# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 23:34:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-ethyl-5-{3-[2-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(ccc2OC)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
 6DR  6DR  6-ethyl-5-{3-[2-methoxy-5-(pyridin-4-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  48  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_6DR
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
 6DR  N1    N  N     0  -0.504  -4.0646  -1.1272  -1.8940
 6DR  C2    C  CR6   0   0.534  -5.2482  -0.9690  -1.3035
 6DR  N3    N  N     0  -0.498  -5.4666  -0.4389  -0.0956
 6DR  C4    C  CR6   0   0.268  -4.3992  -0.0307   0.5807
 6DR  C5    C  CR6   0  -0.319  -3.1080  -0.1415   0.0707
 6DR  C6    C  CR6   0   0.462  -2.9949  -0.7180  -1.2230
 6DR  CAA   C  CH3   0  -0.664  -4.5965  -0.5894   3.0072
 6DR  CAB   C  CH3   0  -0.438   0.4529   4.1632  -0.7582
 6DR  NAC   N  NH2   0  -0.820  -6.3327  -1.3551  -2.0024
 6DR  NAD   N  NH2   0  -0.823  -1.8000  -0.8473  -1.8148
 6DR  CAE   C  CSP   0   0.045  -0.9232   0.6111   1.3125
 6DR  CAF   C  CSP   0   0.140  -1.9478   0.2751   0.7697
 6DR  CAG   C  CR16  0  -0.062   6.1530  -2.1550  -1.2491
 6DR  CAH   C  CR16  0  -0.062   5.9160  -2.4780   0.9788
 6DR  CAI   C  CR16  0  -0.386   5.1714  -1.1783  -1.2673
 6DR  CAJ   C  CR16  0  -0.388   4.9276  -1.5120   1.0695
 6DR  CAK   C  CR16  0  -0.308   3.4965   1.2773  -0.9307
 6DR  CAL   C  CR16  0  -0.369   2.5154   2.2571  -0.8964
 6DR  CAM   C  CR16  0  -0.353   2.4425   0.1505   0.8902
 6DR  CAN   C  CH2   0  -0.519  -4.6400   0.5180   1.9543
 6DR  CAO   C  CH2   0  -0.672   0.3296   1.0006   1.9500
 6DR  NAP   N  N     0  -0.410   6.5297  -2.8047  -0.1532
 6DR  OAS   O  O2    0  -0.456   0.4966   3.0776   0.1475
 6DR  CAV   C  CR6   0   0.184   4.5275  -0.8291  -0.0796
 6DR  CAW   C  CR6   0   0.094   3.4825   0.2075  -0.0425
 6DR  CAX   C  CR6   0   0.032   1.4514   1.1114   0.9458
 6DR  CAZ   C  CR6   0   0.362   1.4869   2.1811   0.0383
 6DR  HAA   H  HCH3  0   0.238  -4.7859  -0.1807   3.9996
 6DR  HAAA  H  HCH3  0   0.229  -5.3521  -1.3494   2.8074
 6DR  HAAB  H  HCH3  0   0.230  -3.6219  -1.0781   3.0281
 6DR  HAB   H  HCH3  0   0.232   1.3403   4.7957  -0.6805
 6DR  HABA  H  HCH3  0   0.232   0.3482   3.8245  -1.7918
 6DR  HABB  H  HCH3  0   0.262  -0.4215   4.7510  -0.4913
 6DR  HNAC  H  HNH2  0   0.394  -6.2083  -1.9136  -2.8285
 6DR  HNAA  H  HNH2  0   0.394  -7.2177  -1.4179  -1.5305
 6DR  HNAD  H  HNH2  0   0.400  -0.9531  -0.6825  -1.2989
