# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 10:52:34 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (6R)-6-(pyridin-2-yl)-5,6-dihydrobenzimidazo[1,2-c]quinazoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N1[C@H](n2c3ccccc3nc2c4ccccc14)c5ccccn5
#
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
 1M1  1M1  (6R)-6-(pyridin-2-yl)-5,6-dihydrobenzimidazo[1,2-c]quinazoline  ligand  37  23  .  2021-08-03  2022-07-21
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1M1
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
 1M1  CAS  C  CR16  0  -0.340  -0.1503   3.1393  -0.8109
 1M1  CAT  C  CR16  0  -0.146  -0.3737   4.1894   0.0688
 1M1  CAU  C  CR16  0  -0.324  -0.7170   3.8980   1.3787
 1M1  CAV  C  CR16  0  -0.072  -0.8165   2.5638   1.7522
 1M1  NAW  N  N     0  -0.402  -0.6012   1.5573   0.9177
 1M1  CAR  C  CR6   0   0.274  -0.2798   1.8422  -0.3378
 1M1  CAQ  C  CR16  0  -0.033  -0.0989   0.6598  -1.2753
 1M1  NAE  N  N     0  -0.580   0.6658  -0.3814  -0.6387
 1M1  CAD  C  CR56  0   0.354   2.0129  -0.3927  -0.3865
 1M1  CAI  C  CR16  0  -0.316   3.0562   0.4152  -0.8171
 1M1  CAH  C  CR16  0  -0.277   4.3227   0.0885  -0.3590
 1M1  CAG  C  CR16  0  -0.270   4.5337  -1.0049   0.4930
 1M1  CAF  C  CR16  0  -0.344   3.4856  -1.8029   0.9189
 1M1  CAC  C  CR56  0   0.139   2.2017  -1.4865   0.4776
 1M1  NAB  N  N     0  -0.486   0.9985  -2.0895   0.7513
 1M1  CAA  C  CR56  0   0.525   0.1126  -1.3936   0.0903
 1M1  CAJ  C  CR66  0  -0.030  -1.3175  -1.5892   0.0302
 1M1  CAK  C  CR16  0  -0.320  -1.9802  -2.5287   0.8140
 1M1  CAL  C  CR16  0  -0.275  -3.3486  -2.6980   0.7009
 1M1  CAM  C  CR16  0  -0.249  -4.0562  -1.9160  -0.2095
 1M1  CAN  C  CR16  0  -0.340  -3.4126  -0.9731  -0.9923
 1M1  CAO  C  CR66  0   0.347  -2.0320  -0.7958  -0.8819
 1M1  NAP  N  NR16  0  -0.696  -1.3511   0.0790  -1.6980
 1M1  H1   H  HCR6  0   0.275   0.1230   3.3246  -1.8417
 1M1  H2   H  HCR6  0   0.279  -0.2754   5.2145  -0.2627
 1M1  H3   H  HCR6  0   0.275  -0.8976   4.6819   2.1011
 1M1  H4   H  HCR6  0   0.268  -1.0763   2.2999   2.7712
 1M1  H5   H  HCR6  0   0.298   0.4320   0.9910  -2.1715
 1M1  H6   H  HCR6  0   0.266   2.9004   1.2587  -1.4770
 1M1  H7   H  HCR6  0   0.257   5.1673   0.6915  -0.6655
 1M1  H8   H  HCR6  0   0.254   5.5399  -1.2259   0.8242
 1M1  H9   H  HCR6  0   0.255   3.6530  -2.6465   1.5763
 1M1  H10  H  HCR6  0   0.254  -1.4071  -3.1252   1.5125
 1M1  H11  H  HCR6  0   0.255  -3.8626  -3.4287   1.3101
 1M1  H12  H  HCR6  0   0.261  -5.1272  -2.0386  -0.3078
 1M1  H13  H  HCR6  0   0.266  -3.9771  -0.3709  -1.6934
 1M1  H14  H  HNR6  0   0.399  -1.9197   0.6937  -2.2604

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
