0.390   6.1628   1.1746  -1.2520
 03M  C24   C   CR16  0  -0.444   4.7205   0.9351   0.6524
 03M  C1    C   CR16  0  -0.211  -4.9901   1.8143   0.8570
 03M  C2    C   CR6   0  -0.156  -5.9763   1.1081   0.1546
 03M  C3    C   CR6   0   0.146  -5.7482  -0.1013  -0.4811
 03M  N5    N   NR15  0  -0.688  -3.8840  -1.7197  -0.8764
 03M  C9    C   CR56  0   0.342  -4.4360  -0.5726  -0.3724
 03M  C11   C   CR5   0   0.236   0.2411  -0.9260   0.6401
 03M  N14   N   NR5   0  -0.564   2.4439  -1.3615   0.9182
 03M  O17   O   O     0  -0.439   1.5996   0.3856   2.1625
 03M  C18   C   CH2   0  -0.427   3.8307  -1.3130   1.3339
 03M  C19   C   CR6   0   0.139   4.6642  -0.4395   0.4334
 03M  C23   C   CR6   0   0.413   5.4679   1.7291  -0.1899
 03M  F25   F   F     0  -0.306   5.5367   3.0492   0.0104
 03M  C27   C   CH3   0  -0.722  -6.8093  -0.8413  -1.2349
 03M  CL    CL  CL    0  -0.131  -7.5686   1.8031   0.0844
 03M  H4    H   HCR6  0   0.256  -2.9519   1.8698   1.4892
 03M  H6    H   HCR5  0   0.293  -2.0080  -2.6601  -0.8337
 03M  H10   H   H     0   0.269  -0.9639   0.4943   1.4841
 03M  H20   H   HCR6  0   0.270   5.3298  -2.0543  -0.8136
 03M  H21   H   HCR6  0   0.294   6.6634  -0.6084  -2.3114
 03M  H24   H   HCR6  0   0.287   4.1872   1.3906   1.4776
 03M  H1    H   HCR6  0   0.274  -5.2431   2.7534   1.3294
 03M  H18   H   HCH2  0   0.295   3.8548  -0.9489   2.3601
 03M  H18A  H   HCH2  0   0.297   4.2165  -2.3311   1.3455
 03M  H27   H   HCH3  0   0.263  -7.1047  -0.2971  -2.1330
 03M  H27A  H   HCH3  0   0.243  -6.4782  -1.8296  -1.5477
 03M  H27B  H   HCH3  0   0.259  -7.7048  -0.9774  -0.6293
 03M  HN5   H   HNR5  0   0.423  -4.3625  -2.4222  -1.4161
 03M  H14   H   HNR5  0   0.428   0.0861  -2.4112  -0.8955
 03M  O16   O   O     0  -0.459   2.6148  -3.0817  -0.6214
 03M  F26   F   F     0  -0.305   6.8830   1.9731  -2.0459

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
 03M  C4   C1    aromatic  1.378  0.020  1.378
 03M  C4   H4    single    0.930  0.020  1.080
 03M  C6   C7    aromatic  1.380  0.020  1.380
 03M  C6   N5    aromatic  1.352  0.020  1.352
 03M  C6   H6    single    0.930  0.020  1.080
 03M  C7   C8    aromatic  1.440  0.020  1.440
 03M  C8   C4    aromatic  1.396  0.020  1.396
 03M  C8   C9    aromatic  1.407  0.020  1.407
 03M  C10  C7    single    1.435  0.020  1.435
 03M  C10  H10   single    0.930  0.020  1.080
 03M  N12  C11   single    1.388  0.020  1.388
 03M  C13  N12   single    1.363  0.020  1.363
 03M  C15  O17   double    1.212  0.020  1.212
 03M  C15  C11   single    1.474  0.020  1.474
 03M  C20  C21   aromatic  1.389  0.020  1.389
 03M  C20  H20   single    0.930  0.020  1.080
 03M  C21  H21   single    0.930  0.020  1.080
 03M  C22  C21   aromatic  1.378  0.020  1.378
