# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:29:18 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-ethyl-5-[3-(5-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(OC)cc(c2)c3ccccc3
#
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
 7DR  7DR  6-ethyl-5-[3-(5-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine  ligand  49  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7DR
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
 7DR  N1    N  N     0  -0.502   4.4078  -0.7268  -1.9214
 7DR  C2    C  CR6   0   0.539   5.5806  -0.6038  -1.3005
 7DR  N3    N  N     0  -0.497   5.7661  -0.3772   0.0050
 7DR  C4    C  CR6   0   0.269   4.6767  -0.2610   0.7531
 7DR  C5    C  CR6   0  -0.318   3.3943  -0.3682   0.2194
 7DR  C6    C  CR6   0   0.455   3.3161  -0.6119  -1.1771
 7DR  CAA   C  CH3   0  -0.666   4.8250   1.5480   2.4672
 7DR  CAB   C  CH3   0  -0.437  -1.0659  -3.4402  -1.6434
 7DR  NAC   N  NH2   0  -0.820   6.6850  -0.6925  -2.0624
 7DR  NAD   N  NH2   0  -0.827   2.1266  -0.7621  -1.7842
 7DR  CAE   C  CSP   0   0.023   1.1470  -0.1616   1.5532
 7DR  CAF   C  CSP   0   0.148   2.2081  -0.2547   0.9849
 7DR  CAG   C  CR16  0  -0.266  -6.9163   2.7450   0.2975
 7DR  CAH   C  CR16  0  -0.240  -6.3864   2.3004  -0.9069
 7DR  CAI   C  CR16  0  -0.240  -6.3047   2.3797   1.4894
 7DR  CAJ   C  CR16  0  -0.309  -5.2551   1.4979  -0.9186
 7DR  CAK   C  CR16  0  -0.310  -5.1729   1.5776   1.4770
 7DR  CAL   C  CR16  0  -0.442  -1.1688  -1.3772   0.2478
 7DR  CAM   C  CR16  0  -0.415  -2.3994   0.4689   1.1823
 7DR  CAN   C  CR16  0  -0.427  -3.3186  -0.7700  -0.6608
 7DR  CAO   C  CH2   0  -0.522   4.8803   0.0423   2.2064
 7DR  CAP   C  CH2   0  -0.658  -0.1680  -0.1075   2.1780
 7DR  OAS   O  O2    0  -0.471  -2.1718  -2.5600  -1.6045
 7DR  CAU   C  CR6   0   0.149  -1.2772  -0.3405   1.1738
 7DR  CAW   C  CR6   0   0.424  -2.1883  -1.5892  -0.6730
 7DR  CAX   C  CR6   0   0.085  -4.6324   1.1225   0.2732
 7DR  CAY   C  CR6   0   0.129  -3.4335   0.2587   0.2632
 7DR  HAA   H  HCH3  0   0.230   5.5728   2.0749   1.8742
 7DR  HAAA  H  HCH3  0   0.231   3.8452   1.9571   2.2188
 7DR  HAAB  H  HCH3  0   0.238   5.0197   1.7608   3.5179
 7DR  HAB   H  HCH3  0   0.231  -0.9595  -4.0016  -0.7117
 7DR  HABA  H  HCH3  0   0.263  -1.2547  -4.1387  -2.4547
 7DR  HABB  H  HCH3  0   0.219  -0.1286  -2.9140  -1.8460
 7DR  HNAC  H  HNH2  0   0.395   6.6087  -1.0107  -3.0125
 7DR  HNAA  H  HNH2  0   0.395   7.5844  -0.7535  -1.6187
 7DR  HNAD  H  HNH2  0   0.397   2.0984  -0.7657  -2.7901
