# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:24:38 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-amino-6-(3-formylphenyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]c(c3cccc(C=O)c3)c(C#N)c2c(n1)N4CCCC4
#
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
 NWJ  NWJ  2-amino-6-(3-formylphenyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  41  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NWJ
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
 NWJ  CAV   C  C1    0   0.123  -5.7671  -0.9950   0.9650
 NWJ  OAE   O  O     0  -0.377  -6.9575  -0.7926   0.9525
 NWJ  CAX   C  CR6   0   0.011  -4.7839  -0.2243   0.1843
 NWJ  CAK   C  CR16  0  -0.337  -3.4415  -0.5641   0.2930
 NWJ  CAI   C  CR16  0  -0.269  -5.1770   0.8271  -0.6430
 NWJ  CAH   C  CR16  0  -0.225  -4.2204   1.5206  -1.3620
 NWJ  CAJ   C  CR16  0  -0.292  -2.8791   1.1747  -1.2617
 NWJ  CAY   C  CR6   0   0.073  -2.4715   0.1359  -0.4240
 NWJ  CBA   C  CR5   0   0.420  -1.0656  -0.2390  -0.3075
 NWJ  NAS   N  NR15  0  -0.723  -0.6898  -1.5396  -0.1988
 NWJ  CAZ   C  CR5   0  -0.128   0.0735   0.5425  -0.2474
 NWJ  CAG   C  CSP   0  -0.097  -0.0274   1.9483  -0.2570
 NWJ  NAA   N  NS    0  -0.257  -0.1774   3.0934  -0.2685
 NWJ  C5    C  CR56  0  -0.023   1.2068  -0.3482  -0.1071
 NWJ  C4    C  CR56  0   0.473   0.6605  -1.6405  -0.0975
 NWJ  N3    N  N     0  -0.509   1.2983  -2.8001  -0.0353
 NWJ  C2    C  CR6   0   0.526   2.6179  -2.6528   0.0098
 NWJ  NAB   N  NH2   0  -0.825   3.3688  -3.7792   0.0175
 NWJ  N1    N  N     0  -0.532   3.2845  -1.4976   0.0172
 NWJ  C6    C  CR6   0   0.482   2.6343  -0.3334  -0.0312
 NWJ  NBF   N  NT    0  -0.495   3.4096   0.7558  -0.0149
 NWJ  CAN   C  CH2   0  -0.259   4.8676   0.6550  -0.0534
 NWJ  CAL   C  CH2   0  -0.484   5.3094   2.0945  -0.2763
 NWJ  CAM   C  CH2   0  -0.472   4.2383   2.8957   0.4519
 NWJ  CAO   C  CH2   0  -0.285   2.9596   2.1312   0.1278
 NWJ  HAV   H  H     0   0.202  -5.3316  -1.7993   1.5837
 NWJ  HAK   H  HCR6  0   0.277  -3.1552  -1.3735   0.9558
 NWJ  HAI   H  HCR6  0   0.275  -6.2224   1.0942  -0.7253
 NWJ  HAH   H  HCR6  0   0.276  -4.5135   2.3297  -2.0170
 NWJ  HAJ   H  HCR6  0   0.276  -2.1540   1.7062  -1.8625
 NWJ  HAS   H  HNR5  0   0.425  -1.3089  -2.3322  -0.2821
 NWJ  HAB1  H  HNH2  0   0.390   2.9155  -4.6467   0.2476
 NWJ  HAB2  H  HNH2  0   0.389   4.3341  -3.6981   0.2857
 NWJ  HAN1  H  HCH2  0   0.234   5.2531   0.2609   0.8918
 NWJ  HAN2  H  HCH2  0   0.249   5.1919  -0.0185  -0.8457
 NWJ  HAO1  H  HCH2  0   0.244   2.5140   2.4948  -0.8014
 NWJ  HAO2  H  HCH2  0   0.253   2.2246   2.2240   0.9268
 NWJ  HAL1  H  HCH2  0   0.253   6.3151   2.2774   0.1001
 NWJ  HAL2  H  HCH2  0   0.239   5.3024   2.3303  -1.3427
 NWJ  HAM1  H  HCH2  0   0.242   4.4216   2.8779   1.5284
 NWJ  HAM2  H  HCH2  0   0.255   4.1797   3.9375   0.1399

