# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:24:08 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1C)C(=O)N[C@@H]2CCc3ccc(cc23)c4cn5CCCc5n4
#
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
 G2D  G2D  N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide  ligand  54  29  .  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_G2D
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
 G2D  C05  C  CR16  0  -0.271  -3.7832  -1.8360  -1.5523
 G2D  C06  C  CR6   0   0.004  -5.1277  -1.9241  -1.2283
 G2D  C13  C  CR15  0  -0.153  -0.4277   1.8867   1.1783
 G2D  C18  C  CR16  0  -0.304   2.1569   3.1108  -1.1521
 G2D  C17  C  CR56  0   0.086   1.0226   2.9710  -0.3647
 G2D  C16  C  CR56  0   0.103   0.8905   1.8517   0.4475
 G2D  C15  C  CH2   0  -0.500  -0.1721   3.8732  -0.2290
 G2D  C19  C  CR16  0  -0.336   3.1403   2.1337  -1.1060
 G2D  C20  C  CR6   0   0.037   3.0156   1.0057  -0.2852
 G2D  C21  C  CR5   0   0.117   4.0672  -0.0089  -0.2293
 G2D  C22  C  CR15  0  -0.113   5.2986   0.0025  -0.8485
 G2D  C24  C  CR55  0   0.464   5.0445  -1.8046   0.3573
 G2D  C11  C  CR16  0  -0.416  -4.7120  -0.4134   0.6236
 G2D  C03  C  CR6   0  -0.027  -3.3672  -0.3225   0.2633
 G2D  C04  C  CR16  0  -0.318  -2.9005  -1.0475  -0.8241
 G2D  C27  C  CH2   0  -0.268   7.1353  -1.8581  -0.7038
 G2D  O01  O  O     0  -0.495  -2.7957   0.8583   2.2438
 G2D  C07  C  CH3   0  -0.712  -6.0714  -2.7696  -2.0274
 G2D  C08  C  CR6   0   0.381  -5.5861  -1.1970  -0.1165
 G2D  O09  O  O2    0  -0.465  -6.8978  -1.3211   0.1586
 G2D  C10  C  CH3   0  -0.439  -7.4337  -0.6115   1.2575
 G2D  N12  N  NH1   0  -0.649  -1.3604   0.9922   0.5130
 G2D  C14  C  CH2   0  -0.456  -0.8258   3.3721   1.0683
 G2D  N23  N  N     0  -0.437   5.8984  -1.1493  -0.4471
 G2D  C25  C  CH2   0  -0.543   5.6242  -3.1083   0.7876
 G2D  C26  C  CH2   0  -0.490   7.1086  -2.9315   0.4017
 G2D  N28  N  N     0  -0.496   3.9254  -1.1527   0.5214
 G2D  C29  C  CR16  0  -0.375   1.8632   0.8689   0.4926
 G2D  H1   H  HCR6  0   0.256  -3.4114  -2.4004  -2.3988
 G2D  H2   H  HCR5  0   0.269  -0.3376   1.5690   2.2174
 G2D  H3   H  HCR6  0   0.248   2.2848   3.9728  -1.7955
 G2D  H4   H  HCH2  0   0.255   0.0937   4.9301  -0.1830
 G2D  H5   H  HCH2  0   0.251  -0.8425   3.7539  -1.0857
 G2D  H6   H  HCR6  0   0.240   4.0240   2.2560  -1.7204
 G2D  H7   H  HCR5  0   0.285   5.7795   0.7153  -1.4969
 G2D  H8   H  HCR6  0   0.279  -5.0562   0.1420   1.4852
 G2D  H9   H  HCR6  0   0.249  -1.8566  -1.0367  -1.1096
 G2D  H10  H  HCH2  0   0.261   7.1199  -2.2905  -1.7056
 G2D  H11  H  HCH3  0   0.247  -6.5048  -3.5694  -1.4243
 G2D  H12  H  HCH3  0   0.246  -6.9027  -2.1824  -2.4209
 G2D  H13  H  HCH3  0   0.245  -5.5572  -3.2277  -2.8705
