# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:21:18 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[(1S)-6-(5-phenyl-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]cc(c5ccccc5)c34
#
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
 G4Y  G4Y  N-[(1S)-6-(5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]imidoformamide  ligand  46  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G4Y
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
 G4Y  N3   N  NR15  0  -0.661  -4.5744   1.2935  -0.3274
 G4Y  C4   C  CR56  0   0.085   2.2619  -1.0465   1.0573
 G4Y  N2   N  N     0  -0.422  -3.2229   3.2211   0.0604
 G4Y  C7   C  CH2   0  -0.499   3.5814  -1.7568   1.1671
 G4Y  C6   C  CR16  0  -0.356   1.3034   0.9182   0.0312
 G4Y  C9   C  CR15  0  -0.135   3.8126   0.2651  -0.1839
 G4Y  C13  C  CR56  0   0.008  -2.3851   0.9336  -0.0282
 G4Y  C20  C  CR16  0  -0.242  -2.4272  -4.0358  -0.0305
 G4Y  C21  C  CR16  0  -0.312  -2.9777  -2.7742   0.1502
 G4Y  C8   C  CH2   0  -0.456   4.5899  -0.6708   0.7673
 G4Y  C18  C  CR16  0  -0.229  -0.7500  -3.0959  -1.4667
 G4Y  C16  C  CR6   0   0.015  -2.4224  -1.6588  -0.4764
 G4Y  C19  C  CR16  0  -0.270  -1.3090  -4.2007  -0.8366
 G4Y  C1   C  CR6   0   0.019   0.0554   0.5643   0.5478
 G4Y  C2   C  CR16  0  -0.274  -0.0666  -0.5827   1.3324
 G4Y  C3   C  CR16  0  -0.299   1.0319  -1.3898   1.5925
 G4Y  C5   C  CR56  0   0.108   2.3898   0.1043   0.2862
 G4Y  C10  C  CR6   0   0.186  -1.1139   1.4238   0.2925
 G4Y  N1   N  N     0  -0.438  -0.9239   2.7377   0.3982
 G4Y  C11  C  CR16  0   0.024  -1.9632   3.5576   0.2673
 G4Y  C12  C  CR56  0   0.501  -3.4010   1.9172  -0.0846
 G4Y  C14  C  CR15  0  -0.025  -4.3463  -0.0475  -0.4662
 G4Y  C15  C  CR5   0  -0.079  -3.0176  -0.3290  -0.3028
 G4Y  C17  C  CR16  0  -0.293  -1.3033  -1.8380  -1.2906
 G4Y  N4   N  NH1   0  -0.605   4.2397   1.6397  -0.1920
 G4Y  C22  C  C1    0   0.118   5.3207   2.0885  -0.8745
 G4Y  H1   H  HNR5  0   0.420  -5.4665   1.7486  -0.4399
 G4Y  H3   H  HCH2  0   0.254   3.6118  -2.5960   0.4652
 G4Y  H4   H  HCR6  0   0.246   1.4070   1.8150  -0.5680
 G4Y  H5   H  HCR5  0   0.267   3.8849  -0.1128  -1.2115
 G4Y  H6   H  HCR6  0   0.253  -2.8684  -4.8892   0.4683
 G4Y  H7   H  HCR6  0   0.246  -3.8348  -2.6508   0.8011
 G4Y  H8   H  HCH2  0   0.243   4.8849  -0.0990   1.6504
 G4Y  H9   H  HCH2  0   0.246   5.4960  -1.0708   0.3131
 G4Y  H10  H  H     0   0.326   5.8292   0.4969  -1.8017
 G4Y  H11  H  HCR6  0   0.251   0.1206  -3.2129  -2.0989
