# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:28:40 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-[4-[[4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-5-methyl-pyrimidin-2-yl]amino]phenyl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc(Nc2ccc(CC#N)cc2)nc1Nc3cc([nH]n3)C4CC4
#
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
 EBD  EBD  2-[4-[[4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-5-methyl-pyrimidin-2-yl]amino]phenyl]ethanenitrile  ligand  45  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EBD
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
 EBD  N1    N  N     0  -0.493  -1.0525   2.3979   0.0679
 EBD  C2    C  CR6   0   0.613  -0.5036   1.2029  -0.0463
 EBD  N3    N  N     0  -0.527   0.8031   0.9315  -0.0243
 EBD  C4    C  CR6   0   0.536   1.6372   1.9458   0.1216
 EBD  C5    C  CR6   0  -0.095   1.1734   3.2808   0.2484
 EBD  C6    C  CR16  0  -0.042  -0.1909   3.4112   0.2120
 EBD  NAG   N  NH1   0  -0.761   2.9683   1.7029   0.1519
 EBD  CAH   C  CR5   0   0.454   3.6295   0.4865   0.0780
 EBD  NAI   N  NH1   0  -0.774  -1.2843   0.0916  -0.2057
 EBD  CAJ   C  CR6   0   0.361  -2.6580  -0.0700  -0.2815
 EBD  CAK   C  CR16  0  -0.346  -3.1222  -1.3746  -0.4991
 EBD  CAL   C  CR16  0  -0.271  -4.4737  -1.6439  -0.5853
 EBD  CAM   C  CR6   0   0.087  -5.4124  -0.6244  -0.4602
 EBD  CAN   C  CR16  0  -0.277  -4.9530   0.6669  -0.2455
 EBD  CAO   C  CR16  0  -0.303  -3.5986   0.9561  -0.1564
 EBD  NAP   N  N     0  -0.327   4.9485   0.5189   0.0990
 EBD  NAQ   N  NR15  0  -0.522   5.3188  -0.7638   0.0313
 EBD  CAR   C  CR5   0   0.493   4.2817  -1.6143  -0.0330
 EBD  CAS   C  CR15  0  -0.544   3.1426  -0.8335  -0.0066
 EBD  CAT   C  CH1   0  -0.371   4.4037  -3.0757  -0.1075
 EBD  CAU   C  CH2   0  -0.475   5.4799  -3.8086   0.6497
 EBD  CAV   C  CH2   0  -0.630  -6.8905  -0.9215  -0.5375
 EBD  CAW   C  CH2   0  -0.477   5.5444  -3.7316  -0.8385
 EBD  CAX   C  CH3   0  -0.760   2.0949   4.4467   0.4138
 EBD  CAY   C  CSP   0   0.138  -7.4196  -1.3241   0.7596
 EBD  NAZ   N  NS    0  -0.277  -7.8220  -1.6364   1.7915
 EBD  H6    H  HCR6  0   0.259  -0.6336   4.3980   0.3072
 EBD  HNAG  H  HNH1  0   0.419   3.5804   2.4983   0.2488
 EBD  HNAI  H  HNH1  0   0.407  -0.7444  -0.7551  -0.2991
 EBD  HAK   H  HCR6  0   0.270  -2.4115  -2.1861  -0.6038
 EBD  HAL   H  HCR6  0   0.260  -4.7972  -2.6635  -0.7577
 EBD  HAN   H  HCR6  0   0.258  -5.6630   1.4794  -0.1464
 EBD  HAO   H  HCR6  0   0.286  -3.2755   1.9707   0.0077
 EBD  HNAQ  H  HNR5  0   0.418   6.3015  -0.9848   0.0296
 EBD  HAS   H  HCR5  0   0.272   2.1236  -1.1694  -0.0438
 EBD  HAT   H  HCH1  0   0.276   3.4452  -3.5748  -0.1749
 EBD  HAU   H  HCH2  0   0.257   6.1847  -3.2212   1.2254
 EBD  HAUA  H  HCH2  0   0.266   5.2089  -4.7507   1.1076
 EBD  HAV   H  HCH2  0   0.328  -7.4533  -0.0482  -0.8720
 EBD  HAVA  H  HCH2  0   0.328  -7.0983  -1.7235  -1.2486
 EBD  HAW   H  HCH2  0   0.266   5.3183  -4.6203  -1.4125
 EBD  HAWA  H  HCH2  0   0.257   6.2948  -3.0933  -1.2885
