# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:37:22 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 5-[(8-chloroisoquinolin-3-yl)amino]-3-{[(2R)-1-(dimethylamino)propan-2-yl]oxy}pyrazine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CN(C)C)Oc1nc(Nc2cc3cccc(Cl)c3cn2)cnc1C#N
#
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
 YM8  YM8  5-[(8-chloroisoquinolin-3-yl)amino]-3-{[(2R)-1-(dimethylamino)propan-2-yl]oxy}pyrazine-2-carbonitrile  ligand  46  27  .  2021-08-25  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_YM8
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
 YM8  CAA   C   CH3   0  -0.675  -1.7940   2.1756   2.9310
 YM8  CAB   C   CH3   0  -0.510  -3.7386   2.8420  -1.4768
 YM8  CAC   C   CH3   0  -0.547  -1.4115   2.2917  -1.5550
 YM8  NAD   N   NS    0  -0.259  -6.0232  -0.3756   0.7002
 YM8  CAG   C   CR16  0  -0.258   5.9950  -1.7202   0.1510
 YM8  CAH   C   CR16  0  -0.221   6.0533  -0.3179   0.2948
 YM8  CAI   C   CR16  0  -0.301   4.8239  -2.3499  -0.1592
 YM8  CAJ   C   CR16  0  -0.196  -2.2743  -2.2941  -1.3090
 YM8  CAK   C   CR16  0  -0.084   2.4739   0.5191  -0.3990
 YM8  CAL   C   CR16  0  -0.466   2.4071  -2.1882  -0.6485
 YM8  CAM   C   CH2   0  -0.259  -2.4636   2.7424   0.5650
 YM8  NAN   N   N     0  -0.342  -3.4825  -1.9981  -0.9149
 YM8  NAO   N   N     0  -0.395   1.3426  -0.0509  -0.7062
 YM8  NAP   N   N     0  -0.434  -1.3037  -0.6709   0.1400
 YM8  OAR   O   O2    0  -0.468  -2.7248   0.5478   1.4538
 YM8  CAS   C   CR6   0  -0.133   4.9209   0.4258   0.1229
 YM8  CAT   C   CR6   0   0.023  -3.6361  -1.0295  -0.0112
 YM8  CAU   C   CR6   0   0.497  -1.1515  -1.6129  -0.7723
 YM8  CAV   C   CR6   0   0.511   1.3036  -1.3900  -0.8187
 YM8  CAW   C   CR6   0   0.575  -2.5251  -0.3546   0.5108
 YM8  CAX   C   CR66  0   0.226   3.6440  -1.5925  -0.3428
 YM8  CAY   C   CR66  0   0.100   3.6842  -0.1830  -0.1994
 YM8  CAZ   C   CH1   0  -0.028  -1.8573   1.7019   1.4971
 YM8  NBA   N   NT    0  -0.404  -2.6293   2.2337  -0.7784
 YM8  HAA   H   HCH3  0   0.240  -1.1459   3.0490   2.9983
 YM8  HAAA  H   HCH3  0   0.233  -2.7792   2.4580   3.3052
 YM8  HAAB  H   HCH3  0   0.247  -1.3821   1.4060   3.5831
 YM8  HAB   H   HCH3  0   0.191  -3.6035   3.9173  -1.6712
 YM8  HABA  H   HCH3  0   0.229  -3.8831   2.3500  -2.4397
 YM8  HABB  H   HCH3  0   0.231  -4.6574   2.7182  -0.9022
 YM8  HAC   H   HCH3  0   0.264  -0.6054   1.7488  -1.0614
 YM8  HACA  H   HCH3  0   0.226  -1.5707   1.8158  -2.5242
 YM8  HACB  H   HCH3  0   0.191  -1.0706   3.3227  -1.7411
 YM8  HAG   H   HCR6  0   0.278   6.9005  -2.2946   0.2936
 YM8  HAH   H   HCR6  0   0.289   6.9918   0.1585   0.5420
 YM8  HAI   H   HCR6  0   0.268   4.7863  -3.4262  -0.2645
 YM8  HAJ   H   HCR6  0   0.288  -2.1525  -3.0731  -2.0522
 YM8  HAK   H   HCR6  0   0.268   2.4554   1.5994  -0.3146
 YM8  HAL   H   HCR6  0   0.284   2.3333  -3.2644  -0.7394
 YM8  HAM   H   HCH2  0   0.235  -3.4444   3.0176   0.9628
