# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:29:24 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-(phenylethynyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]cc(C#Cc3ccccc3)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
 XP0  XP0  5-(phenylethynyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine  ligand  40  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XP0
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
 XP0  CAL   C  CH2   0  -0.255  -1.7954  -3.0610   0.2683
 XP0  CAJ   C  CH2   0  -0.484  -0.5461  -3.8987   0.5046
 XP0  CAK   C  CH2   0  -0.477   0.5086  -3.1812  -0.3274
 XP0  CAM   C  CH2   0  -0.274   0.1751  -1.7106  -0.1036
 XP0  NAW   N  NT    0  -0.497  -1.2660  -1.7109   0.0868
 XP0  C6    C  CR6   0   0.440  -2.0773  -0.6470   0.0108
 XP0  C5    C  CR56  0  -0.118  -1.6674   0.7175  -0.0791
 XP0  N1    N  N     0  -0.533  -3.3827  -0.9307   0.0309
 XP0  C2    C  CR6   0   0.512  -4.2897   0.0430  -0.0556
 XP0  NAA   N  NH2   0  -0.826  -5.5919  -0.3490  -0.0766
 XP0  N3    N  N     0  -0.510  -4.0446   1.3412  -0.1655
 XP0  C4    C  CR56  0   0.485  -2.7445   1.6169  -0.1661
 XP0  NAP   N  NR15  0  -0.656  -2.2498   2.8773  -0.2335
 XP0  CAI   C  CR15  0  -0.065  -0.8936   2.8427  -0.1775
 XP0  CAS   C  CR5   0  -0.151  -0.4686   1.5411  -0.0781
 XP0  CAC   C  CSP   0   0.118   0.9075   1.2444   0.0183
 XP0  CAB   C  CSP   0   0.053   2.1004   1.0640   0.0983
 XP0  CAQ   C  CR6   0  -0.112   3.4945   0.7967   0.1800
 XP0  CAG   C  CR16  0  -0.304   4.4192   1.8403   0.2995
 XP0  CAE   C  CR16  0  -0.247   5.7755   1.5654   0.3739
 XP0  CAD   C  CR16  0  -0.261   6.2303   0.2531   0.3312
 XP0  CAF   C  CR16  0  -0.243   5.3180  -0.7887   0.2134
 XP0  CAH   C  CR16  0  -0.317   3.9607  -0.5225   0.1377
 XP0  HAL1  H  HCH2  0   0.231  -2.3321  -3.3908  -0.6264
 XP0  HAL2  H  HCH2  0   0.245  -2.4961  -3.0986   1.1016
 XP0  HAJ1  H  HCH2  0   0.238  -0.2719  -3.8786   1.5617
 XP0  HAJ2  H  HCH2  0   0.251  -0.6907  -4.9394   0.2170
 XP0  HAK1  H  HCH2  0   0.253   1.5308  -3.4165  -0.0325
 XP0  HAK2  H  HCH2  0   0.240   0.3976  -3.4356  -1.3836
 XP0  HAM1  H  HCH2  0   0.237   0.6862  -1.3258   0.7824
 XP0  HAM2  H  HCH2  0   0.251   0.4628  -1.0944  -0.9544
 XP0  HAA1  H  HNH2  0   0.384  -5.7963  -1.2722   0.2657
 XP0  HAA2  H  HNH2  0   0.384  -6.2823   0.3503   0.1380
 XP0  HAP   H  HNR5  0   0.415  -2.8113   3.7109  -0.3030
 XP0  HAI   H  HCR5  0   0.296  -0.3050   3.7444  -0.2075
 XP0  HAG   H  HCR6  0   0.257   4.0693   2.8639   0.3334
 XP0  HAH   H  HCR6  0   0.258   3.2541  -1.3370   0.0444
 XP0  HAE   H  HCR6  0   0.262   6.4813   2.3803   0.4658
 XP0  HAD   H  HCR6  0   0.261   7.2904   0.0442   0.3884
