# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:03:44 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-{2-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenyl}hex-5-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C#CCCCC(O)=O)c(Cc2cnc3nc(N)nc(N)c3c2C)c1
#
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
 D2R  D2R  '6-{2-[(2,4-diamino-5-methylpyrido[2,3-d]pyrimidin-6-yl)methyl]-4-methoxyphenyl}hex-5-ynoic acid'  ligand  52  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D2R
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
 D2R  N1    N  N      0  -0.505  -0.7772   4.6363  -0.5157
 D2R  C2    C  CR6    0   0.535   0.5641   4.6394  -0.4276
 D2R  N3    N  N      0  -0.496   1.3262   3.6195  -0.0907
 D2R  C4    C  CR6    0   0.344   0.6916   2.5041   0.3093
 D2R  C5    C  CR6    0  -0.187  -0.7228   2.4022   0.3827
 D2R  C6    C  CR6    0   0.456  -1.4228   3.5457  -0.1619
 D2R  CAA   C  CH3    0  -0.438  -6.0621  -3.8302  -0.1605
 D2R  NAC   N  NH2    0  -0.818   1.1654   5.8111  -0.7166
 D2R  NAD   N  NH2    0  -0.820  -2.7513   3.5671  -0.3507
 D2R  OAE   O  O      0  -0.603   5.6599  -0.2767   1.0616
 D2R  OAF   O  OC    -1  -0.634   7.2748  -0.8086  -0.3771
 D2R  CAG   C  CSP    0   0.065   1.3218  -2.2862  -0.9953
 D2R  CAI   C  CR16   0  -0.393  -3.3854  -3.4187  -0.9093
 D2R  CAJ   C  CR16   0  -0.293  -2.0469  -3.1983  -1.1923
 D2R  CAK   C  C1     0  -0.094   0.9205   0.3815   1.0897
 D2R  CAL   C  CR16   0  -0.425  -3.1009  -2.1787   1.1329
 D2R  CAM   C  CH2    0  -0.619   2.7223  -2.2525  -1.3975
 D2R  CAN   C  CH2    0  -0.424   3.6331  -1.4922  -0.4285
 D2R  CAO   C  CH2    0  -0.583   5.0842  -1.5577  -0.8724
 D2R  NAQ   N  N      0  -0.435   1.4876   1.4800   0.6623
 D2R  CAU   C  C      0   0.409   6.0904  -0.8105   0.0217
 D2R  CAX   C  C      0   0.167  -1.3019   1.2401   0.9491
 D2R  CAY   C  CR6    0   0.397  -3.9204  -2.9094   0.2703
 D2R  CAZ   C  CR6    0  -0.149  -1.2193  -2.4733  -0.3350
 D2R  CBA   C  C      0   0.043  -0.4552   0.1864   1.2667
 D2R  CBB   C  CR6    0   0.188  -1.7683  -1.9407   0.8470
 D2R  HAA   H  HCH3   0   0.230  -6.1901  -3.3819  -1.1491
 D2R  HAAA  H  HCH3   0   0.230  -5.7071  -4.8567  -0.2812
 D2R  HAAB  H  HCH3   0   0.261  -7.0258  -3.8500   0.3421
 D2R  HAB   H  HCH3   0   0.268  -3.3540   0.7823   0.4371
 D2R  HABA  H  HCH3   0   0.272  -2.9249   0.4420   2.0944
 D2R  HABB  H  HCH3   0   0.273  -3.1688   2.0987   1.6052
 D2R  HNAC  H  HNH2   0   0.392   0.6355   6.5240  -1.1864
 D2R  HNAA  H  HNH2   0   0.392   2.1612   5.8187  -0.8523
 D2R  HNAD  H  HNH2   0   0.420  -3.2949   2.7253  -0.3966
 D2R  HNAB  H  HNH2   0   0.401  -3.1225   4.3560  -0.8550
 D2R  HAI   H  HCR6   0   0.282  -3.9804  -3.9908  -1.6077
 D2R  HAJ   H  HCR6   0   0.257  -1.6302  -3.6100  -2.1022
 D2R  HAK   H  H      0   0.258   1.5941  -0.4303   1.3487
