# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:10:10 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccc(c1)c2cn3CCCc3n2)c4ccccc4
#
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
 G1Y  G1Y  N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}benzamide  ligand  43  24  .  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_G1Y
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
 G1Y  O01  O  O     0  -0.488  -3.9022   1.3320   1.6267
 G1Y  C02  C  C     0   0.532  -3.7514   0.3969   0.8518
 G1Y  C03  C  CR6   0  -0.033  -4.8793  -0.0747  -0.0105
 G1Y  C04  C  CR16  0  -0.295  -4.6750  -0.6630  -1.2573
 G1Y  C05  C  CR16  0  -0.240  -5.7565  -1.0574  -2.0322
 G1Y  C06  C  CR16  0  -0.251  -7.0510  -0.8729  -1.5664
 G1Y  C07  C  CR16  0  -0.243  -7.2609  -0.2814  -0.3268
 G1Y  C08  C  CR16  0  -0.269  -6.1818   0.1262   0.4417
 G1Y  N09  N  NH1   0  -0.639  -2.5951  -0.2763   0.7202
 G1Y  C10  C  CH2   0  -0.365  -1.3705   0.0706   1.4010
 G1Y  C11  C  CR6   0   0.142  -0.3131   0.6109   0.4681
 G1Y  C12  C  CR16  0  -0.318  -0.6210   1.5893  -0.4733
 G1Y  C13  C  CR16  0  -0.218   0.3756   2.0873  -1.3003
 G1Y  C14  C  CR16  0  -0.356   1.6769   1.6212  -1.1972
 G1Y  C15  C  CR6   0   0.064   2.0060   0.6396  -0.2608
 G1Y  C16  C  CR5   0   0.114   3.3707   0.1308  -0.1405
 G1Y  C17  C  CR15  0  -0.109   4.4563   0.4115  -0.9425
 G1Y  N18  N  N     0  -0.436   5.4823  -0.2891  -0.3933
 G1Y  C19  C  CH2   0  -0.269   6.8757  -0.5582  -0.6869
 G1Y  C20  C  CH2   0  -0.489   7.3438  -1.2075   0.6291
 G1Y  C21  C  CH2   0  -0.543   6.0762  -1.7938   1.2865
 G1Y  C22  C  CR55  0   0.462   5.0062  -0.9587   0.6710
 G1Y  N23  N  N     0  -0.495   3.7348  -0.7349   0.8640
 G1Y  C24  C  CR16  0  -0.382   0.9918   0.1457   0.5633
 G1Y  H1   H  HCR6  0   0.259  -3.6755  -0.7974  -1.6522
 G1Y  H2   H  HCR6  0   0.265  -5.5846  -1.5051  -3.0021
 G1Y  H3   H  HCR6  0   0.264  -7.8945  -1.1828  -2.1695
 G1Y  H4   H  HCR6  0   0.263  -8.2679  -0.1336   0.0402
 G1Y  H5   H  HCR6  0   0.261  -6.3527   0.5953   1.4015
 G1Y  H6   H  HNH1  0   0.409  -2.5612  -1.0796   0.1137
 G1Y  H7   H  HCH2  0   0.271  -1.6054   0.8088   2.1675
 G1Y  H8   H  HCH2  0   0.267  -0.9872  -0.8106   1.9184
 G1Y  H9   H  HCR6  0   0.249  -1.6319   1.9679  -0.5633
 G1Y  H10  H  HCR6  0   0.255   0.1392   2.8505  -2.0306
 G1Y  H11  H  HCR6  0   0.242   2.4366   2.0319  -1.8506
 G1Y  H12  H  HCR5  0   0.286   4.5717   1.0321  -1.8151
 G1Y  H13  H  HCH2  0   0.261   6.9545  -1.2374  -1.5377
 G1Y  H14  H  HCH2  0   0.262   8.1118  -1.9586   0.4572
 G1Y  H15  H  HCH2  0   0.266   5.9372  -2.8466   1.0268
 G1Y  H17  H  HCR6  0   0.245   1.2283  -0.6223   1.2905
 G1Y  H18  H  HCH2  0   0.269   7.4143   0.3572  -0.9250
 G1Y  H19  H  HCH2  0   0.260   7.7696  -0.4414   1.2771
 G1Y  H20  H  HCH2  0   0.272   6.0986  -1.7249   2.3733

