# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:11:28 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-({6-[(piperidin-4-ylmethyl)amino]pyrimidin-4-yl}amino)pyrazine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cnc(Nc2cc(NCC3CCNCC3)ncn2)cn1
#
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
 YM7  YM7  5-({6-[(piperidin-4-ylmethyl)amino]pyrimidin-4-yl}amino)pyrazine-2-carbonitrile  ligand  41  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YM7
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
 YM7  CAI   C  CH2   0  -0.427  -5.3709  -1.5434   0.6183
 YM7  CAG   C  CH2   0  -0.316  -6.8852  -1.4874   0.4316
 YM7  NAP   N  NH1   0  -0.576  -7.3050  -0.9256  -0.8417
 YM7  CAH   C  CH2   0  -0.315  -6.7018   0.3766  -1.0747
 YM7  CAJ   C  CH2   0  -0.423  -5.1798   0.3946  -0.9471
 YM7  CAW   C  CH1   0  -0.291  -4.7357  -0.1706   0.4021
 YM7  CAK   C  CH2   0  -0.240  -3.2222  -0.2742   0.5216
 YM7  NAQ   N  NH1   0  -0.657  -2.5960   1.0259   0.4556
 YM7  C6    C  CR6   0   0.546  -1.2725   1.2263   0.4040
 YM7  C5    C  CR16  0  -0.529  -0.3509   0.1783   0.2974
 YM7  N1    N  N     0  -0.471  -0.8531   2.5055   0.4517
 YM7  C2    C  CR16  0   0.060   0.4443   2.7002   0.3840
 YM7  N3    N  N     0  -0.454   1.4053   1.7942   0.2712
 YM7  C4    C  CR6   0   0.557   0.9898   0.5320   0.2278
 YM7  NAR   N  NH1   0  -0.758   1.9073  -0.4948   0.1135
 YM7  CAT   C  CR6   0   0.507   3.2624  -0.4886  -0.0024
 YM7  CAE   C  CR16  0  -0.170   3.9061  -1.7512  -0.1113
 YM7  NAN   N  N     0  -0.345   5.1987  -1.8521  -0.2287
 YM7  CAS   C  CR6   0   0.123   5.9030  -0.7122  -0.2423
 YM7  CAB   C  CSP   0   0.060   7.3217  -0.8118  -0.3709
 YM7  NAA   N  NS    0  -0.242   8.4675  -0.8784  -0.4692
 YM7  CAD   C  CR16  0  -0.037   5.2809   0.5193  -0.1364
 YM7  NAO   N  N     0  -0.382   3.9668   0.6296  -0.0174
 YM7  HAI1  H  HCH2  0   0.230  -5.1358  -1.9180   1.6189
 YM7  HAI2  H  HCH2  0   0.215  -4.9429  -2.2587  -0.0941
 YM7  HAG1  H  HCH2  0   0.235  -7.3117  -2.4875   0.5336
 YM7  HAG2  H  HCH2  0   0.214  -7.3223  -0.8795   1.2316
 YM7  HAW   H  HCH1  0   0.230  -5.0986   0.4975   1.1958
 YM7  HAP   H  HNH1  0   0.337  -7.0217  -1.5543  -1.5850
 YM7  HAH1  H  HCH2  0   0.235  -6.9986   0.7282  -2.0650
 YM7  HAH2  H  HCH2  0   0.214  -7.1300   1.0829  -0.3545
 YM7  HAJ1  H  HCH2  0   0.214  -4.7372  -0.2055  -1.7511
 YM7  HAJ2  H  HCH2  0   0.230  -4.8184   1.4172  -1.0857
 YM7  HAK1  H  HCH2  0   0.240  -2.9591  -0.7772   1.4603
 YM7  HAK2  H  HCH2  0   0.231  -2.8453  -0.9020  -0.2927
 YM7  HAQ   H  HNH1  0   0.390  -3.1616   1.8421   0.6308