 G2D  H14  H  HCH3  0   0.261  -8.4943  -0.8476   1.2898
 G2D  H15  H  HCH3  0   0.230  -6.9755  -0.9149   2.2022
 G2D  H16  H  HCH3  0   0.229  -7.3171   0.4690   1.1412
 G2D  H17  H  HNH1  0   0.405  -1.2248   0.8335  -0.4724
 G2D  H18  H  HCH2  0   0.249  -1.9051   3.5162   1.0996
 G2D  H19  H  HCH2  0   0.247  -0.3983   3.9067   1.9192
 G2D  H20  H  HCH2  0   0.271   5.4888  -3.3035   1.8507
 G2D  H21  H  HCH2  0   0.262   7.5677  -3.8603   0.0698
 G2D  H23  H  HCR6  0   0.244   1.7461   0.0047   1.1346
 G2D  H24  H  HCH2  0   0.268   7.9945  -1.1942  -0.6287
 G2D  H25  H  HCH2  0   0.266   5.1613  -3.9339   0.2410
 G2D  H26  H  HCH2  0   0.260   7.6700  -2.5754   1.2659
 G2D  C02  C  C     0   0.548  -2.4896   0.5562   1.0971

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
 G2D  C07  C06  single    1.498  0.020  1.498
 G2D  C05  C06  aromatic  1.386  0.020  1.386
 G2D  C05  C04  aromatic  1.390  0.020  1.390
 G2D  C06  C08  aromatic  1.405  0.020  1.405
 G2D  C04  C03  aromatic  1.388  0.020  1.388
 G2D  C08  O09  single    1.346  0.020  1.346
 G2D  C08  C11  aromatic  1.388  0.020  1.388
 G2D  O09  C10  single    1.414  0.020  1.414
 G2D  C03  C11  aromatic  1.395  0.020  1.395
 G2D  C03  C02  single    1.496  0.020  1.496
 G2D  C02  N12  single    1.344  0.020  1.344
 G2D  C02  O01  double    1.225  0.020  1.225
 G2D  N12  C13  single    1.453  0.020  1.453
 G2D  C14  C13  single    1.542  0.020  1.542
 G2D  C14  C15  single    1.537  0.020  1.537
 G2D  C13  C16  single    1.508  0.020  1.508
 G2D  C15  C17  single    1.503  0.020  1.503
 G2D  C16  C17  aromatic  1.389  0.020  1.389
 G2D  C16  C29  aromatic  1.383  0.020  1.383
 G2D  C17  C18  aromatic  1.388  0.020  1.388
 G2D  C29  C20  aromatic  1.397  0.020  1.397
 G2D  C18  C19  aromatic  1.387  0.020  1.387
 G2D  C20  C19  aromatic  1.401  0.020  1.401
 G2D  C20  C21  single    1.462  0.020  1.462
 G2D  N28  C21  aromatic  1.375  0.020  1.375
 G2D  N28  C24  aromatic  1.305  0.020  1.305
 G2D  C21  C22  aromatic  1.378  0.020  1.378
 G2D  C24  C25  single    1.490  0.020  1.490
 G2D  C24  N23  aromatic  1.344  0.020  1.344
 G2D  C22  N23  aromatic  1.359  0.020  1.359
 G2D  C25  C26  single    1.544  0.020  1.544
 G2D  N23  C27  single    1.449  0.020  1.449
 G2D  C27  C26  single    1.541  0.020  1.541
 G2D  C05  H1   single    0.930  0.020  1.080
 G2D  C13  H2   single    0.970  0.020  1.090
 G2D  C18  H3   single    0.930  0.020  1.080
 G2D  C15  H4   single    0.970  0.020  1.090
 G2D  C15  H5   single    0.970  0.020  1.090
 G2D  C19  H6   single    0.930  0.020  1.080
 G2D  C22  H7   single    0.930  0.020  1.080
 G2D  C11  H8   single    0.930  0.020  1.080
 G2D  C04  H9   single    0.930  0.020  1.080