 6DR  HNAB  H  HNH2  0   0.397  -1.7293  -1.3639  -2.6743
 6DR  HAG   H  HCR6  0   0.264   6.6551  -2.4268  -2.1712
 6DR  HAH   H  HCR6  0   0.264   6.2293  -3.0091   1.8709
 6DR  HAI   H  HCR6  0   0.266   4.9073  -0.7135  -2.2080
 6DR  HAJ   H  HCR6  0   0.266   4.4953  -1.2899   2.0362
 6DR  HAK   H  HCR6  0   0.261   4.2934   1.3764  -1.6566
 6DR  HAL   H  HCR6  0   0.284   2.5739   3.0739  -1.6024
 6DR  HAM   H  HCR6  0   0.256   2.3878  -0.6798   1.5842
 6DR  HAN   H  HCH2  0   0.244  -3.8940   1.2778   2.1911
 6DR  HANA  H  HCH2  0   0.249  -5.6182   1.0009   1.9699
 6DR  HAO   H  HCH2  0   0.287   0.1919   1.9454   2.4829
 6DR  HAOA  H  HCH2  0   0.284   0.5987   0.2606   2.7079

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
 6DR  C2   N1    aromatic  1.332  0.020  1.332
 6DR  C6   N1    aromatic  1.327  0.020  1.327
 6DR  N3   C2    aromatic  1.337  0.020  1.337
 6DR  C2   NAC   single    1.347  0.020  1.347
 6DR  C4   N3    aromatic  1.328  0.020  1.328
 6DR  CAN  C4    single    1.499  0.020  1.499
 6DR  C4   C5    aromatic  1.393  0.020  1.393
 6DR  CAF  C5    single    1.417  0.020  1.417
 6DR  C5   C6    aromatic  1.421  0.020  1.421
 6DR  C6   NAD   single    1.340  0.020  1.340
 6DR  CAA  CAN   single    1.529  0.020  1.529
 6DR  CAA  HAA   single    0.970  0.020  1.090
 6DR  CAA  HAAA  single    0.970  0.020  1.090
 6DR  CAA  HAAB  single    0.970  0.020  1.090
 6DR  OAS  CAB   single    1.414  0.020  1.414
 6DR  CAB  HAB   single    0.970  0.020  1.090
 6DR  CAB  HABA  single    0.970  0.020  1.090
 6DR  CAB  HABB  single    0.970  0.020  1.090
 6DR  NAC  HNAC  single    0.890  0.020  1.040
 6DR  NAC  HNAA  single    0.890  0.020  1.040
 6DR  NAD  HNAD  single    0.860  0.020  1.020
 6DR  NAD  HNAB  single    0.860  0.020  1.020
 6DR  CAO  CAE   single    1.459  0.020  1.459
 6DR  CAE  CAF   triple    1.207  0.020  1.207
 6DR  CAI  CAG   aromatic  1.385  0.020  1.385
 6DR  CAG  NAP   aromatic  1.329  0.020  1.329
 6DR  CAG  HAG   single    0.930  0.020  1.080
 6DR  NAP  CAH   aromatic  1.328  0.020  1.328
 6DR  CAJ  CAH   aromatic  1.385  0.020  1.385
 6DR  CAH  HAH   single    0.930  0.020  1.080
 6DR  CAI  CAV   aromatic  1.395  0.020  1.395
 6DR  CAI  HAI   single    0.930  0.020  1.080
 6DR  CAV  CAJ   aromatic  1.395  0.020  1.395
 6DR  CAJ  HAJ   single    0.930  0.020  1.080
 6DR  CAL  CAK   aromatic  1.387  0.020  1.387
 6DR  CAK  CAW   aromatic  1.391  0.020  1.391
 6DR  CAK  HAK   single    0.930  0.020  1.080
 6DR  CAL  CAZ   aromatic  1.392  0.020  1.392
