# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:28:43 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7-dimethylnaphthalene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2cc(ccc2c(C)c1Nc3ncnc(Nc4ccc(cc4)C#N)n3)C#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
 639  639  6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7-dimethylnaphthalene-2-carbonitrile  ligand  47  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_639
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
 639  CBD  C  CR6   0   0.388   -4.9160  -0.3680   0.1539
 639  CBC  C  CR6   0   0.091    2.8036   0.0048   0.8960
 639  NAW  N  NH1   0  -0.749    0.8624  -1.3920   0.5094
 639  CAG  C  CR16  0  -0.229   -7.2795  -0.7912   0.4497
 639  CAK  C  CR66  0   0.080    4.1569   0.3148   0.5787
 639  NAT  N  N     0  -0.479   -2.3032   0.8234  -0.5520
 639  CBE  C  CR6   0   0.628   -2.4148  -0.3530   0.0637
 639  CAZ  C  CR66  0   0.150    4.8737  -0.5150  -0.3203
 639  NAS  N  N     0  -0.497   -1.3965  -1.1216   0.4312
 639  CBF  C  CR6   0   0.594   -0.1918  -0.6403   0.1420
 639  CAJ  C  CR16  0  -0.421    4.2349  -1.6321  -0.9010
 639  NAV  N  NH1   0  -0.766   -3.6392  -0.8558   0.3680
 639  NAU  N  N     0  -0.444    0.0375   0.5233  -0.4821
 639  CBB  C  CR6   0   0.108    2.9247  -1.9125  -0.6355
 639  NAD  N  NS    0  -0.260  -10.0245   1.1604  -0.4907
 639  CBG  C  CR16  0   0.110   -1.0541   1.1893  -0.7907
 639  CBH  C  CR6   0   0.215    2.2133  -1.0680   0.2637
 639  CCA  C  CR16  0  -0.320    4.8218   1.4353   1.1356
 639  CCB  C  CR16  0  -0.238    6.1216   1.7175   0.8281
 639  CCC  C  CR6   0   0.001    6.8281   0.8774  -0.0635
 639  CAA  C  CR16  0  -0.310    6.2158  -0.2164  -0.6268
 639  CCD  C  CSP   0   0.053    8.1874   1.1701  -0.3821
 639  CAC  C  CH3   0  -0.764    2.0661   0.8357   1.9010
 639  CAI  C  CR16  0  -0.344   -5.9680  -1.1758   0.6109
 639  CBA  C  CR6   0  -0.016   -7.5763   0.4208  -0.1776
 639  CAH  C  CR16  0  -0.297   -5.2177   0.8465  -0.4724
 639  CAF  C  CR16  0  -0.230   -6.5359   1.2286  -0.6332
 639  CAE  C  CSP   0   0.050   -8.9290   0.8283  -0.3501
 639  H1   H  HNH1  0   0.409    0.6442  -2.3157   0.8545
 639  H2   H  HCR6  0   0.283   -8.0747  -1.4303   0.8090
 639  H3   H  HCR6  0   0.259    4.7965  -2.2602  -1.5820
 639  H4   H  HNH1  0   0.419   -3.5924  -1.7475   0.8404
 639  H5   H  HCR6  0   0.271   -0.9193   2.1390  -1.2980
 639  H6   H  HCR6  0   0.269    4.2963   2.0939   1.8124
 639  H7   H  HCR6  0   0.279    6.6129   2.5789   1.2588
