# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:29:57 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)C(=O)N(CC2CC2)Cc3cccc(c3)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
 G2J  G2J  N-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide  ligand  57  30  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G2J
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
 G2J  O01  O  O     0  -0.484  -2.2097   0.7316   2.9544
 G2J  C02  C  C     0   0.525  -2.2907   0.6278   1.7378
 G2J  C03  C  CR6   0  -0.068  -3.0121  -0.5522   1.1624
 G2J  C04  C  CR16  0  -0.297  -4.3444  -0.7709   1.5044
 G2J  C05  C  CR16  0  -0.235  -4.9816  -1.9057   1.0333
 G2J  C06  C  CR16  0  -0.382  -4.3071  -2.8417   0.2574
 G2J  C07  C  CR6   0   0.399  -2.9665  -2.6323  -0.0586
 G2J  O08  O  O2    0  -0.470  -2.2149  -3.4780  -0.7850
 G2J  C09  C  CH3   0  -0.438  -2.7979  -4.6857  -1.2338
 G2J  C10  C  CR16  0  -0.347  -2.3262  -1.4758   0.3900
 G2J  N11  N  NT    0  -0.442  -1.7181   1.4977   0.8767
 G2J  C12  C  CH2   0  -0.325  -2.1156   1.6333  -0.5196
 G2J  C13  C  CH1   0  -0.244  -2.9797   2.8441  -0.7615
 G2J  C14  C  CH2   0  -0.483  -4.4140   2.8158  -0.3351
 G2J  C15  C  CH2   0  -0.486  -4.0642   2.7631  -1.7918
 G2J  C16  C  CH2   0  -0.384  -0.8838   2.5691   1.4003
 G2J  C17  C  CR6   0   0.123   0.3976   2.7020   0.6196
 G2J  C18  C  CR16  0  -0.328   0.7264   3.8919  -0.0160
 G2J  C19  C  CR16  0  -0.220   1.9192   3.9926  -0.7245
 G2J  C20  C  CR16  0  -0.352   2.7808   2.9132  -0.8024
 G2J  C21  C  CR6   0   0.061   2.4662   1.7050  -0.1699
 G2J  C22  C  CR5   0   0.115   3.3671   0.5558  -0.2347
 G2J  C23  C  CR15  0  -0.108   4.5508   0.4386  -0.9311
 G2J  N24  N  N     0  -0.438   4.9831  -0.8227  -0.6689
 G2J  C25  C  CH2   0  -0.268   6.1431  -1.6399  -0.9620
 G2J  C26  C  CH2   0  -0.490   5.6686  -3.0285  -0.4915
 G2J  C27  C  CH2   0  -0.543   4.5450  -2.7721   0.5358
 G2J  C28  C  CR55  0   0.463   4.0943  -1.4035   0.1561
 G2J  N29  N  N     0  -0.493   3.0983  -0.6103   0.4427
 G2J  C30  C  CR16  0  -0.353   1.2684   1.6199   0.5362
 G2J  H1   H  HCR6  0   0.259  -4.8785  -0.0591   2.1199
 G2J  H2   H  HCR6  0   0.264  -6.0219  -2.0779   1.2759
 G2J  H3   H  HCR6  0   0.284  -4.8377  -3.7188  -0.0872
 G2J  H4   H  HCH3  0   0.230  -3.1521  -5.3004  -0.4023
 G2J  H5   H  HCH3  0   0.230  -3.6295  -4.5084  -1.9205
 G2J  H6   H  HCH3  0   0.261  -2.0175  -5.2276  -1.7617
 G2J  H7   H  HCR6  0   0.266  -1.2865  -1.3128   0.1291
 G2J  H8   H  HCH2  0   0.262  -1.2167   1.6831  -1.1381
 G2J  H9   H  HCH2  0   0.268  -2.6511   0.7402  -0.8316
 G2J  H10  H  HCH1  0   0.259  -2.4764   3.8025  -0.6852
 G2J  H11  H  HCH2  0   0.243  -4.7901   1.9109   0.1286
 G2J  H12  H  HCH2  0   0.253  -4.8479   3.7259   0.0576
 G2J  H13  H  HCH2  0   0.254  -4.2573   3.6373  -2.3999
 G2J  H14  H  HCH2  0   0.247  -4.1999   1.8222  -2.3119
