# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 15:25:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[2-(1H-indol-3-ylmethyl)-1H-benzimidazol-5-yl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc2[nH]c(Cc3c[nH]c4ccccc34)nc2c1)[C@@H]5CCCN5
#
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
 0QY  0QY  N-[2-(1H-indol-3-ylmethyl)-1H-benzimidazol-5-yl]-L-prolinamide  ligand  48  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0QY
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
 0QY  O01  O  O     0  -0.468  -3.7578   0.8607   1.4027
 0QY  C02  C  C     0   0.520  -4.2614   0.2024   0.5093
 0QY  C03  C  CH1   0  -0.225  -5.7280   0.3163   0.1456
 0QY  N04  N  NH1   0  -0.580  -6.5130   0.8769   1.2273
 0QY  C05  C  CH2   0  -0.330  -7.7135   1.3776   0.5708
 0QY  C06  C  CH2   0  -0.460  -7.2779   1.9401  -0.7958
 0QY  C07  C  CH2   0  -0.467  -5.9448   1.2297  -1.0930
 0QY  N08  N  NH1   0  -0.738  -3.5769  -0.6565  -0.2818
 0QY  C09  C  CR6   0   0.355  -2.1898  -0.8855  -0.3144
 0QY  C10  C  CR16  0  -0.356  -1.6527  -1.3010  -1.5488
 0QY  C11  C  CR16  0  -0.299  -0.3097  -1.5840  -1.7048
 0QY  C12  C  CR16  0  -0.403  -1.3767  -0.7471   0.8017
 0QY  C13  C  CR56  0   0.150  -0.0183  -1.0203   0.6499
 0QY  C14  C  CR56  0   0.330   0.4993  -1.4305  -0.5875
 0QY  N15  N  NR15  0  -0.695   1.8381  -1.6091  -0.3610
 0QY  C16  C  CR5   0   0.466   2.0732  -1.3146   0.9424
 0QY  C17  C  CH2   0  -0.643   3.4375  -1.4215   1.5400
 0QY  C18  C  CR5   0  -0.010   4.4994  -0.8522   0.6579
 0QY  C19  C  CR15  0  -0.079   5.5225  -1.5254   0.0529
 0QY  N20  N  NR15  0  -0.688   6.2810  -0.6604  -0.6825
 0QY  C21  C  CR56  0   0.358   5.7654   0.5986  -0.5741
 0QY  C22  C  CR16  0  -0.304   6.1861   1.8031  -1.1360
 0QY  C23  C  CR16  0  -0.282   5.4493   2.9345  -0.8416
 0QY  C24  C  CR16  0  -0.268   4.3194   2.8758  -0.0083
 0QY  C25  C  CR16  0  -0.366   3.9058   1.6805   0.5467
 0QY  C26  C  CR56  0   0.040   4.6336   0.5188   0.2661
 0QY  N27  N  N     0  -0.487   0.9913  -0.9567   1.5818
 0QY  H1   H  HCH1  0   0.268  -6.1172  -0.6822  -0.0844
 0QY  H2   H  HNH1  0   0.343  -6.0005   1.6599   1.6190
 0QY  H4   H  HCH2  0   0.225  -8.4116   0.5485   0.4285
 0QY  H5   H  HCH2  0   0.243  -8.2124   2.1141   1.2001
 0QY  H6   H  HCH2  0   0.238  -8.0268   1.7595  -1.5670
 0QY  H7   H  HCH2  0   0.235  -7.1303   3.0189  -0.7375
 0QY  H8   H  HCH2  0   0.244  -5.1336   1.9545  -1.1853
 0QY  H9   H  HCH2  0   0.246  -5.9667   0.6514  -2.0168
 0QY  H10  H  HNH1  0   0.412  -4.1041  -1.1008  -1.0185
 0QY  H11  H  HCR6  0   0.268  -2.3134  -1.3992  -2.4015