 03M  C22  F26   single    1.337  0.020  1.337
 03M  C24  C19   aromatic  1.393  0.020  1.393
 03M  C24  C23   aromatic  1.378  0.020  1.378
 03M  C24  H24   single    0.930  0.020  1.080
 03M  C1   C2    aromatic  1.402  0.020  1.402
 03M  C1   H1    single    0.930  0.020  1.080
 03M  C2   CL    single    1.739  0.020  1.739
 03M  C3   C2    aromatic  1.385  0.020  1.385
 03M  C3   C27   single    1.497  0.020  1.497
 03M  N5   C9    aromatic  1.369  0.020  1.369
 03M  N5   HN5   single    0.860  0.020  1.020
 03M  C9   C3    aromatic  1.399  0.020  1.399
 03M  C11  C10   double    1.342  0.020  1.342
 03M  N14  C13   single    1.389  0.020  1.389
 03M  N14  C15   single    1.374  0.020  1.374
 03M  O16  C13   double    1.209  0.020  1.209
 03M  C18  N14   single    1.449  0.020  1.449
 03M  C18  C19   single    1.506  0.020  1.506
 03M  C18  H18   single    0.970  0.020  1.090
 03M  C18  H18A  single    0.970  0.020  1.090
 03M  C19  C20   aromatic  1.390  0.020  1.390
 03M  C23  C22   aromatic  1.385  0.020  1.385
 03M  F25  C23   single    1.337  0.020  1.337
 03M  C27  H27   single    0.970  0.020  1.090
 03M  C27  H27A  single    0.970  0.020  1.090
 03M  C27  H27B  single    0.970  0.020  1.090
 03M  N12  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
 03M  H4    C4   C1    119.88  3.000
 03M  H4    C4   C8    121.48  3.000
 03M  C1    C4   C8    118.64  3.000
 03M  H6    C6   N5    119.08  3.000
 03M  H6    C6   C7    130.94  3.000
 03M  N5    C6   C7    109.95  3.000
 03M  C10   C7   C8    124.51  3.000
 03M  C10   C7   C6    129.87  3.000
 03M  C8    C7   C6    105.61  3.000
 03M  C9    C8   C7    107.35  3.000
 03M  C9    C8   C4    119.15  3.000
 03M  C7    C8   C4    133.50  3.000
 03M  H10   C10  C11   114.49  3.000
 03M  C11   C10  C7    129.36  3.000
 03M  H10   C10  C7    116.15  3.000
 03M  H14   N12  C11   126.12  3.000
 03M  H14   N12  C13   121.05  3.000
 03M  C11   N12  C13   111.50  3.000
 03M  O16   C13  N14   125.86  3.000
 03M  O16   C13  N12   127.85  3.000
 03M  N14   C13  N12   106.29  3.000
 03M  O17   C15  N14   126.02  3.000
 03M  N14   C15  C11   105.12  3.000
 03M  O17   C15  C11   128.86  3.000
 03M  H20   C20  C19   120.02  3.000
 03M  C19   C20  C21   120.81  3.000
 03M  H20   C20  C21   119.17  3.000
 03M  H21   C21  C22   119.81  3.000
 03M  C22   C21  C20   119.24  3.000
 03M  H21   C21  C20   120.95  3.000
 03M  F26   C22  C23   119.12  3.000
 03M  C23   C22  C21   120.30  3.000
 03M  F26   C22  C21   120.57  3.000
 03M  H24   C24  C23   119.38  3.000
 03M  H24   C24  C19   120.99  3.000
 03M  C23   C24  C19   119.63  3.000
 03M  H1    C1   C2    119.47  3.000
 03M  H1    C1   C4    120.18  3.000
 03M  C2    C1   C4    120.35  3.000
 03M  CL    C2   C3    118.76  3.000
 03M  C3    C2   C1    123.65  3.000
