# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:22:42 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R)-3-methyl-5-(1-methylpyrazol-4-yl)-3-(phenylmethyl)-1H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2ccc3NC(=O)[C@](C)(Cc4ccccc4)c3c2
#
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
 A0J  A0J  (3R)-3-methyl-5-(1-methylpyrazol-4-yl)-3-(phenylmethyl)-1H-indol-2-one  ligand  43  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0J
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
 A0J  C1    C  CH3   0  -0.645  -1.6073   0.2466   1.9801
 A0J  C2    C  CR5   0  -0.318  -1.3664  -0.3902   0.6151
 A0J  C3    C  CR56  0   0.152   0.0744  -0.7643   0.3904
 A0J  C4    C  CR16  0  -0.423   1.2114   0.0110   0.3735
 A0J  C5    C  CR6   0   0.096   2.4553  -0.5805   0.1073
 A0J  C6    C  CR16  0  -0.349   2.5021  -1.9537  -0.1426
 A0J  C7    C  CR16  0  -0.286   1.3585  -2.7451  -0.1395
 A0J  C8    C  CR56  0   0.349   0.1519  -2.1297   0.1318
 A0J  N9    N  NR15  0  -0.737  -1.1195  -2.6821   0.2069
 A0J  C10   C  CR5   0   0.583  -2.0603  -1.7565   0.5442
 A0J  O11   O  O     0  -0.445  -3.2312  -1.9856   0.7573
 A0J  C12   C  CR5   0  -0.137   3.6721   0.2290   0.0953
 A0J  C13   C  CR15  0  -0.101   3.9000   1.4768   0.7103
 A0J  N14   N  N     0  -0.281   5.1249   1.9142   0.4873
 A0J  N15   N  NR5   0  -0.265   5.7005   0.9823  -0.2637
 A0J  C16   C  CR15  0   0.007   4.8774  -0.0458  -0.5242
 A0J  C17   C  CH3   0  -0.506   7.0722   1.1345  -0.6854
 A0J  C18   C  CH2   0  -0.499  -1.8330   0.5170  -0.5551
 A0J  C19   C  CR6   0   0.153  -3.2826   0.9131  -0.5585
 A0J  C20   C  CR16  0  -0.309  -3.7171   2.0357   0.1439
 A0J  C21   C  CR16  0  -0.244  -5.0529   2.4146   0.1299
 A0J  C22   C  CR16  0  -0.271  -5.9777   1.6770  -0.5973
 A0J  C23   C  CR16  0  -0.247  -5.5550   0.5630  -1.3115
 A0J  C24   C  CR16  0  -0.293  -4.2196   0.1863  -1.2896
 A0J  H11C  H  HCH3  0   0.242  -1.0941   1.2064   2.0497
 A0J  H12C  H  HCH3  0   0.249  -2.6691   0.4163   2.1534
 A0J  H13C  H  HCH3  0   0.248  -1.2298  -0.3909   2.7801
 A0J  H181  H  HCH2  0   0.267  -1.2135   1.4168  -0.5150
 A0J  H182  H  HCH2  0   0.264  -1.5853   0.0209  -1.4969
 A0J  H4    H  HCR6  0   0.246   1.1434   1.0780   0.5530
 A0J  H6    H  HCR6  0   0.251   3.4559  -2.4290  -0.3353
 A0J  H7    H  HCR6  0   0.268   1.4238  -3.8076  -0.3332
 A0J  H9    H  HNR5  0   0.409  -1.3215  -3.6659   0.1095
 A0J  H13   H  HCR5  0   0.256   3.2196   2.0589   1.3142
 A0J  H16   H  HCR5  0   0.290   5.1912  -0.8800  -1.1314
 A0J  H171  H  HCH3  0   0.260   7.7427   1.0944   0.1710
 A0J  H172  H  HCH3  0   0.258   7.3231   0.3282  -1.3683
 A0J  H173  H  HCH3  0   0.261   7.2025   2.0848  -1.1985
 A0J  H20   H  HCR6  0   0.247  -3.0008   2.6263   0.7032
 A0J  H24   H  HCR6  0   0.242  -3.9004  -0.6811  -1.8546