 D2R  HAL   H  HCR6   0   0.262  -3.5313  -1.7891   2.0480
 D2R  HAM   H  HCH2   0   0.254   3.0791  -3.2820  -1.5060
 D2R  HAMA  H  HCH2   0   0.256   2.7930  -1.8070  -2.3948
 D2R  HAN   H  HCH2   0   0.233   3.3040  -0.4536  -0.3609
 D2R  HANA  H  HCH2   0   0.215   3.5269  -1.9157   0.5728
 D2R  HAO   H  HCH2   0   0.222   5.4019  -2.6055  -0.9389
 D2R  HAOA  H  HCH2   0   0.220   5.1778  -1.1704  -1.8936
 D2R  HAP   H  HCH2   0   0.279  -0.0402  -1.7278   2.0767
 D2R  HAPA  H  HCH2   0   0.281  -1.4785  -1.0077   2.7420
 D2R  CAB   C  CH3    0  -0.812  -2.7618   1.1436   1.2814
 D2R  CAP   C  CH2    0  -0.682  -0.9241  -1.1417   1.8097
 D2R  OAT   O  O2     0  -0.469  -5.1972  -3.0672   0.6583
 D2R  CAH   C  CSP    0   0.113   0.1616  -2.3341  -0.6644

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
 D2R  C2   N1    aromatic  1.344  0.020  1.344
 D2R  N1   C6    aromatic  1.316  0.020  1.316
 D2R  N3   C2    aromatic  1.317  0.020  1.317
 D2R  NAC  C2    single    1.348  0.020  1.348
 D2R  N3   C4    aromatic  1.344  0.020  1.344
 D2R  NAQ  C4    aromatic  1.344  0.020  1.344
 D2R  C4   C5    aromatic  1.420  0.020  1.420
 D2R  C5   CAX   aromatic  1.417  0.020  1.417
 D2R  C5   C6    aromatic  1.447  0.020  1.447
 D2R  C6   NAD   single    1.342  0.020  1.342
 D2R  OAT  CAA   single    1.414  0.020  1.414
 D2R  CAA  HAA   single    0.970  0.020  1.090
 D2R  CAA  HAAA  single    0.970  0.020  1.090
 D2R  CAA  HAAB  single    0.970  0.020  1.090
 D2R  CAX  CAB   single    1.500  0.020  1.500
 D2R  CAB  HAB   single    0.970  0.020  1.090
 D2R  CAB  HABA  single    0.970  0.020  1.090
 D2R  CAB  HABB  single    0.970  0.020  1.090
 D2R  NAC  HNAC  single    0.890  0.020  1.040
 D2R  NAC  HNAA  single    0.890  0.020  1.040
 D2R  NAD  HNAD  single    0.890  0.020  1.040
 D2R  NAD  HNAB  single    0.890  0.020  1.040
 D2R  OAE  CAU   deloc     1.246  0.020  1.246
 D2R  CAU  OAF   deloc     1.250  0.020  1.250
 D2R  CAM  CAG   single    1.458  0.020  1.458
 D2R  CAG  CAH   triple    1.207  0.020  1.207
 D2R  CAH  CAZ   single    1.427  0.020  1.427
 D2R  CAJ  CAI   aromatic  1.386  0.020  1.386
 D2R  CAI  CAY   aromatic  1.392  0.020  1.392
 D2R  CAI  HAI   single    0.930  0.020  1.080
 D2R  CAZ  CAJ   aromatic  1.395  0.020  1.395
 D2R  CAJ  HAJ   single    0.930  0.020  1.080
 D2R  NAQ  CAK   aromatic  1.308  0.020  1.308
 D2R  CAK  CBA   aromatic  1.401  0.020  1.401
 D2R  CAK  HAK   single    0.930  0.020  1.080
 D2R  CBB  CAL   aromatic  1.384  0.020  1.384
 D2R  CAL  CAY   aromatic  1.396  0.020  1.396
 D2R  CAL  HAL   single    0.930  0.020  1.080
 D2R  CAM  CAN   single    1.532  0.020  1.532
 D2R  CAM  HAM   single    0.970  0.020  1.090
 D2R  CAM  HAMA  single    0.970  0.020  1.090
 D2R  CAO  CAN   single    1.519  0.020  1.519
 D2R  CAN  HAN   single    0.970  0.020  1.090