 03M  CL    C2   C1    117.59  3.000
 03M  C27   C3   C9    122.52  3.000
 03M  C9    C3   C2    114.39  3.000
 03M  C27   C3   C2    123.09  3.000
 03M  HN5   N5   C9    126.18  3.000
 03M  HN5   N5   C6    123.72  3.000
 03M  C9    N5   C6    110.10  3.000
 03M  N5    C9   C3    129.20  3.000
 03M  C3    C9   C8    123.82  3.000
 03M  N5    C9   C8    106.99  3.000
 03M  C15   C11  N12   105.42  3.000
 03M  C15   C11  C10   123.99  3.000
 03M  N12   C11  C10   130.58  3.000
 03M  C18   N14  C15   124.96  3.000
 03M  C18   N14  C13   123.38  3.000
 03M  C15   N14  C13   111.58  3.000
 03M  H18A  C18  H18   107.14  3.000
 03M  H18A  C18  C19   110.64  3.000
 03M  H18   C18  C19   110.93  3.000
 03M  H18A  C18  N14   108.12  3.000
 03M  H18   C18  N14   107.62  3.000
 03M  C19   C18  N14   112.19  3.000
 03M  C18   C19  C24   120.04  3.000
 03M  C18   C19  C20   120.61  3.000
 03M  C24   C19  C20   119.34  3.000
 03M  F25   C23  C24   120.35  3.000
 03M  F25   C23  C22   118.97  3.000
 03M  C24   C23  C22   120.68  3.000
 03M  H27B  C27  H27A  107.24  3.000
 03M  H27B  C27  H27   107.30  3.000
 03M  H27A  C27  H27   107.39  3.000
 03M  H27B  C27  C3    111.37  3.000
 03M  H27A  C27  C3    112.20  3.000
 03M  H27   C27  C3    111.09  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
 03M  CONST_01  C3   C2   C1   C4     0.00   0.0  0
 03M  CONST_02  C6   C7   C8   C4   180.00   0.0  0
 03M  CONST_03  N5   C9   C8   C4   180.00   0.0  0
 03M  CONST_04  C3   C9   C8   C4     0.00   0.0  0
 03M  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 03M  CONST_06  C8   C9   N5   C6     0.00   0.0  0
 03M  CONST_07  C3   C9   N5   C6   180.00   0.0  0
 03M  CONST_08  C9   N5   C6   C7     0.00   0.0  0
 03M  CONST_09  C1   C4   C8   C7   180.00   0.0  0
 03M  CONST_10  N5   C9   C8   C7     0.00   0.0  0
 03M  CONST_11  C3   C9   C8   C7   180.00   0.0  0
 03M  CONST_12  N5   C6   C7   C8     0.00   0.0  0
 03M  CONST_13  C2   C1   C4   C8     0.00   0.0  0
 03M  CONST_14  C2   C3   C9   C8     0.00   0.0  0
 03M  CONST_15  C23  C22  C21  C20    0.00   0.0  0
 03M  CONST_16  C23  C24  C19  C20    0.00   0.0  0
 03M  CONST_17  C24  C19  C20  C21    0.00   0.0  0
 03M  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 03M  CONST_19  C19  C20  C21  C22    0.00   0.0  0
 03M  CONST_20  C19  C24  C23  C22    0.00   0.0  0
 03M  CONST_21  C9   C8   C4   C1     0.00   0.0  0
 03M  CONST_22  C9   C3   C2   C1     0.00   0.0  0
 03M  CONST_23  N5   C9   C3   C2   180.00   0.0  0
 03M  CONST_24  N14  C15  C11  N12    0.00   0.0  0
 03M  CONST_25  C15  N14  C13  N12    0.00   0.0  0
 03M  CONST_26  C15  C11  N12  C13    0.00   0.0  0
 03M  CONST_27  C11  C15  N14  C13    0.00   0.0  0
 03M  CONST_28  N14  C13  N12  C11    0.00   0.0  0