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
 NWJ  CAV  OAE   double    1.208  0.020  1.208
 NWJ  CAV  CAX   single    1.473  0.020  1.473
 NWJ  CAV  HAV   single    0.930  0.020  1.080
 NWJ  CAX  CAK   aromatic  1.389  0.020  1.389
 NWJ  CAX  CAI   aromatic  1.394  0.020  1.394
 NWJ  CAK  CAY   aromatic  1.395  0.020  1.395
 NWJ  CAI  CAH   aromatic  1.383  0.020  1.383
 NWJ  CAH  CAJ   aromatic  1.389  0.020  1.389
 NWJ  CAJ  CAY   aromatic  1.395  0.020  1.395
 NWJ  CAY  CBA   single    1.460  0.020  1.460
 NWJ  CBA  NAS   aromatic  1.358  0.020  1.358
 NWJ  CBA  CAZ   aromatic  1.383  0.020  1.383
 NWJ  NAS  C4    aromatic  1.358  0.020  1.358
 NWJ  CAZ  CAG   single    1.409  0.020  1.409
 NWJ  CAZ  C5    aromatic  1.448  0.020  1.448
 NWJ  CAG  NAA   triple    1.155  0.020  1.155
 NWJ  C5   C4    aromatic  1.403  0.020  1.403
 NWJ  C5   C6    aromatic  1.430  0.020  1.430
 NWJ  C4   N3    aromatic  1.325  0.020  1.325
 NWJ  N3   C2    aromatic  1.329  0.020  1.329
 NWJ  C2   NAB   single    1.354  0.020  1.354
 NWJ  C2   N1    aromatic  1.334  0.020  1.334
 NWJ  N1   C6    aromatic  1.334  0.020  1.334
 NWJ  C6   NBF   single    1.337  0.020  1.337
 NWJ  NBF  CAN   single    1.462  0.020  1.462
 NWJ  NBF  CAO   single    1.454  0.020  1.454
 NWJ  CAN  CAL   single    1.522  0.020  1.522
 NWJ  CAL  CAM   single    1.523  0.020  1.523
 NWJ  CAM  CAO   single    1.525  0.020  1.525
 NWJ  CAK  HAK   single    0.930  0.020  1.080
 NWJ  CAI  HAI   single    0.930  0.020  1.080
 NWJ  CAH  HAH   single    0.930  0.020  1.080
 NWJ  CAJ  HAJ   single    0.930  0.020  1.080
 NWJ  NAS  HAS   single    0.860  0.020  1.020
 NWJ  NAB  HAB1  single    0.890  0.020  1.040
 NWJ  NAB  HAB2  single    0.890  0.020  1.040
 NWJ  CAN  HAN1  single    0.970  0.020  1.090
 NWJ  CAN  HAN2  single    0.970  0.020  1.090
 NWJ  CAO  HAO1  single    0.970  0.020  1.090
 NWJ  CAO  HAO2  single    0.970  0.020  1.090
 NWJ  CAL  HAL1  single    0.970  0.020  1.090
 NWJ  CAL  HAL2  single    0.970  0.020  1.090
 NWJ  CAM  HAM1  single    0.970  0.020  1.090
 NWJ  CAM  HAM2  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
 NWJ  HAV   CAV  CAX   114.51  3.000
 NWJ  HAV   CAV  OAE   121.11  3.000
 NWJ  CAX   CAV  OAE   124.38  3.000
 NWJ  CAI   CAX  CAK   120.22  3.000
 NWJ  CAI   CAX  CAV   121.38  3.000
 NWJ  CAK   CAX  CAV   118.40  3.000
 NWJ  HAK   CAK  CAY   120.35  3.000
 NWJ  HAK   CAK  CAX   119.04  3.000
 NWJ  CAY   CAK  CAX   120.61  3.000
 NWJ  HAI   CAI  CAH   120.33  3.000
 NWJ  HAI   CAI  CAX   120.24  3.000
 NWJ  CAH   CAI  CAX   119.44  3.000
 NWJ  HAH   CAH  CAJ   119.46  3.000
 NWJ  HAH   CAH  CAI   120.17  3.000
 NWJ  CAJ   CAH  CAI   120.37  3.000
 NWJ  HAJ   CAJ  CAY   120.24  3.000
 NWJ  HAJ   CAJ  CAH   119.02  3.000
 NWJ  CAY   CAJ  CAH   120.72  3.000
 NWJ  CBA   CAY  CAJ   121.36  3.000