 G4Y  H12  H  HCR6  0   0.253  -0.8757  -5.1832  -0.9726
 G4Y  H13  H  HCR6  0   0.258  -1.0259  -0.8374   1.7638
 G4Y  H14  H  HCR6  0   0.247   0.9218  -2.2705   2.2129
 G4Y  H15  H  HCR6  0   0.253  -1.7517   4.6171   0.3586
 G4Y  H16  H  HCR5  0   0.300  -5.1555  -0.7185  -0.7064
 G4Y  H17  H  HCR6  0   0.244  -0.8635  -0.9858  -1.7931
 G4Y  H18  H  HNH1  0   0.396   3.8986   2.2304   0.5497
 G4Y  H19  H  H     0   0.245   5.5216   3.1405  -0.6783
 G4Y  H2   H  HCH2  0   0.256   3.7677  -2.1666   2.1604
 G4Y  N5   N  N     0  -0.673   6.0803   1.4763  -1.6962

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
 G4Y  C22  N4   single    1.355  0.020  1.355
 G4Y  C22  N5   double    1.276  0.020  1.276
 G4Y  N4   C9   single    1.439  0.020  1.439
 G4Y  C20  C19  aromatic  1.388  0.020  1.388
 G4Y  C20  C21  aromatic  1.388  0.020  1.388
 G4Y  C8   C9   single    1.544  0.020  1.544
 G4Y  C8   C7   single    1.535  0.020  1.535
 G4Y  C9   C5   single    1.507  0.020  1.507
 G4Y  C19  C18  aromatic  1.389  0.020  1.389
 G4Y  C21  C16  aromatic  1.395  0.020  1.395
 G4Y  C7   C4   single    1.503  0.020  1.503
 G4Y  C5   C6   aromatic  1.381  0.020  1.381
 G4Y  C5   C4   aromatic  1.391  0.020  1.391
 G4Y  C6   C1   aromatic  1.396  0.020  1.396
 G4Y  C4   C3   aromatic  1.385  0.020  1.385
 G4Y  C18  C17  aromatic  1.386  0.020  1.386
 G4Y  C16  C17  aromatic  1.395  0.020  1.395
 G4Y  C16  C15  single    1.467  0.020  1.467
 G4Y  C1   C10  single    1.473  0.020  1.473
 G4Y  C1   C2   aromatic  1.395  0.020  1.395
 G4Y  C3   C2   aromatic  1.388  0.020  1.388
 G4Y  C15  C13  aromatic  1.439  0.020  1.439
 G4Y  C15  C14  aromatic  1.368  0.020  1.368
 G4Y  C10  C13  aromatic  1.400  0.020  1.400
 G4Y  C10  N1   aromatic  1.332  0.020  1.332
 G4Y  C13  C12  aromatic  1.415  0.020  1.415
 G4Y  C14  N3   aromatic  1.367  0.020  1.367
 G4Y  N1   C11  aromatic  1.330  0.020  1.330
 G4Y  C12  N3   aromatic  1.351  0.020  1.351
 G4Y  C12  N2   aromatic  1.324  0.020  1.324
 G4Y  C11  N2   aromatic  1.320  0.020  1.320
 G4Y  N3   H1   single    0.860  0.020  1.020
 G4Y  C7   H2   single    0.970  0.020  1.090
 G4Y  C7   H3   single    0.970  0.020  1.090
 G4Y  C6   H4   single    0.930  0.020  1.080
 G4Y  C9   H5   single    0.970  0.020  1.090
 G4Y  C20  H6   single    0.930  0.020  1.080
 G4Y  C21  H7   single    0.930  0.020  1.080
 G4Y  C8   H8   single    0.970  0.020  1.090
 G4Y  C8   H9   single    0.970  0.020  1.090
 G4Y  N5   H10  single    0.890  0.020  1.040