 XP0  HAF   H  HCR6  0   0.262   5.6641  -1.8135   0.1789

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
 XP0  CAL  CAJ   single    1.523  0.020  1.523
 XP0  CAL  NAW   single    1.462  0.020  1.462
 XP0  CAJ  CAK   single    1.523  0.020  1.523
 XP0  CAK  CAM   single    1.524  0.020  1.524
 XP0  CAM  NAW   single    1.454  0.020  1.454
 XP0  NAW  C6    single    1.340  0.020  1.340
 XP0  C6   C5    aromatic  1.428  0.020  1.428
 XP0  C6   N1    aromatic  1.336  0.020  1.336
 XP0  C5   C4    aromatic  1.406  0.020  1.406
 XP0  C5   CAS   aromatic  1.454  0.020  1.454
 XP0  N1   C2    aromatic  1.334  0.020  1.334
 XP0  C2   NAA   single    1.360  0.020  1.360
 XP0  C2   N3    aromatic  1.326  0.020  1.326
 XP0  N3   C4    aromatic  1.329  0.020  1.329
 XP0  C4   NAP   aromatic  1.356  0.020  1.356
 XP0  NAP  CAI   aromatic  1.358  0.020  1.358
 XP0  CAI  CAS   aromatic  1.373  0.020  1.373
 XP0  CAS  CAC   single    1.411  0.020  1.411
 XP0  CAC  CAB   triple    1.209  0.020  1.209
 XP0  CAB  CAQ   single    1.422  0.020  1.422
 XP0  CAQ  CAG   aromatic  1.399  0.020  1.399
 XP0  CAQ  CAH   aromatic  1.400  0.020  1.400
 XP0  CAG  CAE   aromatic  1.386  0.020  1.386
 XP0  CAE  CAD   aromatic  1.390  0.020  1.390
 XP0  CAD  CAF   aromatic  1.390  0.020  1.390
 XP0  CAF  CAH   aromatic  1.385  0.020  1.385
 XP0  CAL  HAL1  single    0.970  0.020  1.090
 XP0  CAL  HAL2  single    0.970  0.020  1.090
 XP0  CAJ  HAJ1  single    0.970  0.020  1.090
 XP0  CAJ  HAJ2  single    0.970  0.020  1.090
 XP0  CAK  HAK1  single    0.970  0.020  1.090
 XP0  CAK  HAK2  single    0.970  0.020  1.090
 XP0  CAM  HAM1  single    0.970  0.020  1.090
 XP0  CAM  HAM2  single    0.970  0.020  1.090
 XP0  NAA  HAA1  single    0.890  0.020  1.040
 XP0  NAA  HAA2  single    0.890  0.020  1.040
 XP0  NAP  HAP   single    0.860  0.020  1.020
 XP0  CAI  HAI   single    0.930  0.020  1.080
 XP0  CAG  HAG   single    0.930  0.020  1.080
 XP0  CAH  HAH   single    0.930  0.020  1.080
 XP0  CAE  HAE   single    0.930  0.020  1.080
 XP0  CAD  HAD   single    0.930  0.020  1.080
 XP0  CAF  HAF   single    0.930  0.020  1.080

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
 XP0  HAL2  CAL  HAL1  107.44  3.000
 XP0  HAL2  CAL  NAW   111.09  3.000
 XP0  HAL1  CAL  NAW   110.77  3.000
 XP0  HAL2  CAL  CAJ   112.96  3.000
 XP0  HAL1  CAL  CAJ   111.31  3.000
 XP0  NAW   CAL  CAJ   103.31  3.000
 XP0  HAJ2  CAJ  HAJ1  107.85  3.000
 XP0  HAJ2  CAJ  CAK   113.44  3.000
 XP0  HAJ1  CAJ  CAK   110.26  3.000
 XP0  HAJ2  CAJ  CAL   112.07  3.000
 XP0  HAJ1  CAJ  CAL   110.24  3.000
 XP0  CAK   CAJ  CAL   102.96  3.000
 XP0  HAK2  CAK  HAK1  107.87  3.000
 XP0  HAK2  CAK  CAM   110.15  3.000
 XP0  HAK1  CAK  CAM   111.95  3.000