 EBD  HAX   H  HCH3  0   0.250   2.7792   4.5542  -0.4315
 EBD  HAXA  H  HCH3  0   0.264   1.5280   5.3736   0.4880
 EBD  HAXB  H  HCH3  0   0.251   2.7036   4.3658   1.3178

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
 EBD  N1   C2    aromatic  1.320  0.020  1.320
 EBD  N1   C6    aromatic  1.338  0.020  1.338
 EBD  C2   N3    aromatic  1.335  0.020  1.335
 EBD  C2   NAI   single    1.367  0.020  1.367
 EBD  N3   C4    aromatic  1.321  0.020  1.321
 EBD  C4   C5    aromatic  1.419  0.020  1.419
 EBD  C4   NAG   single    1.353  0.020  1.353
 EBD  C5   C6    aromatic  1.371  0.020  1.371
 EBD  C5   CAX   single    1.495  0.020  1.495
 EBD  NAG  CAH   single    1.386  0.020  1.386
 EBD  CAH  NAP   aromatic  1.320  0.020  1.320
 EBD  CAH  CAS   aromatic  1.409  0.020  1.409
 EBD  NAI  CAJ   single    1.385  0.020  1.385
 EBD  CAJ  CAK   aromatic  1.402  0.020  1.402
 EBD  CAJ  CAO   aromatic  1.398  0.020  1.398
 EBD  CAK  CAL   aromatic  1.381  0.020  1.381
 EBD  CAL  CAM   aromatic  1.391  0.020  1.391
 EBD  CAM  CAN   aromatic  1.387  0.020  1.387
 EBD  CAM  CAV   single    1.510  0.020  1.510
 EBD  CAN  CAO   aromatic  1.388  0.020  1.388
 EBD  NAP  NAQ   aromatic  1.337  0.020  1.337
 EBD  NAQ  CAR   aromatic  1.343  0.020  1.343
 EBD  CAR  CAS   aromatic  1.381  0.020  1.381
 EBD  CAR  CAT   single    1.468  0.020  1.468
 EBD  CAT  CAU   single    1.506  0.020  1.506
 EBD  CAT  CAW   single    1.505  0.020  1.505
 EBD  CAU  CAW   single    1.492  0.020  1.492
 EBD  CAV  CAY   single    1.458  0.020  1.458
 EBD  CAY  NAZ   triple    1.151  0.020  1.151
 EBD  C6   H6    single    0.930  0.020  1.080
 EBD  NAG  HNAG  single    0.860  0.020  1.020
 EBD  NAI  HNAI  single    0.860  0.020  1.020
 EBD  CAK  HAK   single    0.930  0.020  1.080
 EBD  CAL  HAL   single    0.930  0.020  1.080
 EBD  CAN  HAN   single    0.930  0.020  1.080
 EBD  CAO  HAO   single    0.930  0.020  1.080
 EBD  NAQ  HNAQ  single    0.860  0.020  1.020
 EBD  CAS  HAS   single    0.930  0.020  1.080
 EBD  CAT  HAT   single    0.970  0.020  1.090
 EBD  CAU  HAU   single    0.970  0.020  1.090
 EBD  CAU  HAUA  single    0.970  0.020  1.090
 EBD  CAV  HAV   single    0.970  0.020  1.090
 EBD  CAV  HAVA  single    0.970  0.020  1.090
 EBD  CAW  HAW   single    0.970  0.020  1.090
 EBD  CAW  HAWA  single    0.970  0.020  1.090
 EBD  CAX  HAX   single    0.970  0.020  1.090
 EBD  CAX  HAXA  single    0.970  0.020  1.090
 EBD  CAX  HAXB  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
 EBD  C6    N1   C2    115.29  3.000
 EBD  NAI   C2   N3    113.30  3.000
 EBD  NAI   C2   N1    120.56  3.000
 EBD  N3    C2   N1    126.14  3.000
 EBD  C4    N3   C2    117.63  3.000
 EBD  NAG   C4   C5    119.23  3.000
 EBD  NAG   C4   N3    119.05  3.000
 EBD  C5    C4   N3    121.72  3.000
 EBD  CAX   C5   C6    122.82  3.000
 EBD  CAX   C5   C4    122.82  3.000
 EBD  C6    C5   C4    114.35  3.000
 EBD  H6    C6   C5    119.33  3.000
 EBD  H6    C6   N1    115.80  3.000
