# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:24:03 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: N-[(1S)-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]imidoformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=CN[C@H]1CCc2ccc(cc12)c3ncnc4[nH]ccc34
#
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
 HB4  HB4  N-[(1S)-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]imidoformamide  ligand  36  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HB4
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
 HB4  C4    C  CR56  0   0.112  -1.9764  -0.4677   0.0034
 HB4  C7    C  CR6   0   0.210   1.6731   0.3402  -0.2209
 HB4  C6    C  CR6   0   0.057   0.4099  -0.4174  -0.2310
 HB4  C9    C  CR15  0  -0.474   3.4242  -1.4630   0.6008
 HB4  C20   C  C1    0   0.112  -4.5528   2.1800   0.2521
 HB4  C8    C  CR56  0  -0.001   2.9082  -0.2134   0.1349
 HB4  C18   C  CH2   0  -0.500  -3.3962  -2.3620  -0.2264
 HB4  C16   C  CR15  0  -0.096  -3.3764   0.0274   0.2639
 HB4  C1    C  CR16  0  -0.316   0.3891  -1.7846  -0.5169
 HB4  C2    C  CR16  0  -0.312  -0.8045  -2.4953  -0.5391
 HB4  C3    C  CR56  0   0.084  -1.9905  -1.8318  -0.2728
 HB4  C5    C  CR16  0  -0.355  -0.7952   0.2459   0.0222
 HB4  C10   C  CR15  0   0.008   4.7650  -1.2862   0.7678
 HB4  N11   N  NR15  0  -0.658   5.1154  -0.0033   0.4386
 HB4  C12   C  CR56  0   0.495   4.0081   0.6738   0.0619
 HB4  N13   N  N     0  -0.423   3.9479   1.9485  -0.2931
 HB4  C14   C  CR16  0   0.026   2.7235   2.3538  -0.5766
 HB4  N15   N  N     0  -0.447   1.6096   1.6277  -0.5580
 HB4  C17   C  CH2   0  -0.459  -4.2444  -1.0887  -0.3539
 HB4  N19   N  NH1   0  -0.607  -3.6088   1.3497  -0.2487
 HB4  N21   N  N     0  -0.661  -5.2363   1.9219   1.2968
 HB4  HC9   H  HCR5  0   0.262   2.8879  -2.3746   0.8034
 HB4  H18A  H  HCH2  0   0.256  -3.6027  -3.0982  -1.0042
 HB4  H18B  H  HCH2  0   0.254  -3.5761  -2.8555   0.7338
 HB4  HC16  H  HCR5  0   0.269  -3.5490   0.0669   1.3438
 HB4  HC1   H  HCR6  0   0.257   1.3079  -2.2983  -0.7653
 HB4  HC2   H  HCR6  0   0.253  -0.7990  -3.5515  -0.7782
 HB4  HC5   H  HCR6  0   0.247  -0.7928   1.3083   0.2312
 HB4  HC10  H  HCR5  0   0.296   5.5125  -1.9856   1.1049
 HB4  HN11  H  HNR5  0   0.418   6.0465   0.3794   0.4853
 HB4  HC14  H  HCR6  0   0.252   2.6111   3.3939  -0.8622
 HB4  H17B  H  HCH2  0   0.238  -4.4063  -0.8586  -1.4101
 HB4  H17A  H  HCH2  0   0.245  -5.2207  -1.1679   0.1227
 HB4  H34   H  HNH1  0   0.391  -3.2694   1.5505  -1.1750
 HB4  H1    H  H     0   0.233  -4.6411   3.0982  -0.3310
 HB4  H2    H  H     0   0.333  -5.8428   2.7057   1.5024

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
 HB4  C20  N19   single    1.353  0.020  1.353
 HB4  C20  N21   double    1.275  0.020  1.275
 HB4  N19  C16   single    1.437  0.020  1.437
 HB4  C17  C16   single    1.543  0.020  1.543
 HB4  C17  C18   single    1.535  0.020  1.535
 HB4  C16  C4    single    1.508  0.020  1.508
 HB4  C18  C3    single    1.503  0.020  1.503
 HB4  C4   C3    aromatic  1.392  0.020  1.392
 HB4  C4   C5    aromatic  1.380  0.020  1.380
 HB4  C3   C2    aromatic  1.385  0.020  1.385
 HB4  C5   C6    aromatic  1.399  0.020  1.399
 HB4  C2   C1    aromatic  1.389  0.020  1.389
 HB4  C6   C1    aromatic  1.397  0.020  1.397
 HB4  C6   C7    single    1.473  0.020  1.473
 HB4  C9   C8    aromatic  1.430  0.020  1.430