 G2D  C27  H10  single    0.970  0.020  1.090
 G2D  C07  H11  single    0.970  0.020  1.090
 G2D  C07  H12  single    0.970  0.020  1.090
 G2D  C07  H13  single    0.970  0.020  1.090
 G2D  C10  H14  single    0.970  0.020  1.090
 G2D  C10  H15  single    0.970  0.020  1.090
 G2D  C10  H16  single    0.970  0.020  1.090
 G2D  N12  H17  single    0.860  0.020  1.020
 G2D  C14  H18  single    0.970  0.020  1.090
 G2D  C14  H19  single    0.970  0.020  1.090
 G2D  C25  H20  single    0.970  0.020  1.090
 G2D  C26  H21  single    0.970  0.020  1.090
 G2D  C29  H23  single    0.930  0.020  1.080
 G2D  C27  H24  single    0.970  0.020  1.090
 G2D  C25  H25  single    0.970  0.020  1.090
 G2D  C26  H26  single    0.970  0.020  1.090

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
 G2D  H1   C05  C04  119.15  3.000
 G2D  H1   C05  C06  118.85  3.000
 G2D  C04  C05  C06  121.99  3.000
 G2D  C08  C06  C07  120.57  3.000
 G2D  C08  C06  C05  117.94  3.000
 G2D  C07  C06  C05  121.49  3.000
 G2D  H2   C13  C14  111.72  3.000
 G2D  H2   C13  N12  108.06  3.000
 G2D  C14  C13  N12  113.24  3.000
 G2D  H2   C13  C16  112.51  3.000
 G2D  C14  C13  C16  102.33  3.000
 G2D  N12  C13  C16  108.96  3.000
 G2D  H3   C18  C19  119.77  3.000
 G2D  H3   C18  C17  120.91  3.000
 G2D  C19  C18  C17  119.32  3.000
 G2D  C15  C17  C16  110.81  3.000
 G2D  C16  C17  C18  119.38  3.000
 G2D  C15  C17  C18  129.82  3.000
 G2D  C29  C16  C17  121.64  3.000
 G2D  C29  C16  C13  127.99  3.000
 G2D  C17  C16  C13  110.35  3.000
 G2D  H5   C15  H4   106.74  3.000
 G2D  H5   C15  C14  111.39  3.000
 G2D  H4   C15  C14  112.58  3.000
 G2D  H5   C15  C17  110.53  3.000
 G2D  H4   C15  C17  113.06  3.000
 G2D  C14  C15  C17  102.62  3.000
 G2D  H6   C19  C20  119.73  3.000
 G2D  H6   C19  C18  118.69  3.000
 G2D  C20  C19  C18  121.58  3.000
 G2D  C29  C20  C21  120.26  3.000
 G2D  C21  C20  C19  121.15  3.000
 G2D  C29  C20  C19  118.59  3.000
 G2D  N28  C21  C22  110.13  3.000
 G2D  C22  C21  C20  128.28  3.000
 G2D  N28  C21  C20  121.58  3.000
 G2D  H7   C22  N23  122.79  3.000
 G2D  H7   C22  C21  132.45  3.000
 G2D  N23  C22  C21  104.75  3.000
 G2D  N28  C24  C25  137.23  3.000
 G2D  C25  C24  N23  110.62  3.000
 G2D  N28  C24  N23  112.11  3.000
 G2D  H8   C11  C08  120.96  3.000
 G2D  H8   C11  C03  118.63  3.000
 G2D  C08  C11  C03  120.41  3.000
 G2D  C04  C03  C02  123.12  3.000
 G2D  C02  C03  C11  117.38  3.000
 G2D  C04  C03  C11  119.50  3.000
 G2D  H9   C04  C03  121.72  3.000
 G2D  H9   C04  C05  118.70  3.000
 G2D  C03  C04  C05  119.57  3.000
 G2D  H24  C27  H10  108.43  3.000
 G2D  H24  C27  C26  112.89  3.000
 G2D  H10  C27  C26  112.48  3.000
 G2D  H24  C27  N23  111.31  3.000
 G2D  H10  C27  N23  110.15  3.000
 G2D  C26  C27  N23  101.47  3.000
