# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:05:51 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-ethyl-5-{3-[3-methoxy-5-(pyridin-4-yl)phenyl]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)c3ccncc3
#
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
 9DR  9DR  6-ethyl-5-{3-[3-methoxy-5-(pyridin-4-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  48  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9DR
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
 9DR  N1    N  N     0  -0.502  -4.3672   0.7251  -1.9432
 9DR  C2    C  CR6   0   0.540  -5.5448   0.6032  -1.3310
 9DR  N3    N  N     0  -0.497  -5.7405   0.3798  -0.0265
 9DR  C4    C  CR6   0   0.270  -4.6570   0.2684   0.7309
 9DR  C5    C  CR6   0  -0.320  -3.3705   0.3769   0.2072
 9DR  C6    C  CR6   0   0.455  -3.2814   0.6143  -1.1900
 9DR  CAA   C  CH3   0  -0.665  -4.8140  -1.5343   2.4509
 9DR  CAB   C  CH3   0  -0.438   1.0751   3.4745  -1.6335
 9DR  NAC   N  NH2   0  -0.820  -6.6428   0.6898  -2.1019
 9DR  NAD   N  NH2   0  -0.826  -2.0874   0.7622  -1.7884
 9DR  CAE   C  CSP   0   0.024  -1.1318   0.1956   1.5583
 9DR  CAF   C  CSP   0   0.149  -2.1903   0.2709   0.9827
 9DR  CAG   C  CR16  0  -0.060   6.4385  -2.2183  -0.8063
 9DR  CAH   C  CR16  0  -0.060   6.3101  -2.3573   1.4519
 9DR  CAI   C  CR16  0  -0.378   5.3100  -1.4178  -0.8760
 9DR  CAJ   C  CR16  0  -0.378   5.1752  -1.5635   1.4911
 9DR  CAK   C  CR16  0  -0.436   1.1862   1.4183   0.2660
 9DR  CAL   C  CR16  0  -0.411   2.4171  -0.4238   1.2054
 9DR  CAM   C  CR16  0  -0.423   3.3372   0.8161  -0.6406
 9DR  CAN   C  CH2   0  -0.522  -4.8716  -0.0299   2.1836
 9DR  CAO   C  CH2   0  -0.658   0.1794   0.1466   2.1913
 9DR  NAP   N  N     0  -0.407   6.9414  -2.6861   0.3306
 9DR  OAS   O  O2    0  -0.470   2.1890   2.6044  -1.5839
 9DR  CAU   C  CR6   0   0.150   1.2924   0.3817   1.1924
 9DR  CAW   C  CR6   0   0.428   2.2062   1.6343  -0.6533
 9DR  CAX   C  CR6   0   0.170   4.6487  -1.0683   0.2998
 9DR  CAY   C  CR6   0   0.135   3.4490  -0.2089   0.2866
 9DR  HAA   H  HCH3  0   0.231  -3.8323  -1.9419   2.2082
 9DR  HAAA  H  HCH3  0   0.238  -5.0126  -1.7433   3.5018
 9DR  HAAB  H  HCH3  0   0.230  -5.5579  -2.0653   1.8566
 9DR  HAB   H  HCH3  0   0.264   1.2630   4.1707  -2.4467
 9DR  HABA  H  HCH3  0   0.220   0.1443   2.9382  -1.8398
 9DR  HABB  H  HCH3  0   0.233   0.9579   4.0389  -0.7050
 9DR  HNAC  H  HNH2  0   0.395  -6.5586   1.0004  -3.0537
 9DR  HNAA  H  HNH2  0   0.396  -7.5470   0.7466  -1.6676