 D2R  CAN  HANA  single    0.970  0.020  1.090
 D2R  CAO  CAU   single    1.539  0.020  1.539
 D2R  CAO  HAO   single    0.970  0.020  1.090
 D2R  CAO  HAOA  single    0.970  0.020  1.090
 D2R  CBA  CAP   single    1.509  0.020  1.509
 D2R  CAP  CBB   single    1.509  0.020  1.509
 D2R  CAP  HAP   single    0.970  0.020  1.090
 D2R  CAP  HAPA  single    0.970  0.020  1.090
 D2R  CAY  OAT   single    1.344  0.020  1.344
 D2R  CBA  CAX   aromatic  1.389  0.020  1.389
 D2R  CAZ  CBB   aromatic  1.408  0.020  1.408

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
 D2R  C6    N1   C2    118.28  3.000
 D2R  NAC   C2   N3    118.01  3.000
 D2R  NAC   C2   N1    115.65  3.000
 D2R  N3    C2   N1    126.33  3.000
 D2R  C4    N3   C2    116.46  3.000
 D2R  NAQ   C4   C5    121.44  3.000
 D2R  C5    C4   N3    123.04  3.000
 D2R  NAQ   C4   N3    115.52  3.000
 D2R  CAX   C5   C6    126.94  3.000
 D2R  C6    C5   C4    113.93  3.000
 D2R  CAX   C5   C4    119.13  3.000
 D2R  NAD   C6   C5    122.99  3.000
 D2R  NAD   C6   N1    115.76  3.000
 D2R  C5    C6   N1    121.25  3.000
 D2R  HAAB  CAA  HAAA  108.78  3.000
 D2R  HAAB  CAA  HAA   108.77  3.000
 D2R  HAAA  CAA  HAA   108.87  3.000
 D2R  HAAB  CAA  OAT   106.51  3.000
 D2R  HAAA  CAA  OAT   111.84  3.000
 D2R  HAA   CAA  OAT   111.96  3.000
 D2R  HNAA  NAC  HNAC  117.00  3.000
 D2R  HNAA  NAC  C2    118.51  3.000
 D2R  HNAC  NAC  C2    118.79  3.000
 D2R  HNAB  NAD  HNAD  115.76  3.000
 D2R  HNAB  NAD  C6    116.60  3.000
 D2R  HNAD  NAD  C6    121.97  3.000
 D2R  CAM   CAG  CAH   180.00  3.000
 D2R  HAI   CAI  CAY   121.97  3.000
 D2R  HAI   CAI  CAJ   118.93  3.000
 D2R  CAY   CAI  CAJ   119.09  3.000
 D2R  HAJ   CAJ  CAZ   119.08  3.000
 D2R  HAJ   CAJ  CAI   118.89  3.000
 D2R  CAZ   CAJ  CAI   122.02  3.000
 D2R  HAK   CAK  CBA   118.35  3.000
 D2R  HAK   CAK  NAQ   115.90  3.000
 D2R  CBA   CAK  NAQ   125.74  3.000
 D2R  HAL   CAL  CBB   119.68  3.000
 D2R  HAL   CAL  CAY   118.47  3.000
 D2R  CBB   CAL  CAY   121.85  3.000
 D2R  HAMA  CAM  HAM   105.75  3.000
 D2R  HAMA  CAM  CAN   109.63  3.000
 D2R  HAM   CAM  CAN   109.61  3.000
 D2R  HAMA  CAM  CAG   108.84  3.000
 D2R  HAM   CAM  CAG   108.58  3.000
 D2R  CAN   CAM  CAG   114.09  3.000
 D2R  HANA  CAN  HAN   106.42  3.000
 D2R  HANA  CAN  CAO   110.13  3.000
 D2R  HAN   CAN  CAO   110.32  3.000
 D2R  HANA  CAN  CAM   109.25  3.000
 D2R  HAN   CAN  CAM   109.40  3.000
 D2R  CAO   CAN  CAM   111.21  3.000
 D2R  HAOA  CAO  HAO   104.85  3.000
 D2R  HAOA  CAO  CAU   108.29  3.000
 D2R  HAO   CAO  CAU   108.03  3.000
 D2R  HAOA  CAO  CAN   109.79  3.000
 D2R  HAO   CAO  CAN   109.61  3.000
 D2R  CAU   CAO  CAN   115.71  3.000
 D2R  CAK   NAQ  C4    117.96  3.000
 D2R  CAO   CAU  OAF   115.77  3.000
 D2R  CAO   CAU  OAE   117.83  3.000
 D2R  OAF   CAU  OAE   126.39  3.000