 G4Y  C18  H11  single    0.930  0.020  1.080
 G4Y  C19  H12  single    0.930  0.020  1.080
 G4Y  C2   H13  single    0.930  0.020  1.080
 G4Y  C3   H14  single    0.930  0.020  1.080
 G4Y  C11  H15  single    0.930  0.020  1.080
 G4Y  C14  H16  single    0.930  0.020  1.080
 G4Y  C17  H17  single    0.930  0.020  1.080
 G4Y  N4   H18  single    0.860  0.020  1.020
 G4Y  C22  H19  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
 G4Y  H1   N3   C14  125.40  3.000
 G4Y  H1   N3   C12  125.48  3.000
 G4Y  C14  N3   C12  109.03  3.000
 G4Y  C5   C4   C3   120.07  3.000
 G4Y  C3   C4   C7   129.39  3.000
 G4Y  C5   C4   C7   110.54  3.000
 G4Y  C12  N2   C11  113.37  3.000
 G4Y  H3   C7   H2   106.93  3.000
 G4Y  H3   C7   C8   110.93  3.000
 G4Y  H2   C7   C8   113.01  3.000
 G4Y  H3   C7   C4   109.88  3.000
 G4Y  H2   C7   C4   113.22  3.000
 G4Y  C8   C7   C4   102.91  3.000
 G4Y  H4   C6   C5   120.97  3.000
 G4Y  H4   C6   C1   119.99  3.000
 G4Y  C5   C6   C1   119.03  3.000
 G4Y  H5   C9   N4   107.70  3.000
 G4Y  H5   C9   C5   108.52  3.000
 G4Y  N4   C9   C5   112.57  3.000
 G4Y  H5   C9   C8   109.57  3.000
 G4Y  C5   C9   C8   102.61  3.000
 G4Y  N4   C9   C8   115.65  3.000
 G4Y  C15  C13  C12  106.67  3.000
 G4Y  C12  C13  C10  114.69  3.000
 G4Y  C15  C13  C10  138.62  3.000
 G4Y  H6   C20  C19  120.14  3.000
 G4Y  H6   C20  C21  119.66  3.000
 G4Y  C19  C20  C21  120.19  3.000
 G4Y  H7   C21  C16  119.59  3.000
 G4Y  H7   C21  C20  119.70  3.000
 G4Y  C16  C21  C20  120.70  3.000
 G4Y  H9   C8   H8   107.73  3.000
 G4Y  H9   C8   C9   112.60  3.000
 G4Y  H8   C8   C9   108.46  3.000
 G4Y  H9   C8   C7   113.28  3.000
 G4Y  H8   C8   C7   109.70  3.000
 G4Y  C9   C8   C7   104.98  3.000
 G4Y  H11  C18  C17  119.58  3.000
 G4Y  H11  C18  C19  120.17  3.000
 G4Y  C17  C18  C19  120.24  3.000
 G4Y  C17  C16  C15  120.72  3.000
 G4Y  C15  C16  C21  120.67  3.000
 G4Y  C17  C16  C21  118.60  3.000
 G4Y  H12  C19  C18  120.25  3.000
 G4Y  H12  C19  C20  120.21  3.000
 G4Y  C18  C19  C20  119.54  3.000
 G4Y  C10  C1   C2   120.51  3.000
 G4Y  C2   C1   C6   119.65  3.000
 G4Y  C10  C1   C6   119.82  3.000
 G4Y  H13  C2   C3   119.34  3.000
 G4Y  H13  C2   C1   119.69  3.000
 G4Y  C3   C2   C1   120.96  3.000
 G4Y  H14  C3   C2   120.00  3.000
 G4Y  H14  C3   C4   120.89  3.000
 G4Y  C2   C3   C4   119.11  3.000
 G4Y  C9   C5   C6   128.47  3.000
 G4Y  C6   C5   C4   121.17  3.000
 G4Y  C9   C5   C4   110.36  3.000
 G4Y  N1   C10  C1   116.65  3.000
 G4Y  N1   C10  C13  119.55  3.000