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
 G1Y  C20  C19  single    1.540  0.020  1.540
 G1Y  C20  C21  single    1.544  0.020  1.544
 G1Y  C19  N18  single    1.449  0.020  1.449
 G1Y  C21  C22  single    1.490  0.020  1.490
 G1Y  N18  C22  aromatic  1.345  0.020  1.345
 G1Y  N18  C17  aromatic  1.358  0.020  1.358
 G1Y  C22  N23  aromatic  1.305  0.020  1.305
 G1Y  C17  C16  aromatic  1.379  0.020  1.379
 G1Y  N23  C16  aromatic  1.375  0.020  1.375
 G1Y  C16  C15  single    1.461  0.020  1.461
 G1Y  C14  C15  aromatic  1.396  0.020  1.396
 G1Y  C14  C13  aromatic  1.386  0.020  1.386
 G1Y  C15  C24  aromatic  1.397  0.020  1.397
 G1Y  C13  C12  aromatic  1.387  0.020  1.387
 G1Y  C24  C11  aromatic  1.389  0.020  1.389
 G1Y  C12  C11  aromatic  1.392  0.020  1.392
 G1Y  C11  C10  single    1.510  0.020  1.510
 G1Y  C10  N09  single    1.443  0.020  1.443
 G1Y  O01  C02  double    1.224  0.020  1.224
 G1Y  C02  N09  single    1.344  0.020  1.344
 G1Y  C02  C03  single    1.496  0.020  1.496
 G1Y  C03  C08  aromatic  1.393  0.020  1.393
 G1Y  C03  C04  aromatic  1.394  0.020  1.394
 G1Y  C08  C07  aromatic  1.386  0.020  1.386
 G1Y  C04  C05  aromatic  1.388  0.020  1.388
 G1Y  C07  C06  aromatic  1.389  0.020  1.389
 G1Y  C05  C06  aromatic  1.388  0.020  1.388
 G1Y  C04  H1   single    0.930  0.020  1.080
 G1Y  C05  H2   single    0.930  0.020  1.080
 G1Y  C06  H3   single    0.930  0.020  1.080
 G1Y  C07  H4   single    0.930  0.020  1.080
 G1Y  C08  H5   single    0.930  0.020  1.080
 G1Y  N09  H6   single    0.860  0.020  1.020
 G1Y  C10  H7   single    0.970  0.020  1.090
 G1Y  C10  H8   single    0.970  0.020  1.090
 G1Y  C12  H9   single    0.930  0.020  1.080
 G1Y  C13  H10  single    0.930  0.020  1.080
 G1Y  C14  H11  single    0.930  0.020  1.080
 G1Y  C17  H12  single    0.930  0.020  1.080
 G1Y  C19  H13  single    0.970  0.020  1.090
 G1Y  C20  H14  single    0.970  0.020  1.090
 G1Y  C21  H15  single    0.970  0.020  1.090
 G1Y  C24  H17  single    0.930  0.020  1.080
 G1Y  C19  H18  single    0.970  0.020  1.090
 G1Y  C20  H19  single    0.970  0.020  1.090
 G1Y  C21  H20  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
 G1Y  N09  C02  C03  115.73  3.000
 G1Y  C03  C02  O01  120.86  3.000
 G1Y  N09  C02  O01  123.40  3.000
 G1Y  C08  C03  C04  119.23  3.000
 G1Y  C04  C03  C02  122.56  3.000
 G1Y  C08  C03  C02  118.18  3.000
 G1Y  H1   C04  C05  118.71  3.000
 G1Y  H1   C04  C03  120.92  3.000
 G1Y  C05  C04  C03  120.35  3.000
 G1Y  H2   C05  C06  120.27  3.000
 G1Y  H2   C05  C04  119.62  3.000
 G1Y  C06  C05  C04  120.11  3.000
 G1Y  H3   C06  C07  120.09  3.000
 G1Y  H3   C06  C05  120.12  3.000
 G1Y  C07  C06  C05  119.80  3.000
 G1Y  H4   C07  C08  119.76  3.000
 G1Y  H4   C07  C06  120.09  3.000
 G1Y  C08  C07  C06  120.14  3.000
 G1Y  H5   C08  C07  119.76  3.000
 G1Y  H5   C08  C03  119.88  3.000