 9DR  HNAD  H  HNH2  0   0.401  -1.2478   0.4902  -1.3055
 9DR  HNAB  H  HNH2  0   0.397  -2.0511   0.7668  -2.7938
 9DR  HAG   H  HCR6  0   0.266   6.9576  -2.4949  -1.7173
 9DR  HAH   H  HCR6  0   0.266   6.7307  -2.7385   2.3758
 9DR  HAI   H  HCR6  0   0.270   4.9474  -1.0921  -1.8419
 9DR  HAJ   H  HCR6  0   0.270   4.7270  -1.3237   2.4461
 9DR  HAK   H  HCR6  0   0.282   0.3033   2.0446   0.2814
 9DR  HAL   H  HCR6  0   0.256   2.4825  -1.2411   1.9127
 9DR  HAM   H  HCR6  0   0.265   4.1305   1.0081  -1.3529
 9DR  HAN   H  HCH2  0   0.245  -4.1161   0.4778   2.7859
 9DR  HANA  H  HCH2  0   0.250  -5.8459   0.3611   2.4790
 9DR  HAO   H  HCH2  0   0.293   0.2323   0.9019   2.9824
 9DR  HAOA  H  HCH2  0   0.284   0.3246  -0.8180   2.6833

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
 9DR  C2   N1    aromatic  1.333  0.020  1.333
 9DR  C6   N1    aromatic  1.326  0.020  1.326
 9DR  N3   C2    aromatic  1.338  0.020  1.338
 9DR  C2   NAC   single    1.344  0.020  1.344
 9DR  C4   N3    aromatic  1.327  0.020  1.327
 9DR  CAN  C4    single    1.499  0.020  1.499
 9DR  C4   C5    aromatic  1.393  0.020  1.393
 9DR  CAF  C5    single    1.416  0.020  1.416
 9DR  C5   C6    aromatic  1.420  0.020  1.420
 9DR  C6   NAD   single    1.344  0.020  1.344
 9DR  CAA  CAN   single    1.529  0.020  1.529
 9DR  CAA  HAA   single    0.970  0.020  1.090
 9DR  CAA  HAAA  single    0.970  0.020  1.090
 9DR  CAA  HAAB  single    0.970  0.020  1.090
 9DR  OAS  CAB   single    1.414  0.020  1.414
 9DR  CAB  HAB   single    0.970  0.020  1.090
 9DR  CAB  HABA  single    0.970  0.020  1.090
 9DR  CAB  HABB  single    0.970  0.020  1.090
 9DR  NAC  HNAC  single    0.890  0.020  1.040
 9DR  NAC  HNAA  single    0.890  0.020  1.040
 9DR  NAD  HNAD  single    0.890  0.020  1.040
 9DR  NAD  HNAB  single    0.890  0.020  1.040
 9DR  CAO  CAE   single    1.457  0.020  1.457
 9DR  CAE  CAF   triple    1.207  0.020  1.207
 9DR  CAG  CAI   aromatic  1.385  0.020  1.385
 9DR  CAG  NAP   aromatic  1.328  0.020  1.328
 9DR  CAG  HAG   single    0.930  0.020  1.080
 9DR  NAP  CAH   aromatic  1.328  0.020  1.328
 9DR  CAH  CAJ   aromatic  1.385  0.020  1.385
 9DR  CAH  HAH   single    0.930  0.020  1.080
 9DR  CAI  CAX   aromatic  1.394  0.020  1.394
 9DR  CAI  HAI   single    0.930  0.020  1.080
 9DR  CAX  CAJ   aromatic  1.393  0.020  1.393
 9DR  CAJ  HAJ   single    0.930  0.020  1.080
 9DR  CAW  CAK   aromatic  1.390  0.020  1.390
 9DR  CAK  CAU   aromatic  1.394  0.020  1.394
 9DR  CAK  HAK   single    0.930  0.020  1.080