 639  H8   H  HCR6  0   0.281    6.7583  -0.8564  -1.3109
 639  H9   H  HCH3  0   0.251    1.8772  -3.7963  -0.5371
 639  H10  H  HCH3  0   0.253    1.3668  -2.7570  -1.8556
 639  H11  H  HCH3  0   0.257    2.9114  -3.6040  -1.9478
 639  H12  H  HCH3  0   0.258    1.7812   1.8027   1.4839
 639  H13  H  HCH3  0   0.262    1.1592   0.3451   2.2433
 639  H14  H  HCH3  0   0.254    2.6808   1.0258   2.7806
 639  H15  H  HCR6  0   0.287   -5.7481  -2.1171   1.0994
 639  H16  H  HCR6  0   0.302   -4.4301   1.4879  -0.8306
 639  H17  H  HCR6  0   0.282   -6.7566   2.1688  -1.1202
 639  CAB  C  CH3   0  -0.729    2.2348  -3.0776  -1.2775
 639  NAB  N  NS    0  -0.251    9.2860   1.4096  -0.6351

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
 639  NAT  CBG  aromatic  1.323  0.020  1.323
 639  NAT  CBE  aromatic  1.333  0.020  1.333
 639  CAI  CAG  aromatic  1.376  0.020  1.376
 639  CAI  CBD  aromatic  1.403  0.020  1.403
 639  NAV  CBE  single    1.358  0.020  1.358
 639  NAV  CBD  single    1.383  0.020  1.383
 639  CBG  NAU  aromatic  1.315  0.020  1.315
 639  CAG  CBA  aromatic  1.397  0.020  1.397
 639  CBE  NAS  aromatic  1.328  0.020  1.328
 639  CBD  CAH  aromatic  1.399  0.020  1.399
 639  NAU  CBF  aromatic  1.340  0.020  1.340
 639  CBA  CAE  single    1.423  0.020  1.423
 639  CBA  CAF  aromatic  1.394  0.020  1.394
 639  NAS  CBF  aromatic  1.329  0.020  1.329
 639  CAH  CAF  aromatic  1.382  0.020  1.382
 639  CAE  NAD  triple    1.153  0.020  1.153
 639  CBF  NAW  single    1.346  0.020  1.346
 639  NAW  CBH  single    1.411  0.020  1.411
 639  CAB  CBB  single    1.499  0.020  1.499
 639  CBH  CBB  aromatic  1.424  0.020  1.424
 639  CBH  CBC  aromatic  1.378  0.020  1.378
 639  CBB  CAJ  aromatic  1.366  0.020  1.366
 639  CAC  CBC  single    1.498  0.020  1.498
 639  CBC  CAK  aromatic  1.424  0.020  1.424
 639  CAJ  CAZ  aromatic  1.412  0.020  1.412
 639  CAK  CAZ  aromatic  1.418  0.020  1.418
 639  CAK  CCA  aromatic  1.417  0.020  1.417
 639  CAZ  CAA  aromatic  1.409  0.020  1.409
 639  CCA  CCB  aromatic  1.365  0.020  1.365
 639  CAA  CCC  aromatic  1.374  0.020  1.374
 639  CCB  CCC  aromatic  1.414  0.020  1.414
 639  CCC  CCD  single    1.427  0.020  1.427
 639  CCD  NAB  triple    1.152  0.020  1.152
 639  NAW  H1   single    0.860  0.020  1.020
 639  CAG  H2   single    0.930  0.020  1.080
 639  CAJ  H3   single    0.930  0.020  1.080
 639  NAV  H4   single    0.860  0.020  1.020
 639  CBG  H5   single    0.930  0.020  1.080
 639  CCA  H6   single    0.930  0.020  1.080