 7DR  HNAB  H  HNH2  0   0.401   1.2843  -0.4853  -1.3084
 7DR  HAG   H  HCR6  0   0.258  -7.7991   3.3709   0.3067
 7DR  HAH   H  HCR6  0   0.258  -6.8511   2.5827  -1.8428
 7DR  HAI   H  HCR6  0   0.258  -6.7136   2.7127   2.4346
 7DR  HAJ   H  HCR6  0   0.255  -4.8413   1.1785  -1.8671
 7DR  HAK   H  HCR6  0   0.255  -4.7192   1.2873   2.4164
 7DR  HAL   H  HCR6  0   0.278  -0.2879  -2.0061   0.2657
 7DR  HAM   H  HCR6  0   0.252  -2.4631   1.2875   1.8886
 7DR  HAN   H  HCR6  0   0.260  -4.1125  -0.9632  -1.3722
 7DR  HAO   H  HCH2  0   0.245   4.1183  -0.4605   2.8045
 7DR  HAOA  H  HCH2  0   0.250   5.8511  -0.3504   2.5112
 7DR  HAP   H  HCH2  0   0.292  -0.2273  -0.8614   2.9701
 7DR  HAPA  H  HCH2  0   0.284  -0.3128   0.8582   2.6676

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
 7DR  N1   C6    aromatic  1.326  0.020  1.326
 7DR  N1   C2    aromatic  1.333  0.020  1.333
 7DR  NAC  C2    single    1.345  0.020  1.345
 7DR  C2   N3    aromatic  1.338  0.020  1.338
 7DR  N3   C4    aromatic  1.327  0.020  1.327
 7DR  C5   C4    aromatic  1.393  0.020  1.393
 7DR  C4   CAO   single    1.498  0.020  1.498
 7DR  C6   C5    aromatic  1.420  0.020  1.420
 7DR  C5   CAF   single    1.416  0.020  1.416
 7DR  NAD  C6    single    1.344  0.020  1.344
 7DR  CAO  CAA   single    1.529  0.020  1.529
 7DR  CAA  HAA   single    0.970  0.020  1.090
 7DR  CAA  HAAA  single    0.970  0.020  1.090
 7DR  CAA  HAAB  single    0.970  0.020  1.090
 7DR  CAB  OAS   single    1.414  0.020  1.414
 7DR  CAB  HAB   single    0.970  0.020  1.090
 7DR  CAB  HABA  single    0.970  0.020  1.090
 7DR  CAB  HABB  single    0.970  0.020  1.090
 7DR  NAC  HNAC  single    0.890  0.020  1.040
 7DR  NAC  HNAA  single    0.890  0.020  1.040
 7DR  NAD  HNAD  single    0.890  0.020  1.040
 7DR  NAD  HNAB  single    0.890  0.020  1.040
 7DR  CAF  CAE   triple    1.207  0.020  1.207
 7DR  CAE  CAP   single    1.457  0.020  1.457
 7DR  CAH  CAG   aromatic  1.389  0.020  1.389
 7DR  CAG  CAI   aromatic  1.389  0.020  1.389
 7DR  CAG  HAG   single    0.930  0.020  1.080
 7DR  CAJ  CAH   aromatic  1.387  0.020  1.387
 7DR  CAH  HAH   single    0.930  0.020  1.080
 7DR  CAK  CAI   aromatic  1.387  0.020  1.387
 7DR  CAI  HAI   single    0.930  0.020  1.080
 7DR  CAJ  CAX   aromatic  1.396  0.020  1.396
 7DR  CAJ  HAJ   single    0.930  0.020  1.080
 7DR  CAX  CAK   aromatic  1.396  0.020  1.396
 7DR  CAK  HAK   single    0.930  0.020  1.080
 7DR  CAU  CAL   aromatic  1.394  0.020  1.394
 7DR  CAL  CAW   aromatic  1.390  0.020  1.390
 7DR  CAL  HAL   single    0.930  0.020  1.080