 A0J  H21   H  HCR6  0   0.253  -5.3692   3.2918   0.6797
 A0J  H22   H  HCR6  0   0.253  -7.0186   1.9733  -0.6152
 A0J  H23   H  HCR6  0   0.252  -6.2659  -0.0116  -1.8914

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
 A0J  C1   C2    single    1.525  0.020  1.525
 A0J  C2   C3    single    1.505  0.020  1.505
 A0J  C2   C10   single    1.534  0.020  1.534
 A0J  C2   C18   single    1.552  0.020  1.552
 A0J  C3   C4    aromatic  1.376  0.020  1.376
 A0J  C3   C8    aromatic  1.392  0.020  1.392
 A0J  C4   C5    aromatic  1.403  0.020  1.403
 A0J  C5   C6    aromatic  1.397  0.020  1.397
 A0J  C5   C12   single    1.461  0.020  1.461
 A0J  C6   C7    aromatic  1.391  0.020  1.391
 A0J  C7   C8    aromatic  1.381  0.020  1.381
 A0J  C8   N9    single    1.388  0.020  1.388
 A0J  N9   C10   single    1.362  0.020  1.362
 A0J  C10  O11   double    1.212  0.020  1.212
 A0J  C12  C13   aromatic  1.410  0.020  1.410
 A0J  C12  C16   aromatic  1.383  0.020  1.383
 A0J  C13  N14   aromatic  1.320  0.020  1.320
 A0J  N14  N15   aromatic  1.328  0.020  1.328
 A0J  N15  C16   aromatic  1.343  0.020  1.343
 A0J  N15  C17   single    1.443  0.020  1.443
 A0J  C18  C19   single    1.503  0.020  1.503
 A0J  C19  C20   aromatic  1.394  0.020  1.394
 A0J  C19  C24   aromatic  1.393  0.020  1.393
 A0J  C20  C21   aromatic  1.389  0.020  1.389
 A0J  C21  C22   aromatic  1.389  0.020  1.389
 A0J  C22  C23   aromatic  1.389  0.020  1.389
 A0J  C23  C24   aromatic  1.388  0.020  1.388
 A0J  C1   H11C  single    0.970  0.020  1.090
 A0J  C1   H12C  single    0.970  0.020  1.090
 A0J  C1   H13C  single    0.970  0.020  1.090
 A0J  C18  H181  single    0.970  0.020  1.090
 A0J  C18  H182  single    0.970  0.020  1.090
 A0J  C4   H4    single    0.930  0.020  1.080
 A0J  C6   H6    single    0.930  0.020  1.080
 A0J  C7   H7    single    0.930  0.020  1.080
 A0J  N9   H9    single    0.860  0.020  1.020
 A0J  C13  H13   single    0.930  0.020  1.080
 A0J  C16  H16   single    0.930  0.020  1.080
 A0J  C17  H171  single    0.970  0.020  1.090
 A0J  C17  H172  single    0.970  0.020  1.090
 A0J  C17  H173  single    0.970  0.020  1.090
 A0J  C20  H20   single    0.930  0.020  1.080
 A0J  C24  H24   single    0.930  0.020  1.080
 A0J  C21  H21   single    0.930  0.020  1.080
 A0J  C22  H22   single    0.930  0.020  1.080
 A0J  C23  H23   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
 A0J  H13C  C1   H12C  108.17  3.000
 A0J  H13C  C1   H11C  107.75  3.000
 A0J  H12C  C1   H11C  108.15  3.000
 A0J  H13C  C1   C2    110.96  3.000
 A0J  H12C  C1   C2    111.19  3.000
 A0J  H11C  C1   C2    110.50  3.000
 A0J  C18   C2   C10   110.47  3.000
 A0J  C18   C2   C3    108.68  3.000
 A0J  C10   C2   C3    101.81  3.000
 A0J  C18   C2   C1    112.53  3.000
 A0J  C10   C2   C1    109.98  3.000
 A0J  C3    C2   C1    112.86  3.000