 YM8  HAMA  H   HCH2  0   0.210  -1.8433   3.6531   0.6009
 YM8  HNAQ  H   HNH1  0   0.426   0.1538  -2.8405  -1.6921
 YM8  HAZ   H   HCH1  0   0.261  -0.8595   1.4096   1.1612
 YM8  NAQ   N   NH1   0  -0.754   0.0897  -1.9719  -1.1825
 YM8  CAF   C   CSP   0   0.057  -4.9544  -0.6705   0.3830
 YM8  CL    CL  CL    0  -0.115   5.0068   2.1446   0.3045

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
 YM8  CAA  CAZ   single    1.511  0.020  1.511
 YM8  CAA  HAA   single    0.970  0.020  1.090
 YM8  CAA  HAAA  single    0.970  0.020  1.090
 YM8  CAA  HAAB  single    0.970  0.020  1.090
 YM8  NBA  CAB   single    1.445  0.020  1.445
 YM8  CAB  HAB   single    0.970  0.020  1.090
 YM8  CAB  HABA  single    0.970  0.020  1.090
 YM8  CAB  HABB  single    0.970  0.020  1.090
 YM8  NBA  CAC   single    1.445  0.020  1.445
 YM8  CAC  HAC   single    0.970  0.020  1.090
 YM8  CAC  HACA  single    0.970  0.020  1.090
 YM8  CAC  HACB  single    0.970  0.020  1.090
 YM8  CAF  NAD   triple    1.153  0.020  1.153
 YM8  CL   CAS   single    1.731  0.020  1.731
 YM8  CAT  CAF   single    1.422  0.020  1.422
 YM8  CAH  CAG   aromatic  1.411  0.020  1.411
 YM8  CAG  CAI   aromatic  1.365  0.020  1.365
 YM8  CAG  HAG   single    0.930  0.020  1.080
 YM8  CAS  CAH   aromatic  1.366  0.020  1.366
 YM8  CAH  HAH   single    0.930  0.020  1.080
 YM8  CAX  CAI   aromatic  1.414  0.020  1.414
 YM8  CAI  HAI   single    0.930  0.020  1.080
 YM8  CAU  CAJ   aromatic  1.419  0.020  1.419
 YM8  CAJ  NAN   aromatic  1.305  0.020  1.305
 YM8  CAJ  HAJ   single    0.930  0.020  1.080
 YM8  CAK  NAO   aromatic  1.304  0.020  1.304
 YM8  CAK  CAY   aromatic  1.413  0.020  1.413
 YM8  CAK  HAK   single    0.930  0.020  1.080
 YM8  CAV  CAL   aromatic  1.373  0.020  1.373
 YM8  CAX  CAL   aromatic  1.406  0.020  1.406
 YM8  CAL  HAL   single    0.930  0.020  1.080
 YM8  CAZ  CAM   single    1.523  0.020  1.523
 YM8  CAM  NBA   single    1.446  0.020  1.446
 YM8  CAM  HAM   single    0.970  0.020  1.090
 YM8  CAM  HAMA  single    0.970  0.020  1.090
 YM8  NAN  CAT   aromatic  1.334  0.020  1.334
 YM8  NAO  CAV   aromatic  1.344  0.020  1.344
 YM8  CAU  NAP   aromatic  1.320  0.020  1.320
 YM8  NAP  CAW   aromatic  1.315  0.020  1.315
 YM8  CAV  NAQ   single    1.394  0.020  1.394
 YM8  NAQ  CAU   single    1.356  0.020  1.356
 YM8  NAQ  HNAQ  single    0.860  0.020  1.020
 YM8  CAW  OAR   single    1.320  0.020  1.320
 YM8  CAZ  OAR   single    1.444  0.020  1.444
 YM8  CAS  CAY   aromatic  1.416  0.020  1.416
 YM8  CAW  CAT   aromatic  1.401  0.020  1.401
 YM8  CAY  CAX   aromatic  1.417  0.020  1.417
 YM8  CAZ  HAZ   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
 YM8  HAAB  CAA  HAAA  108.60  3.000
 YM8  HAAB  CAA  HAA   107.72  3.000
 YM8  HAAA  CAA  HAA   107.97  3.000
 YM8  HAAB  CAA  CAZ   111.23  3.000
 YM8  HAAA  CAA  CAZ   111.63  3.000
 YM8  HAA   CAA  CAZ   109.55  3.000
 YM8  HABB  CAB  HABA  107.58  3.000
 YM8  HABB  CAB  HAB   107.89  3.000
