# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:15:10 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: 3,4-dichloro-2-cyclopropyl-1-[(piperidin-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(Cl)c2c(Cl)c(C3CC3)n(CC4CCNCC4)c2n1
#
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
 ROY  ROY  3,4-dichloro-2-cyclopropyl-1-[(piperidin-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide  ligand  44  24  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ROY
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
 ROY  CAV   C   CH2   0  -0.479  74.5117  39.5593   2.9242
 ROY  CAW   C   CH2   0  -0.475  74.5412  38.4712   3.9427
 ROY  CAU   C   CH1   0  -0.351  75.5529  38.4866   2.8254
 ROY  CAH   C   CR5   0   0.500  75.5184  37.4754   1.7572
 ROY  CAI   C   CR5   0  -0.363  75.2098  37.6168   0.4264
 ROY  CLAX  CL  CL    0  -0.144  74.7621  39.0767  -0.3512
 ROY  CAE   C   CR56  0   0.316  75.3861  36.3605  -0.2036
 ROY  CAD   C   CR6   0  -0.057  75.2596  35.8030  -1.4692
 ROY  CLAJ  CL  CL    0  -0.101  74.7057  36.7373  -2.8039
 ROY  CAA   C   CR16  0  -0.309  75.5788  34.4704  -1.6494
 ROY  CAB   C   CR6   0   0.099  76.0221  33.7177  -0.5543
 ROY  CAK   C   C     0   0.472  76.3534  32.2553  -0.6817
 ROY  OAS   O   O     0  -0.467  76.2316  31.5063   0.2725
 ROY  NAT   N   NH2   0  -0.809  76.7673  31.8564  -1.8930
 ROY  NAC   N   N     0  -0.431  76.1411  34.2098   0.6674
 ROY  CAF   C   CR56  0   0.448  75.8271  35.4789   0.8151
 ROY  NAG   N   NR5   0  -0.590  75.8896  36.1687   1.9862
 ROY  CAL   C   CH2   0  -0.302  76.3256  35.6025   3.2530
 ROY  CAM   C   CH1   0  -0.254  75.4601  34.4533   3.7630
 ROY  CAR   C   CH2   0  -0.482  73.9926  34.8212   3.9403
 ROY  CAQ   C   CH2   0  -0.261  73.1736  33.5849   4.3303
 ROY  NAP   N   NH1   0  -0.609  73.9956  32.6288   5.0647
 ROY  CAO   C   CH2   0  -0.302  74.9372  33.2905   5.9486
 ROY  CAN   C   CH2   0  -0.420  76.0264  33.9620   5.1058
 ROY  H1    H   HCH2  0   0.263  74.8499  40.5465   3.2088
 ROY  H2    H   HCH2  0   0.256  73.6958  39.5551   2.2153
 ROY  H3    H   HCH2  0   0.263  74.9010  38.6910   4.9392
 ROY  H4    H   HCH2  0   0.262  73.7564  37.7281   3.9004
 ROY  H5    H   HCH1  0   0.301  76.5576  38.7756   3.1212
 ROY  H6    H   HCR6  0   0.292  75.4591  34.0217  -2.6254
 ROY  H7    H   HNH2  0   0.409  77.0040  30.8897  -2.0469
 ROY  H8    H   HNH2  0   0.415  77.0012  32.5041  -2.6251
 ROY  H9    H   HCH2  0   0.269  77.3584  35.2627   3.1433
 ROY  H10   H   HCH2  0   0.273  76.3316  36.4120   3.9812
 ROY  H11   H   HCH1  0   0.254  75.5223  33.6362   3.0403
 ROY  H12   H   HCH2  0   0.226  73.9046  35.5922   4.7124
 ROY  H13   H   HCH2  0   0.242  73.5730  35.2538   3.0294
 ROY  H14   H   HCH2  0   0.203  72.2935  33.9109   4.9021
 ROY  H15   H   HCH2  0   0.216  72.7957  33.0964   3.4275
 ROY  H16   H   HNH1  0   0.350  73.3996  32.0073   5.5937
 ROY  H18   H   HCH2  0   0.235  75.3829  32.5470   6.6114