 0QY  H12  H  HCR6  0   0.270   0.0815  -1.9046  -2.6609
 0QY  H13  H  HCR6  0   0.268  -1.7655  -0.4510   1.7632
 0QY  H14  H  HNR5  0   0.415   2.5360  -1.8771  -1.0376
 0QY  H15  H  HCH2  0   0.274   3.4104  -0.9169   2.5077
 0QY  H16  H  HCH2  0   0.287   3.6548  -2.4740   1.7448
 0QY  H17  H  HCR5  0   0.287   5.7701  -2.5747   0.0953
 0QY  H18  H  HNR5  0   0.410   7.0975  -0.9183  -1.2105
 0QY  H19  H  HCR6  0   0.260   7.0558   1.8516  -1.7790
 0QY  H20  H  HCR6  0   0.250   5.7483   3.8861  -1.2618
 0QY  H21  H  HCR6  0   0.247   3.7676   3.7838   0.1984
 0QY  H22  H  HCR6  0   0.239   3.0338   1.6451   1.1892

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
 0QY  N20  C19  aromatic  1.365  0.020  1.365
 0QY  N20  C21  aromatic  1.365  0.020  1.365
 0QY  C19  C18  aromatic  1.366  0.020  1.366
 0QY  C22  C21  aromatic  1.394  0.020  1.394
 0QY  C22  C23  aromatic  1.382  0.020  1.382
 0QY  C21  C26  aromatic  1.412  0.020  1.412
 0QY  C18  C26  aromatic  1.432  0.020  1.432
 0QY  C18  C17  single    1.493  0.020  1.493
 0QY  C26  C25  aromatic  1.399  0.020  1.399
 0QY  C23  C24  aromatic  1.405  0.020  1.405
 0QY  C17  C16  single    1.493  0.020  1.493
 0QY  C24  C25  aromatic  1.381  0.020  1.381
 0QY  N27  C16  aromatic  1.307  0.020  1.307
 0QY  N27  C13  aromatic  1.375  0.020  1.375
 0QY  C16  N15  aromatic  1.357  0.020  1.357
 0QY  C13  C12  aromatic  1.394  0.020  1.394
 0QY  C13  C14  aromatic  1.403  0.020  1.403
 0QY  N15  C14  aromatic  1.370  0.020  1.370
 0QY  C12  C09  aromatic  1.388  0.020  1.388
 0QY  C14  C11  aromatic  1.388  0.020  1.388
 0QY  O01  C02  double    1.219  0.020  1.219
 0QY  C05  N04  single    1.457  0.020  1.457
 0QY  C05  C06  single    1.541  0.020  1.541
 0QY  N04  C03  single    1.449  0.020  1.449
 0QY  C09  N08  single    1.406  0.020  1.406
 0QY  C09  C10  aromatic  1.409  0.020  1.409
 0QY  C02  N08  single    1.354  0.020  1.354
 0QY  C02  C03  single    1.515  0.020  1.515
 0QY  C11  C10  aromatic  1.381  0.020  1.381
 0QY  C03  C07  single    1.554  0.020  1.554
 0QY  C06  C07  single    1.540  0.020  1.540
 0QY  C03  H1   single    0.970  0.020  1.090
 0QY  N04  H2   single    0.890  0.020  1.040
 0QY  C05  H4   single    0.970  0.020  1.090
 0QY  C05  H5   single    0.970  0.020  1.090
 0QY  C06  H6   single    0.970  0.020  1.090
 0QY  C06  H7   single    0.970  0.020  1.090
 0QY  C07  H8   single    0.970  0.020  1.090
 0QY  C07  H9   single    0.970  0.020  1.090
 0QY  N08  H10  single    0.860  0.020  1.020
 0QY  C10  H11  single    0.930  0.020  1.080
 0QY  C11  H12  single    0.930  0.020  1.080