 A0J  C8    C3   C4    120.29  3.000
 A0J  C8    C3   C2    108.95  3.000
 A0J  C4    C3   C2    130.73  3.000
 A0J  H4    C4   C5    120.13  3.000
 A0J  H4    C4   C3    120.04  3.000
 A0J  C5    C4   C3    119.83  3.000
 A0J  C12   C5   C6    121.01  3.000
 A0J  C12   C5   C4    120.42  3.000
 A0J  C6    C5   C4    118.57  3.000
 A0J  H6    C6   C7    118.35  3.000
 A0J  H6    C6   C5    119.53  3.000
 A0J  C7    C6   C5    122.11  3.000
 A0J  H7    C7   C8    121.70  3.000
 A0J  H7    C7   C6    120.58  3.000
 A0J  C8    C7   C6    117.72  3.000
 A0J  N9    C8   C7    129.29  3.000
 A0J  N9    C8   C3    109.23  3.000
 A0J  C7    C8   C3    121.48  3.000
 A0J  H9    N9   C10   123.24  3.000
 A0J  H9    N9   C8    124.48  3.000
 A0J  C10   N9   C8    112.06  3.000
 A0J  O11   C10  N9    125.62  3.000
 A0J  O11   C10  C2    126.67  3.000
 A0J  N9    C10  C2    107.71  3.000
 A0J  C16   C12  C13   103.32  3.000
 A0J  C16   C12  C5    128.26  3.000
 A0J  C13   C12  C5    128.41  3.000
 A0J  H13   C13  N14   120.04  3.000
 A0J  H13   C13  C12   128.25  3.000
 A0J  N14   C13  C12   111.70  3.000
 A0J  N15   N14  C13   105.39  3.000
 A0J  C17   N15  C16   127.36  3.000
 A0J  C17   N15  N14   120.22  3.000
 A0J  C16   N15  N14   112.42  3.000
 A0J  H16   C16  N15   121.55  3.000
 A0J  H16   C16  C12   131.27  3.000
 A0J  N15   C16  C12   107.17  3.000
 A0J  H173  C17  H172  108.92  3.000
 A0J  H173  C17  H171  109.24  3.000
 A0J  H172  C17  H171  108.98  3.000
 A0J  H173  C17  N15   110.11  3.000
 A0J  H172  C17  N15   108.97  3.000
 A0J  H171  C17  N15   110.60  3.000
 A0J  H182  C18  H181  106.07  3.000
 A0J  H182  C18  C19   109.65  3.000
 A0J  H181  C18  C19   109.26  3.000
 A0J  H182  C18  C2    108.43  3.000
 A0J  H181  C18  C2    106.44  3.000
 A0J  C19   C18  C2    116.46  3.000
 A0J  C24   C19  C20   118.36  3.000
 A0J  C24   C19  C18   120.83  3.000
 A0J  C20   C19  C18   120.79  3.000
 A0J  H20   C20  C21   119.49  3.000
 A0J  H20   C20  C19   119.53  3.000
 A0J  C21   C20  C19   120.97  3.000
 A0J  H21   C21  C22   120.12  3.000
 A0J  H21   C21  C20   119.80  3.000
 A0J  C22   C21  C20   120.07  3.000
 A0J  H22   C22  C23   120.25  3.000
 A0J  H22   C22  C21   120.25  3.000
 A0J  C23   C22  C21   119.51  3.000
 A0J  H23   C23  C24   119.75  3.000
 A0J  H23   C23  C22   120.08  3.000
 A0J  C24   C23  C22   120.16  3.000
 A0J  H24   C24  C23   119.51  3.000
 A0J  H24   C24  C19   119.56  3.000
 A0J  C23   C24  C19   120.93  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
 A0J  CONST_01  C6    C5   C4   C3     0.00   0.0  0
 A0J  CONST_02  C12   C5   C4   C3   180.00   0.0  0
 A0J  CONST_03  C6    C7   C8   C3     0.00   0.0  0
 A0J  CONST_04  C7    C8   C3   C4     0.00   0.0  0
 A0J  CONST_05  C7    C6   C5   C4     0.00   0.0  0
 A0J  CONST_08  C8    C3   C4   C5     0.00   0.0  0