 ROY  H19   H   HCH2  0   0.193  74.4563  34.0343   6.6032
 ROY  H20   H   HCH2  0   0.231  76.8461  33.2642   4.9214
 ROY  H21   H   HCH2  0   0.217  76.4477  34.7990   5.6713

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
 ROY  CLAJ  CAD  single    1.721  0.020  1.721
 ROY  NAT   CAK  single    1.341  0.020  1.341
 ROY  CAA   CAD  aromatic  1.382  0.020  1.382
 ROY  CAA   CAB  aromatic  1.401  0.020  1.401
 ROY  CAD   CAE  aromatic  1.389  0.020  1.389
 ROY  CAK   CAB  single    1.505  0.020  1.505
 ROY  CAK   OAS  double    1.219  0.020  1.219
 ROY  CAB   NAC  aromatic  1.322  0.020  1.322
 ROY  CLAX  CAI  single    1.714  0.020  1.714
 ROY  CAE   CAI  aromatic  1.416  0.020  1.416
 ROY  CAE   CAF  aromatic  1.418  0.020  1.418
 ROY  CAI   CAH  aromatic  1.373  0.020  1.373
 ROY  NAC   CAF  aromatic  1.316  0.020  1.316
 ROY  CAF   NAG  aromatic  1.361  0.020  1.361
 ROY  CAH   NAG  aromatic  1.377  0.020  1.377
 ROY  CAH   CAU  single    1.471  0.020  1.471
 ROY  NAG   CAL  single    1.454  0.020  1.454
 ROY  CAV   CAU  single    1.498  0.020  1.498
 ROY  CAV   CAW  single    1.491  0.020  1.491
 ROY  CAU   CAW  single    1.507  0.020  1.507
 ROY  CAL   CAM  single    1.526  0.020  1.526
 ROY  CAM   CAR  single    1.523  0.020  1.523
 ROY  CAM   CAN  single    1.538  0.020  1.538
 ROY  CAR   CAQ  single    1.533  0.020  1.533
 ROY  CAQ   NAP  single    1.459  0.020  1.459
 ROY  CAN   CAO  single    1.532  0.020  1.532
 ROY  NAP   CAO  single    1.451  0.020  1.451
 ROY  CAV   H1   single    0.970  0.020  1.090
 ROY  CAV   H2   single    0.970  0.020  1.090
 ROY  CAW   H3   single    0.970  0.020  1.090
 ROY  CAW   H4   single    0.970  0.020  1.090
 ROY  CAU   H5   single    0.970  0.020  1.090
 ROY  CAA   H6   single    0.930  0.020  1.080
 ROY  NAT   H7   single    0.860  0.020  1.020
 ROY  NAT   H8   single    0.860  0.020  1.020
 ROY  CAL   H9   single    0.970  0.020  1.090
 ROY  CAL   H10  single    0.970  0.020  1.090
 ROY  CAM   H11  single    0.970  0.020  1.090
 ROY  CAR   H12  single    0.970  0.020  1.090
 ROY  CAR   H13  single    0.970  0.020  1.090
 ROY  CAQ   H14  single    0.970  0.020  1.090
 ROY  CAQ   H15  single    0.970  0.020  1.090
 ROY  NAP   H16  single    0.890  0.020  1.040
 ROY  CAO   H18  single    0.970  0.020  1.090
 ROY  CAO   H19  single    0.970  0.020  1.090
 ROY  CAN   H20  single    0.970  0.020  1.090
 ROY  CAN   H21  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
 ROY  H2    CAV  H1    114.33  3.000
 ROY  H2    CAV  CAU   118.60  3.000
 ROY  H1    CAV  CAU   116.97  3.000
 ROY  H2    CAV  CAW   117.40  3.000
 ROY  H1    CAV  CAW   118.70  3.000
 ROY  CAU   CAV  CAW    60.57  3.000
 ROY  H4    CAW  H3    114.64  3.000
 ROY  H4    CAW  CAU   117.71  3.000
 ROY  H3    CAW  CAU   117.22  3.000
 ROY  H4    CAW  CAV   117.41  3.000
 ROY  H3    CAW  CAV   119.18  3.000
 ROY  CAU   CAW  CAV    59.96  3.000
 ROY  H5    CAU  CAH   113.71  3.000