 0QY  C12  H13  single    0.930  0.020  1.080
 0QY  N15  H14  single    0.860  0.020  1.020
 0QY  C17  H15  single    0.970  0.020  1.090
 0QY  C17  H16  single    0.970  0.020  1.090
 0QY  C19  H17  single    0.930  0.020  1.080
 0QY  N20  H18  single    0.860  0.020  1.020
 0QY  C22  H19  single    0.930  0.020  1.080
 0QY  C23  H20  single    0.930  0.020  1.080
 0QY  C24  H21  single    0.930  0.020  1.080
 0QY  C25  H22  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
 0QY  N08  C02  C03  113.38  3.000
 0QY  C03  C02  O01  122.37  3.000
 0QY  N08  C02  O01  124.21  3.000
 0QY  H1   C03  C07  108.58  3.000
 0QY  H1   C03  N04  108.46  3.000
 0QY  C07  C03  N04  106.97  3.000
 0QY  H1   C03  C02  109.00  3.000
 0QY  C07  C03  C02  111.74  3.000
 0QY  N04  C03  C02  111.97  3.000
 0QY  H2   N04  C05  108.97  3.000
 0QY  H2   N04  C03  108.24  3.000
 0QY  C05  N04  C03  104.06  3.000
 0QY  H5   C05  H4   107.18  3.000
 0QY  H5   C05  C06  113.26  3.000
 0QY  H4   C05  C06  110.00  3.000
 0QY  H5   C05  N04  110.44  3.000
 0QY  H4   C05  N04  108.92  3.000
 0QY  C06  C05  N04  106.99  3.000
 0QY  H7   C06  H6   107.14  3.000
 0QY  H7   C06  C07  110.46  3.000
 0QY  H6   C06  C07  112.45  3.000
 0QY  H7   C06  C05  110.61  3.000
 0QY  H6   C06  C05  111.89  3.000
 0QY  C07  C06  C05  104.34  3.000
 0QY  H9   C07  H8   107.19  3.000
 0QY  H9   C07  C06  113.02  3.000
 0QY  H8   C07  C06  110.69  3.000
 0QY  H9   C07  C03  111.49  3.000
 0QY  H8   C07  C03  110.73  3.000
 0QY  C06  C07  C03  103.77  3.000
 0QY  H10  N08  C09  115.27  3.000
 0QY  H10  N08  C02  116.22  3.000
 0QY  C09  N08  C02  128.00  3.000
 0QY  C12  C09  C10  120.71  3.000
 0QY  C10  C09  N08  116.38  3.000
 0QY  C12  C09  N08  122.89  3.000
 0QY  H11  C10  C11  119.05  3.000
 0QY  H11  C10  C09  118.95  3.000
 0QY  C11  C10  C09  122.00  3.000
 0QY  H12  C11  C14  122.25  3.000
 0QY  H12  C11  C10  120.81  3.000
 0QY  C14  C11  C10  116.95  3.000
 0QY  H13  C12  C13  120.14  3.000
 0QY  H13  C12  C09  122.22  3.000
 0QY  C13  C12  C09  117.64  3.000
 0QY  N27  C13  C14  109.90  3.000
 0QY  C14  C13  C12  120.86  3.000
 0QY  N27  C13  C12  129.24  3.000
 0QY  N15  C14  C13  104.65  3.000
 0QY  N15  C14  C11  133.51  3.000
 0QY  C13  C14  C11  121.83  3.000
 0QY  H14  N15  C16  125.62  3.000
 0QY  H14  N15  C14  126.89  3.000
 0QY  C16  N15  C14  107.46  3.000
 0QY  N27  C16  C17  125.47  3.000
 0QY  N27  C16  N15  112.71  3.000
 0QY  C17  C16  N15  121.82  3.000
 0QY  H16  C17  H15  106.48  3.000
 0QY  H16  C17  C18  109.64  3.000
 0QY  H15  C17  C18  111.42  3.000
 0QY  H16  C17  C16  108.98  3.000