 6DR  CAL  HAL   single    0.930  0.020  1.080
 6DR  CAW  CAM   aromatic  1.398  0.020  1.398
 6DR  CAX  CAM   aromatic  1.382  0.020  1.382
 6DR  CAM  HAM   single    0.930  0.020  1.080
 6DR  CAN  HAN   single    0.970  0.020  1.090
 6DR  CAN  HANA  single    0.970  0.020  1.090
 6DR  CAX  CAO   single    1.510  0.020  1.510
 6DR  CAO  HAO   single    0.970  0.020  1.090
 6DR  CAO  HAOA  single    0.970  0.020  1.090
 6DR  OAS  CAZ   single    1.340  0.020  1.340
 6DR  CAW  CAV   single    1.472  0.020  1.472
 6DR  CAZ  CAX   aromatic  1.403  0.020  1.403

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
 6DR  C6    N1   C2    117.08  3.000
 6DR  NAC   C2   N3    116.80  3.000
 6DR  NAC   C2   N1    116.84  3.000
 6DR  N3    C2   N1    126.35  3.000
 6DR  C4    N3   C2    116.79  3.000
 6DR  CAN   C4   C5    120.92  3.000
 6DR  C5    C4   N3    122.29  3.000
 6DR  CAN   C4   N3    116.76  3.000
 6DR  CAF   C5   C6    120.22  3.000
 6DR  C6    C5   C4    116.07  3.000
 6DR  CAF   C5   C4    123.71  3.000
 6DR  NAD   C6   C5    120.82  3.000
 6DR  NAD   C6   N1    117.75  3.000
 6DR  C5    C6   N1    121.41  3.000
 6DR  HAAB  CAA  HAAA  108.10  3.000
 6DR  HAAB  CAA  HAA   107.82  3.000
 6DR  HAAA  CAA  HAA   107.93  3.000
 6DR  HAAB  CAA  CAN   111.30  3.000
 6DR  HAAA  CAA  CAN   111.04  3.000
 6DR  HAA   CAA  CAN   110.52  3.000
 6DR  HABB  CAB  HABA  108.84  3.000
 6DR  HABB  CAB  HAB   108.83  3.000
 6DR  HABA  CAB  HAB   108.94  3.000
 6DR  HABB  CAB  OAS   106.42  3.000
 6DR  HABA  CAB  OAS   111.76  3.000
 6DR  HAB   CAB  OAS   111.94  3.000
 6DR  HNAA  NAC  HNAC  117.41  3.000
 6DR  HNAA  NAC  C2    118.91  3.000
 6DR  HNAC  NAC  C2    119.09  3.000
 6DR  HNAB  NAD  HNAD  117.63  3.000
 6DR  HNAB  NAD  C6    119.34  3.000
 6DR  HNAD  NAD  C6    120.59  3.000
 6DR  CAO   CAE  CAF   180.00  3.000
 6DR  CAE   CAF  C5    180.00  3.000
 6DR  HAG   CAG  NAP   116.58  3.000
 6DR  HAG   CAG  CAI   119.58  3.000
 6DR  NAP   CAG  CAI   123.83  3.000
 6DR  HAH   CAH  NAP   116.56  3.000
 6DR  HAH   CAH  CAJ   119.59  3.000
 6DR  NAP   CAH  CAJ   123.85  3.000
 6DR  HAI   CAI  CAV   121.32  3.000
 6DR  HAI   CAI  CAG   119.17  3.000
 6DR  CAV   CAI  CAG   119.50  3.000
 6DR  HAJ   CAJ  CAV   121.38  3.000
 6DR  HAJ   CAJ  CAH   119.13  3.000
 6DR  CAV   CAJ  CAH   119.48  3.000
 6DR  HAK   CAK  CAW   120.41  3.000
 6DR  HAK   CAK  CAL   118.20  3.000
 6DR  CAW   CAK  CAL   121.37  3.000
 6DR  HAL   CAL  CAZ   121.32  3.000
 6DR  HAL   CAL  CAK   118.64  3.000