 ROY  H5    CAU  CAW   114.93  3.000
 ROY  CAH   CAU  CAW   121.02  3.000
 ROY  H5    CAU  CAV   115.74  3.000
 ROY  CAW   CAU  CAV    59.47  3.000
 ROY  CAH   CAU  CAV   121.58  3.000
 ROY  NAG   CAH  CAI   108.63  3.000
 ROY  NAG   CAH  CAU   121.66  3.000
 ROY  CAI   CAH  CAU   129.64  3.000
 ROY  CAE   CAI  CLAX  125.90  3.000
 ROY  CAE   CAI  CAH   108.16  3.000
 ROY  CLAX  CAI  CAH   125.89  3.000
 ROY  CAF   CAE  CAD   115.69  3.000
 ROY  CAF   CAE  CAI   105.71  3.000
 ROY  CAD   CAE  CAI   138.60  3.000
 ROY  CAA   CAD  CLAJ  119.78  3.000
 ROY  CAA   CAD  CAE   119.01  3.000
 ROY  CLAJ  CAD  CAE   121.21  3.000
 ROY  H6    CAA  CAB   121.19  3.000
 ROY  H6    CAA  CAD   119.50  3.000
 ROY  CAB   CAA  CAD   119.29  3.000
 ROY  NAC   CAB  CAK   114.83  3.000
 ROY  NAC   CAB  CAA   123.42  3.000
 ROY  CAK   CAB  CAA   121.71  3.000
 ROY  NAT   CAK  OAS   123.71  3.000
 ROY  OAS   CAK  CAB   120.59  3.000
 ROY  NAT   CAK  CAB   115.69  3.000
 ROY  H8    NAT  H7    116.90  3.000
 ROY  H8    NAT  CAK   122.56  3.000
 ROY  H7    NAT  CAK   119.76  3.000
 ROY  CAF   NAC  CAB   116.18  3.000
 ROY  NAG   CAF  NAC   125.08  3.000
 ROY  NAG   CAF  CAE   108.51  3.000
 ROY  NAC   CAF  CAE   126.40  3.000
 ROY  CAL   NAG  CAF   124.47  3.000
 ROY  CAL   NAG  CAH   126.51  3.000
 ROY  CAF   NAG  CAH   108.99  3.000
 ROY  H10   CAL  H9    107.04  3.000
 ROY  H10   CAL  CAM   109.84  3.000
 ROY  H9    CAL  CAM   109.60  3.000
 ROY  H10   CAL  NAG   107.14  3.000
 ROY  H9    CAL  NAG   108.47  3.000
 ROY  CAM   CAL  NAG   114.47  3.000
 ROY  H11   CAM  CAN   108.52  3.000
 ROY  H11   CAM  CAR   108.21  3.000
 ROY  CAN   CAM  CAR   109.29  3.000
 ROY  H11   CAM  CAL   108.04  3.000
 ROY  CAN   CAM  CAL   108.87  3.000
 ROY  CAR   CAM  CAL   113.79  3.000
 ROY  H13   CAR  H12   106.17  3.000
 ROY  H13   CAR  CAQ   109.04  3.000
 ROY  H12   CAR  CAQ   110.21  3.000
 ROY  H13   CAR  CAM   111.64  3.000
 ROY  H12   CAR  CAM   109.24  3.000
 ROY  CAQ   CAR  CAM   110.45  3.000
 ROY  H15   CAQ  H14   106.58  3.000
 ROY  H15   CAQ  NAP   108.51  3.000
 ROY  H14   CAQ  NAP   112.56  3.000
 ROY  H15   CAQ  CAR   109.55  3.000
 ROY  H14   CAQ  CAR   108.72  3.000
 ROY  NAP   CAQ  CAR   110.82  3.000
 ROY  H16   NAP  CAO   110.14  3.000
 ROY  H16   NAP  CAQ   109.53  3.000
 ROY  CAO   NAP  CAQ   111.92  3.000
 ROY  H19   CAO  H18   106.11  3.000
 ROY  H19   CAO  CAN   109.96  3.000
 ROY  H18   CAO  CAN   110.02  3.000
 ROY  H19   CAO  NAP   112.75  3.000
 ROY  H18   CAO  NAP   108.92  3.000
 ROY  CAN   CAO  NAP   109.03  3.000
 ROY  H21   CAN  H20   106.67  3.000
 ROY  H21   CAN  CAO   108.94  3.000
 ROY  H20   CAN  CAO   110.27  3.000
 ROY  H21   CAN  CAM   110.40  3.000
 ROY  H20   CAN  CAM   109.46  3.000
 ROY  CAO   CAN  CAM   111.01  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
 ROY  CONST_01  CAD   CAE  CAI  CAH    180.00   0.0  0
 ROY  CONST_02  CAF   CAE  CAI  CAH      0.00   0.0  0
 ROY  CONST_03  CAE   CAF  NAG  CAH      0.00   0.0  0