 YM8  HABA  CAB  HAB   107.51  3.000
 YM8  HABB  CAB  NBA   110.14  3.000
 YM8  HABA  CAB  NBA   109.78  3.000
 YM8  HAB   CAB  NBA   113.72  3.000
 YM8  HACB  CAC  HACA  107.65  3.000
 YM8  HACB  CAC  HAC   108.29  3.000
 YM8  HACA  CAC  HAC   107.03  3.000
 YM8  HACB  CAC  NBA   112.89  3.000
 YM8  HACA  CAC  NBA   109.67  3.000
 YM8  HAC   CAC  NBA   111.08  3.000
 YM8  HAG   CAG  CAI   120.20  3.000
 YM8  HAG   CAG  CAH   118.67  3.000
 YM8  CAI   CAG  CAH   121.13  3.000
 YM8  HAH   CAH  CAS   120.57  3.000
 YM8  HAH   CAH  CAG   119.81  3.000
 YM8  CAS   CAH  CAG   119.62  3.000
 YM8  HAI   CAI  CAX   119.41  3.000
 YM8  HAI   CAI  CAG   120.71  3.000
 YM8  CAX   CAI  CAG   119.88  3.000
 YM8  HAJ   CAJ  CAU   121.05  3.000
 YM8  HAJ   CAJ  NAN   118.32  3.000
 YM8  CAU   CAJ  NAN   120.64  3.000
 YM8  HAK   CAK  CAY   119.92  3.000
 YM8  HAK   CAK  NAO   116.06  3.000
 YM8  CAY   CAK  NAO   124.01  3.000
 YM8  HAL   CAL  CAX   119.95  3.000
 YM8  HAL   CAL  CAV   120.86  3.000
 YM8  CAX   CAL  CAV   119.19  3.000
 YM8  HAMA  CAM  HAM   106.56  3.000
 YM8  HAMA  CAM  NBA   112.66  3.000
 YM8  HAM   CAM  NBA   108.89  3.000
 YM8  HAMA  CAM  CAZ   108.69  3.000
 YM8  HAM   CAM  CAZ   107.84  3.000
 YM8  NBA   CAM  CAZ   111.95  3.000
 YM8  CAT   NAN  CAJ   118.43  3.000
 YM8  CAV   NAO  CAK   118.71  3.000
 YM8  CAW   NAP  CAU   118.26  3.000
 YM8  CAZ   OAR  CAW   118.47  3.000
 YM8  CAY   CAS  CAH   121.26  3.000
 YM8  CAY   CAS  CL    119.63  3.000
 YM8  CAH   CAS  CL    119.12  3.000
 YM8  CAW   CAT  NAN   120.74  3.000
 YM8  CAW   CAT  CAF   120.69  3.000
 YM8  NAN   CAT  CAF   118.55  3.000
 YM8  NAQ   CAU  NAP   120.24  3.000
 YM8  NAQ   CAU  CAJ   118.88  3.000
 YM8  NAP   CAU  CAJ   120.85  3.000
 YM8  NAQ   CAV  NAO   117.56  3.000
 YM8  NAQ   CAV  CAL   119.32  3.000
 YM8  NAO   CAV  CAL   123.06  3.000
 YM8  CAT   CAW  OAR   118.39  3.000
 YM8  CAT   CAW  NAP   121.04  3.000
 YM8  OAR   CAW  NAP   120.41  3.000
 YM8  CAY   CAX  CAL   117.91  3.000
 YM8  CAY   CAX  CAI   119.72  3.000
 YM8  CAL   CAX  CAI   122.36  3.000
 YM8  CAX   CAY  CAS   118.39  3.000
 YM8  CAX   CAY  CAK   117.09  3.000
 YM8  CAS   CAY  CAK   124.52  3.000
 YM8  HAZ   CAZ  OAR   108.99  3.000
 YM8  HAZ   CAZ  CAM   110.99  3.000
 YM8  OAR   CAZ  CAM   106.76  3.000
 YM8  HAZ   CAZ  CAA   109.71  3.000
 YM8  OAR   CAZ  CAA   107.70  3.000
 YM8  CAM   CAZ  CAA   112.53  3.000
 YM8  CAM   NBA  CAC   112.86  3.000
 YM8  CAM   NBA  CAB   112.88  3.000
 YM8  CAC   NBA  CAB   111.73  3.000
 YM8  HNAQ  NAQ  CAV   115.83  3.000
 YM8  HNAQ  NAQ  CAU   116.03  3.000
 YM8  CAV   NAQ  CAU   127.42  3.000
 YM8  CAT   CAF  NAD   180.00  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
 YM8  CONST_01  CAY  CAS  CAH  CAG     0.00   0.0  0
 YM8  CONST_02  CAL  CAX  CAI  CAG   180.00   0.0  0
 YM8  CONST_03  CAY  CAX  CAI  CAG     0.00   0.0  0
 YM8  CONST_04  CAX  CAI  CAG  CAH     0.00   0.0  0
 YM8  CONST_05  CAK  CAY  CAS  CAH   180.00   0.0  0