 6DR  CAZ   CAL  CAK   120.05  3.000
 6DR  HAM   CAM  CAX   118.10  3.000
 6DR  HAM   CAM  CAW   119.74  3.000
 6DR  CAX   CAM  CAW   122.15  3.000
 6DR  HANA  CAN  HAN   107.56  3.000
 6DR  HANA  CAN  CAA   109.66  3.000
 6DR  HAN   CAN  CAA   109.61  3.000
 6DR  HANA  CAN  C4    108.62  3.000
 6DR  HAN   CAN  C4    110.13  3.000
 6DR  CAA   CAN  C4    111.19  3.000
 6DR  HAOA  CAO  HAO   106.15  3.000
 6DR  HAOA  CAO  CAX   109.14  3.000
 6DR  HAO   CAO  CAX   110.75  3.000
 6DR  HAOA  CAO  CAE   109.50  3.000
 6DR  HAO   CAO  CAE   109.61  3.000
 6DR  CAX   CAO  CAE   111.53  3.000
 6DR  CAH   NAP  CAG   116.85  3.000
 6DR  CAZ   OAS  CAB   118.95  3.000
 6DR  CAW   CAV  CAJ   121.83  3.000
 6DR  CAW   CAV  CAI   121.68  3.000
 6DR  CAJ   CAV  CAI   116.50  3.000
 6DR  CAV   CAW  CAM   121.07  3.000
 6DR  CAV   CAW  CAK   121.23  3.000
 6DR  CAM   CAW  CAK   117.71  3.000
 6DR  CAZ   CAX  CAO   120.32  3.000
 6DR  CAZ   CAX  CAM   119.08  3.000
 6DR  CAO   CAX  CAM   120.58  3.000
 6DR  CAX   CAZ  OAS   116.01  3.000
 6DR  CAX   CAZ  CAL   119.64  3.000
 6DR  OAS   CAZ  CAL   124.34  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
 6DR  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 6DR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 6DR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 6DR  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 6DR  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 6DR  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 6DR  CONST_07  CAJ   CAV  CAI  CAG     0.00   0.0  0
 6DR  CONST_08  CAW   CAV  CAI  CAG   180.00   0.0  0
 6DR  CONST_09  CAJ   CAH  NAP  CAG     0.00   0.0  0
 6DR  CONST_10  CAI   CAG  NAP  CAH     0.00   0.0  0
 6DR  CONST_11  CAI   CAV  CAJ  CAH     0.00   0.0  0
 6DR  CONST_12  CAW   CAV  CAJ  CAH   180.00   0.0  0
 6DR  CONST_17  CAX   CAZ  CAL  CAK     0.00   0.0  0
 6DR  CONST_18  CAX   CAM  CAW  CAK     0.00   0.0  0
 6DR  CONST_19  CAM   CAW  CAK  CAL     0.00   0.0  0
 6DR  CONST_20  CAV   CAW  CAK  CAL   180.00   0.0  0
 6DR  CONST_21  CAM   CAX  CAZ  CAL     0.00   0.0  0
 6DR  CONST_22  CAV   CAI  CAG  NAP     0.00   0.0  0
 6DR  CONST_23  CAV   CAJ  CAH  NAP     0.00   0.0  0
 6DR  CONST_24  CAX   CAM  CAW  CAV   180.00   0.0  0
 6DR  CONST_25  CAZ   CAL  CAK  CAW     0.00   0.0  0
 6DR  CONST_26  CAZ   CAX  CAM  CAW     0.00   0.0  0
 6DR  CONST_27  CAF   C5   C6   N1    180.00   0.0  0
 6DR  CONST_28  NAD   C6   N1   C2    180.00   0.0  0
 6DR  CONST_29  CAN   C4   N3   C2    180.00   0.0  0