 XP0  HAK2  CAK  CAJ   110.38  3.000
 XP0  HAK1  CAK  CAJ   113.59  3.000
 XP0  CAM   CAK  CAJ   102.87  3.000
 XP0  HAM2  CAM  HAM1  108.09  3.000
 XP0  HAM2  CAM  NAW   111.37  3.000
 XP0  HAM1  CAM  NAW   110.95  3.000
 XP0  HAM2  CAM  CAK   111.92  3.000
 XP0  HAM1  CAM  CAK   110.88  3.000
 XP0  NAW   CAM  CAK   103.65  3.000
 XP0  C6    NAW  CAM   126.34  3.000
 XP0  C6    NAW  CAL   121.41  3.000
 XP0  CAM   NAW  CAL   112.06  3.000
 XP0  N1    C6   C5    118.98  3.000
 XP0  N1    C6   NAW   114.96  3.000
 XP0  C5    C6   NAW   126.06  3.000
 XP0  CAS   C5   C4    105.62  3.000
 XP0  CAS   C5   C6    141.06  3.000
 XP0  C4    C5   C6    113.29  3.000
 XP0  C2    N1   C6    120.57  3.000
 XP0  N3    C2   NAA   117.26  3.000
 XP0  N3    C2   N1    126.49  3.000
 XP0  NAA   C2   N1    116.22  3.000
 XP0  HAA2  NAA  HAA1  115.22  3.000
 XP0  HAA2  NAA  C2    116.97  3.000
 XP0  HAA1  NAA  C2    117.00  3.000
 XP0  C4    N3   C2    112.59  3.000
 XP0  NAP   C4   N3    123.36  3.000
 XP0  NAP   C4   C5    108.56  3.000
 XP0  N3    C4   C5    128.08  3.000
 XP0  HAP   NAP  CAI   125.49  3.000
 XP0  HAP   NAP  C4    124.70  3.000
 XP0  CAI   NAP  C4    109.80  3.000
 XP0  HAI   CAI  CAS   128.79  3.000
 XP0  HAI   CAI  NAP   121.55  3.000
 XP0  CAS   CAI  NAP   109.66  3.000
 XP0  CAC   CAS  CAI   120.41  3.000
 XP0  CAC   CAS  C5    133.23  3.000
 XP0  CAI   CAS  C5    106.35  3.000
 XP0  CAB   CAC  CAS   180.00  3.000
 XP0  CAQ   CAB  CAC   180.00  3.000
 XP0  CAH   CAQ  CAG   119.03  3.000
 XP0  CAH   CAQ  CAB   120.13  3.000
 XP0  CAG   CAQ  CAB   120.84  3.000
 XP0  HAG   CAG  CAE   120.15  3.000
 XP0  HAG   CAG  CAQ   119.63  3.000
 XP0  CAE   CAG  CAQ   120.22  3.000
 XP0  HAE   CAE  CAD   120.03  3.000
 XP0  HAE   CAE  CAG   119.57  3.000
 XP0  CAD   CAE  CAG   120.40  3.000
 XP0  HAD   CAD  CAF   120.19  3.000
 XP0  HAD   CAD  CAE   120.10  3.000
 XP0  CAF   CAD  CAE   119.71  3.000
 XP0  HAF   CAF  CAH   119.58  3.000
 XP0  HAF   CAF  CAD   120.17  3.000
 XP0  CAH   CAF  CAD   120.25  3.000
 XP0  HAH   CAH  CAF   119.99  3.000
 XP0  HAH   CAH  CAQ   119.63  3.000
 XP0  CAF   CAH  CAQ   120.38  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
 XP0  CONST_01  N3   C4   C5   C6     0.00   0.0  0
 XP0  CONST_02  NAP  C4   C5   C6   180.00   0.0  0
 XP0  CONST_03  CAI  CAS  C5   C6   180.00   0.0  0
 XP0  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 XP0  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 XP0  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 XP0  CONST_07  CAI  NAP  C4   C5     0.00   0.0  0
 XP0  CONST_08  NAP  CAI  CAS  C5     0.00   0.0  0
 XP0  CONST_09  C4   C5   C6   N1     0.00   0.0  0
 XP0  CONST_10  CAS  C5   C6   N1   180.00   0.0  0
