# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 14:49:50 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2c(cccc2C(N)=O)n1c3nc4CCOCc4c(NCc5ccccc5)n3
#
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
 JDP  JDP  1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide  ligand  54  31  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JDP
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
 JDP  C22  C  CR16  0  -0.244  -2.3609   4.0991  -0.1810
 JDP  C21  C  CR16  0  -0.269  -2.7478   3.8708   1.1339
 JDP  O01  O  O     0  -0.485   5.6863   1.5454   0.5921
 JDP  C03  C  CR6   0  -0.128   3.4210   2.1617   0.2377
 JDP  C04  C  CR16  0  -0.306   2.5121   3.1901   0.4475
 JDP  C05  C  CR16  0  -0.278   1.1389   2.9459   0.4895
 JDP  C06  C  CR16  0  -0.282   0.6259   1.6735   0.3075
 JDP  C07  C  CR56  0   0.334   1.5305   0.6407   0.0884
 JDP  C08  C  CR56  0   0.094   2.9253   0.8575   0.0755
 JDP  C09  C  CR15  0  -0.460   3.5350  -0.4157  -0.1399
 JDP  C10  C  CR5   0   0.359   2.5472  -1.3475  -0.2335
 JDP  C11  C  CH3   0  -0.725   2.7148  -2.7990  -0.5066
 JDP  N12  N  NR5   0  -0.678   1.3184  -0.7168  -0.0948
 JDP  C13  C  CR6   0   0.551   0.0666  -1.3507  -0.1112
 JDP  N14  N  N     0  -0.486  -0.9095  -0.6899  -0.7043
 JDP  C15  C  CR6   0   0.565  -2.1062  -1.2745  -0.7278
 JDP  N16  N  NH1   0  -0.685  -3.1190  -0.5997  -1.2974
 JDP  C17  C  CH2   0  -0.334  -2.9888   0.7378  -1.8154
 JDP  C18  C  CR6   0   0.073  -2.9144   1.8186  -0.7603
 JDP  C19  C  CR16  0  -0.287  -3.3098   1.6005   0.5541
 JDP  C20  C  CR16  0  -0.243  -3.2224   2.6185   1.4965
 JDP  C23  C  CR16  0  -0.285  -2.4408   3.0789  -1.1169
 JDP  C24  C  CR6   0  -0.145  -2.2937  -2.5682  -0.1906
 JDP  C25  C  CH2   0  -0.210  -3.6172  -3.2787  -0.2459
 JDP  O26  O  O2    0  -0.477  -3.5131  -4.6346   0.0941
 JDP  C27  C  CH2   0  -0.203  -2.7748  -4.8364   1.2815
 JDP  C28  C  CH2   0  -0.523  -1.3155  -4.4818   1.0597
 JDP  C29  C  CR6   0   0.263  -1.1971  -3.1367   0.4131
 JDP  N30  N  N     0  -0.470  -0.0053  -2.5243   0.4725
 JDP  N31  N  NH2   0  -0.809   5.2850   3.6209  -0.1836
 JDP  H1   H  HCR6  0   0.256  -1.9857   5.0705  -0.4766
 JDP  H2   H  HCR6  0   0.254  -2.6774   4.6615   1.8694
 JDP  H3   H  HCR6  0   0.253   2.8604   4.2023   0.6106
 JDP  H4   H  HCR6  0   0.255   0.4566   3.7664   0.6648
 JDP  H5   H  HCR6  0   0.292  -0.4411   1.5092   0.3217
 JDP  H6   H  HCR5  0   0.248   4.5860  -0.6292  -0.2326
 JDP  H7   H  HCH3  0   0.260   2.4423  -3.4134   0.3490
 JDP  H8   H  HCH3  0   0.250   2.1054  -3.1300  -1.3483
 JDP  H9   H  HCH3  0   0.253   3.7583  -2.9885  -0.7515
 JDP  H10  H  HNH1  0   0.415  -4.0389  -1.0047  -1.2932
 JDP  H11  H  HCH2  0   0.261  -2.1072   0.8004  -2.4550
 JDP  H12  H  HCH2  0   0.279  -3.8529   0.9115  -2.4584
 JDP  H13  H  HCR6  0   0.243  -3.6792   0.6287   0.8574
 JDP  H14  H  HCR6  0   0.254  -3.5252   2.4278   2.5183