 6DR  CONST_30  CAF   C5   C4   N3    180.00   0.0  0
 6DR  CONST_31  NAC   C2   N3   C4    180.00   0.0  0
 6DR  CONST_32  NAD   C6   C5   C4    180.00   0.0  0
 6DR  CONST_33  NAC   C2   N1   C6    180.00   0.0  0
 6DR  CONST_34  CAN   C4   C5   C6    180.00   0.0  0
 6DR  CONST_35  OAS   CAZ  CAL  CAK   180.00   0.0  0
 6DR  CONST_36  CAO   CAX  CAZ  CAL   180.00   0.0  0
 6DR  CONST_37  OAS   CAZ  CAX  CAM   180.00   0.0  0
 6DR  CONST_38  CAW   CAM  CAX  CAO   180.00   0.0  0
 6DR  CONST_39  HAH   CAH  NAP  CAG   180.00   0.0  0
 6DR  CONST_40  HAG   CAG  NAP  CAH   180.00   0.0  0
 6DR  CONST_41  HAJ   CAJ  CAV  CAI   180.00   0.0  0
 6DR  CONST_42  HAI   CAI  CAV  CAJ   180.00   0.0  0
 6DR  CONST_43  HAM   CAM  CAW  CAK   180.00   0.0  0
 6DR  CONST_44  HAK   CAK  CAW  CAM   180.00   0.0  0
 6DR  CONST_45  HAL   CAL  CAK  CAW   180.00   0.0  0
 6DR  CONST_46  HNAC  NAC  C2   N1      0.00   0.0  0
 6DR  CONST_47  HNAA  NAC  C2   N1    180.00   0.0  0
 6DR  CONST_48  HNAD  NAD  C6   N1    180.00   0.0  0
 6DR  CONST_49  HNAB  NAD  C6   N1      0.00   0.0  0
 6DR  Var_01    CAA   CAN  C4   N3     89.19  30.0  1
 6DR  Var_02    CAL   CAZ  OAS  CAB     1.73  30.0  2
 6DR  Var_03    CAM   CAX  CAO  CAE  -106.40  30.0  2
 6DR  Var_04    CAX   CAO  CAE  CAF    35.08  30.0  1
 6DR  Var_05    HAA   CAA  CAN  C4   -179.25  30.0  3
 6DR  Var_06    HAB   CAB  OAS  CAZ   -61.44  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
 6DR  plan-1  N1    0.020
 6DR  plan-1  C2    0.020
 6DR  plan-1  N3    0.020
 6DR  plan-1  C4    0.020
 6DR  plan-1  C5    0.020
 6DR  plan-1  C6    0.020
 6DR  plan-1  NAC   0.020
 6DR  plan-1  NAD   0.020
 6DR  plan-1  CAE   0.020
 6DR  plan-1  CAF   0.020
 6DR  plan-1  CAN   0.020
 6DR  plan-2  CAG   0.020
 6DR  plan-2  CAH   0.020
 6DR  plan-2  CAI   0.020
 6DR  plan-2  CAJ   0.020
 6DR  plan-2  NAP   0.020
 6DR  plan-2  CAV   0.020
 6DR  plan-2  CAW   0.020
 6DR  plan-2  HAG   0.020
 6DR  plan-2  HAH   0.020
 6DR  plan-2  HAI   0.020
 6DR  plan-2  HAJ   0.020
 6DR  plan-3  CAK   0.020
 6DR  plan-3  CAL   0.020
 6DR  plan-3  CAM   0.020
 6DR  plan-3  CAO   0.020
 6DR  plan-3  OAS   0.020
 6DR  plan-3  CAV   0.020
 6DR  plan-3  CAW   0.020
 6DR  plan-3  CAX   0.020
 6DR  plan-3  CAZ   0.020
 6DR  plan-3  HAK   0.020
 6DR  plan-3  HAL   0.020
 6DR  plan-3  HAM   0.020
 6DR  plan-4  C2    0.020
 6DR  plan-4  NAC   0.020
 6DR  plan-4  HNAC  0.020
 6DR  plan-4  HNAA  0.020
 6DR  plan-5  C6    0.020
 6DR  plan-5  NAD   0.020
 6DR  plan-5  HNAD  0.020
 6DR  plan-5  HNAB  0.020