 9DR  CAY  CAL   aromatic  1.398  0.020  1.398
 9DR  CAL  CAU   aromatic  1.383  0.020  1.383
 9DR  CAL  HAL   single    0.930  0.020  1.080
 9DR  CAM  CAW   aromatic  1.396  0.020  1.396
 9DR  CAM  CAY   aromatic  1.387  0.020  1.387
 9DR  CAM  HAM   single    0.930  0.020  1.080
 9DR  CAN  HAN   single    0.970  0.020  1.090
 9DR  CAN  HANA  single    0.970  0.020  1.090
 9DR  CAU  CAO   single    1.514  0.020  1.514
 9DR  CAO  HAO   single    0.970  0.020  1.090
 9DR  CAO  HAOA  single    0.970  0.020  1.090
 9DR  OAS  CAW   single    1.344  0.020  1.344
 9DR  CAX  CAY   single    1.476  0.020  1.476

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
 9DR  C6    N1   C2    117.06  3.000
 9DR  NAC   C2   N3    116.77  3.000
 9DR  NAC   C2   N1    116.90  3.000
 9DR  N3    C2   N1    126.32  3.000
 9DR  C4    N3   C2    116.82  3.000
 9DR  CAN   C4   C5    120.81  3.000
 9DR  C5    C4   N3    122.21  3.000
 9DR  CAN   C4   N3    116.95  3.000
 9DR  CAF   C5   C6    119.93  3.000
 9DR  C6    C5   C4    116.16  3.000
 9DR  CAF   C5   C4    123.91  3.000
 9DR  NAD   C6   C5    120.82  3.000
 9DR  NAD   C6   N1    117.74  3.000
 9DR  C5    C6   N1    121.42  3.000
 9DR  HAAB  CAA  HAAA  107.94  3.000
 9DR  HAAB  CAA  HAA   108.11  3.000
 9DR  HAAA  CAA  HAA   107.88  3.000
 9DR  HAAB  CAA  CAN   110.99  3.000
 9DR  HAAA  CAA  CAN   110.51  3.000
 9DR  HAA   CAA  CAN   111.28  3.000
 9DR  HABB  CAB  HABA  108.79  3.000
 9DR  HABB  CAB  HAB   108.87  3.000
 9DR  HABA  CAB  HAB   108.67  3.000
 9DR  HABB  CAB  OAS   111.86  3.000
 9DR  HABA  CAB  OAS   112.04  3.000
 9DR  HAB   CAB  OAS   106.50  3.000
 9DR  HNAA  NAC  HNAC  117.87  3.000
 9DR  HNAA  NAC  C2    119.39  3.000
 9DR  HNAC  NAC  C2    119.65  3.000
 9DR  HNAB  NAD  HNAD  116.80  3.000
 9DR  HNAB  NAD  C6    118.53  3.000
 9DR  HNAD  NAD  C6    119.87  3.000
 9DR  CAO   CAE  CAF   180.00  3.000
 9DR  CAE   CAF  C5    180.00  3.000
 9DR  HAG   CAG  NAP   116.62  3.000
 9DR  HAG   CAG  CAI   119.67  3.000
 9DR  NAP   CAG  CAI   123.71  3.000
 9DR  HAH   CAH  NAP   116.61  3.000
 9DR  HAH   CAH  CAJ   119.67  3.000
 9DR  NAP   CAH  CAJ   123.72  3.000
 9DR  HAI   CAI  CAX   121.24  3.000
 9DR  HAI   CAI  CAG   119.46  3.000
 9DR  CAX   CAI  CAG   119.28  3.000
 9DR  HAJ   CAJ  CAX   121.29  3.000
 9DR  HAJ   CAJ  CAH   119.43  3.000
 9DR  CAX   CAJ  CAH   119.27  3.000
 9DR  HAK   CAK  CAW   121.19  3.000
 9DR  HAK   CAK  CAU   118.87  3.000
 9DR  CAW   CAK  CAU   119.94  3.000
 9DR  HAL   CAL  CAY   120.04  3.000
 9DR  HAL   CAL  CAU   119.66  3.000