 7DR  CAU  CAM   aromatic  1.384  0.020  1.384
 7DR  CAM  CAY   aromatic  1.399  0.020  1.399
 7DR  CAM  HAM   single    0.930  0.020  1.080
 7DR  CAY  CAN   aromatic  1.387  0.020  1.387
 7DR  CAW  CAN   aromatic  1.396  0.020  1.396
 7DR  CAN  HAN   single    0.930  0.020  1.080
 7DR  CAO  HAO   single    0.970  0.020  1.090
 7DR  CAO  HAOA  single    0.970  0.020  1.090
 7DR  CAP  CAU   single    1.514  0.020  1.514
 7DR  CAP  HAP   single    0.970  0.020  1.090
 7DR  CAP  HAPA  single    0.970  0.020  1.090
 7DR  CAW  OAS   single    1.346  0.020  1.346
 7DR  CAY  CAX   single    1.478  0.020  1.478

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
 7DR  C6    N1   C2    117.06  3.000
 7DR  NAC   C2   N3    116.75  3.000
 7DR  N3    C2   N1    126.32  3.000
 7DR  NAC   C2   N1    116.92  3.000
 7DR  C4    N3   C2    116.82  3.000
 7DR  CAO   C4   C5    120.81  3.000
 7DR  CAO   C4   N3    116.94  3.000
 7DR  C5    C4   N3    122.21  3.000
 7DR  CAF   C5   C6    119.95  3.000
 7DR  CAF   C5   C4    123.90  3.000
 7DR  C6    C5   C4    116.15  3.000
 7DR  NAD   C6   C5    120.81  3.000
 7DR  NAD   C6   N1    117.74  3.000
 7DR  C5    C6   N1    121.44  3.000
 7DR  HAAB  CAA  HAAA  107.88  3.000
 7DR  HAAB  CAA  HAA   107.91  3.000
 7DR  HAAA  CAA  HAA   108.12  3.000
 7DR  HAAB  CAA  CAO   110.51  3.000
 7DR  HAAA  CAA  CAO   111.29  3.000
 7DR  HAA   CAA  CAO   111.00  3.000
 7DR  HABB  CAB  HABA  108.64  3.000
 7DR  HABB  CAB  HAB   108.76  3.000
 7DR  HABA  CAB  HAB   108.85  3.000
 7DR  HABB  CAB  OAS   112.07  3.000
 7DR  HABA  CAB  OAS   106.54  3.000
 7DR  HAB   CAB  OAS   111.87  3.000
 7DR  HNAA  NAC  HNAC  117.80  3.000
 7DR  HNAA  NAC  C2    119.28  3.000
 7DR  HNAC  NAC  C2    119.62  3.000
 7DR  HNAB  NAD  HNAD  116.76  3.000
 7DR  HNAB  NAD  C6    119.77  3.000
 7DR  HNAD  NAD  C6    118.47  3.000
 7DR  CAP   CAE  CAF   180.00  3.000
 7DR  CAE   CAF  C5    180.00  3.000
 7DR  HAG   CAG  CAI   120.27  3.000
 7DR  HAG   CAG  CAH   120.25  3.000
 7DR  CAI   CAG  CAH   119.48  3.000
 7DR  HAH   CAH  CAJ   119.59  3.000
 7DR  HAH   CAH  CAG   120.16  3.000
 7DR  CAJ   CAH  CAG   120.24  3.000
 7DR  HAI   CAI  CAK   119.60  3.000
 7DR  HAI   CAI  CAG   120.15  3.000
 7DR  CAK   CAI  CAG   120.25  3.000
 7DR  HAJ   CAJ  CAX   119.86  3.000
 7DR  HAJ   CAJ  CAH   119.32  3.000
 7DR  CAX   CAJ  CAH   120.81  3.000
 7DR  HAK   CAK  CAX   119.90  3.000
 7DR  HAK   CAK  CAI   119.28  3.000
 7DR  CAX   CAK  CAI   120.81  3.000
 7DR  HAL   CAL  CAW   121.28  3.000
 7DR  HAL   CAL  CAU   118.96  3.000
 7DR  CAW   CAL  CAU   119.76  3.000