 G2D  H13  C07  H12  107.88  3.000
 G2D  H13  C07  H11  107.89  3.000
 G2D  H12  C07  H11  106.92  3.000
 G2D  H13  C07  C06  110.67  3.000
 G2D  H12  C07  C06  111.63  3.000
 G2D  H11  C07  C06  111.65  3.000
 G2D  O09  C08  C11  123.84  3.000
 G2D  C11  C08  C06  120.57  3.000
 G2D  O09  C08  C06  115.59  3.000
 G2D  C10  O09  C08  118.82  3.000
 G2D  H16  C10  H15  108.76  3.000
 G2D  H16  C10  H14  108.78  3.000
 G2D  H15  C10  H14  108.85  3.000
 G2D  H16  C10  O09  111.91  3.000
 G2D  H15  C10  O09  111.94  3.000
 G2D  H14  C10  O09  106.50  3.000
 G2D  H17  N12  C02  119.16  3.000
 G2D  H17  N12  C13  117.28  3.000
 G2D  C02  N12  C13  122.67  3.000
 G2D  H19  C14  H18  107.50  3.000
 G2D  H19  C14  C15  109.37  3.000
 G2D  H18  C14  C15  113.74  3.000
 G2D  H19  C14  C13  108.36  3.000
 G2D  H18  C14  C13  112.41  3.000
 G2D  C15  C14  C13  105.34  3.000
 G2D  C27  N23  C24  114.21  3.000
 G2D  C27  N23  C22  137.66  3.000
 G2D  C24  N23  C22  108.03  3.000
 G2D  H25  C25  H20  107.46  3.000
 G2D  H25  C25  C26  111.63  3.000
 G2D  H20  C25  C26  112.58  3.000
 G2D  H25  C25  C24  110.59  3.000
 G2D  H20  C25  C24  112.96  3.000
 G2D  C26  C25  C24  101.64  3.000
 G2D  H26  C26  H21  107.66  3.000
 G2D  H26  C26  C25  109.53  3.000
 G2D  H21  C26  C25  112.60  3.000
 G2D  H26  C26  C27  109.40  3.000
 G2D  H21  C26  C27  111.62  3.000
 G2D  C25  C26  C27  106.00  3.000
 G2D  C24  N28  C21  104.97  3.000
 G2D  H23  C29  C20  119.83  3.000
 G2D  H23  C29  C16  120.67  3.000
 G2D  C20  C29  C16  119.49  3.000
 G2D  N12  C02  O01  122.48  3.000
 G2D  O01  C02  C03  121.34  3.000
 G2D  N12  C02  C03  116.18  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
 G2D  CONST_01  C11  C08  C06  C05     0.00   0.0  0
 G2D  CONST_02  C11  C03  C04  C05     0.00   0.0  0
 G2D  CONST_03  C03  C04  C05  C06     0.00   0.0  0
 G2D  CONST_04  C03  C11  C08  C06     0.00   0.0  0
 G2D  CONST_05  C29  C16  C17  C18     0.00   0.0  0
 G2D  CONST_06  C29  C20  C19  C18     0.00   0.0  0
 G2D  CONST_07  C21  C20  C19  C18   180.00   0.0  0
 G2D  CONST_08  C20  C29  C16  C17     0.00   0.0  0
 G2D  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 G2D  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 G2D  CONST_11  C19  C20  C29  C16     0.00   0.0  0
 G2D  CONST_12  C21  C20  C29  C16   180.00   0.0  0
 G2D  CONST_13  N28  C21  C20  C19   180.00   0.0  0
 G2D  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 G2D  CONST_15  C24  N28  C21  C20   180.00   0.0  0
 G2D  CONST_16  N23  C22  C21  C20   180.00   0.0  0
 G2D  CONST_17  N23  C24  N28  C21     0.00   0.0  0
 G2D  CONST_18  C24  N23  C22  C21     0.00   0.0  0
 G2D  CONST_19  C29  C20  C21  C22   180.00   0.0  0