 1M1  CAU  CAT  aromatic  1.385  0.020  1.385
 1M1  CAU  CAV  aromatic  1.389  0.020  1.389
 1M1  CAT  CAS  aromatic  1.388  0.020  1.388
 1M1  CAS  CAR  aromatic  1.387  0.020  1.387
 1M1  CAV  NAW  aromatic  1.325  0.020  1.325
 1M1  CAR  NAW  aromatic  1.327  0.020  1.327
 1M1  CAR  CAQ  single    1.520  0.020  1.520
 1M1  CAQ  NAP  single    1.444  0.020  1.444
 1M1  CAQ  NAE  single    1.440  0.020  1.440
 1M1  NAP  CAO  single    1.377  0.020  1.377
 1M1  CAI  CAH  aromatic  1.386  0.020  1.386
 1M1  CAI  CAD  aromatic  1.388  0.020  1.388
 1M1  CAH  CAG  aromatic  1.402  0.020  1.402
 1M1  NAE  CAD  aromatic  1.371  0.020  1.371
 1M1  NAE  CAA  aromatic  1.365  0.020  1.365
 1M1  CAD  CAC  aromatic  1.407  0.020  1.407
 1M1  CAO  CAN  aromatic  1.396  0.020  1.396
 1M1  CAO  CAJ  aromatic  1.404  0.020  1.404
 1M1  CAN  CAM  aromatic  1.384  0.020  1.384
 1M1  CAG  CAF  aromatic  1.384  0.020  1.384
 1M1  CAA  CAJ  aromatic  1.445  0.020  1.445
 1M1  CAA  NAB  aromatic  1.306  0.020  1.306
 1M1  CAJ  CAK  aromatic  1.391  0.020  1.391
 1M1  CAC  CAF  aromatic  1.394  0.020  1.394
 1M1  CAC  NAB  aromatic  1.373  0.020  1.373
 1M1  CAM  CAL  aromatic  1.393  0.020  1.393
 1M1  CAK  CAL  aromatic  1.383  0.020  1.383
 1M1  CAS  H1   single    0.930  0.020  1.080
 1M1  CAT  H2   single    0.930  0.020  1.080
 1M1  CAU  H3   single    0.930  0.020  1.080
 1M1  CAV  H4   single    0.930  0.020  1.080
 1M1  CAQ  H5   single    0.970  0.020  1.090
 1M1  CAI  H6   single    0.930  0.020  1.080
 1M1  CAH  H7   single    0.930  0.020  1.080
 1M1  CAG  H8   single    0.930  0.020  1.080
 1M1  CAF  H9   single    0.930  0.020  1.080
 1M1  CAK  H10  single    0.930  0.020  1.080
 1M1  CAL  H11  single    0.930  0.020  1.080
 1M1  CAM  H12  single    0.930  0.020  1.080
 1M1  CAN  H13  single    0.930  0.020  1.080
 1M1  NAP  H14  single    0.890  0.020  1.040

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
 1M1  H1   CAS  CAR  120.57  3.000
 1M1  H1   CAS  CAT  120.98  3.000
 1M1  CAR  CAS  CAT  118.45  3.000
 1M1  H2   CAT  CAU  120.77  3.000
 1M1  H2   CAT  CAS  120.54  3.000
 1M1  CAU  CAT  CAS  118.69  3.000
 1M1  H3   CAU  CAV  120.31  3.000
 1M1  H3   CAU  CAT  121.38  3.000
 1M1  CAV  CAU  CAT  118.30  3.000
 1M1  H4   CAV  NAW  116.49  3.000
 1M1  H4   CAV  CAU  120.24  3.000
 1M1  NAW  CAV  CAU  123.27  3.000
 1M1  CAR  NAW  CAV  118.18  3.000
 1M1  CAQ  CAR  NAW  116.46  3.000
 1M1  CAQ  CAR  CAS  120.41  3.000
 1M1  NAW  CAR  CAS  123.11  3.000
 1M1  H5   CAQ  NAP  107.65  3.000
 1M1  H5   CAQ  NAE  108.89  3.000
 1M1  NAP  CAQ  NAE  107.40  3.000
 1M1  H5   CAQ  CAR  109.14  3.000
 1M1  NAE  CAQ  CAR  110.67  3.000
 1M1  NAP  CAQ  CAR  112.98  3.000