 7DR  HAM   CAM  CAY   119.90  3.000
 7DR  HAM   CAM  CAU   119.59  3.000
 7DR  CAY   CAM  CAU   120.49  3.000
 7DR  HAN   CAN  CAY   120.59  3.000
 7DR  HAN   CAN  CAW   118.88  3.000
 7DR  CAY   CAN  CAW   120.53  3.000
 7DR  HAOA  CAO  HAO   107.60  3.000
 7DR  HAOA  CAO  CAA   109.82  3.000
 7DR  HAO   CAO  CAA   109.57  3.000
 7DR  HAOA  CAO  C4    108.61  3.000
 7DR  HAO   CAO  C4    110.08  3.000
 7DR  CAA   CAO  C4    111.09  3.000
 7DR  HAPA  CAP  HAP   106.09  3.000
 7DR  HAPA  CAP  CAU   109.64  3.000
 7DR  HAP   CAP  CAU   109.52  3.000
 7DR  HAPA  CAP  CAE   110.16  3.000
 7DR  HAP   CAP  CAE   109.49  3.000
 7DR  CAU   CAP  CAE   111.78  3.000
 7DR  CAW   OAS  CAB   118.54  3.000
 7DR  CAP   CAU  CAM   120.00  3.000
 7DR  CAP   CAU  CAL   119.86  3.000
 7DR  CAM   CAU  CAL   120.14  3.000
 7DR  OAS   CAW  CAN   116.06  3.000
 7DR  OAS   CAW  CAL   124.03  3.000
 7DR  CAN   CAW  CAL   119.90  3.000
 7DR  CAY   CAX  CAK   120.70  3.000
 7DR  CAY   CAX  CAJ   120.89  3.000
 7DR  CAK   CAX  CAJ   118.41  3.000
 7DR  CAX   CAY  CAN   120.33  3.000
 7DR  CAX   CAY  CAM   120.49  3.000
 7DR  CAN   CAY  CAM   119.18  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
 7DR  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 7DR  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 7DR  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 7DR  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 7DR  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 7DR  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 7DR  CONST_07  CAX   CAJ  CAH  CAG    0.00   0.0  0
 7DR  CONST_08  CAX   CAK  CAI  CAG    0.00   0.0  0
 7DR  CONST_09  CAK   CAI  CAG  CAH    0.00   0.0  0
 7DR  CONST_10  CAK   CAX  CAJ  CAH    0.00   0.0  0
 7DR  CONST_11  CAY   CAX  CAJ  CAH  180.00   0.0  0
 7DR  CONST_12  CAJ   CAH  CAG  CAI    0.00   0.0  0
 7DR  CONST_13  CAJ   CAX  CAK  CAI    0.00   0.0  0
 7DR  CONST_14  CAY   CAX  CAK  CAI  180.00   0.0  0
 7DR  CONST_19  CAY   CAM  CAU  CAL    0.00   0.0  0
 7DR  CONST_20  CAY   CAN  CAW  CAL    0.00   0.0  0
 7DR  CONST_21  CAW   CAL  CAU  CAM    0.00   0.0  0
 7DR  CONST_22  CAW   CAN  CAY  CAM    0.00   0.0  0
 7DR  CONST_23  CAU   CAM  CAY  CAN    0.00   0.0  0
 7DR  CONST_24  CAU   CAL  CAW  CAN    0.00   0.0  0
 7DR  CONST_25  CAX   CAY  CAM  CAU  180.00   0.0  0
 7DR  CONST_26  CAX   CAY  CAN  CAW  180.00   0.0  0
 7DR  CONST_27  CAF   C5   C6   N1   180.00   0.0  0
 7DR  CONST_28  NAD   C6   N1   C2   180.00   0.0  0
 7DR  CONST_29  CAO   C4   N3   C2   180.00   0.0  0