 G1Y  C07  C08  C03  120.36  3.000
 G1Y  H6   N09  C10  116.56  3.000
 G1Y  H6   N09  C02  119.16  3.000
 G1Y  C10  N09  C02  124.28  3.000
 G1Y  H8   C10  H7   106.81  3.000
 G1Y  H8   C10  C11  109.62  3.000
 G1Y  H7   C10  C11  110.06  3.000
 G1Y  H8   C10  N09  109.12  3.000
 G1Y  H7   C10  N09  108.16  3.000
 G1Y  C11  C10  N09  112.88  3.000
 G1Y  C24  C11  C12  119.32  3.000
 G1Y  C12  C11  C10  120.95  3.000
 G1Y  C24  C11  C10  119.72  3.000
 G1Y  H9   C12  C13  119.69  3.000
 G1Y  H9   C12  C11  120.55  3.000
 G1Y  C13  C12  C11  119.76  3.000
 G1Y  H10  C13  C14  119.49  3.000
 G1Y  H10  C13  C12  119.89  3.000
 G1Y  C14  C13  C12  120.62  3.000
 G1Y  H11  C14  C15  120.41  3.000
 G1Y  H11  C14  C13  119.09  3.000
 G1Y  C15  C14  C13  120.51  3.000
 G1Y  C24  C15  C16  120.41  3.000
 G1Y  C24  C15  C14  118.24  3.000
 G1Y  C16  C15  C14  121.34  3.000
 G1Y  N23  C16  C17  110.16  3.000
 G1Y  N23  C16  C15  121.77  3.000
 G1Y  C17  C16  C15  128.07  3.000
 G1Y  H12  C17  N18  122.94  3.000
 G1Y  H12  C17  C16  132.31  3.000
 G1Y  N18  C17  C16  104.75  3.000
 G1Y  C22  N18  C19  114.11  3.000
 G1Y  C22  N18  C17  108.02  3.000
 G1Y  C19  N18  C17  137.74  3.000
 G1Y  H18  C19  H13  108.49  3.000
 G1Y  H18  C19  C20  113.02  3.000
 G1Y  H13  C19  C20  112.44  3.000
 G1Y  H18  C19  N18  111.34  3.000
 G1Y  H13  C19  N18  110.05  3.000
 G1Y  C20  C19  N18  101.38  3.000
 G1Y  H19  C20  H14  107.66  3.000
 G1Y  H19  C20  C21  109.55  3.000
 G1Y  H14  C20  C21  112.63  3.000
 G1Y  H19  C20  C19  109.29  3.000
 G1Y  H14  C20  C19  111.75  3.000
 G1Y  C21  C20  C19  105.93  3.000
 G1Y  H20  C21  H15  107.49  3.000
 G1Y  H20  C21  C22  113.04  3.000
 G1Y  H15  C21  C22  110.50  3.000
 G1Y  H20  C21  C20  112.58  3.000
 G1Y  H15  C21  C20  111.66  3.000
 G1Y  C22  C21  C20  101.59  3.000
 G1Y  N23  C22  C21  137.25  3.000
 G1Y  N23  C22  N18  112.12  3.000
 G1Y  C21  C22  N18  110.59  3.000
 G1Y  C22  N23  C16  104.94  3.000
 G1Y  H17  C24  C15  119.21  3.000
 G1Y  H17  C24  C11  119.24  3.000
 G1Y  C15  C24  C11  121.55  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
 G1Y  CONST_01  C06  C07  C08  C03     0.00   0.0  0
 G1Y  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 G1Y  CONST_03  C07  C08  C03  C04     0.00   0.0  0
 G1Y  CONST_04  C07  C06  C05  C04     0.00   0.0  0
 G1Y  CONST_05  C08  C03  C04  C05     0.00   0.0  0
 G1Y  CONST_06  C08  C07  C06  C05     0.00   0.0  0
 G1Y  CONST_07  C16  C15  C24  C11   180.00   0.0  0
 G1Y  CONST_08  C14  C15  C24  C11     0.00   0.0  0
 G1Y  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 G1Y  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 G1Y  CONST_11  C15  C24  C11  C12     0.00   0.0  0
 G1Y  CONST_12  C16  C15  C14  C13   180.00   0.0  0
 G1Y  CONST_13  C24  C15  C14  C13     0.00   0.0  0
 G1Y  CONST_14  C24  C11  C12  C13     0.00   0.0  0