 03M  CONST_29  CL   C2   C1   C4   180.00   0.0  0
 03M  CONST_30  C10  C7   C8   C4     0.00   0.0  0
 03M  CONST_31  C27  C3   C9   C8   180.00   0.0  0
 03M  CONST_32  N5   C6   C7   C10  180.00   0.0  0
 03M  CONST_33  C9   C8   C7   C10  180.00   0.0  0
 03M  CONST_34  F26  C22  C21  C20  180.00   0.0  0
 03M  CONST_35  C18  C19  C20  C21  180.00   0.0  0
 03M  CONST_36  F25  C23  C22  C21  180.00   0.0  0
 03M  CONST_37  F26  C22  C23  C24  180.00   0.0  0
 03M  CONST_38  C27  C3   C2   C1   180.00   0.0  0
 03M  CONST_39  C27  C3   C9   N5     0.00   0.0  0
 03M  CONST_40  CL   C2   C3   C9   180.00   0.0  0
 03M  CONST_41  C23  C24  C19  C18  180.00   0.0  0
 03M  CONST_42  F25  C23  C24  C19  180.00   0.0  0
 03M  CONST_43  C18  N14  C13  N12  180.00   0.0  0
 03M  CONST_44  O17  C15  N14  C13  180.00   0.0  0
 03M  CONST_45  O16  C13  N14  C15  180.00   0.0  0
 03M  CONST_46  O16  C13  N12  C11  180.00   0.0  0
 03M  CONST_47  C18  N14  C15  C11  180.00   0.0  0
 03M  CONST_48  HN5  N5   C6   C7   180.00   0.0  0
 03M  CONST_49  H4   C4   C8   C7     0.00   0.0  0
 03M  CONST_50  H6   C6   C7   C8   180.00   0.0  0
 03M  CONST_51  H1   C1   C4   C8   180.00   0.0  0
 03M  CONST_52  H24  C24  C19  C20  180.00   0.0  0
 03M  CONST_53  H20  C20  C21  C22  180.00   0.0  0
 03M  CONST_54  H21  C21  C20  C19  180.00   0.0  0
 03M  CONST_55  H14  N12  C11  C15  180.00   0.0  0
 03M  CONST_56  C18  N14  C13  O16    0.00   0.0  0
 03M  CONST_57  C18  N14  C15  O17    0.00   0.0  0
 03M  Var_01    C11  C10  C7   C6     9.94  30.0  2
 03M  Var_02    N12  C11  C10  C7     1.43  30.0  2
 03M  Var_03    C19  C18  N14  C13   85.87  30.0  2
 03M  Var_04    N14  C18  C19  C20  -94.06  30.0  2
 03M  Var_05    H27  C27  C3   C2    67.53  30.0  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
 03M  plan-1  C10  0.020
 03M  plan-1  N12  0.020
 03M  plan-1  C13  0.020
 03M  plan-1  C15  0.020
 03M  plan-1  C11  0.020
 03M  plan-1  N14  0.020
 03M  plan-1  O17  0.020
 03M  plan-1  C18  0.020
 03M  plan-1  H14  0.020
 03M  plan-1  O16  0.020
 03M  plan-2  C20  0.020
 03M  plan-2  C21  0.020
 03M  plan-2  C22  0.020
 03M  plan-2  C24  0.020
 03M  plan-2  C18  0.020
 03M  plan-2  C19  0.020
 03M  plan-2  C23  0.020
 03M  plan-2  F25  0.020
 03M  plan-2  H20  0.020
 03M  plan-2  H21  0.020
 03M  plan-2  H24  0.020
 03M  plan-2  F26  0.020
 03M  plan-3  C4   0.020
 03M  plan-3  C6   0.020
 03M  plan-3  C7   0.020
 03M  plan-3  C8   0.020
 03M  plan-3  C10  0.020
 03M  plan-3  C1   0.020
 03M  plan-3  C2   0.020
 03M  plan-3  C3   0.020
 03M  plan-3  N5   0.020
 03M  plan-3  C9   0.020
 03M  plan-3  C27  0.020
 03M  plan-3  CL   0.020
 03M  plan-3  H4   0.020
 03M  plan-3  H6   0.020
 03M  plan-3  H1   0.020
 03M  plan-3  HN5  0.020