 YM7  H5    H  HCR6  0   0.289  -0.6598  -0.8575   0.2706
 YM7  H2    H  HCR6  0   0.254   0.7742   3.7336   0.4255
 YM7  HAR   H  HNH1  0   0.429   1.4937  -1.4157   0.1022
 YM7  HAE   H  HCR6  0   0.298   3.3273  -2.6690  -0.0984
 YM7  HAD   H  HCR6  0   0.296   5.8565   1.4373  -0.1489

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
 YM7  CAI  CAG   single    1.527  0.020  1.527
 YM7  CAI  CAW   single    1.528  0.020  1.528
 YM7  CAG  NAP   single    1.454  0.020  1.454
 YM7  NAP  CAH   single    1.454  0.020  1.454
 YM7  CAH  CAJ   single    1.528  0.020  1.528
 YM7  CAJ  CAW   single    1.529  0.020  1.529
 YM7  CAW  CAK   single    1.522  0.020  1.522
 YM7  CAK  NAQ   single    1.445  0.020  1.445
 YM7  NAQ  C6    single    1.340  0.020  1.340
 YM7  C6   C5    aromatic  1.400  0.020  1.400
 YM7  C6   N1    aromatic  1.347  0.020  1.347
 YM7  C5   C4    aromatic  1.388  0.020  1.388
 YM7  N1   C2    aromatic  1.314  0.020  1.314
 YM7  C2   N3    aromatic  1.325  0.020  1.325
 YM7  N3   C4    aromatic  1.330  0.020  1.330
 YM7  C4   NAR   single    1.382  0.020  1.382
 YM7  NAR  CAT   single    1.360  0.020  1.360
 YM7  CAT  CAE   aromatic  1.421  0.020  1.421
 YM7  CAT  NAO   aromatic  1.322  0.020  1.322
 YM7  CAE  NAN   aromatic  1.302  0.020  1.302
 YM7  NAN  CAS   aromatic  1.340  0.020  1.340
 YM7  CAS  CAB   single    1.428  0.020  1.428
 YM7  CAS  CAD   aromatic  1.384  0.020  1.384
 YM7  CAB  NAA   triple    1.152  0.020  1.152
 YM7  CAD  NAO   aromatic  1.324  0.020  1.324
 YM7  CAI  HAI1  single    0.970  0.020  1.090
 YM7  CAI  HAI2  single    0.970  0.020  1.090
 YM7  CAG  HAG1  single    0.970  0.020  1.090
 YM7  CAG  HAG2  single    0.970  0.020  1.090
 YM7  CAW  HAW   single    0.970  0.020  1.090
 YM7  NAP  HAP   single    0.890  0.020  1.040
 YM7  CAH  HAH1  single    0.970  0.020  1.090
 YM7  CAH  HAH2  single    0.970  0.020  1.090
 YM7  CAJ  HAJ1  single    0.970  0.020  1.090
 YM7  CAJ  HAJ2  single    0.970  0.020  1.090
 YM7  CAK  HAK1  single    0.970  0.020  1.090
 YM7  CAK  HAK2  single    0.970  0.020  1.090
 YM7  NAQ  HAQ   single    0.860  0.020  1.020
 YM7  C5   H5    single    0.930  0.020  1.080
 YM7  C2   H2    single    0.930  0.020  1.080
 YM7  NAR  HAR   single    0.860  0.020  1.020
 YM7  CAE  HAE   single    0.930  0.020  1.080
 YM7  CAD  HAD   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
 YM7  HAI2  CAI  HAI1  106.67  3.000
 YM7  HAI2  CAI  CAW   109.38  3.000
 YM7  HAI1  CAI  CAW   110.35  3.000
 YM7  HAI2  CAI  CAG   109.36  3.000
 YM7  HAI1  CAI  CAG   109.73  3.000