 G2J  H15  H  HCH2  0   0.262  -1.4310   3.5160   1.3925
 G2J  H16  H  HCH2  0   0.284  -0.6601   2.3468   2.4420
 G2J  H17  H  HCR6  0   0.250   0.0538   4.7399   0.0375
 G2J  H18  H  HCR6  0   0.255   2.1754   4.9197  -1.2211
 G2J  H19  H  HCR6  0   0.242   3.7052   3.0135  -1.3577
 G2J  H20  H  HCR5  0   0.286   5.0848   1.1176  -1.5744
 G2J  H21  H  HCH2  0   0.268   6.3887  -1.6132  -2.0220
 G2J  H22  H  HCH2  0   0.260   5.2676  -3.5812  -1.3413
 G2J  H23  H  HCH2  0   0.272   3.7491  -3.5132   0.4765
 G2J  H25  H  HCR6  0   0.242   1.0113   0.6883   1.0263
 G2J  H26  H  HCH2  0   0.262   7.0060  -1.2805  -0.3992
 G2J  H27  H  HCH2  0   0.262   6.4883  -3.6111  -0.0764
 G2J  H28  H  HCH2  0   0.266   4.9239  -2.7801   1.5610

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
 G2J  C09  O08  single    1.414  0.020  1.414
 G2J  O08  C07  single    1.345  0.020  1.345
 G2J  C07  C06  aromatic  1.393  0.020  1.393
 G2J  C07  C10  aromatic  1.396  0.020  1.396
 G2J  C06  C05  aromatic  1.390  0.020  1.390
 G2J  C26  C27  single    1.544  0.020  1.544
 G2J  C26  C25  single    1.541  0.020  1.541
 G2J  C10  C03  aromatic  1.386  0.020  1.386
 G2J  C05  C04  aromatic  1.384  0.020  1.384
 G2J  C27  C28  single    1.490  0.020  1.490
 G2J  C25  N24  single    1.449  0.020  1.449
 G2J  C04  C03  aromatic  1.393  0.020  1.393
 G2J  C03  C02  single    1.498  0.020  1.498
 G2J  C28  N24  aromatic  1.345  0.020  1.345
 G2J  C28  N29  aromatic  1.305  0.020  1.305
 G2J  N24  C23  aromatic  1.359  0.020  1.359
 G2J  O01  C02  double    1.224  0.020  1.224
 G2J  N29  C22  aromatic  1.375  0.020  1.375
 G2J  C02  N11  single    1.351  0.020  1.351
 G2J  C23  C22  aromatic  1.378  0.020  1.378
 G2J  C22  C21  single    1.462  0.020  1.462
 G2J  N11  C12  single    1.458  0.020  1.458
 G2J  N11  C16  single    1.455  0.020  1.455
 G2J  C30  C21  aromatic  1.393  0.020  1.393
 G2J  C30  C17  aromatic  1.391  0.020  1.391
 G2J  C21  C20  aromatic  1.400  0.020  1.400
 G2J  C12  C13  single    1.507  0.020  1.507
 G2J  C16  C17  single    1.506  0.020  1.506
 G2J  C17  C18  aromatic  1.388  0.020  1.388
 G2J  C20  C19  aromatic  1.383  0.020  1.383
 G2J  C13  C15  single    1.498  0.020  1.498
 G2J  C13  C14  single    1.497  0.020  1.497
 G2J  C18  C19  aromatic  1.391  0.020  1.391
 G2J  C15  C14  single    1.499  0.020  1.499
 G2J  C04  H1   single    0.930  0.020  1.080
 G2J  C05  H2   single    0.930  0.020  1.080
 G2J  C06  H3   single    0.930  0.020  1.080
 G2J  C09  H4   single    0.970  0.020  1.090
 G2J  C09  H5   single    0.970  0.020  1.090
 G2J  C09  H6   single    0.970  0.020  1.090
 G2J  C10  H7   single    0.930  0.020  1.080
 G2J  C12  H8   single    0.970  0.020  1.090
 G2J  C12  H9   single    0.970  0.020  1.090
 G2J  C13  H10  single    0.970  0.020  1.090
 G2J  C14  H11  single    0.970  0.020  1.090
 G2J  C14  H12  single    0.970  0.020  1.090