 HB4  C9   C10   aromatic  1.363  0.020  1.363
 HB4  C7   C8    aromatic  1.399  0.020  1.399
 HB4  C7   N15   aromatic  1.332  0.020  1.332
 HB4  C8   C12   aromatic  1.415  0.020  1.415
 HB4  C10  N11   aromatic  1.370  0.020  1.370
 HB4  N15  C14   aromatic  1.330  0.020  1.330
 HB4  C12  N11   aromatic  1.351  0.020  1.351
 HB4  C12  N13   aromatic  1.325  0.020  1.325
 HB4  C14  N13   aromatic  1.320  0.020  1.320
 HB4  C9   HC9   single    0.930  0.020  1.080
 HB4  C18  H18A  single    0.970  0.020  1.090
 HB4  C18  H18B  single    0.970  0.020  1.090
 HB4  C16  HC16  single    0.970  0.020  1.090
 HB4  C1   HC1   single    0.930  0.020  1.080
 HB4  C2   HC2   single    0.930  0.020  1.080
 HB4  C5   HC5   single    0.930  0.020  1.080
 HB4  C10  HC10  single    0.930  0.020  1.080
 HB4  N11  HN11  single    0.860  0.020  1.020
 HB4  C14  HC14  single    0.930  0.020  1.080
 HB4  C17  H17B  single    0.970  0.020  1.090
 HB4  C17  H17A  single    0.970  0.020  1.090
 HB4  N19  H34   single    0.860  0.020  1.020
 HB4  C20  H1    single    0.930  0.020  1.080
 HB4  N21  H2    single    0.890  0.020  1.040

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
 HB4  C5    C4   C3    121.21  3.000
 HB4  C5    C4   C16   128.50  3.000
 HB4  C3    C4   C16   110.29  3.000
 HB4  N15   C7   C8    119.25  3.000
 HB4  N15   C7   C6    117.02  3.000
 HB4  C8    C7   C6    123.72  3.000
 HB4  C5    C6   C1    119.24  3.000
 HB4  C1    C6   C7    121.17  3.000
 HB4  C5    C6   C7    119.58  3.000
 HB4  HC9   C9   C10   125.22  3.000
 HB4  HC9   C9   C8    128.42  3.000
 HB4  C10   C9   C8    106.35  3.000
 HB4  H1    C20  N21   124.39  3.000
 HB4  H1    C20  N19   112.02  3.000
 HB4  N21   C20  N19   123.58  3.000
 HB4  C12   C8   C9    106.51  3.000
 HB4  C12   C8   C7    115.15  3.000
 HB4  C9    C8   C7    138.33  3.000
 HB4  H18B  C18  H18A  106.87  3.000
 HB4  H18B  C18  C17   110.85  3.000
 HB4  H18A  C18  C17   113.33  3.000
 HB4  H18B  C18  C3    109.87  3.000
 HB4  H18A  C18  C3    113.16  3.000
 HB4  C17   C18  C3    102.80  3.000
 HB4  HC16  C16  N19   107.06  3.000
 HB4  HC16  C16  C17   109.42  3.000
 HB4  N19   C16  C17   115.58  3.000
 HB4  HC16  C16  C4    109.20  3.000
 HB4  C17   C16  C4    102.45  3.000
 HB4  N19   C16  C4    113.00  3.000
 HB4  HC1   C1   C2    118.90  3.000
 HB4  HC1   C1   C6    119.95  3.000
 HB4  C2    C1   C6    121.11  3.000
 HB4  HC2   C2   C3    120.94  3.000
 HB4  HC2   C2   C1    119.87  3.000
 HB4  C3    C2   C1    119.18  3.000
 HB4  C2    C3   C18   129.63  3.000
 HB4  C2    C3   C4    119.94  3.000
 HB4  C18   C3   C4    110.44  3.000
 HB4  HC5   C5   C6    119.90  3.000
 HB4  HC5   C5   C4    120.78  3.000
 HB4  C6    C5   C4    119.32  3.000
 HB4  HC10  C10  N11   120.36  3.000
 HB4  HC10  C10  C9    129.54  3.000
 HB4  N11   C10  C9    110.10  3.000
 HB4  HN11  N11  C12   125.43  3.000
 HB4  HN11  N11  C10   125.50  3.000
 HB4  C12   N11  C10   109.06  3.000
 HB4  N13   C12  N11   126.45  3.000
 HB4  N13   C12  C8    125.58  3.000
 HB4  N11   C12  C8    107.97  3.000
 HB4  C14   N13  C12   113.27  3.000
 HB4  HC14  C14  N15   116.13  3.000
 HB4  HC14  C14  N13   116.56  3.000
 HB4  N15   C14  N13   127.31  3.000
 HB4  C14   N15  C7    119.42  3.000
 HB4  H17A  C17  H17B  107.78  3.000
 HB4  H17A  C17  C16   112.43  3.000
 HB4  H17B  C17  C16   108.54  3.000
 HB4  H17A  C17  C18   113.49  3.000
 HB4  H17B  C17  C18   109.67  3.000