 G1Y  CONST_15  C17  C16  C15  C14     0.00   0.0  0
 G1Y  CONST_16  N23  C16  C15  C14   180.00   0.0  0
 G1Y  CONST_17  N18  C17  C16  C15   180.00   0.0  0
 G1Y  CONST_18  C22  N23  C16  C15   180.00   0.0  0
 G1Y  CONST_19  C22  N18  C17  C16     0.00   0.0  0
 G1Y  CONST_20  N18  C22  N23  C16     0.00   0.0  0
 G1Y  CONST_21  N23  C22  N18  C17     0.00   0.0  0
 G1Y  CONST_22  C22  N23  C16  C17     0.00   0.0  0
 G1Y  CONST_23  C24  C15  C16  C17   180.00   0.0  0
 G1Y  CONST_24  N23  C16  C17  N18     0.00   0.0  0
 G1Y  CONST_25  C24  C15  C16  N23     0.00   0.0  0
 G1Y  CONST_26  C07  C08  C03  C02   180.00   0.0  0
 G1Y  CONST_27  C05  C04  C03  C02   180.00   0.0  0
 G1Y  CONST_28  C15  C24  C11  C10   180.00   0.0  0
 G1Y  CONST_29  C13  C12  C11  C10   180.00   0.0  0
 G1Y  CONST_30  H4   C07  C08  C03   180.00   0.0  0
 G1Y  CONST_31  H2   C05  C04  C03   180.00   0.0  0
 G1Y  CONST_32  H5   C08  C03  C04   180.00   0.0  0
 G1Y  CONST_33  H3   C06  C05  C04   180.00   0.0  0
 G1Y  CONST_34  H1   C04  C05  C06   180.00   0.0  0
 G1Y  CONST_35  H10  C13  C12  C11   180.00   0.0  0
 G1Y  CONST_36  H11  C14  C13  C12   180.00   0.0  0
 G1Y  CONST_37  H17  C24  C11  C12   180.00   0.0  0
 G1Y  CONST_38  H9   C12  C13  C14   180.00   0.0  0
 G1Y  CONST_39  H12  C17  C16  C15     0.00   0.0  0
 G1Y  CONST_40  C10  N09  C02  C03   180.00   0.0  0
 G1Y  CONST_41  H6   N09  C02  C03     0.00   0.0  0
 G1Y  CONST_42  C10  N09  C02  O01     0.00   0.0  0
 G1Y  Var_01    C20  C19  N18  C17   168.62  30.0  1
 G1Y  Var_02    C21  C20  C19  N18    24.25  30.0  1
 G1Y  Var_03    C20  C21  C22  N18    14.52  30.0  1
 G1Y  Var_04    C22  C21  C20  C19   -23.73  30.0  1
 G1Y  Var_05    C08  C03  C02  O01   -27.18  30.0  2
 G1Y  Var_06    C24  C11  C10  N09  -134.05  30.0  3
 G1Y  Var_07    C11  C10  N09  C02  -110.34  30.0  1

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
 G1Y  plan-1  C02  0.020
 G1Y  plan-1  C03  0.020
 G1Y  plan-1  C04  0.020
 G1Y  plan-1  C05  0.020
 G1Y  plan-1  C06  0.020
 G1Y  plan-1  C07  0.020
 G1Y  plan-1  C08  0.020
 G1Y  plan-1  H1   0.020
 G1Y  plan-1  H2   0.020
 G1Y  plan-1  H3   0.020
 G1Y  plan-1  H4   0.020
 G1Y  plan-1  H5   0.020
 G1Y  plan-2  C10  0.020
 G1Y  plan-2  C11  0.020
 G1Y  plan-2  C12  0.020
 G1Y  plan-2  C13  0.020
 G1Y  plan-2  C14  0.020
 G1Y  plan-2  C15  0.020
 G1Y  plan-2  C16  0.020
 G1Y  plan-2  C24  0.020
 G1Y  plan-2  H9   0.020
 G1Y  plan-2  H10  0.020
 G1Y  plan-2  H11  0.020
 G1Y  plan-2  H17  0.020
 G1Y  plan-3  C15  0.020
 G1Y  plan-3  C16  0.020
 G1Y  plan-3  C17  0.020
 G1Y  plan-3  N18  0.020
 G1Y  plan-3  C19  0.020
 G1Y  plan-3  C21  0.020
 G1Y  plan-3  C22  0.020
 G1Y  plan-3  N23  0.020
 G1Y  plan-3  H12  0.020
 G1Y  plan-4  O01  0.020
 G1Y  plan-4  C02  0.020
 G1Y  plan-4  C03  0.020
 G1Y  plan-4  N09  0.020
 G1Y  plan-4  C10  0.020
 G1Y  plan-4  H6   0.020