 JDP  H15  H  HCR6  0   0.248  -2.1199   3.2632  -2.1360
 JDP  H16  H  HCH2  0   0.227  -4.3388  -2.7650   0.4098
 JDP  H17  H  HCH2  0   0.253  -4.0277  -3.2426  -1.2598
 JDP  H18  H  HCH2  0   0.216  -3.1875  -4.2341   2.1016
 JDP  H19  H  HCH2  0   0.250  -2.8845  -5.8857   1.5546
 JDP  H20  H  HCH2  0   0.262  -0.7734  -4.4780   2.0071
 JDP  H21  H  HCH2  0   0.267  -0.8300  -5.2291   0.4249
 JDP  H22  H  HNH2  0   0.403   6.2662   3.8458  -0.2119
 JDP  H23  H  HNH2  0   0.410   4.6515   4.2790  -0.6021
 JDP  C02  C  C     0   0.466   4.8918   2.4051   0.2319

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
 JDP  O01  C02  double    1.225  0.020  1.225
 JDP  N31  C02  single    1.344  0.020  1.344
 JDP  C02  C03  single    1.491  0.020  1.491
 JDP  C09  C08  aromatic  1.428  0.020  1.428
 JDP  C09  C10  aromatic  1.361  0.020  1.361
 JDP  C03  C08  aromatic  1.405  0.020  1.405
 JDP  C03  C04  aromatic  1.388  0.020  1.388
 JDP  C08  C07  aromatic  1.412  0.020  1.412
 JDP  C11  C10  single    1.486  0.020  1.486
 JDP  C04  C05  aromatic  1.395  0.020  1.395
 JDP  C10  N12  aromatic  1.388  0.020  1.388
 JDP  C07  N12  aromatic  1.386  0.020  1.386
 JDP  C07  C06  aromatic  1.390  0.020  1.390
 JDP  N12  C13  single    1.403  0.020  1.403
 JDP  C05  C06  aromatic  1.384  0.020  1.384
 JDP  C13  N30  aromatic  1.313  0.020  1.313
 JDP  C13  N14  aromatic  1.320  0.020  1.320
 JDP  N30  C29  aromatic  1.341  0.020  1.341
 JDP  N14  C15  aromatic  1.332  0.020  1.332
 JDP  C29  C28  single    1.497  0.020  1.497
 JDP  C29  C24  aromatic  1.375  0.020  1.375
 JDP  C28  C27  single    1.518  0.020  1.518
 JDP  C15  C24  aromatic  1.413  0.020  1.413
 JDP  C15  N16  single    1.344  0.020  1.344
 JDP  C22  C21  aromatic  1.389  0.020  1.389
 JDP  C22  C23  aromatic  1.387  0.020  1.387
 JDP  C24  C25  single    1.503  0.020  1.503
 JDP  C21  C20  aromatic  1.387  0.020  1.387
 JDP  C23  C18  aromatic  1.393  0.020  1.393
 JDP  N16  C17  single    1.440  0.020  1.440
 JDP  C27  O26  single    1.413  0.020  1.413
 JDP  C20  C19  aromatic  1.390  0.020  1.390
 JDP  C18  C19  aromatic  1.390  0.020  1.390
 JDP  C18  C17  single    1.512  0.020  1.512
 JDP  C25  O26  single    1.402  0.020  1.402
 JDP  C22  H1   single    0.930  0.020  1.080
 JDP  C21  H2   single    0.930  0.020  1.080
 JDP  C04  H3   single    0.930  0.020  1.080
 JDP  C05  H4   single    0.930  0.020  1.080
 JDP  C06  H5   single    0.930  0.020  1.080
 JDP  C09  H6   single    0.930  0.020  1.080
 JDP  C11  H7   single    0.970  0.020  1.090
 JDP  C11  H8   single    0.970  0.020  1.090
 JDP  C11  H9   single    0.970  0.020  1.090
 JDP  N16  H10  single    0.860  0.020  1.020
 JDP  C17  H11  single    0.970  0.020  1.090
 JDP  C17  H12  single    0.970  0.020  1.090
 JDP  C19  H13  single    0.930  0.020  1.080
 JDP  C20  H14  single    0.930  0.020  1.080