 0QY  H15  C17  C16  107.40  3.000
 0QY  C18  C17  C16  112.71  3.000
 0QY  C26  C18  C19  106.29  3.000
 0QY  C26  C18  C17  126.38  3.000
 0QY  C19  C18  C17  127.33  3.000
 0QY  H17  C19  N20  120.65  3.000
 0QY  H17  C19  C18  129.33  3.000
 0QY  N20  C19  C18  110.02  3.000
 0QY  H18  N20  C21  125.79  3.000
 0QY  H18  N20  C19  124.83  3.000
 0QY  C21  N20  C19  109.38  3.000
 0QY  C26  C21  C22  122.05  3.000
 0QY  C26  C21  N20  107.34  3.000
 0QY  C22  C21  N20  130.61  3.000
 0QY  H19  C22  C23  121.21  3.000
 0QY  H19  C22  C21  121.37  3.000
 0QY  C23  C22  C21  117.42  3.000
 0QY  H20  C23  C24  119.28  3.000
 0QY  H20  C23  C22  119.33  3.000
 0QY  C24  C23  C22  121.39  3.000
 0QY  H21  C24  C25  119.77  3.000
 0QY  H21  C24  C23  119.22  3.000
 0QY  C25  C24  C23  121.02  3.000
 0QY  H22  C25  C26  120.68  3.000
 0QY  H22  C25  C24  120.50  3.000
 0QY  C26  C25  C24  118.82  3.000
 0QY  C25  C26  C21  119.30  3.000
 0QY  C25  C26  C18  133.72  3.000
 0QY  C21  C26  C18  106.98  3.000
 0QY  C16  N27  C13  105.28  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
 0QY  CONST_01  N27  C13  C12  C09   180.00   0.0  0
 0QY  CONST_02  C14  C13  C12  C09     0.00   0.0  0
 0QY  CONST_03  C14  C11  C10  C09     0.00   0.0  0
 0QY  CONST_04  C13  C12  C09  C10     0.00   0.0  0
 0QY  CONST_05  C13  C14  C11  C10     0.00   0.0  0
 0QY  CONST_06  N15  C14  C11  C10   180.00   0.0  0
 0QY  CONST_07  N27  C13  C14  C11   180.00   0.0  0
 0QY  CONST_08  C12  C13  C14  C11     0.00   0.0  0
 0QY  CONST_09  C16  N15  C14  C11   180.00   0.0  0
 0QY  CONST_10  C12  C09  C10  C11     0.00   0.0  0
 0QY  CONST_11  C16  N27  C13  C12   180.00   0.0  0
 0QY  CONST_12  N15  C14  C13  C12   180.00   0.0  0
 0QY  CONST_13  N15  C16  N27  C13     0.00   0.0  0
 0QY  CONST_14  C16  N15  C14  C13     0.00   0.0  0
 0QY  CONST_15  C16  N27  C13  C14     0.00   0.0  0
 0QY  CONST_16  N27  C16  N15  C14     0.00   0.0  0
 0QY  CONST_17  N27  C13  C14  N15     0.00   0.0  0
 0QY  CONST_18  C21  N20  C19  C18     0.00   0.0  0
 0QY  CONST_19  N20  C21  C26  C18     0.00   0.0  0
 0QY  CONST_20  C22  C21  C26  C18   180.00   0.0  0
 0QY  CONST_21  C24  C25  C26  C18   180.00   0.0  0
 0QY  CONST_22  C22  C21  N20  C19   180.00   0.0  0
 0QY  CONST_23  C26  C21  N20  C19     0.00   0.0  0
 0QY  CONST_24  C21  C26  C18  C19     0.00   0.0  0
 0QY  CONST_25  C25  C26  C18  C19   180.00   0.0  0
 0QY  CONST_26  C26  C18  C19  N20     0.00   0.0  0
 0QY  CONST_27  C23  C22  C21  N20   180.00   0.0  0
 0QY  CONST_28  C25  C26  C21  N20   180.00   0.0  0
 0QY  CONST_29  C24  C23  C22  C21     0.00   0.0  0