 HB4  C16   C17  C18   104.83  3.000
 HB4  H34   N19  C16   117.21  3.000
 HB4  H34   N19  C20   116.96  3.000
 HB4  C16   N19  C20   123.05  3.000
 HB4  H2    N21  C20   109.33  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
 HB4  CONST_01  C1    C2   C3   C4     0.00   0.0  0
 HB4  CONST_02  C1    C6   C5   C4     0.00   0.0  0
 HB4  CONST_03  C7    C6   C5   C4   180.00   0.0  0
 HB4  CONST_04  C2    C1   C6   C7   180.00   0.0  0
 HB4  CONST_05  C10   C9   C8   C7   180.00   0.0  0
 HB4  CONST_06  N11   C12  C8   C7   180.00   0.0  0
 HB4  CONST_07  N13   C12  C8   C7     0.00   0.0  0
 HB4  CONST_08  N13   C14  N15  C7     0.00   0.0  0
 HB4  CONST_09  C3    C4   C5   C6     0.00   0.0  0
 HB4  CONST_10  C3    C2   C1   C6     0.00   0.0  0
 HB4  CONST_11  C9    C8   C7   C6     0.00   0.0  0
 HB4  CONST_12  C12   C8   C7   C6   180.00   0.0  0
 HB4  CONST_13  C14   N15  C7   C6   180.00   0.0  0
 HB4  CONST_14  N15   C7   C8   C9   180.00   0.0  0
 HB4  CONST_15  N11   C12  C8   C9     0.00   0.0  0
 HB4  CONST_16  N13   C12  C8   C9   180.00   0.0  0
 HB4  CONST_17  C12   N11  C10  C9     0.00   0.0  0
 HB4  CONST_18  N11   C10  C9   C8     0.00   0.0  0
 HB4  CONST_21  C14   N15  C7   C8     0.00   0.0  0
 HB4  CONST_22  C10   N11  C12  C8     0.00   0.0  0
 HB4  CONST_23  C14   N13  C12  C8     0.00   0.0  0
 HB4  CONST_25  C5    C4   C3   C2     0.00   0.0  0
 HB4  CONST_26  C5    C6   C1   C2     0.00   0.0  0
 HB4  CONST_28  C12   C8   C9   C10    0.00   0.0  0
 HB4  CONST_29  N13   C12  N11  C10  180.00   0.0  0
 HB4  CONST_30  C14   N13  C12  N11  180.00   0.0  0
 HB4  CONST_31  N15   C7   C8   C12    0.00   0.0  0
 HB4  CONST_32  N15   C14  N13  C12    0.00   0.0  0
 HB4  CONST_33  HC2   C2   C3   C4   180.00   0.0  0
 HB4  CONST_34  HC5   C5   C6   C7     0.00   0.0  0
 HB4  CONST_35  HC1   C1   C6   C7     0.00   0.0  0
 HB4  CONST_36  HC9   C9   C8   C7     0.00   0.0  0
 HB4  CONST_37  HC14  C14  N15  C7   180.00   0.0  0
 HB4  CONST_38  HN11  N11  C10  C9   180.00   0.0  0
 HB4  CONST_39  HC10  C10  C9   C8   180.00   0.0  0
 HB4  CONST_40  N21   C20  N19  C16    0.00   0.0  0
 HB4  CONST_41  H1    C20  N19  C16  180.00   0.0  0
 HB4  CONST_42  H2    N21  C20  N19  180.00   0.0  0
 HB4  CONST_43  H34   N19  C20  N21  180.00   0.0  0
 HB4  Var_01    C17   C18  C3   C4    18.19  30.0  1
 HB4  Var_02    C3    C18  C17  C16  -28.86  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
 HB4  chir_01  C16  N19  C17  C4  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
 HB4  plan-1  C7    0.020
 HB4  plan-1  C6    0.020
 HB4  plan-1  C9    0.020
 HB4  plan-1  C8    0.020
 HB4  plan-1  C10   0.020
 HB4  plan-1  N11   0.020
 HB4  plan-1  C12   0.020
 HB4  plan-1  N13   0.020
 HB4  plan-1  C14   0.020
 HB4  plan-1  N15   0.020
 HB4  plan-1  HC9   0.020
 HB4  plan-1  HC10  0.020
 HB4  plan-1  HN11  0.020
 HB4  plan-1  HC14  0.020
 HB4  plan-2  C4    0.020
 HB4  plan-2  C7    0.020
 HB4  plan-2  C6    0.020
 HB4  plan-2  C18   0.020
 HB4  plan-2  C16   0.020
 HB4  plan-2  C1    0.020
 HB4  plan-2  C2    0.020
 HB4  plan-2  C3    0.020
 HB4  plan-2  C5    0.020
 HB4  plan-2  HC1   0.020
 HB4  plan-2  HC2   0.020
 HB4  plan-2  HC5   0.020
 HB4  plan-3  C20   0.020
 HB4  plan-3  C16   0.020
 HB4  plan-3  N19   0.020
 HB4  plan-3  N21   0.020
 HB4  plan-3  H34   0.020
 HB4  plan-3  H1    0.020
 HB4  plan-3  H2    0.020