 1M1  CAA  NAE  CAD  107.10  3.000
 1M1  CAA  NAE  CAQ  123.87  3.000
 1M1  CAD  NAE  CAQ  127.53  3.000
 1M1  CAC  CAD  CAI  122.83  3.000
 1M1  CAC  CAD  NAE  104.56  3.000
 1M1  CAI  CAD  NAE  132.61  3.000
 1M1  H6   CAI  CAH  121.12  3.000
 1M1  H6   CAI  CAD  122.31  3.000
 1M1  CAH  CAI  CAD  116.56  3.000
 1M1  H7   CAH  CAG  119.29  3.000
 1M1  H7   CAH  CAI  119.23  3.000
 1M1  CAG  CAH  CAI  121.48  3.000
 1M1  H8   CAG  CAF  119.48  3.000
 1M1  H8   CAG  CAH  119.02  3.000
 1M1  CAF  CAG  CAH  121.50  3.000
 1M1  H9   CAF  CAC  120.77  3.000
 1M1  H9   CAF  CAG  121.26  3.000
 1M1  CAC  CAF  CAG  117.97  3.000
 1M1  NAB  CAC  CAF  130.10  3.000
 1M1  NAB  CAC  CAD  110.25  3.000
 1M1  CAF  CAC  CAD  119.65  3.000
 1M1  CAA  NAB  CAC  105.03  3.000
 1M1  CAJ  CAA  NAB  128.34  3.000
 1M1  NAB  CAA  NAE  113.00  3.000
 1M1  CAJ  CAA  NAE  118.65  3.000
 1M1  CAO  CAJ  CAK  120.33  3.000
 1M1  CAK  CAJ  CAA  122.65  3.000
 1M1  CAO  CAJ  CAA  117.01  3.000
 1M1  H10  CAK  CAL  120.59  3.000
 1M1  H10  CAK  CAJ  118.90  3.000
 1M1  CAL  CAK  CAJ  120.51  3.000
 1M1  H11  CAL  CAM  120.40  3.000
 1M1  H11  CAL  CAK  120.45  3.000
 1M1  CAM  CAL  CAK  119.15  3.000
 1M1  H12  CAM  CAN  119.06  3.000
 1M1  H12  CAM  CAL  119.89  3.000
 1M1  CAN  CAM  CAL  121.05  3.000
 1M1  H13  CAN  CAO  119.73  3.000
 1M1  H13  CAN  CAM  120.17  3.000
 1M1  CAO  CAN  CAM  120.10  3.000
 1M1  NAP  CAO  CAN  121.53  3.000
 1M1  CAN  CAO  CAJ  118.86  3.000
 1M1  NAP  CAO  CAJ  119.50  3.000
 1M1  H14  NAP  CAO  116.04  3.000
 1M1  H14  NAP  CAQ  114.02  3.000
 1M1  CAO  NAP  CAQ  120.74  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
 1M1  CONST_01  CAV  CAU  CAT  CAS    0.00   0.0  0
 1M1  CONST_02  CAV  NAW  CAR  CAS    0.00   0.0  0
 1M1  CONST_03  NAW  CAV  CAU  CAT    0.00   0.0  0
 1M1  CONST_04  NAW  CAR  CAS  CAT    0.00   0.0  0
 1M1  CONST_05  CAR  CAS  CAT  CAU    0.00   0.0  0
 1M1  CONST_06  CAR  NAW  CAV  CAU    0.00   0.0  0
 1M1  CONST_07  CAH  CAI  CAD  NAE  180.00   0.0  0
 1M1  CONST_08  CAF  CAC  CAD  NAE  180.00   0.0  0
 1M1  CONST_09  NAB  CAC  CAD  NAE    0.00   0.0  0
 1M1  CONST_10  CAO  CAJ  CAA  NAE    0.00   0.0  0
 1M1  CONST_11  CAK  CAJ  CAA  NAE  180.00   0.0  0
 1M1  CONST_12  CAC  NAB  CAA  NAE    0.00   0.0  0
 1M1  CONST_13  CAG  CAH  CAI  CAD    0.00   0.0  0
 1M1  CONST_14  CAJ  CAA  NAE  CAD  180.00   0.0  0
 1M1  CONST_15  NAB  CAA  NAE  CAD    0.00   0.0  0
 1M1  CONST_16  CAG  CAF  CAC  CAD    0.00   0.0  0
 1M1  CONST_17  CAA  NAB  CAC  CAD    0.00   0.0  0
 1M1  CONST_18  CAF  CAG  CAH  CAI    0.00   0.0  0
 1M1  CONST_19  CAA  NAE  CAD  CAI  180.00   0.0  0
 1M1  CONST_20  CAF  CAC  CAD  CAI    0.00   0.0  0
 1M1  CONST_21  NAB  CAC  CAD  CAI  180.00   0.0  0