 639  CCB  H7   single    0.930  0.020  1.080
 639  CAA  H8   single    0.930  0.020  1.080
 639  CAB  H9   single    0.970  0.020  1.090
 639  CAB  H10  single    0.970  0.020  1.090
 639  CAB  H11  single    0.970  0.020  1.090
 639  CAC  H12  single    0.970  0.020  1.090
 639  CAC  H13  single    0.970  0.020  1.090
 639  CAC  H14  single    0.970  0.020  1.090
 639  CAI  H15  single    0.930  0.020  1.080
 639  CAH  H16  single    0.930  0.020  1.080
 639  CAF  H17  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
 639  CAH  CBD  CAI  118.94  3.000
 639  CAH  CBD  NAV  125.05  3.000
 639  CAI  CBD  NAV  116.02  3.000
 639  CAC  CBC  CBH  121.92  3.000
 639  CAC  CBC  CAK  119.77  3.000
 639  CBH  CBC  CAK  118.31  3.000
 639  H1   NAW  CBH  118.46  3.000
 639  H1   NAW  CBF  115.77  3.000
 639  CBH  NAW  CBF  125.05  3.000
 639  H2   CAG  CBA  120.38  3.000
 639  H2   CAG  CAI  119.77  3.000
 639  CBA  CAG  CAI  119.84  3.000
 639  CCA  CAK  CAZ  118.34  3.000
 639  CCA  CAK  CBC  122.04  3.000
 639  CAZ  CAK  CBC  119.62  3.000
 639  CBG  NAT  CBE  113.98  3.000
 639  NAV  CBE  NAS  114.53  3.000
 639  NAS  CBE  NAT  125.08  3.000
 639  NAV  CBE  NAT  120.39  3.000
 639  CAA  CAZ  CAJ  120.62  3.000
 639  CAA  CAZ  CAK  119.70  3.000
 639  CAJ  CAZ  CAK  119.67  3.000
 639  CBF  NAS  CBE  115.17  3.000
 639  NAU  CBF  NAS  124.80  3.000
 639  NAS  CBF  NAW  116.64  3.000
 639  NAU  CBF  NAW  118.56  3.000
 639  H3   CAJ  CBB  120.03  3.000
 639  H3   CAJ  CAZ  118.86  3.000
 639  CBB  CAJ  CAZ  121.10  3.000
 639  H4   NAV  CBE  112.94  3.000
 639  H4   NAV  CBD  115.24  3.000
 639  CBE  NAV  CBD  131.82  3.000
 639  CBG  NAU  CBF  114.01  3.000
 639  CAB  CBB  CBH  120.11  3.000
 639  CBH  CBB  CAJ  118.70  3.000
 639  CAB  CBB  CAJ  121.20  3.000
 639  H5   CBG  NAU  116.73  3.000
 639  H5   CBG  NAT  116.33  3.000
 639  NAU  CBG  NAT  126.94  3.000
 639  CBB  CBH  NAW  116.88  3.000
 639  CBB  CBH  CBC  122.51  3.000
 639  NAW  CBH  CBC  120.59  3.000
 639  H6   CCA  CCB  118.56  3.000
 639  H6   CCA  CAK  119.99  3.000
 639  CCB  CCA  CAK  121.45  3.000
 639  H7   CCB  CCC  119.83  3.000
 639  H7   CCB  CCA  120.50  3.000
 639  CCC  CCB  CCA  119.66  3.000
 639  CCD  CCC  CAA  119.76  3.000
 639  CCD  CCC  CCB  119.67  3.000
 639  CAA  CCC  CCB  120.57  3.000
 639  H8   CAA  CCC  120.41  3.000
 639  H8   CAA  CAZ  119.32  3.000
 639  CCC  CAA  CAZ  120.27  3.000
 639  CCC  CCD  NAB  180.00  3.000
 639  H14  CAC  H13  107.18  3.000
 639  H14  CAC  H12  107.53  3.000
 639  H13  CAC  H12  107.62  3.000