 JDP  C23  H15  single    0.930  0.020  1.080
 JDP  C25  H16  single    0.970  0.020  1.090
 JDP  C25  H17  single    0.970  0.020  1.090
 JDP  C27  H18  single    0.970  0.020  1.090
 JDP  C27  H19  single    0.970  0.020  1.090
 JDP  C28  H20  single    0.970  0.020  1.090
 JDP  C28  H21  single    0.970  0.020  1.090
 JDP  N31  H22  single    0.860  0.020  1.020
 JDP  N31  H23  single    0.860  0.020  1.020

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
 JDP  H1   C22  C23  119.72  3.000
 JDP  H1   C22  C21  120.16  3.000
 JDP  C23  C22  C21  120.12  3.000
 JDP  H2   C21  C20  120.27  3.000
 JDP  H2   C21  C22  120.33  3.000
 JDP  C20  C21  C22  119.40  3.000
 JDP  C08  C03  C04  118.31  3.000
 JDP  C04  C03  C02  121.70  3.000
 JDP  C08  C03  C02  119.95  3.000
 JDP  H3   C04  C05  118.40  3.000
 JDP  H3   C04  C03  120.30  3.000
 JDP  C05  C04  C03  121.27  3.000
 JDP  H4   C05  C06  119.01  3.000
 JDP  H4   C05  C04  119.53  3.000
 JDP  C06  C05  C04  121.45  3.000
 JDP  H5   C06  C07  122.14  3.000
 JDP  H5   C06  C05  120.30  3.000
 JDP  C07  C06  C05  117.55  3.000
 JDP  N12  C07  C08  107.48  3.000
 JDP  N12  C07  C06  130.45  3.000
 JDP  C08  C07  C06  122.02  3.000
 JDP  C09  C08  C07  106.64  3.000
 JDP  C07  C08  C03  119.35  3.000
 JDP  C09  C08  C03  134.00  3.000
 JDP  H6   C09  C10  124.53  3.000
 JDP  H6   C09  C08  127.35  3.000
 JDP  C10  C09  C08  108.12  3.000
 JDP  N12  C10  C11  124.18  3.000
 JDP  N12  C10  C09  108.93  3.000
 JDP  C11  C10  C09  126.82  3.000
 JDP  H9   C11  H8   108.01  3.000
 JDP  H9   C11  H7   108.59  3.000
 JDP  H8   C11  H7   107.19  3.000
 JDP  H9   C11  C10  108.63  3.000
 JDP  H8   C11  C10  112.03  3.000
 JDP  H7   C11  C10  112.26  3.000
 JDP  C13  N12  C10  125.68  3.000
 JDP  C13  N12  C07  125.48  3.000
 JDP  C10  N12  C07  108.83  3.000
 JDP  N30  C13  N14  127.38  3.000
 JDP  N14  C13  N12  116.03  3.000
 JDP  N30  C13  N12  116.58  3.000
 JDP  C15  N14  C13  116.91  3.000
 JDP  C24  C15  N16  121.39  3.000
 JDP  N16  C15  N14  117.66  3.000
 JDP  C24  C15  N14  120.95  3.000
 JDP  H10  N16  C17  117.28  3.000
 JDP  H10  N16  C15  119.06  3.000
 JDP  C17  N16  C15  123.42  3.000
 JDP  H12  C17  H11  106.58  3.000
 JDP  H12  C17  C18  109.66  3.000
 JDP  H11  C17  C18  109.16  3.000
 JDP  H12  C17  N16  106.76  3.000
 JDP  H11  C17  N16  109.71  3.000
 JDP  C18  C17  N16  114.66  3.000
 JDP  C23  C18  C19  118.75  3.000
 JDP  C19  C18  C17  122.25  3.000
 JDP  C23  C18  C17  119.00  3.000
 JDP  H13  C19  C20  119.26  3.000
 JDP  H13  C19  C18  120.18  3.000
 JDP  C20  C19  C18  120.56  3.000
 JDP  H14  C20  C19  119.56  3.000
 JDP  H14  C20  C21  120.08  3.000
 JDP  C19  C20  C21  120.36  3.000
 JDP  H15  C23  C18  119.68  3.000
 JDP  H15  C23  C22  119.49  3.000
 JDP  C18  C23  C22  120.83  3.000
 JDP  C29  C24  C25  121.53  3.000
 JDP  C25  C24  C15  122.38  3.000
 JDP  C29  C24  C15  116.08  3.000