 NWJ  CBA   CAY  CAK   119.99  3.000
 NWJ  CAJ   CAY  CAK   118.63  3.000
 NWJ  CAZ   CBA  NAS   108.05  3.000
 NWJ  CAZ   CBA  CAY   130.67  3.000
 NWJ  NAS   CBA  CAY   121.26  3.000
 NWJ  HAS   NAS  C4    123.91  3.000
 NWJ  HAS   NAS  CBA   125.15  3.000
 NWJ  C4    NAS  CBA   110.63  3.000
 NWJ  C5    CAZ  CAG   132.07  3.000
 NWJ  C5    CAZ  CBA   107.53  3.000
 NWJ  CAG   CAZ  CBA   120.30  3.000
 NWJ  NAA   CAG  CAZ   180.00  3.000
 NWJ  C6    C5   C4    113.45  3.000
 NWJ  C6    C5   CAZ   141.28  3.000
 NWJ  C4    C5   CAZ   105.21  3.000
 NWJ  N3    C4   C5    128.25  3.000
 NWJ  N3    C4   NAS   123.18  3.000
 NWJ  C5    C4   NAS   108.56  3.000
 NWJ  C2    N3   C4    112.50  3.000
 NWJ  N1    C2   NAB   116.32  3.000
 NWJ  N1    C2   N3    126.35  3.000
 NWJ  NAB   C2   N3    117.31  3.000
 NWJ  HAB2  NAB  HAB1  116.20  3.000
 NWJ  HAB2  NAB  C2    117.84  3.000
 NWJ  HAB1  NAB  C2    117.98  3.000
 NWJ  C6    N1   C2    120.79  3.000
 NWJ  NBF   C6   N1    115.33  3.000
 NWJ  NBF   C6   C5    126.02  3.000
 NWJ  N1    C6   C5    118.65  3.000
 NWJ  CAO   NBF  CAN   112.11  3.000
 NWJ  CAO   NBF  C6    126.32  3.000
 NWJ  CAN   NBF  C6    121.45  3.000
 NWJ  HAN2  CAN  HAN1  107.50  3.000
 NWJ  HAN2  CAN  CAL   113.06  3.000
 NWJ  HAN1  CAN  CAL   111.40  3.000
 NWJ  HAN2  CAN  NBF   111.02  3.000
 NWJ  HAN1  CAN  NBF   110.70  3.000
 NWJ  CAL   CAN  NBF   103.19  3.000
 NWJ  HAL2  CAL  HAL1  107.89  3.000
 NWJ  HAL2  CAL  CAM   110.41  3.000
 NWJ  HAL1  CAL  CAM   113.31  3.000
 NWJ  HAL2  CAL  CAN   110.20  3.000
 NWJ  HAL1  CAL  CAN   112.09  3.000
 NWJ  CAM   CAL  CAN   102.91  3.000
 NWJ  HAM2  CAM  HAM1  107.88  3.000
 NWJ  HAM2  CAM  CAO   111.93  3.000
 NWJ  HAM1  CAM  CAO   110.00  3.000
 NWJ  HAM2  CAM  CAL   113.83  3.000
 NWJ  HAM1  CAM  CAL   110.17  3.000
 NWJ  CAO   CAM  CAL   102.97  3.000
 NWJ  HAO2  CAO  HAO1  108.68  3.000
 NWJ  HAO2  CAO  CAM   111.54  3.000
 NWJ  HAO1  CAO  CAM   110.85  3.000
 NWJ  HAO2  CAO  NBF   111.18  3.000
 NWJ  HAO1  CAO  NBF   110.94  3.000
 NWJ  CAM   CAO  NBF   103.62  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
 NWJ  CONST_01  CAJ  CAY  CAK  CAX     0.00   0.0  0
 NWJ  CONST_02  CBA  CAY  CAK  CAX   180.00   0.0  0
 NWJ  CONST_03  CAJ  CAH  CAI  CAX     0.00   0.0  0
 NWJ  CONST_04  CAH  CAI  CAX  CAK     0.00   0.0  0
 NWJ  CONST_05  CAH  CAJ  CAY  CAK     0.00   0.0  0
 NWJ  CONST_08  CAY  CAK  CAX  CAI     0.00   0.0  0
 NWJ  CONST_09  CAY  CAJ  CAH  CAI     0.00   0.0  0
 NWJ  CONST_10  CBA  CAY  CAJ  CAH   180.00   0.0  0
 NWJ  CONST_13  C4   NAS  CBA  CAY   180.00   0.0  0
 NWJ  CONST_14  C5   CAZ  CBA  CAY   180.00   0.0  0
 NWJ  CONST_15  C5   C4   NAS  CBA     0.00   0.0  0
 NWJ  CONST_16  N3   C4   NAS  CBA   180.00   0.0  0
 NWJ  CONST_17  C4   C5   CAZ  CBA     0.00   0.0  0
 NWJ  CONST_18  C6   C5   CAZ  CBA   180.00   0.0  0