 7DR  CONST_30  CAF   C5   C4   N3   180.00   0.0  0
 7DR  CONST_31  NAC   C2   N3   C4   180.00   0.0  0
 7DR  CONST_32  NAD   C6   C5   C4   180.00   0.0  0
 7DR  CONST_33  NAC   C2   N1   C6   180.00   0.0  0
 7DR  CONST_34  CAO   C4   C5   C6   180.00   0.0  0
 7DR  CONST_35  CAW   CAL  CAU  CAP  180.00   0.0  0
 7DR  CONST_36  CAY   CAM  CAU  CAP  180.00   0.0  0
 7DR  CONST_37  CAU   CAL  CAW  OAS  180.00   0.0  0
 7DR  CONST_38  CAY   CAN  CAW  OAS  180.00   0.0  0
 7DR  CONST_39  HAJ   CAJ  CAH  CAG  180.00   0.0  0
 7DR  CONST_40  HAK   CAK  CAI  CAG  180.00   0.0  0
 7DR  CONST_41  HAI   CAI  CAG  CAH  180.00   0.0  0
 7DR  CONST_42  HAH   CAH  CAG  CAI  180.00   0.0  0
 7DR  CONST_43  HAG   CAG  CAH  CAJ  180.00   0.0  0
 7DR  CONST_44  HAM   CAM  CAU  CAL  180.00   0.0  0
 7DR  CONST_45  HAN   CAN  CAW  CAL  180.00   0.0  0
 7DR  CONST_46  HAL   CAL  CAU  CAM  180.00   0.0  0
 7DR  CONST_47  HNAD  NAD  C6   N1     0.00   0.0  0
 7DR  CONST_48  HNAB  NAD  C6   N1   180.00   0.0  0
 7DR  CONST_49  HNAC  NAC  C2   N1     0.00   0.0  0
 7DR  CONST_50  HNAA  NAC  C2   N1   180.00   0.0  0
 7DR  Var_01    CAA   CAO  C4   N3    93.39  30.0  2
 7DR  Var_02    CAL   CAW  OAS  CAB    1.21  30.0  1
 7DR  Var_03    CAL   CAU  CAP  CAE   45.21  30.0  2
 7DR  Var_04    CAU   CAP  CAE  CAF  -29.50  30.0  3
 7DR  Var_05    HAA   CAA  CAO  C4   -57.70  30.0  3
 7DR  Var_06    HAB   CAB  OAS  CAW   60.92  30.0  3

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
 7DR  plan-1  N1    0.020
 7DR  plan-1  C2    0.020
 7DR  plan-1  N3    0.020
 7DR  plan-1  C4    0.020
 7DR  plan-1  C5    0.020
 7DR  plan-1  C6    0.020
 7DR  plan-1  NAC   0.020
 7DR  plan-1  NAD   0.020
 7DR  plan-1  CAE   0.020
 7DR  plan-1  CAF   0.020
 7DR  plan-1  CAO   0.020
 7DR  plan-2  CAG   0.020
 7DR  plan-2  CAH   0.020
 7DR  plan-2  CAI   0.020
 7DR  plan-2  CAJ   0.020
 7DR  plan-2  CAK   0.020
 7DR  plan-2  CAX   0.020
 7DR  plan-2  CAY   0.020
 7DR  plan-2  HAG   0.020
 7DR  plan-2  HAH   0.020
 7DR  plan-2  HAI   0.020
 7DR  plan-2  HAJ   0.020
 7DR  plan-2  HAK   0.020
 7DR  plan-3  CAL   0.020
 7DR  plan-3  CAM   0.020
 7DR  plan-3  CAN   0.020
 7DR  plan-3  CAP   0.020
 7DR  plan-3  OAS   0.020
 7DR  plan-3  CAU   0.020
 7DR  plan-3  CAW   0.020
 7DR  plan-3  CAX   0.020
 7DR  plan-3  CAY   0.020
 7DR  plan-3  HAL   0.020
 7DR  plan-3  HAM   0.020
 7DR  plan-3  HAN   0.020
 7DR  plan-4  C2    0.020
 7DR  plan-4  NAC   0.020
 7DR  plan-4  HNAC  0.020
 7DR  plan-4  HNAA  0.020
 7DR  plan-5  C6    0.020
 7DR  plan-5  NAD   0.020
 7DR  plan-5  HNAD  0.020
 7DR  plan-5  HNAB  0.020