 9DR  CAY   CAL  CAU   120.29  3.000
 9DR  HAM   CAM  CAY   120.77  3.000
 9DR  HAM   CAM  CAW   118.91  3.000
 9DR  CAY   CAM  CAW   120.31  3.000
 9DR  HANA  CAN  HAN   107.59  3.000
 9DR  HANA  CAN  CAA   109.82  3.000
 9DR  HAN   CAN  CAA   109.58  3.000
 9DR  HANA  CAN  C4    108.61  3.000
 9DR  HAN   CAN  C4    110.07  3.000
 9DR  CAA   CAN  C4    111.10  3.000
 9DR  HAOA  CAO  HAO   106.09  3.000
 9DR  HAOA  CAO  CAU   109.67  3.000
 9DR  HAO   CAO  CAU   109.51  3.000
 9DR  HAOA  CAO  CAE   110.19  3.000
 9DR  HAO   CAO  CAE   109.52  3.000
 9DR  CAU   CAO  CAE   111.70  3.000
 9DR  CAH   NAP  CAG   117.09  3.000
 9DR  CAW   OAS  CAB   118.57  3.000
 9DR  CAO   CAU  CAL   120.07  3.000
 9DR  CAO   CAU  CAK   119.86  3.000
 9DR  CAL   CAU  CAK   120.07  3.000
 9DR  OAS   CAW  CAM   116.08  3.000
 9DR  OAS   CAW  CAK   124.09  3.000
 9DR  CAM   CAW  CAK   119.83  3.000
 9DR  CAY   CAX  CAJ   121.45  3.000
 9DR  CAY   CAX  CAI   121.63  3.000
 9DR  CAJ   CAX  CAI   116.93  3.000
 9DR  CAX   CAY  CAM   120.13  3.000
 9DR  CAX   CAY  CAL   120.31  3.000
 9DR  CAM   CAY  CAL   119.56  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
 9DR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 9DR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 9DR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 9DR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 9DR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 9DR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 9DR  CONST_07  CAJ   CAX  CAI  CAG     0.00   0.0  0
 9DR  CONST_08  CAY   CAX  CAI  CAG   180.00   0.0  0
 9DR  CONST_09  CAJ   CAH  NAP  CAG     0.00   0.0  0
 9DR  CONST_10  CAI   CAG  NAP  CAH     0.00   0.0  0
 9DR  CONST_11  CAI   CAX  CAJ  CAH     0.00   0.0  0
 9DR  CONST_12  CAY   CAX  CAJ  CAH   180.00   0.0  0
 9DR  CONST_17  CAY   CAM  CAW  CAK     0.00   0.0  0
 9DR  CONST_18  CAY   CAL  CAU  CAK     0.00   0.0  0
 9DR  CONST_19  CAW   CAM  CAY  CAL     0.00   0.0  0
 9DR  CONST_20  CAW   CAK  CAU  CAL     0.00   0.0  0
 9DR  CONST_21  CAU   CAK  CAW  CAM     0.00   0.0  0
 9DR  CONST_22  CAU   CAL  CAY  CAM     0.00   0.0  0
 9DR  CONST_23  CAX   CAI  CAG  NAP     0.00   0.0  0
 9DR  CONST_24  CAX   CAJ  CAH  NAP     0.00   0.0  0
 9DR  CONST_25  CAX   CAY  CAL  CAU   180.00   0.0  0
 9DR  CONST_26  CAX   CAY  CAM  CAW   180.00   0.0  0
 9DR  CONST_27  CAF   C5   C6   N1    180.00   0.0  0
 9DR  CONST_28  NAD   C6   N1   C2    180.00   0.0  0
 9DR  CONST_29  CAN   C4   N3   C2    180.00   0.0  0