 EBD  C5    C6   N1    124.87  3.000
 EBD  HNAG  NAG  CAH   114.06  3.000
 EBD  HNAG  NAG  C4    117.23  3.000
 EBD  CAH   NAG  C4    128.70  3.000
 EBD  CAS   CAH  NAP   111.67  3.000
 EBD  CAS   CAH  NAG   131.31  3.000
 EBD  NAP   CAH  NAG   117.02  3.000
 EBD  HNAI  NAI  CAJ   115.34  3.000
 EBD  HNAI  NAI  C2    112.79  3.000
 EBD  CAJ   NAI  C2    131.86  3.000
 EBD  CAO   CAJ  CAK   118.32  3.000
 EBD  CAO   CAJ  NAI   125.23  3.000
 EBD  CAK   CAJ  NAI   116.45  3.000
 EBD  HAK   CAK  CAL   119.33  3.000
 EBD  HAK   CAK  CAJ   119.66  3.000
 EBD  CAL   CAK  CAJ   121.02  3.000
 EBD  HAL   CAL  CAM   120.16  3.000
 EBD  HAL   CAL  CAK   119.06  3.000
 EBD  CAM   CAL  CAK   120.78  3.000
 EBD  CAV   CAM  CAN   121.02  3.000
 EBD  CAV   CAM  CAL   120.78  3.000
 EBD  CAN   CAM  CAL   118.20  3.000
 EBD  HAN   CAN  CAO   118.51  3.000
 EBD  HAN   CAN  CAM   119.68  3.000
 EBD  CAO   CAN  CAM   121.81  3.000
 EBD  HAO   CAO  CAN   119.92  3.000
 EBD  HAO   CAO  CAJ   120.21  3.000
 EBD  CAN   CAO  CAJ   119.87  3.000
 EBD  NAQ   NAP  CAH   104.63  3.000
 EBD  HNAQ  NAQ  CAR   127.91  3.000
 EBD  HNAQ  NAQ  NAP   118.74  3.000
 EBD  CAR   NAQ  NAP   113.35  3.000
 EBD  CAT   CAR  CAS   129.21  3.000
 EBD  CAT   CAR  NAQ   124.65  3.000
 EBD  CAS   CAR  NAQ   106.14  3.000
 EBD  HAS   CAS  CAR   127.24  3.000
 EBD  HAS   CAS  CAH   128.54  3.000
 EBD  CAR   CAS  CAH   104.22  3.000
 EBD  HAT   CAT  CAW   116.09  3.000
 EBD  HAT   CAT  CAU   116.07  3.000
 EBD  CAW   CAT  CAU    59.38  3.000
 EBD  HAT   CAT  CAR   112.85  3.000
 EBD  CAW   CAT  CAR   121.42  3.000
 EBD  CAU   CAT  CAR   121.21  3.000
 EBD  HAUA  CAU  HAU   114.22  3.000
 EBD  HAUA  CAU  CAW   118.55  3.000
 EBD  HAU   CAU  CAW   118.30  3.000
 EBD  HAUA  CAU  CAT   117.22  3.000
 EBD  HAU   CAU  CAT   117.92  3.000
 EBD  CAW   CAU  CAT    60.28  3.000
 EBD  HAVA  CAV  HAV   106.85  3.000
 EBD  HAVA  CAV  CAY   107.91  3.000
 EBD  HAV   CAV  CAY   107.85  3.000
 EBD  HAVA  CAV  CAM   111.36  3.000
 EBD  HAV   CAV  CAM   111.29  3.000
 EBD  CAY   CAV  CAM   111.36  3.000
 EBD  HAWA  CAW  HAW   114.11  3.000
 EBD  HAWA  CAW  CAU   118.35  3.000
 EBD  HAW   CAW  CAU   118.55  3.000
 EBD  HAWA  CAW  CAT   118.03  3.000
 EBD  HAW   CAW  CAT   117.21  3.000
 EBD  CAU   CAW  CAT    60.34  3.000
 EBD  HAXB  CAX  HAXA  107.25  3.000
 EBD  HAXB  CAX  HAX   107.36  3.000
 EBD  HAXA  CAX  HAX   107.15  3.000
 EBD  HAXB  CAX  C5    112.15  3.000
 EBD  HAXA  CAX  C5    110.51  3.000
 EBD  HAX   CAX  C5    112.15  3.000
 EBD  NAZ   CAY  CAV   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
 EBD  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 EBD  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 EBD  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 EBD  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 EBD  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 EBD  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 EBD  CONST_07  CAR   NAQ  NAP  CAH     0.00   0.0  0