 G2J  C15  H13  single    0.970  0.020  1.090
 G2J  C15  H14  single    0.970  0.020  1.090
 G2J  C16  H15  single    0.970  0.020  1.090
 G2J  C16  H16  single    0.970  0.020  1.090
 G2J  C18  H17  single    0.930  0.020  1.080
 G2J  C19  H18  single    0.930  0.020  1.080
 G2J  C20  H19  single    0.930  0.020  1.080
 G2J  C23  H20  single    0.930  0.020  1.080
 G2J  C25  H21  single    0.970  0.020  1.090
 G2J  C26  H22  single    0.970  0.020  1.090
 G2J  C27  H23  single    0.970  0.020  1.090
 G2J  C30  H25  single    0.930  0.020  1.080
 G2J  C25  H26  single    0.970  0.020  1.090
 G2J  C26  H27  single    0.970  0.020  1.090
 G2J  C27  H28  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
 G2J  N11  C02  C03  117.80  3.000
 G2J  N11  C02  O01  123.43  3.000
 G2J  C03  C02  O01  118.73  3.000
 G2J  C10  C03  C04  120.38  3.000
 G2J  C04  C03  C02  119.34  3.000
 G2J  C10  C03  C02  120.05  3.000
 G2J  H1   C04  C05  120.38  3.000
 G2J  H1   C04  C03  120.56  3.000
 G2J  C05  C04  C03  119.05  3.000
 G2J  H2   C05  C06  118.97  3.000
 G2J  H2   C05  C04  119.79  3.000
 G2J  C06  C05  C04  121.24  3.000
 G2J  H3   C06  C07  121.45  3.000
 G2J  H3   C06  C05  119.07  3.000
 G2J  C07  C06  C05  119.48  3.000
 G2J  C10  C07  O08  116.00  3.000
 G2J  C10  C07  C06  119.54  3.000
 G2J  O08  C07  C06  124.47  3.000
 G2J  C09  O08  C07  118.57  3.000
 G2J  H6   C09  H5   108.79  3.000
 G2J  H6   C09  H4   108.77  3.000
 G2J  H5   C09  H4   108.82  3.000
 G2J  H6   C09  O08  106.50  3.000
 G2J  H5   C09  O08  111.99  3.000
 G2J  H4   C09  O08  111.87  3.000
 G2J  H7   C10  C07  119.15  3.000
 G2J  H7   C10  C03  120.57  3.000
 G2J  C07  C10  C03  120.28  3.000
 G2J  C16  N11  C12  115.61  3.000
 G2J  C16  N11  C02  119.18  3.000
 G2J  C12  N11  C02  123.69  3.000
 G2J  H9   C12  H8   106.28  3.000
 G2J  H9   C12  C13  109.36  3.000
 G2J  H8   C12  C13  110.15  3.000
 G2J  H9   C12  N11  109.43  3.000
 G2J  H8   C12  N11  108.80  3.000
 G2J  C13  C12  N11  112.63  3.000
 G2J  H10  C13  C15  115.59  3.000
 G2J  H10  C13  C14  116.18  3.000
 G2J  C15  C13  C14   60.08  3.000
 G2J  H10  C13  C12  115.61  3.000
 G2J  C14  C13  C12  119.24  3.000
 G2J  C15  C13  C12  118.82  3.000
 G2J  H12  C14  H11  114.06  3.000
 G2J  H12  C14  C15  118.41  3.000
 G2J  H11  C14  C15  117.86  3.000
 G2J  H12  C14  C13  118.15  3.000
 G2J  H11  C14  C13  118.05  3.000
 G2J  C15  C14  C13   60.01  3.000
 G2J  H14  C15  H13  114.17  3.000
 G2J  H14  C15  C14  117.88  3.000
 G2J  H13  C15  C14  118.43  3.000
 G2J  H14  C15  C13  117.88  3.000
 G2J  H13  C15  C13  118.16  3.000
 G2J  C14  C15  C13   59.91  3.000
 G2J  H16  C16  H15  106.64  3.000
 G2J  H16  C16  C17  109.83  3.000
 G2J  H15  C16  C17  110.21  3.000
 G2J  H16  C16  N11  108.17  3.000
 G2J  H15  C16  N11  110.37  3.000
 G2J  C17  C16  N11  111.48  3.000
 G2J  C30  C17  C18  119.39  3.000