 1M1  CONST_22  CAC  CAD  CAI  CAH    0.00   0.0  0
 1M1  CONST_23  CAC  CAF  CAG  CAH    0.00   0.0  0
 1M1  CONST_24  NAB  CAC  CAF  CAG  180.00   0.0  0
 1M1  CONST_25  CAA  NAB  CAC  CAF  180.00   0.0  0
 1M1  CONST_26  CAA  NAE  CAD  CAC    0.00   0.0  0
 1M1  CONST_27  CAJ  CAA  NAB  CAC  180.00   0.0  0
 1M1  CONST_28  CAO  CAJ  CAA  NAB  180.00   0.0  0
 1M1  CONST_29  CAK  CAJ  CAA  NAB    0.00   0.0  0
 1M1  CONST_30  CAN  CAO  CAJ  CAA  180.00   0.0  0
 1M1  CONST_31  CAL  CAK  CAJ  CAA  180.00   0.0  0
 1M1  CONST_32  CAM  CAN  CAO  CAJ    0.00   0.0  0
 1M1  CONST_33  CAM  CAL  CAK  CAJ    0.00   0.0  0
 1M1  CONST_34  CAN  CAO  CAJ  CAK    0.00   0.0  0
 1M1  CONST_35  CAN  CAM  CAL  CAK    0.00   0.0  0
 1M1  CONST_36  CAO  CAN  CAM  CAL    0.00   0.0  0
 1M1  CONST_37  CAO  CAJ  CAK  CAL    0.00   0.0  0
 1M1  CONST_38  CAQ  CAR  CAS  CAT  180.00   0.0  0
 1M1  CONST_39  CAQ  CAR  NAW  CAV  180.00   0.0  0
 1M1  CONST_40  H3   CAU  CAT  CAS  180.00   0.0  0
 1M1  CONST_41  H4   CAV  CAU  CAT  180.00   0.0  0
 1M1  CONST_42  H1   CAS  CAT  CAU  180.00   0.0  0
 1M1  CONST_43  H2   CAT  CAU  CAV  180.00   0.0  0
 1M1  CONST_44  H6   CAI  CAD  NAE    0.00   0.0  0
 1M1  CONST_45  H7   CAH  CAI  CAD  180.00   0.0  0
 1M1  CONST_46  H9   CAF  CAC  CAD  180.00   0.0  0
 1M1  CONST_47  H8   CAG  CAH  CAI  180.00   0.0  0
 1M1  CONST_48  H10  CAK  CAJ  CAA    0.00   0.0  0
 1M1  CONST_49  H13  CAN  CAO  CAJ  180.00   0.0  0
 1M1  CONST_50  H11  CAL  CAK  CAJ  180.00   0.0  0
 1M1  CONST_51  H12  CAM  CAL  CAK  180.00   0.0  0
 1M1  Var_01    CAN  CAO  NAP  CAQ  155.12  30.0  1

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
 1M1  chir_01  CAQ  CAR  NAP  NAE  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
 1M1  plan-1  CAS  0.020
 1M1  plan-1  CAT  0.020
 1M1  plan-1  CAU  0.020
 1M1  plan-1  CAV  0.020
 1M1  plan-1  NAW  0.020
 1M1  plan-1  CAR  0.020
 1M1  plan-1  CAQ  0.020
 1M1  plan-1  H1   0.020
 1M1  plan-1  H2   0.020
 1M1  plan-1  H3   0.020
 1M1  plan-1  H4   0.020
 1M1  plan-2  CAQ  0.020
 1M1  plan-2  NAE  0.020
 1M1  plan-2  CAD  0.020
 1M1  plan-2  CAI  0.020
 1M1  plan-2  CAH  0.020
 1M1  plan-2  CAG  0.020
 1M1  plan-2  CAF  0.020
 1M1  plan-2  CAC  0.020
 1M1  plan-2  NAB  0.020
 1M1  plan-2  CAA  0.020
 1M1  plan-2  CAJ  0.020
 1M1  plan-2  H6   0.020
 1M1  plan-2  H7   0.020
 1M1  plan-2  H8   0.020
 1M1  plan-2  H9   0.020
 1M1  plan-3  CAA  0.020
 1M1  plan-3  CAJ  0.020
 1M1  plan-3  CAK  0.020
 1M1  plan-3  CAL  0.020
 1M1  plan-3  CAM  0.020
 1M1  plan-3  CAN  0.020
 1M1  plan-3  CAO  0.020
 1M1  plan-3  NAP  0.020
 1M1  plan-3  H10  0.020
 1M1  plan-3  H11  0.020
 1M1  plan-3  H12  0.020
 1M1  plan-3  H13  0.020