 JDP  H17  C25  H16  106.87  3.000
 JDP  H17  C25  O26  106.52  3.000
 JDP  H16  C25  O26  110.81  3.000
 JDP  H17  C25  C24  110.41  3.000
 JDP  H16  C25  C24  109.53  3.000
 JDP  O26  C25  C24  112.51  3.000
 JDP  C27  O26  C25  112.39  3.000
 JDP  H19  C27  H18  107.65  3.000
 JDP  H19  C27  C28  111.00  3.000
 JDP  H18  C27  C28  110.01  3.000
 JDP  H19  C27  O26  107.19  3.000
 JDP  H18  C27  O26  110.67  3.000
 JDP  C28  C27  O26  110.26  3.000
 JDP  H21  C28  H20  106.60  3.000
 JDP  H21  C28  C29  109.15  3.000
 JDP  H20  C28  C29  109.42  3.000
 JDP  H21  C28  C27  110.59  3.000
 JDP  H20  C28  C27  110.57  3.000
 JDP  C29  C28  C27  110.43  3.000
 JDP  N30  C29  C28  117.47  3.000
 JDP  C28  C29  C24  119.87  3.000
 JDP  N30  C29  C24  122.64  3.000
 JDP  C29  N30  C13  115.92  3.000
 JDP  H23  N31  H22  117.14  3.000
 JDP  H23  N31  C02  122.48  3.000
 JDP  H22  N31  C02  119.74  3.000
 JDP  N31  C02  C03  115.96  3.000
 JDP  C03  C02  O01  121.62  3.000
 JDP  N31  C02  O01  122.43  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
 JDP  CONST_01  C19  C20  C21  C22    0.00   0.0  0
 JDP  CONST_02  C19  C18  C23  C22    0.00   0.0  0
 JDP  CONST_03  C18  C23  C22  C21    0.00   0.0  0
 JDP  CONST_04  C18  C19  C20  C21    0.00   0.0  0
 JDP  CONST_05  C10  C09  C08  C03  180.00   0.0  0
 JDP  CONST_06  N12  C07  C08  C03  180.00   0.0  0
 JDP  CONST_07  C06  C07  C08  C03    0.00   0.0  0
 JDP  CONST_08  C06  C05  C04  C03    0.00   0.0  0
 JDP  CONST_09  C09  C08  C03  C04  180.00   0.0  0
 JDP  CONST_10  C07  C08  C03  C04    0.00   0.0  0
 JDP  CONST_11  C07  C06  C05  C04    0.00   0.0  0
 JDP  CONST_12  C08  C03  C04  C05    0.00   0.0  0
 JDP  CONST_13  C08  C07  C06  C05    0.00   0.0  0
 JDP  CONST_14  N12  C07  C06  C05  180.00   0.0  0
 JDP  CONST_15  C09  C08  C07  C06  180.00   0.0  0
 JDP  CONST_16  C10  N12  C07  C06  180.00   0.0  0
 JDP  CONST_17  C13  N12  C07  C06    0.00   0.0  0
 JDP  CONST_18  C10  C09  C08  C07    0.00   0.0  0
 JDP  CONST_19  C09  C10  N12  C07    0.00   0.0  0
 JDP  CONST_22  N12  C10  C09  C08    0.00   0.0  0
 JDP  CONST_23  C10  N12  C07  C08    0.00   0.0  0
 JDP  CONST_24  C13  N12  C07  C08  180.00   0.0  0
 JDP  CONST_25  N12  C07  C08  C09    0.00   0.0  0
 JDP  CONST_26  C13  N12  C10  C09  180.00   0.0  0
 JDP  CONST_29  C29  N30  C13  N12  180.00   0.0  0
 JDP  CONST_30  C15  N14  C13  N12  180.00   0.0  0
 JDP  CONST_31  C24  C29  N30  C13    0.00   0.0  0
 JDP  CONST_32  C24  C15  N14  C13    0.00   0.0  0
 JDP  CONST_33  C29  N30  C13  N14    0.00   0.0  0
 JDP  CONST_34  C29  C24  C15  N14    0.00   0.0  0
 JDP  CONST_35  N30  C13  N14  C15    0.00   0.0  0
 JDP  CONST_36  N30  C29  C24  C15    0.00   0.0  0
 JDP  CONST_37  C23  C22  C21  C20    0.00   0.0  0
 JDP  CONST_38  C23  C18  C19  C20    0.00   0.0  0
 JDP  CONST_39  C17  C18  C23  C22  180.00   0.0  0