 G4Y  C1   C10  C13  123.79  3.000
 G4Y  C11  N1   C10  119.26  3.000
 G4Y  H15  C11  N1   116.21  3.000
 G4Y  H15  C11  N2   116.64  3.000
 G4Y  N1   C11  N2   127.14  3.000
 G4Y  C13  C12  N2   125.70  3.000
 G4Y  N2   C12  N3   126.25  3.000
 G4Y  C13  C12  N3   108.05  3.000
 G4Y  H16  C14  C15  128.86  3.000
 G4Y  H16  C14  N3   120.51  3.000
 G4Y  C15  C14  N3   110.60  3.000
 G4Y  C14  C15  C16  124.50  3.000
 G4Y  C14  C15  C13  105.61  3.000
 G4Y  C16  C15  C13  129.77  3.000
 G4Y  H17  C17  C16  119.70  3.000
 G4Y  H17  C17  C18  119.57  3.000
 G4Y  C16  C17  C18  120.73  3.000
 G4Y  H18  N4   C22  116.53  3.000
 G4Y  H18  N4   C9   117.08  3.000
 G4Y  C22  N4   C9   123.77  3.000
 G4Y  H19  C22  N4   112.11  3.000
 G4Y  H19  C22  N5   118.03  3.000
 G4Y  N4   C22  N5   129.84  3.000
 G4Y  H10  N5   C22  112.47  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
 G4Y  CONST_01  C16  C15  C14  N3   180.00   0.0  0
 G4Y  CONST_02  C13  C15  C14  N3     0.00   0.0  0
 G4Y  CONST_03  C15  C13  C12  N3     0.00   0.0  0
 G4Y  CONST_04  C10  C13  C12  N3   180.00   0.0  0
 G4Y  CONST_05  C11  N2   C12  N3   180.00   0.0  0
 G4Y  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 G4Y  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 G4Y  CONST_08  C15  C13  C12  N2   180.00   0.0  0
 G4Y  CONST_09  C10  C13  C12  N2     0.00   0.0  0
 G4Y  CONST_10  C14  N3   C12  N2   180.00   0.0  0
 G4Y  CONST_11  C10  N1   C11  N2     0.00   0.0  0
 G4Y  CONST_12  C3   C4   C5   C6     0.00   0.0  0
 G4Y  CONST_15  C3   C2   C1   C6     0.00   0.0  0
 G4Y  CONST_19  C11  N1   C10  C13    0.00   0.0  0
 G4Y  CONST_20  C14  N3   C12  C13    0.00   0.0  0
 G4Y  CONST_21  C11  N2   C12  C13    0.00   0.0  0
 G4Y  CONST_22  C17  C18  C19  C20    0.00   0.0  0
 G4Y  CONST_23  C17  C16  C21  C20    0.00   0.0  0
 G4Y  CONST_24  C15  C16  C21  C20  180.00   0.0  0
 G4Y  CONST_25  C18  C19  C20  C21    0.00   0.0  0
 G4Y  CONST_26  C18  C17  C16  C21    0.00   0.0  0
 G4Y  CONST_28  C15  C16  C17  C18  180.00   0.0  0
 G4Y  CONST_29  C19  C20  C21  C16    0.00   0.0  0
 G4Y  CONST_30  C19  C18  C17  C16    0.00   0.0  0
 G4Y  CONST_31  C10  C13  C15  C16    0.00   0.0  0
 G4Y  CONST_32  C12  C13  C15  C16  180.00   0.0  0
 G4Y  CONST_33  C15  C13  C10  C1     0.00   0.0  0
 G4Y  CONST_34  C12  C13  C10  C1   180.00   0.0  0
 G4Y  CONST_35  C11  N1   C10  C1   180.00   0.0  0
 G4Y  CONST_36  C5   C6   C1   C2     0.00   0.0  0
 G4Y  CONST_38  C5   C4   C3   C2     0.00   0.0  0
 G4Y  CONST_39  C10  C1   C2   C3   180.00   0.0  0