 YM8  CONST_06  CAX  CAY  CAS  CAH     0.00   0.0  0
 YM8  CONST_07  CAS  CAH  CAG  CAI     0.00   0.0  0
 YM8  CONST_08  CAV  CAL  CAX  CAI   180.00   0.0  0
 YM8  CONST_09  CAK  CAY  CAX  CAI   180.00   0.0  0
 YM8  CONST_10  CAS  CAY  CAX  CAI     0.00   0.0  0
 YM8  CONST_11  CAW  NAP  CAU  CAJ     0.00   0.0  0
 YM8  CONST_12  CAW  CAT  NAN  CAJ     0.00   0.0  0
 YM8  CONST_13  CAL  CAV  NAO  CAK     0.00   0.0  0
 YM8  CONST_14  CAL  CAX  CAY  CAK     0.00   0.0  0
 YM8  CONST_15  CAS  CAY  CAX  CAL   180.00   0.0  0
 YM8  CONST_16  NAP  CAU  CAJ  NAN     0.00   0.0  0
 YM8  CONST_17  NAP  CAW  CAT  NAN     0.00   0.0  0
 YM8  CONST_18  CAS  CAY  CAK  NAO   180.00   0.0  0
 YM8  CONST_19  CAX  CAY  CAK  NAO     0.00   0.0  0
 YM8  CONST_20  CAX  CAL  CAV  NAO     0.00   0.0  0
 YM8  CONST_21  CAU  CAJ  NAN  CAT     0.00   0.0  0
 YM8  CONST_22  CAU  NAP  CAW  CAT     0.00   0.0  0
 YM8  CONST_23  CAY  CAX  CAL  CAV     0.00   0.0  0
 YM8  CONST_24  CAY  CAK  NAO  CAV     0.00   0.0  0
 YM8  CONST_25  CAG  CAH  CAS  CL    180.00   0.0  0
 YM8  CONST_26  CAK  CAY  CAS  CL      0.00   0.0  0
 YM8  CONST_27  CAX  CAY  CAS  CL    180.00   0.0  0
 YM8  CONST_28  CAJ  NAN  CAT  CAF   180.00   0.0  0
 YM8  CONST_29  NAP  CAW  CAT  CAF   180.00   0.0  0
 YM8  CONST_30  NAQ  CAV  NAO  CAK   180.00   0.0  0
 YM8  CONST_31  NAQ  CAU  CAJ  NAN   180.00   0.0  0
 YM8  CONST_32  OAR  CAW  CAT  NAN   180.00   0.0  0
 YM8  CONST_33  CAX  CAL  CAV  NAQ   180.00   0.0  0
 YM8  CONST_34  CAW  NAP  CAU  NAQ   180.00   0.0  0
 YM8  CONST_35  CAU  NAP  CAW  OAR   180.00   0.0  0
 YM8  CONST_36  HAI  CAI  CAG  CAH   180.00   0.0  0
 YM8  CONST_37  HAH  CAH  CAG  CAI   180.00   0.0  0
 YM8  CONST_38  HAL  CAL  CAX  CAI     0.00   0.0  0
 YM8  CONST_39  HAJ  CAJ  CAU  NAP   180.00   0.0  0
 YM8  CONST_40  HAG  CAG  CAH  CAS   180.00   0.0  0
 YM8  CONST_41  HAK  CAK  CAY  CAS     0.00   0.0  0
 YM8  Var_01    CAV  NAQ  CAU  CAJ   177.05  30.0  2
 YM8  Var_02    CAU  NAQ  CAV  CAL   143.28  30.0  2
 YM8  Var_03    CAZ  CAM  NBA  CAB   150.49  30.0  1
 YM8  Var_04    HAC  CAC  NBA  CAB  -174.65  30.0  3
 YM8  Var_05    HAB  CAB  NBA  CAC   -62.99  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
 YM8  chir_01  CAZ  CAA  CAM  OAR  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
 YM8  plan-1  NAD  0.020
 YM8  plan-1  CAJ  0.020
 YM8  plan-1  NAN  0.020
 YM8  plan-1  NAP  0.020
 YM8  plan-1  OAR  0.020
 YM8  plan-1  CAT  0.020
 YM8  plan-1  CAU  0.020
 YM8  plan-1  CAW  0.020
 YM8  plan-1  HAJ  0.020
 YM8  plan-1  NAQ  0.020
 YM8  plan-1  CAF  0.020
 YM8  plan-2  CAG  0.020
 YM8  plan-2  CAH  0.020
 YM8  plan-2  CAI  0.020
 YM8  plan-2  CAK  0.020
 YM8  plan-2  CAL  0.020
 YM8  plan-2  NAO  0.020
 YM8  plan-2  CAS  0.020
 YM8  plan-2  CAV  0.020
 YM8  plan-2  CAX  0.020
 YM8  plan-2  CAY  0.020
 YM8  plan-2  HAG  0.020
 YM8  plan-2  HAH  0.020
 YM8  plan-2  HAI  0.020
 YM8  plan-2  HAK  0.020
 YM8  plan-2  HAL  0.020
 YM8  plan-2  NAQ  0.020
 YM8  plan-2  CL   0.020