 639  H14  CAC  CBC  111.14  3.000
 639  H13  CAC  CBC  111.83  3.000
 639  H12  CAC  CBC  111.33  3.000
 639  H15  CAI  CAG  119.29  3.000
 639  H15  CAI  CBD  119.68  3.000
 639  CAG  CAI  CBD  121.03  3.000
 639  CAE  CBA  CAF  120.26  3.000
 639  CAF  CBA  CAG  119.42  3.000
 639  CAE  CBA  CAG  120.32  3.000
 639  H16  CAH  CAF  119.62  3.000
 639  H16  CAH  CBD  120.53  3.000
 639  CAF  CAH  CBD  119.85  3.000
 639  H17  CAF  CAH  119.17  3.000
 639  H17  CAF  CBA  119.91  3.000
 639  CAH  CAF  CBA  120.92  3.000
 639  CBA  CAE  NAD  180.00  3.000
 639  H11  CAB  H10  108.08  3.000
 639  H11  CAB  H9   107.63  3.000
 639  H10  CAB  H9   106.98  3.000
 639  H11  CAB  CBB  110.72  3.000
 639  H10  CAB  CBB  111.39  3.000
 639  H9   CAB  CBB  111.84  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
 639  CONST_01  CBA  CAG  CAI  CBD    0.00   0.0  0
 639  CONST_02  CBA  CAF  CAH  CBD    0.00   0.0  0
 639  CONST_03  CAJ  CBB  CBH  CBC    0.00   0.0  0
 639  CONST_04  CAJ  CAZ  CAK  CBC    0.00   0.0  0
 639  CONST_05  CAA  CAZ  CAK  CBC  180.00   0.0  0
 639  CONST_06  CCB  CCA  CAK  CBC  180.00   0.0  0
 639  CONST_07  CAH  CBD  CAI  CAG    0.00   0.0  0
 639  CONST_08  CAH  CAF  CBA  CAG    0.00   0.0  0
 639  CONST_09  CBB  CBH  CBC  CAK    0.00   0.0  0
 639  CONST_10  CBB  CAJ  CAZ  CAK    0.00   0.0  0
 639  CONST_11  CCC  CAA  CAZ  CAK    0.00   0.0  0
 639  CONST_12  CCC  CCB  CCA  CAK    0.00   0.0  0
 639  CONST_13  CBF  NAU  CBG  NAT    0.00   0.0  0
 639  CONST_14  CBF  NAS  CBE  NAT    0.00   0.0  0
 639  CONST_15  NAU  CBG  NAT  CBE    0.00   0.0  0
 639  CONST_16  NAU  CBF  NAS  CBE    0.00   0.0  0
 639  CONST_17  CBH  CBB  CAJ  CAZ    0.00   0.0  0
 639  CONST_18  CBH  CBC  CAK  CAZ    0.00   0.0  0
 639  CONST_19  CCB  CCA  CAK  CAZ    0.00   0.0  0
 639  CONST_20  CCB  CCC  CAA  CAZ    0.00   0.0  0
 639  CONST_21  CBG  NAT  CBE  NAS    0.00   0.0  0
 639  CONST_22  CBG  NAU  CBF  NAS    0.00   0.0  0
 639  CONST_23  CCA  CAK  CAZ  CAJ  180.00   0.0  0
 639  CONST_24  CCC  CAA  CAZ  CAJ  180.00   0.0  0
 639  CONST_25  CAA  CAZ  CAJ  CBB  180.00   0.0  0
 639  CONST_26  CCA  CAK  CBC  CBH  180.00   0.0  0
 639  CONST_27  CAA  CAZ  CAK  CCA    0.00   0.0  0
 639  CONST_28  CAA  CCC  CCB  CCA    0.00   0.0  0
 639  CONST_29  CAF  CBA  CAG  CAI    0.00   0.0  0
 639  CONST_30  CAF  CAH  CBD  CAI    0.00   0.0  0
 639  CONST_31  CAB  CBB  CBH  CBC  180.00   0.0  0
 639  CONST_32  CBG  NAU  CBF  NAW  180.00   0.0  0
 639  CONST_33  CBE  NAS  CBF  NAW  180.00   0.0  0
 639  CONST_34  CAJ  CBB  CBH  NAW  180.00   0.0  0