 EBD  CONST_08  NAQ   CAR  CAS  CAH     0.00   0.0  0
 EBD  CONST_09  CAM   CAL  CAK  CAJ     0.00   0.0  0
 EBD  CONST_10  CAM   CAN  CAO  CAJ     0.00   0.0  0
 EBD  CONST_11  CAN   CAO  CAJ  CAK     0.00   0.0  0
 EBD  CONST_12  CAN   CAM  CAL  CAK     0.00   0.0  0
 EBD  CONST_13  CAO   CAJ  CAK  CAL     0.00   0.0  0
 EBD  CONST_14  CAO   CAN  CAM  CAL     0.00   0.0  0
 EBD  CONST_15  CAR   CAS  CAH  NAP     0.00   0.0  0
 EBD  CONST_16  CAS   CAR  NAQ  NAP     0.00   0.0  0
 EBD  CONST_17  CAS   CAH  NAP  NAQ     0.00   0.0  0
 EBD  CONST_18  CAT   CAR  CAS  CAH   180.00   0.0  0
 EBD  CONST_19  CAT   CAR  NAQ  NAP   180.00   0.0  0
 EBD  CONST_20  CAX   C5   C6   N1    180.00   0.0  0
 EBD  CONST_21  NAG   C4   N3   C2    180.00   0.0  0
 EBD  CONST_22  CAX   C5   C4   N3    180.00   0.0  0
 EBD  CONST_23  NAI   C2   N3   C4    180.00   0.0  0
 EBD  CONST_24  NAI   C2   N1   C6    180.00   0.0  0
 EBD  CONST_25  NAG   C4   C5   C6    180.00   0.0  0
 EBD  CONST_26  NAQ   NAP  CAH  NAG   180.00   0.0  0
 EBD  CONST_27  CAR   CAS  CAH  NAG   180.00   0.0  0
 EBD  CONST_28  CAL   CAK  CAJ  NAI   180.00   0.0  0
 EBD  CONST_29  CAN   CAO  CAJ  NAI   180.00   0.0  0
 EBD  CONST_30  CAV   CAM  CAL  CAK   180.00   0.0  0
 EBD  CONST_31  CAV   CAM  CAN  CAO   180.00   0.0  0
 EBD  CONST_32  H6    C6   N1   C2    180.00   0.0  0
 EBD  CONST_33  HNAQ  NAQ  NAP  CAH   180.00   0.0  0
 EBD  CONST_34  HAL   CAL  CAK  CAJ   180.00   0.0  0
 EBD  CONST_35  HAN   CAN  CAO  CAJ   180.00   0.0  0
 EBD  CONST_36  HAO   CAO  CAJ  CAK   180.00   0.0  0
 EBD  CONST_37  HAK   CAK  CAL  CAM   180.00   0.0  0
 EBD  CONST_38  HAS   CAS  CAH  NAP   180.00   0.0  0
 EBD  Var_01    CAU   CAT  CAR  NAQ    36.94  30.0  2
 EBD  Var_02    CAW   CAU  CAT  CAR  -110.47  30.0  1
 EBD  Var_03    CAJ   NAI  C2   N1      0.03  30.0  2
 EBD  Var_04    CAK   CAJ  NAI  C2    177.77  30.0  2
 EBD  Var_05    CAH   NAG  C4   N3     -1.60  30.0  2
 EBD  Var_06    NAP   CAH  NAG  C4    178.49  30.0  2
 EBD  Var_07    CAY   CAV  CAM  CAL    85.42  30.0  2
 EBD  Var_08    HAX   CAX  C5   C4     60.31  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
 EBD  chir_01  CAT  CAR  CAU  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
 EBD  plan-1  NAG   0.020
 EBD  plan-1  CAH   0.020
 EBD  plan-1  NAP   0.020
 EBD  plan-1  NAQ   0.020
 EBD  plan-1  CAR   0.020
 EBD  plan-1  CAS   0.020
 EBD  plan-1  CAT   0.020
 EBD  plan-1  HNAQ  0.020
 EBD  plan-1  HAS   0.020
 EBD  plan-2  N1    0.020
 EBD  plan-2  C2    0.020
 EBD  plan-2  N3    0.020
 EBD  plan-2  C4    0.020
 EBD  plan-2  C5    0.020
 EBD  plan-2  C6    0.020
 EBD  plan-2  NAG   0.020
 EBD  plan-2  NAI   0.020
 EBD  plan-2  CAX   0.020
 EBD  plan-2  H6    0.020
 EBD  plan-3  NAI   0.020
 EBD  plan-3  CAJ   0.020
 EBD  plan-3  CAK   0.020
 EBD  plan-3  CAL   0.020
 EBD  plan-3  CAM   0.020
 EBD  plan-3  CAN   0.020
 EBD  plan-3  CAO   0.020
 EBD  plan-3  CAV   0.020
 EBD  plan-3  HAK   0.020
 EBD  plan-3  HAL   0.020
 EBD  plan-3  HAN   0.020
 EBD  plan-3  HAO   0.020