 G2J  C18  C17  C16  120.95  3.000
 G2J  C30  C17  C16  119.66  3.000
 G2J  H17  C18  C19  120.05  3.000
 G2J  H17  C18  C17  120.07  3.000
 G2J  C19  C18  C17  119.89  3.000
 G2J  H18  C19  C20  119.68  3.000
 G2J  H18  C19  C18  119.91  3.000
 G2J  C20  C19  C18  120.42  3.000
 G2J  H19  C20  C21  120.23  3.000
 G2J  H19  C20  C19  119.22  3.000
 G2J  C21  C20  C19  120.55  3.000
 G2J  C30  C21  C22  120.30  3.000
 G2J  C30  C21  C20  118.36  3.000
 G2J  C22  C21  C20  121.34  3.000
 G2J  N29  C22  C23  110.17  3.000
 G2J  C23  C22  C21  128.21  3.000
 G2J  N29  C22  C21  121.62  3.000
 G2J  H20  C23  N24  122.86  3.000
 G2J  H20  C23  C22  132.38  3.000
 G2J  N24  C23  C22  104.75  3.000
 G2J  C28  N24  C25  114.19  3.000
 G2J  C28  N24  C23  108.00  3.000
 G2J  C25  N24  C23  137.67  3.000
 G2J  H26  C25  H21  108.41  3.000
 G2J  H26  C25  C26  112.50  3.000
 G2J  H21  C25  C26  112.89  3.000
 G2J  H26  C25  N24  110.06  3.000
 G2J  H21  C25  N24  111.34  3.000
 G2J  C26  C25  N24  101.54  3.000
 G2J  H27  C26  H22  107.64  3.000
 G2J  H27  C26  C27  112.55  3.000
 G2J  H22  C26  C27  109.59  3.000
 G2J  H27  C26  C25  111.53  3.000
 G2J  H22  C26  C25  109.39  3.000
 G2J  C27  C26  C25  106.12  3.000
 G2J  H28  C27  H23  107.42  3.000
 G2J  H28  C27  C28  110.52  3.000
 G2J  H23  C27  C28  112.96  3.000
 G2J  H28  C27  C26  111.75  3.000
 G2J  H23  C27  C26  112.50  3.000
 G2J  C28  C27  C26  101.72  3.000
 G2J  N29  C28  C27  137.14  3.000
 G2J  N29  C28  N24  112.13  3.000
 G2J  C27  C28  N24  110.68  3.000
 G2J  C28  N29  C22  104.95  3.000
 G2J  H25  C30  C21  119.06  3.000
 G2J  H25  C30  C17  119.53  3.000
 G2J  C21  C30  C17  121.40  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
 G2J  CONST_01  C06  C07  C10  C03     0.00   0.0  0
 G2J  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 G2J  CONST_03  C07  C06  C05  C04     0.00   0.0  0
 G2J  CONST_04  C07  C10  C03  C04     0.00   0.0  0
 G2J  CONST_05  C10  C07  C06  C05     0.00   0.0  0
 G2J  CONST_06  C10  C03  C04  C05     0.00   0.0  0
 G2J  CONST_07  C22  C21  C30  C17   180.00   0.0  0
 G2J  CONST_08  C20  C21  C30  C17     0.00   0.0  0
 G2J  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 G2J  CONST_10  C21  C30  C17  C18     0.00   0.0  0
 G2J  CONST_11  C21  C20  C19  C18     0.00   0.0  0
 G2J  CONST_12  C22  C21  C20  C19   180.00   0.0  0
 G2J  CONST_13  C30  C21  C20  C19     0.00   0.0  0
 G2J  CONST_14  C30  C17  C18  C19     0.00   0.0  0
 G2J  CONST_15  N29  C22  C21  C20   180.00   0.0  0
 G2J  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 G2J  CONST_17  C28  N29  C22  C21   180.00   0.0  0
 G2J  CONST_18  N24  C23  C22  C21   180.00   0.0  0
 G2J  CONST_19  N24  C28  N29  C22     0.00   0.0  0
 G2J  CONST_20  C28  N24  C23  C22     0.00   0.0  0
 G2J  CONST_21  N29  C28  N24  C23     0.00   0.0  0