 639  CONST_35  CAK  CBC  CBH  NAW  180.00   0.0  0
 639  CONST_36  NAV  CBD  CAI  CAG  180.00   0.0  0
 639  CONST_37  CAB  CBB  CAJ  CAZ  180.00   0.0  0
 639  CONST_38  CAC  CBC  CAK  CAZ  180.00   0.0  0
 639  CONST_39  CCD  CCC  CAA  CAZ  180.00   0.0  0
 639  CONST_40  NAV  CBE  NAS  CBF  180.00   0.0  0
 639  CONST_41  CBG  NAT  CBE  NAV  180.00   0.0  0
 639  CONST_42  CAF  CAH  CBD  NAV  180.00   0.0  0
 639  CONST_43  CAC  CBC  CBH  CBB  180.00   0.0  0
 639  CONST_44  CAC  CBC  CAK  CCA    0.00   0.0  0
 639  CONST_45  CCD  CCC  CCB  CCA  180.00   0.0  0
 639  CONST_46  CAE  CBA  CAG  CAI  180.00   0.0  0
 639  CONST_47  CAE  CBA  CAF  CAH  180.00   0.0  0
 639  CONST_48  H2   CAG  CAI  CBD  180.00   0.0  0
 639  CONST_49  H17  CAF  CAH  CBD  180.00   0.0  0
 639  CONST_50  H6   CCA  CAK  CBC    0.00   0.0  0
 639  CONST_51  H3   CAJ  CAZ  CAK  180.00   0.0  0
 639  CONST_52  H8   CAA  CAZ  CAK  180.00   0.0  0
 639  CONST_53  H7   CCB  CCA  CAK  180.00   0.0  0
 639  CONST_54  H5   CBG  NAT  CBE  180.00   0.0  0
 639  CONST_55  H16  CAH  CBD  CAI  180.00   0.0  0
 639  CONST_56  H15  CAI  CAG  CBA  180.00   0.0  0
 639  Var_01    NAT  CBE  NAV  CBD    0.25  30.0  2
 639  Var_02    CBF  NAW  CBH  CBC   67.80  30.0  2
 639  Var_03    CAI  CBD  NAV  CBE  179.93  30.0  2
 639  Var_04    CBH  NAW  CBF  NAS  178.44  30.0  2
 639  Var_05    H12  CAC  CBC  CAK   74.90  30.0  2
 639  Var_06    H9   CAB  CBB  CAJ  119.28  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
 639  plan-1  NAW  0.020
 639  plan-1  NAT  0.020
 639  plan-1  CBE  0.020
 639  plan-1  NAS  0.020
 639  plan-1  CBF  0.020
 639  plan-1  NAV  0.020
 639  plan-1  NAU  0.020
 639  plan-1  CBG  0.020
 639  plan-1  H5   0.020
 639  plan-2  CBD  0.020
 639  plan-2  CAG  0.020
 639  plan-2  NAV  0.020
 639  plan-2  NAD  0.020
 639  plan-2  CAI  0.020
 639  plan-2  CBA  0.020
 639  plan-2  CAH  0.020
 639  plan-2  CAF  0.020
 639  plan-2  CAE  0.020
 639  plan-2  H2   0.020
 639  plan-2  H15  0.020
 639  plan-2  H16  0.020
 639  plan-2  H17  0.020
 639  plan-3  CBC  0.020
 639  plan-3  NAW  0.020
 639  plan-3  CAK  0.020
 639  plan-3  CAZ  0.020
 639  plan-3  CAJ  0.020
 639  plan-3  CBB  0.020
 639  plan-3  CBH  0.020
 639  plan-3  CCA  0.020
 639  plan-3  CCB  0.020
 639  plan-3  CCC  0.020
 639  plan-3  CAA  0.020
 639  plan-3  CCD  0.020
 639  plan-3  CAC  0.020
 639  plan-3  H3   0.020
 639  plan-3  H6   0.020
 639  plan-3  H7   0.020
 639  plan-3  H8   0.020
 639  plan-3  CAB  0.020
 639  plan-3  NAB  0.020