 G2D  CONST_20  C24  N28  C21  C22     0.00   0.0  0
 G2D  CONST_21  N28  C24  N23  C22     0.00   0.0  0
 G2D  CONST_22  C08  C06  C05  C04     0.00   0.0  0
 G2D  CONST_23  C08  C11  C03  C04     0.00   0.0  0
 G2D  CONST_24  N28  C21  C22  N23     0.00   0.0  0
 G2D  CONST_25  C29  C20  C21  N28     0.00   0.0  0
 G2D  CONST_26  O09  C08  C06  C05   180.00   0.0  0
 G2D  CONST_27  C02  C03  C04  C05   180.00   0.0  0
 G2D  CONST_28  C07  C06  C08  C11   180.00   0.0  0
 G2D  CONST_29  C08  C11  C03  C02   180.00   0.0  0
 G2D  CONST_30  O09  C08  C11  C03   180.00   0.0  0
 G2D  CONST_31  C07  C06  C05  C04   180.00   0.0  0
 G2D  CONST_32  H9   C04  C05  C06   180.00   0.0  0
 G2D  CONST_33  H8   C11  C08  C06   180.00   0.0  0
 G2D  CONST_34  H23  C29  C16  C13     0.00   0.0  0
 G2D  CONST_35  H6   C19  C18  C17   180.00   0.0  0
 G2D  CONST_36  H3   C18  C17  C16   180.00   0.0  0
 G2D  CONST_37  H7   C22  C21  C20     0.00   0.0  0
 G2D  CONST_38  H1   C05  C04  C03   180.00   0.0  0
 G2D  CONST_39  C03  C02  N12  C13   180.00   0.0  0
 G2D  CONST_40  O01  C02  N12  C13     0.00   0.0  0
 G2D  CONST_41  H17  N12  C02  C03     0.00   0.0  0
 G2D  Var_01    C17  C15  C14  C13   -27.49  30.0  1
 G2D  Var_02    C14  C15  C17  C18  -163.72  30.0  1
 G2D  Var_03    C26  C27  N23  C22   168.73  30.0  1
 G2D  Var_04    C27  C26  C25  C24   -23.21  30.0  1
 G2D  Var_05    C26  C25  C24  N23    14.50  30.0  1
 G2D  Var_06    C25  C26  C27  N23    23.47  30.0  1
 G2D  Var_07    N12  C02  C03  C11  -158.28  30.0  2
 G2D  Var_08    H11  C07  C06  C05   117.69  30.0  2
 G2D  Var_09    H14  C10  O09  C08   179.54  30.0  3

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
 G2D  chir_01  C13  N12  C14  C16  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
 G2D  plan-1  C05  0.020
 G2D  plan-1  C06  0.020
 G2D  plan-1  C11  0.020
 G2D  plan-1  C03  0.020
 G2D  plan-1  C04  0.020
 G2D  plan-1  C07  0.020
 G2D  plan-1  C08  0.020
 G2D  plan-1  O09  0.020
 G2D  plan-1  H1   0.020
 G2D  plan-1  H8   0.020
 G2D  plan-1  H9   0.020
 G2D  plan-1  C02  0.020
 G2D  plan-2  C20  0.020
 G2D  plan-2  C21  0.020
 G2D  plan-2  C22  0.020
 G2D  plan-2  C24  0.020
 G2D  plan-2  C27  0.020
 G2D  plan-2  N23  0.020
 G2D  plan-2  C25  0.020
 G2D  plan-2  N28  0.020
 G2D  plan-2  H7   0.020
 G2D  plan-3  C13  0.020
 G2D  plan-3  C18  0.020
 G2D  plan-3  C17  0.020
 G2D  plan-3  C16  0.020
 G2D  plan-3  C15  0.020
 G2D  plan-3  C19  0.020
 G2D  plan-3  C20  0.020
 G2D  plan-3  C21  0.020
 G2D  plan-3  C29  0.020
 G2D  plan-3  H3   0.020
 G2D  plan-3  H6   0.020
 G2D  plan-3  H23  0.020
 G2D  plan-4  C13  0.020
 G2D  plan-4  C03  0.020
 G2D  plan-4  O01  0.020
 G2D  plan-4  N12  0.020
 G2D  plan-4  H17  0.020
 G2D  plan-4  C02  0.020