 G2J  CONST_22  C28  N29  C22  C23     0.00   0.0  0
 G2J  CONST_23  C30  C21  C22  C23   180.00   0.0  0
 G2J  CONST_24  N29  C22  C23  N24     0.00   0.0  0
 G2J  CONST_25  C30  C21  C22  N29     0.00   0.0  0
 G2J  CONST_26  C07  C10  C03  C02   180.00   0.0  0
 G2J  CONST_27  C05  C04  C03  C02   180.00   0.0  0
 G2J  CONST_28  O08  C07  C10  C03   180.00   0.0  0
 G2J  CONST_29  O08  C07  C06  C05   180.00   0.0  0
 G2J  CONST_30  C21  C30  C17  C16   180.00   0.0  0
 G2J  CONST_31  C19  C18  C17  C16   180.00   0.0  0
 G2J  CONST_32  H2   C05  C04  C03   180.00   0.0  0
 G2J  CONST_33  H3   C06  C05  C04   180.00   0.0  0
 G2J  CONST_34  H7   C10  C03  C04   180.00   0.0  0
 G2J  CONST_35  H1   C04  C05  C06   180.00   0.0  0
 G2J  CONST_36  H18  C19  C18  C17   180.00   0.0  0
 G2J  CONST_37  H25  C30  C17  C18   180.00   0.0  0
 G2J  CONST_38  H19  C20  C19  C18   180.00   0.0  0
 G2J  CONST_39  H17  C18  C19  C20   180.00   0.0  0
 G2J  CONST_40  H20  C23  C22  C21     0.00   0.0  0
 G2J  CONST_42  C16  N11  C02  C03   180.00   0.0  0
 G2J  CONST_44  C16  N11  C02  O01     0.00   0.0  0
 G2J  Var_01    C26  C25  N24  C23  -169.84  30.0  1
 G2J  Var_02    C27  C26  C25  N24   -23.00  30.0  1
 G2J  Var_03    C26  C27  C28  N24   -13.88  30.0  1
 G2J  Var_04    C28  C27  C26  C25    22.56  30.0  1
 G2J  Var_05    C14  C15  C13  C12   109.07  30.0  1
 G2J  Var_06    H11  C14  C15  C13  -108.00  30.0  1
 G2J  Var_07    C10  C03  C02  O01  -116.38  30.0  2
 G2J  Var_08    C10  C07  O08  C09   178.16  30.0  2
 G2J  Var_09    C15  C13  C12  N11  -145.37  30.0  3
 G2J  Var_10    C30  C17  C16  N11   -59.00  30.0  2
 G2J  Var_11    C13  C12  N11  C02   102.26  30.0  3
 G2J  Var_12    C17  C16  N11  C02   134.45  30.0  3
 G2J  Var_13    H4   C09  O08  C07   -59.27  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
 G2J  chir_01  C13  C12  C15  C14  both

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
 G2J  plan-1  C02  0.020
 G2J  plan-1  C03  0.020
 G2J  plan-1  C04  0.020
 G2J  plan-1  C05  0.020
 G2J  plan-1  C06  0.020
 G2J  plan-1  C07  0.020
 G2J  plan-1  O08  0.020
 G2J  plan-1  C10  0.020
 G2J  plan-1  H1   0.020
 G2J  plan-1  H2   0.020
 G2J  plan-1  H3   0.020
 G2J  plan-1  H7   0.020
 G2J  plan-2  C21  0.020
 G2J  plan-2  C22  0.020
 G2J  plan-2  C23  0.020
 G2J  plan-2  N24  0.020
 G2J  plan-2  C25  0.020
 G2J  plan-2  C27  0.020
 G2J  plan-2  C28  0.020
 G2J  plan-2  N29  0.020
 G2J  plan-2  H20  0.020
 G2J  plan-3  C16  0.020
 G2J  plan-3  C17  0.020
 G2J  plan-3  C18  0.020
 G2J  plan-3  C19  0.020
 G2J  plan-3  C20  0.020
 G2J  plan-3  C21  0.020
 G2J  plan-3  C22  0.020
 G2J  plan-3  C30  0.020
 G2J  plan-3  H17  0.020
 G2J  plan-3  H18  0.020
 G2J  plan-3  H19  0.020
 G2J  plan-3  H25  0.020
 G2J  plan-4  O01  0.020
 G2J  plan-4  C02  0.020
 G2J  plan-4  C03  0.020
 G2J  plan-4  N11  0.020
 G2J  plan-4  C12  0.020
 G2J  plan-4  C16  0.020