 JDP  CONST_40  C09  C08  C03  C02    0.00   0.0  0
 JDP  CONST_41  C07  C08  C03  C02  180.00   0.0  0
 JDP  CONST_42  C05  C04  C03  C02  180.00   0.0  0
 JDP  CONST_43  C11  C10  N12  C07  180.00   0.0  0
 JDP  CONST_44  C11  C10  C09  C08  180.00   0.0  0
 JDP  CONST_45  C13  N12  C10  C11    0.00   0.0  0
 JDP  CONST_46  N16  C15  N14  C13  180.00   0.0  0
 JDP  CONST_47  C29  C24  C15  N16  180.00   0.0  0
 JDP  CONST_48  C25  C24  C15  N16    0.00   0.0  0
 JDP  CONST_49  C20  C19  C18  C17  180.00   0.0  0
 JDP  CONST_50  H14  C20  C21  C22  180.00   0.0  0
 JDP  CONST_51  H15  C23  C22  C21  180.00   0.0  0
 JDP  CONST_52  H13  C19  C20  C21  180.00   0.0  0
 JDP  CONST_53  H6   C09  C08  C03    0.00   0.0  0
 JDP  CONST_54  H4   C05  C04  C03  180.00   0.0  0
 JDP  CONST_55  H5   C06  C05  C04  180.00   0.0  0
 JDP  CONST_56  H3   C04  C05  C06  180.00   0.0  0
 JDP  CONST_57  H1   C22  C23  C18  180.00   0.0  0
 JDP  CONST_58  H2   C21  C20  C19  180.00   0.0  0
 JDP  CONST_59  C17  N16  C15  N14    0.00   0.0  0
 JDP  CONST_60  C24  C15  N16  C17  180.00   0.0  0
 JDP  CONST_61  H10  N16  C15  N14  180.00   0.0  0
 JDP  CONST_62  H22  N31  C02  C03  180.00   0.0  0
 JDP  CONST_63  H23  N31  C02  C03    0.00   0.0  0
 JDP  Var_01    O26  C25  C24  C15  167.86  30.0  1
 JDP  Var_02    C27  C28  C29  C24  -16.33  30.0  1
 JDP  Var_03    C28  C27  O26  C25  -68.22  30.0  1
 JDP  Var_04    C29  C28  C27  O26   49.51  30.0  1
 JDP  Var_05    C08  C03  C02  O01  -28.14  30.0  2
 JDP  Var_06    C18  C17  N16  C15  -74.42  30.0  3
 JDP  Var_07    C23  C18  C17  N16  163.19  30.0  2
 JDP  Var_08    H7   C11  C10  C09  112.81  30.0  2

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
 JDP  plan-1  C22  0.020
 JDP  plan-1  C21  0.020
 JDP  plan-1  C17  0.020
 JDP  plan-1  C18  0.020
 JDP  plan-1  C19  0.020
 JDP  plan-1  C20  0.020
 JDP  plan-1  C23  0.020
 JDP  plan-1  H1   0.020
 JDP  plan-1  H2   0.020
 JDP  plan-1  H13  0.020
 JDP  plan-1  H14  0.020
 JDP  plan-1  H15  0.020
 JDP  plan-2  C03  0.020
 JDP  plan-2  C04  0.020
 JDP  plan-2  C05  0.020
 JDP  plan-2  C06  0.020
 JDP  plan-2  C07  0.020
 JDP  plan-2  C08  0.020
 JDP  plan-2  C09  0.020
 JDP  plan-2  C10  0.020
 JDP  plan-2  C11  0.020
 JDP  plan-2  N12  0.020
 JDP  plan-2  C13  0.020
 JDP  plan-2  H3   0.020
 JDP  plan-2  H4   0.020
 JDP  plan-2  H5   0.020
 JDP  plan-2  H6   0.020
 JDP  plan-2  C02  0.020
 JDP  plan-3  O01  0.020
 JDP  plan-3  C03  0.020
 JDP  plan-3  N31  0.020
 JDP  plan-3  H22  0.020
 JDP  plan-3  H23  0.020
 JDP  plan-3  C02  0.020
 JDP  plan-4  C15  0.020
 JDP  plan-4  N16  0.020
 JDP  plan-4  C17  0.020
 JDP  plan-4  H10  0.020
 JDP  plan-5  N12  0.020
 JDP  plan-5  C13  0.020
 JDP  plan-5  N14  0.020
 JDP  plan-5  C15  0.020
 JDP  plan-5  N16  0.020
 JDP  plan-5  C24  0.020
 JDP  plan-5  C25  0.020
 JDP  plan-5  C28  0.020
 JDP  plan-5  C29  0.020
 JDP  plan-5  N30  0.020