 A0J  CONST_09  C8    C7   C6   C5     0.00   0.0  0
 A0J  CONST_10  N14   C13  C12  C5   180.00   0.0  0
 A0J  CONST_11  N15   C16  C12  C5   180.00   0.0  0
 A0J  CONST_14  C12   C5   C6   C7   180.00   0.0  0
 A0J  CONST_15  N15   N14  C13  C12    0.00   0.0  0
 A0J  CONST_16  N14   N15  C16  C12    0.00   0.0  0
 A0J  CONST_17  N15   C16  C12  C13    0.00   0.0  0
 A0J  CONST_18  C16   N15  N14  C13    0.00   0.0  0
 A0J  CONST_19  C16   C12  C13  N14    0.00   0.0  0
 A0J  CONST_20  C22   C21  C20  C19    0.00   0.0  0
 A0J  CONST_21  C22   C23  C24  C19    0.00   0.0  0
 A0J  CONST_22  C23   C24  C19  C20    0.00   0.0  0
 A0J  CONST_23  C23   C22  C21  C20    0.00   0.0  0
 A0J  CONST_24  C24   C19  C20  C21    0.00   0.0  0
 A0J  CONST_25  C24   C23  C22  C21    0.00   0.0  0
 A0J  CONST_26  C8    N9   C10  C2     0.00   0.0  0
 A0J  CONST_27  C17   N15  C16  C12  180.00   0.0  0
 A0J  CONST_28  C17   N15  N14  C13  180.00   0.0  0
 A0J  CONST_29  C21   C20  C19  C18  180.00   0.0  0
 A0J  CONST_30  C23   C24  C19  C18  180.00   0.0  0
 A0J  CONST_31  O11   C10  N9   C8   180.00   0.0  0
 A0J  CONST_32  H4    C4   C3   C2     0.00   0.0  0
 A0J  CONST_33  H7    C7   C8   C3   180.00   0.0  0
 A0J  CONST_34  H6    C6   C5   C4   180.00   0.0  0
 A0J  CONST_35  H13   C13  C12  C5     0.00   0.0  0
 A0J  CONST_36  H16   C16  C12  C5     0.00   0.0  0
 A0J  CONST_37  H21   C21  C20  C19  180.00   0.0  0
 A0J  CONST_38  H23   C23  C24  C19  180.00   0.0  0
 A0J  CONST_39  H24   C24  C19  C20  180.00   0.0  0
 A0J  CONST_40  H22   C22  C21  C20  180.00   0.0  0
 A0J  CONST_41  H20   C20  C21  C22  180.00   0.0  0
 A0J  CONST_42  H9    N9   C10  C2   180.00   0.0  0
 A0J  Var_01    C20   C19  C18  C2    86.75  30.0  2
 A0J  Var_02    H171  C17  N15  N14   65.99  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
 A0J  chir_01  C2  C3  C10  C18  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
 A0J  plan-1  C5   0.020
 A0J  plan-1  C12  0.020
 A0J  plan-1  C13  0.020
 A0J  plan-1  N14  0.020
 A0J  plan-1  N15  0.020
 A0J  plan-1  C16  0.020
 A0J  plan-1  C17  0.020
 A0J  plan-1  H13  0.020
 A0J  plan-1  H16  0.020
 A0J  plan-2  C18  0.020
 A0J  plan-2  C19  0.020
 A0J  plan-2  C20  0.020
 A0J  plan-2  C21  0.020
 A0J  plan-2  C22  0.020
 A0J  plan-2  C23  0.020
 A0J  plan-2  C24  0.020
 A0J  plan-2  H20  0.020
 A0J  plan-2  H24  0.020
 A0J  plan-2  H21  0.020
 A0J  plan-2  H22  0.020
 A0J  plan-2  H23  0.020
 A0J  plan-3  C2   0.020
 A0J  plan-3  C3   0.020
 A0J  plan-3  C4   0.020
 A0J  plan-3  C5   0.020
 A0J  plan-3  C6   0.020
 A0J  plan-3  C7   0.020
 A0J  plan-3  C8   0.020
 A0J  plan-3  N9   0.020
 A0J  plan-3  C10  0.020
 A0J  plan-3  O11  0.020
 A0J  plan-3  C12  0.020
 A0J  plan-3  H4   0.020
 A0J  plan-3  H6   0.020
 A0J  plan-3  H7   0.020
 A0J  plan-3  H9   0.020