 9DR  CONST_30  CAF   C5   C4   N3    180.00   0.0  0
 9DR  CONST_31  NAC   C2   N3   C4    180.00   0.0  0
 9DR  CONST_32  NAD   C6   C5   C4    180.00   0.0  0
 9DR  CONST_33  NAC   C2   N1   C6    180.00   0.0  0
 9DR  CONST_34  CAN   C4   C5   C6    180.00   0.0  0
 9DR  CONST_35  CAW   CAK  CAU  CAO   180.00   0.0  0
 9DR  CONST_36  CAY   CAL  CAU  CAO   180.00   0.0  0
 9DR  CONST_37  CAU   CAK  CAW  OAS   180.00   0.0  0
 9DR  CONST_38  CAY   CAM  CAW  OAS   180.00   0.0  0
 9DR  CONST_39  HAH   CAH  NAP  CAG   180.00   0.0  0
 9DR  CONST_40  HAG   CAG  NAP  CAH   180.00   0.0  0
 9DR  CONST_41  HAJ   CAJ  CAX  CAI   180.00   0.0  0
 9DR  CONST_42  HAI   CAI  CAX  CAJ   180.00   0.0  0
 9DR  CONST_43  HAM   CAM  CAW  CAK   180.00   0.0  0
 9DR  CONST_44  HAL   CAL  CAU  CAK   180.00   0.0  0
 9DR  CONST_45  HAK   CAK  CAU  CAL   180.00   0.0  0
 9DR  CONST_46  HNAC  NAC  C2   N1      0.00   0.0  0
 9DR  CONST_47  HNAA  NAC  C2   N1    180.00   0.0  0
 9DR  CONST_48  HNAD  NAD  C6   N1    180.00   0.0  0
 9DR  CONST_49  HNAB  NAD  C6   N1      0.00   0.0  0
 9DR  Var_01    CAA   CAN  C4   N3     93.45  30.0  1
 9DR  Var_02    CAK   CAW  OAS  CAB     0.62  30.0  2
 9DR  Var_03    CAK   CAU  CAO  CAE    45.33  30.0  2
 9DR  Var_04    CAU   CAO  CAE  CAF   -20.40  30.0  1
 9DR  Var_05    HAA   CAA  CAN  C4     62.54  30.0  3
 9DR  Var_06    HAB   CAB  OAS  CAW  -179.92  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
 9DR  plan-1  N1    0.020
 9DR  plan-1  C2    0.020
 9DR  plan-1  N3    0.020
 9DR  plan-1  C4    0.020
 9DR  plan-1  C5    0.020
 9DR  plan-1  C6    0.020
 9DR  plan-1  NAC   0.020
 9DR  plan-1  NAD   0.020
 9DR  plan-1  CAE   0.020
 9DR  plan-1  CAF   0.020
 9DR  plan-1  CAN   0.020
 9DR  plan-2  CAG   0.020
 9DR  plan-2  CAH   0.020
 9DR  plan-2  CAI   0.020
 9DR  plan-2  CAJ   0.020
 9DR  plan-2  NAP   0.020
 9DR  plan-2  CAX   0.020
 9DR  plan-2  CAY   0.020
 9DR  plan-2  HAG   0.020
 9DR  plan-2  HAH   0.020
 9DR  plan-2  HAI   0.020
 9DR  plan-2  HAJ   0.020
 9DR  plan-3  CAK   0.020
 9DR  plan-3  CAL   0.020
 9DR  plan-3  CAM   0.020
 9DR  plan-3  CAO   0.020
 9DR  plan-3  OAS   0.020
 9DR  plan-3  CAU   0.020
 9DR  plan-3  CAW   0.020
 9DR  plan-3  CAX   0.020
 9DR  plan-3  CAY   0.020
 9DR  plan-3  HAK   0.020
 9DR  plan-3  HAL   0.020
 9DR  plan-3  HAM   0.020
 9DR  plan-4  C2    0.020
 9DR  plan-4  NAC   0.020
 9DR  plan-4  HNAC  0.020
 9DR  plan-4  HNAA  0.020
 9DR  plan-5  C6    0.020
 9DR  plan-5  NAD   0.020
 9DR  plan-5  HNAD  0.020
 9DR  plan-5  HNAB  0.020