 NWJ  CONST_19  C5   CAZ  CBA  NAS     0.00   0.0  0
 NWJ  CONST_20  CAZ  C5   C4   NAS     0.00   0.0  0
 NWJ  CONST_21  C6   C5   C4   NAS   180.00   0.0  0
 NWJ  CONST_22  C2   N3   C4   NAS   180.00   0.0  0
 NWJ  CONST_23  C4   NAS  CBA  CAZ     0.00   0.0  0
 NWJ  CONST_24  N3   C4   C5   CAZ   180.00   0.0  0
 NWJ  CONST_25  N1   C6   C5   CAZ   180.00   0.0  0
 NWJ  CONST_26  C2   N3   C4   C5      0.00   0.0  0
 NWJ  CONST_27  C2   N1   C6   C5      0.00   0.0  0
 NWJ  CONST_28  N1   C6   C5   C4      0.00   0.0  0
 NWJ  CONST_29  N1   C2   N3   C4      0.00   0.0  0
 NWJ  CONST_30  C6   C5   C4   N3      0.00   0.0  0
 NWJ  CONST_31  C6   N1   C2   N3      0.00   0.0  0
 NWJ  CONST_32  NBF  C6   C5   CAZ     0.00   0.0  0
 NWJ  CONST_33  NBF  C6   C5   C4    180.00   0.0  0
 NWJ  CONST_34  NBF  C6   N1   C2    180.00   0.0  0
 NWJ  CONST_35  CAY  CAK  CAX  CAV   180.00   0.0  0
 NWJ  CONST_36  CAH  CAI  CAX  CAV   180.00   0.0  0
 NWJ  CONST_37  CAG  CAZ  CBA  CAY     0.00   0.0  0
 NWJ  CONST_38  CAG  CAZ  CBA  NAS   180.00   0.0  0
 NWJ  CONST_39  C4   C5   CAZ  CAG   180.00   0.0  0
 NWJ  CONST_40  C6   C5   CAZ  CAG     0.00   0.0  0
 NWJ  CONST_41  NAB  C2   N3   C4    180.00   0.0  0
 NWJ  CONST_42  C6   N1   C2   NAB   180.00   0.0  0
 NWJ  CONST_43  HAH  CAH  CAI  CAX   180.00   0.0  0
 NWJ  CONST_44  HAI  CAI  CAX  CAK   180.00   0.0  0
 NWJ  CONST_45  HAJ  CAJ  CAY  CAK   180.00   0.0  0
 NWJ  CONST_46  HAK  CAK  CAX  CAI   180.00   0.0  0
 NWJ  CONST_47  HAS  NAS  CBA  CAY     0.00   0.0  0
 NWJ  Var_01    CAN  NBF  C6   C5   -174.55  30.0  2
 NWJ  Var_02    CAL  CAN  NBF  C6    169.96  30.0  1
 NWJ  Var_03    CAM  CAO  NBF  C6    165.42  30.0  1
 NWJ  Var_04    CAM  CAL  CAN  NBF    32.42  30.0  1
 NWJ  Var_05    CAL  CAM  CAO  NBF    30.62  30.0  1
 NWJ  Var_06    CAO  CAM  CAL  CAN   -39.15  30.0  1
 NWJ  Var_07    CAK  CAX  CAV  OAE   179.99  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
 NWJ  plan-1  CAV   0.020
 NWJ  plan-1  CAX   0.020
 NWJ  plan-1  CAK   0.020
 NWJ  plan-1  CAI   0.020
 NWJ  plan-1  CAH   0.020
 NWJ  plan-1  CAJ   0.020
 NWJ  plan-1  CAY   0.020
 NWJ  plan-1  CBA   0.020
 NWJ  plan-1  HAK   0.020
 NWJ  plan-1  HAI   0.020
 NWJ  plan-1  HAH   0.020
 NWJ  plan-1  HAJ   0.020
 NWJ  plan-2  CAY   0.020
 NWJ  plan-2  CBA   0.020
 NWJ  plan-2  NAS   0.020
 NWJ  plan-2  CAZ   0.020
 NWJ  plan-2  CAG   0.020
 NWJ  plan-2  NAA   0.020
 NWJ  plan-2  C5    0.020
 NWJ  plan-2  C4    0.020
 NWJ  plan-2  N3    0.020
 NWJ  plan-2  C2    0.020
 NWJ  plan-2  NAB   0.020
 NWJ  plan-2  N1    0.020
 NWJ  plan-2  C6    0.020
 NWJ  plan-2  NBF   0.020
 NWJ  plan-2  HAS   0.020
 NWJ  plan-3  C2    0.020
 NWJ  plan-3  NAB   0.020
 NWJ  plan-3  HAB1  0.020
 NWJ  plan-3  HAB2  0.020
 NWJ  plan-4  CAV   0.020
 NWJ  plan-4  OAE   0.020
 NWJ  plan-4  CAX   0.020
 NWJ  plan-4  HAV   0.020