 XP0  CONST_11  C4   N3   C2   N1     0.00   0.0  0
 XP0  CONST_12  NAP  C4   N3   C2   180.00   0.0  0
 XP0  CONST_13  CAS  C5   C4   N3   180.00   0.0  0
 XP0  CONST_14  CAI  NAP  C4   N3   180.00   0.0  0
 XP0  CONST_15  CAI  CAS  C5   C4     0.00   0.0  0
 XP0  CONST_16  CAS  CAI  NAP  C4     0.00   0.0  0
 XP0  CONST_17  CAS  C5   C4   NAP    0.00   0.0  0
 XP0  CONST_18  CAD  CAE  CAG  CAQ    0.00   0.0  0
 XP0  CONST_19  CAD  CAF  CAH  CAQ    0.00   0.0  0
 XP0  CONST_20  CAF  CAH  CAQ  CAG    0.00   0.0  0
 XP0  CONST_21  CAF  CAD  CAE  CAG    0.00   0.0  0
 XP0  CONST_22  CAH  CAQ  CAG  CAE    0.00   0.0  0
 XP0  CONST_23  CAH  CAF  CAD  CAE    0.00   0.0  0
 XP0  CONST_24  C4   C5   C6   NAW  180.00   0.0  0
 XP0  CONST_25  CAS  C5   C6   NAW    0.00   0.0  0
 XP0  CONST_26  C2   N1   C6   NAW  180.00   0.0  0
 XP0  CONST_27  CAC  CAS  C5   C6     0.00   0.0  0
 XP0  CONST_28  NAA  C2   N1   C6   180.00   0.0  0
 XP0  CONST_29  C4   N3   C2   NAA  180.00   0.0  0
 XP0  CONST_30  CAC  CAS  C5   C4   180.00   0.0  0
 XP0  CONST_31  CAC  CAS  CAI  NAP  180.00   0.0  0
 XP0  CONST_32  CAE  CAG  CAQ  CAB  180.00   0.0  0
 XP0  CONST_33  CAF  CAH  CAQ  CAB  180.00   0.0  0
 XP0  CONST_34  HAP  NAP  C4   C5   180.00   0.0  0
 XP0  CONST_35  HAI  CAI  CAS  C5   180.00   0.0  0
 XP0  CONST_36  HAE  CAE  CAG  CAQ  180.00   0.0  0
 XP0  CONST_37  HAF  CAF  CAH  CAQ  180.00   0.0  0
 XP0  CONST_38  HAH  CAH  CAQ  CAG  180.00   0.0  0
 XP0  CONST_39  HAD  CAD  CAE  CAG  180.00   0.0  0
 XP0  CONST_40  HAG  CAG  CAE  CAD  180.00   0.0  0
 XP0  Var_01    CAM  CAK  CAJ  CAL   39.09  30.0  1
 XP0  Var_02    CAK  CAM  NAW  CAL   11.59  30.0  1
 XP0  Var_03    C5   C6   NAW  CAL  175.72  30.0  2
 XP0  Var_04    CAM  NAW  CAL  CAJ   12.80  30.0  1
 XP0  Var_05    NAW  CAM  CAK  CAJ  -31.15  30.0  1
 XP0  Var_06    NAW  CAL  CAJ  CAK  -31.85  30.0  1

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
 XP0  plan-1  CAC   0.020
 XP0  plan-1  CAB   0.020
 XP0  plan-1  CAQ   0.020
 XP0  plan-1  CAG   0.020
 XP0  plan-1  CAE   0.020
 XP0  plan-1  CAD   0.020
 XP0  plan-1  CAF   0.020
 XP0  plan-1  CAH   0.020
 XP0  plan-1  HAG   0.020
 XP0  plan-1  HAH   0.020
 XP0  plan-1  HAE   0.020
 XP0  plan-1  HAD   0.020
 XP0  plan-1  HAF   0.020
 XP0  plan-2  NAW   0.020
 XP0  plan-2  C6    0.020
 XP0  plan-2  C5    0.020
 XP0  plan-2  N1    0.020
 XP0  plan-2  C2    0.020
 XP0  plan-2  NAA   0.020
 XP0  plan-2  N3    0.020
 XP0  plan-2  C4    0.020
 XP0  plan-2  NAP   0.020
 XP0  plan-2  CAI   0.020
 XP0  plan-2  CAS   0.020
 XP0  plan-2  CAC   0.020
 XP0  plan-2  CAB   0.020
 XP0  plan-2  HAP   0.020
 XP0  plan-2  HAI   0.020
 XP0  plan-3  C2    0.020
 XP0  plan-3  NAA   0.020
 XP0  plan-3  HAA1  0.020
 XP0  plan-3  HAA2  0.020