 ROY  CONST_04  NAC   CAF  NAG  CAH    180.00   0.0  0
 ROY  CONST_05  CAA   CAD  CAE  CAI    180.00   0.0  0
 ROY  CONST_06  NAC   CAF  CAE  CAI    180.00   0.0  0
 ROY  CONST_07  NAG   CAF  CAE  CAI      0.00   0.0  0
 ROY  CONST_08  CAF   NAG  CAH  CAI      0.00   0.0  0
 ROY  CONST_09  CAB   CAA  CAD  CAE      0.00   0.0  0
 ROY  CONST_10  NAG   CAH  CAI  CAE      0.00   0.0  0
 ROY  CONST_11  CAB   NAC  CAF  CAE      0.00   0.0  0
 ROY  CONST_12  NAC   CAB  CAA  CAD      0.00   0.0  0
 ROY  CONST_13  NAC   CAF  CAE  CAD      0.00   0.0  0
 ROY  CONST_14  NAG   CAF  CAE  CAD    180.00   0.0  0
 ROY  CONST_15  CAF   CAE  CAD  CAA      0.00   0.0  0
 ROY  CONST_16  CAF   NAC  CAB  CAA      0.00   0.0  0
 ROY  CONST_17  NAG   CAF  NAC  CAB    180.00   0.0  0
 ROY  CONST_18  CAE   CAI  CAH  CAU    180.00   0.0  0
 ROY  CONST_19  CAF   NAG  CAH  CAU    180.00   0.0  0
 ROY  CONST_20  CLAX  CAI  CAH  CAU      0.00   0.0  0
 ROY  CONST_21  CAL   NAG  CAH  CAU      0.00   0.0  0
 ROY  CONST_22  CLAJ  CAD  CAE  CAI      0.00   0.0  0
 ROY  CONST_23  CAL   NAG  CAH  CAI    180.00   0.0  0
 ROY  CONST_24  CAD   CAE  CAI  CLAX     0.00   0.0  0
 ROY  CONST_25  CAF   CAE  CAI  CLAX   180.00   0.0  0
 ROY  CONST_26  NAG   CAH  CAI  CLAX   180.00   0.0  0
 ROY  CONST_27  CAL   NAG  CAF  CAE    180.00   0.0  0
 ROY  CONST_28  CAK   CAB  CAA  CAD    180.00   0.0  0
 ROY  CONST_29  CAB   CAA  CAD  CLAJ   180.00   0.0  0
 ROY  CONST_30  CAF   CAE  CAD  CLAJ   180.00   0.0  0
 ROY  CONST_31  CAF   NAC  CAB  CAK    180.00   0.0  0
 ROY  CONST_32  CAL   NAG  CAF  NAC      0.00   0.0  0
 ROY  CONST_33  H6    CAA  CAD  CAE    180.00   0.0  0
 ROY  CONST_34  H7    NAT  CAK  CAB    180.00   0.0  0
 ROY  CONST_35  H8    NAT  CAK  CAB      0.00   0.0  0
 ROY  Var_01    CAI   CAH  CAU  CAV     40.33  30.0  1
 ROY  Var_02    CAH   CAU  CAW  CAV   -110.78  30.0  1
 ROY  Var_03    NAP   CAQ  CAR  CAM     28.92  30.0  1
 ROY  Var_04    NAP   CAO  CAN  CAM     32.78  30.0  1
 ROY  Var_05    CAO   NAP  CAQ  CAR     37.06  30.0  1
 ROY  Var_06    CAN   CAO  NAP  CAQ    -71.02  30.0  1
 ROY  Var_07    CAM   CAL  NAG  CAH    120.42  30.0  2
 ROY  Var_08    NAT   CAK  CAB  CAA     28.04  30.0  2

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
 ROY  chir_02  CAM  CAL  CAR  CAN  positiv
 ROY  chir_03  CAU  CAH  CAV  CAW  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
 ROY  plan-1  CAB   0.020
 ROY  plan-1  CAK   0.020
 ROY  plan-1  OAS   0.020
 ROY  plan-1  NAT   0.020
 ROY  plan-1  H7    0.020
 ROY  plan-1  H8    0.020
 ROY  plan-2  CAU   0.020
 ROY  plan-2  CAH   0.020
 ROY  plan-2  CAI   0.020
 ROY  plan-2  CLAX  0.020
 ROY  plan-2  CAE   0.020
 ROY  plan-2  CAD   0.020
 ROY  plan-2  CLAJ  0.020
 ROY  plan-2  CAA   0.020
 ROY  plan-2  CAB   0.020
 ROY  plan-2  CAK   0.020
 ROY  plan-2  NAC   0.020
 ROY  plan-2  CAF   0.020
 ROY  plan-2  NAG   0.020
 ROY  plan-2  CAL   0.020
 ROY  plan-2  H6    0.020