 0QY  CONST_30  C24  C25  C26  C21     0.00   0.0  0
 0QY  CONST_31  C25  C26  C21  C22     0.00   0.0  0
 0QY  CONST_32  C25  C24  C23  C22     0.00   0.0  0
 0QY  CONST_33  C26  C21  C22  C23     0.00   0.0  0
 0QY  CONST_34  C26  C25  C24  C23     0.00   0.0  0
 0QY  CONST_35  C13  C12  C09  N08   180.00   0.0  0
 0QY  CONST_36  C11  C10  C09  N08   180.00   0.0  0
 0QY  CONST_37  C17  C16  N27  C13   180.00   0.0  0
 0QY  CONST_38  C17  C16  N15  C14   180.00   0.0  0
 0QY  CONST_39  N20  C19  C18  C17   180.00   0.0  0
 0QY  CONST_40  C21  C26  C18  C17   180.00   0.0  0
 0QY  CONST_41  C25  C26  C18  C17     0.00   0.0  0
 0QY  CONST_42  H12  C11  C10  C09   180.00   0.0  0
 0QY  CONST_43  H13  C12  C09  C10   180.00   0.0  0
 0QY  CONST_44  H14  N15  C14  C11     0.00   0.0  0
 0QY  CONST_45  H11  C10  C09  C12   180.00   0.0  0
 0QY  CONST_46  H18  N20  C19  C18   180.00   0.0  0
 0QY  CONST_47  H22  C25  C26  C18     0.00   0.0  0
 0QY  CONST_48  H19  C22  C21  N20     0.00   0.0  0
 0QY  CONST_49  H17  C19  N20  C21   180.00   0.0  0
 0QY  CONST_50  H20  C23  C22  C21   180.00   0.0  0
 0QY  CONST_51  H21  C24  C23  C22   180.00   0.0  0
 0QY  CONST_52  C09  N08  C02  C03   180.00   0.0  0
 0QY  CONST_56  C09  N08  C02  O01     0.00   0.0  0
 0QY  Var_01    C06  C05  N04  C03   -36.59  30.0  1
 0QY  Var_02    C05  C06  C07  C03    -0.21  30.0  1
 0QY  Var_03    C07  C06  C05  N04    22.28  30.0  1
 0QY  Var_04    C18  C17  C16  N15    43.87  30.0  1
 0QY  Var_05    C19  C18  C17  C16  -114.85  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
 0QY  chir_01  C03  N04  C02  C07  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
 0QY  plan-1  C17  0.020
 0QY  plan-1  C18  0.020
 0QY  plan-1  C19  0.020
 0QY  plan-1  N20  0.020
 0QY  plan-1  C21  0.020
 0QY  plan-1  C22  0.020
 0QY  plan-1  C23  0.020
 0QY  plan-1  C24  0.020
 0QY  plan-1  C25  0.020
 0QY  plan-1  C26  0.020
 0QY  plan-1  H17  0.020
 0QY  plan-1  H18  0.020
 0QY  plan-1  H19  0.020
 0QY  plan-1  H20  0.020
 0QY  plan-1  H21  0.020
 0QY  plan-1  H22  0.020
 0QY  plan-2  N08  0.020
 0QY  plan-2  C09  0.020
 0QY  plan-2  C10  0.020
 0QY  plan-2  C11  0.020
 0QY  plan-2  C12  0.020
 0QY  plan-2  C13  0.020
 0QY  plan-2  C14  0.020
 0QY  plan-2  N15  0.020
 0QY  plan-2  C16  0.020
 0QY  plan-2  C17  0.020
 0QY  plan-2  N27  0.020
 0QY  plan-2  H11  0.020
 0QY  plan-2  H12  0.020
 0QY  plan-2  H13  0.020
 0QY  plan-2  H14  0.020
 0QY  plan-3  O01  0.020
 0QY  plan-3  C02  0.020
 0QY  plan-3  C03  0.020
 0QY  plan-3  N08  0.020
 0QY  plan-3  C09  0.020
 0QY  plan-3  H10  0.020