 YM7  CAW   CAI  CAG   111.23  3.000
 YM7  HAG2  CAG  HAG1  106.51  3.000
 YM7  HAG2  CAG  NAP   108.05  3.000
 YM7  HAG1  CAG  NAP   108.84  3.000
 YM7  HAG2  CAG  CAI   109.07  3.000
 YM7  HAG1  CAG  CAI   110.02  3.000
 YM7  NAP   CAG  CAI   114.06  3.000
 YM7  HAP   NAP  CAH   108.78  3.000
 YM7  HAP   NAP  CAG   108.77  3.000
 YM7  CAH   NAP  CAG   111.51  3.000
 YM7  HAH2  CAH  HAH1  106.40  3.000
 YM7  HAH2  CAH  CAJ   109.07  3.000
 YM7  HAH1  CAH  CAJ   110.04  3.000
 YM7  HAH2  CAH  NAP   108.05  3.000
 YM7  HAH1  CAH  NAP   108.72  3.000
 YM7  CAJ   CAH  NAP   114.24  3.000
 YM7  HAJ2  CAJ  HAJ1  106.58  3.000
 YM7  HAJ2  CAJ  CAW   111.21  3.000
 YM7  HAJ1  CAJ  CAW   109.12  3.000
 YM7  HAJ2  CAJ  CAH   109.25  3.000
 YM7  HAJ1  CAJ  CAH   109.54  3.000
 YM7  CAW   CAJ  CAH   111.03  3.000
 YM7  HAW   CAW  CAK   108.24  3.000
 YM7  HAW   CAW  CAJ   108.46  3.000
 YM7  CAK   CAW  CAJ   112.55  3.000
 YM7  HAW   CAW  CAI   107.86  3.000
 YM7  CAK   CAW  CAI   109.95  3.000
 YM7  CAJ   CAW  CAI   109.65  3.000
 YM7  HAK2  CAK  HAK1  106.91  3.000
 YM7  HAK2  CAK  NAQ   109.44  3.000
 YM7  HAK1  CAK  NAQ   110.36  3.000
 YM7  HAK2  CAK  CAW   108.84  3.000
 YM7  HAK1  CAK  CAW   109.69  3.000
 YM7  NAQ   CAK  CAW   111.49  3.000
 YM7  HAQ   NAQ  C6    116.09  3.000
 YM7  HAQ   NAQ  CAK   118.52  3.000
 YM7  C6    NAQ  CAK   124.38  3.000
 YM7  N1    C6   C5    120.58  3.000
 YM7  N1    C6   NAQ   116.63  3.000
 YM7  C5    C6   NAQ   122.78  3.000
 YM7  H5    C5   C4    121.25  3.000
 YM7  H5    C5   C6    122.08  3.000
 YM7  C4    C5   C6    116.67  3.000
 YM7  C2    N1   C6    116.51  3.000
 YM7  H2    C2   N3    115.69  3.000
 YM7  H2    C2   N1    116.05  3.000
 YM7  N3    C2   N1    128.25  3.000
 YM7  C4    N3   C2    115.16  3.000
 YM7  NAR   C4   N3    120.05  3.000
 YM7  NAR   C4   C5    117.13  3.000
 YM7  N3    C4   C5    122.82  3.000
 YM7  HAR   NAR  CAT   114.29  3.000
 YM7  HAR   NAR  C4    114.00  3.000
 YM7  CAT   NAR  C4    131.70  3.000
 YM7  NAO   CAT  CAE   120.62  3.000
 YM7  NAO   CAT  NAR   122.40  3.000
 YM7  CAE   CAT  NAR   116.98  3.000
 YM7  HAE   CAE  NAN   117.72  3.000
 YM7  HAE   CAE  CAT   120.59  3.000
 YM7  NAN   CAE  CAT   121.69  3.000
 YM7  CAS   NAN  CAE   117.19  3.000
 YM7  CAD   CAS  CAB   121.04  3.000
 YM7  CAD   CAS  NAN   121.33  3.000
 YM7  CAB   CAS  NAN   117.63  3.000
 YM7  NAA   CAB  CAS   180.00  3.000
 YM7  HAD   CAD  NAO   117.23  3.000
 YM7  HAD   CAD  CAS   120.95  3.000
 YM7  NAO   CAD  CAS   121.82  3.000
 YM7  CAD   NAO  CAT   117.35  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