 G4Y  CONST_40  C10  C1   C6   C5   180.00   0.0  0
 G4Y  CONST_41  C14  C15  C13  C10  180.00   0.0  0
 G4Y  CONST_42  C15  C13  C10  N1   180.00   0.0  0
 G4Y  CONST_43  C12  C13  C10  N1     0.00   0.0  0
 G4Y  CONST_44  C12  N2   C11  N1     0.00   0.0  0
 G4Y  CONST_45  C14  C15  C13  C12    0.00   0.0  0
 G4Y  CONST_46  C15  C14  N3   C12    0.00   0.0  0
 G4Y  CONST_48  H4   C6   C5   C4   180.00   0.0  0
 G4Y  CONST_49  H13  C2   C3   C4   180.00   0.0  0
 G4Y  CONST_50  H1   N3   C12  N2     0.00   0.0  0
 G4Y  CONST_51  H14  C3   C4   C7     0.00   0.0  0
 G4Y  CONST_52  H16  C14  C15  C13  180.00   0.0  0
 G4Y  CONST_53  H11  C18  C19  C20  180.00   0.0  0
 G4Y  CONST_54  H12  C19  C20  C21  180.00   0.0  0
 G4Y  CONST_55  H17  C17  C16  C21  180.00   0.0  0
 G4Y  CONST_56  H6   C20  C19  C18  180.00   0.0  0
 G4Y  CONST_57  H7   C21  C20  C19  180.00   0.0  0
 G4Y  CONST_58  H15  C11  N1   C10  180.00   0.0  0
 G4Y  CONST_59  N5   C22  N4   C9     0.00   0.0  0
 G4Y  CONST_60  H19  C22  N4   C9   180.00   0.0  0
 G4Y  CONST_61  H18  N4   C22  N5   180.00   0.0  0
 G4Y  CONST_62  H10  N5   C22  N4     0.00   0.0  0
 G4Y  Var_01    C9   C8   C7   C4   -28.01  30.0  1
 G4Y  Var_02    C5   C4   C7   C8    17.94  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
 G4Y  chir_01  C9  N4  C8  C5  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
 G4Y  plan-1  C20  0.020
 G4Y  plan-1  C21  0.020
 G4Y  plan-1  C18  0.020
 G4Y  plan-1  C16  0.020
 G4Y  plan-1  C19  0.020
 G4Y  plan-1  C15  0.020
 G4Y  plan-1  C17  0.020
 G4Y  plan-1  H6   0.020
 G4Y  plan-1  H7   0.020
 G4Y  plan-1  H11  0.020
 G4Y  plan-1  H12  0.020
 G4Y  plan-1  H17  0.020
 G4Y  plan-2  C4   0.020
 G4Y  plan-2  C7   0.020
 G4Y  plan-2  C6   0.020
 G4Y  plan-2  C9   0.020
 G4Y  plan-2  C1   0.020
 G4Y  plan-2  C2   0.020
 G4Y  plan-2  C3   0.020
 G4Y  plan-2  C5   0.020
 G4Y  plan-2  C10  0.020
 G4Y  plan-2  H4   0.020
 G4Y  plan-2  H13  0.020
 G4Y  plan-2  H14  0.020
 G4Y  plan-3  N3   0.020
 G4Y  plan-3  N2   0.020
 G4Y  plan-3  C13  0.020
 G4Y  plan-3  C16  0.020
 G4Y  plan-3  C1   0.020
 G4Y  plan-3  C10  0.020
 G4Y  plan-3  N1   0.020
 G4Y  plan-3  C11  0.020
 G4Y  plan-3  C12  0.020
 G4Y  plan-3  C14  0.020
 G4Y  plan-3  C15  0.020
 G4Y  plan-3  H1   0.020
 G4Y  plan-3  H15  0.020
 G4Y  plan-3  H16  0.020
 G4Y  plan-4  C9   0.020
 G4Y  plan-4  N4   0.020
 G4Y  plan-4  C22  0.020
 G4Y  plan-4  H10  0.020
 G4Y  plan-4  H18  0.020
 G4Y  plan-4  H19  0.020
 G4Y  plan-4  N5   0.020