 YM7  CONST_01  N3   C4   C5   C6      0.00   0.0  0
 YM7  CONST_02  N3   C2   N1   C6      0.00   0.0  0
 YM7  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 YM7  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 YM7  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 YM7  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 YM7  CONST_07  CAS  NAN  CAE  CAT     0.00   0.0  0
 YM7  CONST_08  CAS  CAD  NAO  CAT     0.00   0.0  0
 YM7  CONST_09  CAD  NAO  CAT  CAE     0.00   0.0  0
 YM7  CONST_10  CAD  CAS  NAN  CAE     0.00   0.0  0
 YM7  CONST_11  NAO  CAT  CAE  NAN     0.00   0.0  0
 YM7  CONST_12  NAO  CAD  CAS  NAN     0.00   0.0  0
 YM7  CONST_13  C4   C5   C6   NAQ   180.00   0.0  0
 YM7  CONST_14  C2   N1   C6   NAQ   180.00   0.0  0
 YM7  CONST_15  NAR  C4   C5   C6    180.00   0.0  0
 YM7  CONST_16  NAR  C4   N3   C2    180.00   0.0  0
 YM7  CONST_17  NAN  CAE  CAT  NAR   180.00   0.0  0
 YM7  CONST_18  CAD  NAO  CAT  NAR   180.00   0.0  0
 YM7  CONST_19  CAB  CAS  NAN  CAE   180.00   0.0  0
 YM7  CONST_20  NAO  CAD  CAS  CAB   180.00   0.0  0
 YM7  CONST_21  H2   C2   N1   C6    180.00   0.0  0
 YM7  CONST_22  H5   C5   C6   N1    180.00   0.0  0
 YM7  CONST_23  HAD  CAD  NAO  CAT   180.00   0.0  0
 YM7  CONST_24  HAE  CAE  NAN  CAS   180.00   0.0  0
 YM7  CONST_25  C5   C6   NAQ  CAK     0.00   0.0  0
 YM7  CONST_26  N1   C6   NAQ  CAK   180.00   0.0  0
 YM7  CONST_27  HAQ  NAQ  C6   C5    180.00   0.0  0
 YM7  Var_01    CAH  NAP  CAG  CAI   -53.23  30.0  1
 YM7  Var_02    CAJ  CAH  NAP  CAG    53.31  30.0  1
 YM7  Var_03    CAW  CAI  CAG  NAP    54.13  30.0  1
 YM7  Var_04    CAW  CAJ  CAH  NAP   -54.07  30.0  1
 YM7  Var_05    CAT  NAR  C4   C5    178.48  30.0  2
 YM7  Var_06    CAE  CAT  NAR  C4   -179.55  30.0  2
 YM7  Var_07    C6   NAQ  CAK  CAW  -173.24  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
 YM7  chir_01  CAW  CAI  CAJ  CAK  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
 YM7  plan-1  NAQ  0.020
 YM7  plan-1  C6   0.020
 YM7  plan-1  C5   0.020
 YM7  plan-1  N1   0.020
 YM7  plan-1  C2   0.020
 YM7  plan-1  N3   0.020
 YM7  plan-1  C4   0.020
 YM7  plan-1  NAR  0.020
 YM7  plan-1  H5   0.020
 YM7  plan-1  H2   0.020
 YM7  plan-2  NAR  0.020
 YM7  plan-2  CAT  0.020
 YM7  plan-2  CAE  0.020
 YM7  plan-2  NAN  0.020
 YM7  plan-2  CAS  0.020
 YM7  plan-2  CAB  0.020
 YM7  plan-2  NAA  0.020
 YM7  plan-2  CAD  0.020
 YM7  plan-2  NAO  0.020
 YM7  plan-2  HAE  0.020
 YM7  plan-2  HAD  0.020
 YM7  plan-3  CAK  0.020
 YM7  plan-3  NAQ  0.020
 YM7  plan-3  C6   0.020
 YM7  plan-3  HAQ  0.020