 D2R  CBA   CAX  CAB   119.59  3.000
 D2R  CBA   CAX  C5    117.69  3.000
 D2R  CAB   CAX  C5    122.63  3.000
 D2R  OAT   CAY  CAL   116.15  3.000
 D2R  OAT   CAY  CAI   124.54  3.000
 D2R  CAL   CAY  CAI   119.31  3.000
 D2R  CBB   CAZ  CAJ   118.77  3.000
 D2R  CBB   CAZ  CAH   122.30  3.000
 D2R  CAJ   CAZ  CAH   118.89  3.000
 D2R  CAX   CBA  CAP   124.09  3.000
 D2R  CAX   CBA  CAK   117.66  3.000
 D2R  CAP   CBA  CAK   118.24  3.000
 D2R  CAZ   CBB  CAP   121.18  3.000
 D2R  CAZ   CBB  CAL   118.94  3.000
 D2R  CAP   CBB  CAL   119.87  3.000
 D2R  HABB  CAB  HABA  106.74  3.000
 D2R  HABB  CAB  HAB   108.52  3.000
 D2R  HABA  CAB  HAB   106.46  3.000
 D2R  HABB  CAB  CAX   111.94  3.000
 D2R  HABA  CAB  CAX   110.70  3.000
 D2R  HAB   CAB  CAX   112.18  3.000
 D2R  HAPA  CAP  HAP   105.51  3.000
 D2R  HAPA  CAP  CBB   108.98  3.000
 D2R  HAP   CAP  CBB   108.91  3.000
 D2R  HAPA  CAP  CBA   110.89  3.000
 D2R  HAP   CAP  CBA   107.96  3.000
 D2R  CBB   CAP  CBA   114.21  3.000
 D2R  CAY   OAT  CAA   118.50  3.000
 D2R  CAZ   CAH  CAG   180.00  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
 D2R  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 D2R  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 D2R  CONST_03  CAX   C5   C6   N1    180.00   0.0  0
 D2R  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 D2R  CONST_05  NAQ   C4   N3   C2    180.00   0.0  0
 D2R  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 D2R  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 D2R  CONST_08  CAK   NAQ  C4   N3    180.00   0.0  0
 D2R  CONST_09  CAX   C5   C4   N3    180.00   0.0  0
 D2R  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 D2R  CONST_11  CBA   CAK  NAQ  C4      0.00   0.0  0
 D2R  CONST_12  CBA   CAX  C5   C4      0.00   0.0  0
 D2R  CONST_13  CAK   NAQ  C4   C5      0.00   0.0  0
 D2R  CONST_14  CAK   CBA  CAX  C5      0.00   0.0  0
 D2R  CONST_15  NAQ   C4   C5   C6    180.00   0.0  0
 D2R  CONST_16  CBA   CAX  C5   C6    180.00   0.0  0
 D2R  CONST_17  CBB   CAZ  CAJ  CAI     0.00   0.0  0
 D2R  CONST_18  CBB   CAL  CAY  CAI     0.00   0.0  0
 D2R  CONST_19  CAL   CAY  CAI  CAJ     0.00   0.0  0
 D2R  CONST_20  CAL   CBB  CAZ  CAJ     0.00   0.0  0
 D2R  CONST_21  CAX   C5   C4   NAQ     0.00   0.0  0
 D2R  CONST_22  CAX   CBA  CAK  NAQ     0.00   0.0  0
 D2R  CONST_23  CAZ   CAJ  CAI  CAY     0.00   0.0  0
 D2R  CONST_24  CAZ   CBB  CAL  CAY     0.00   0.0  0
 D2R  CONST_25  NAD   C6   N1   C2    180.00   0.0  0
 D2R  CONST_26  NAC   C2   N3   C4    180.00   0.0  0
 D2R  CONST_27  CAB   CAX  C5   C4    180.00   0.0  0
 D2R  CONST_28  NAD   C6   C5   C4    180.00   0.0  0
 D2R  CONST_29  CAP   CBA  CAX  C5    180.00   0.0  0
 D2R  CONST_30  NAC   C2   N1   C6    180.00   0.0  0
 D2R  CONST_31  CAB   CAX  C5   C6      0.00   0.0  0
 D2R  CONST_32  CAK   CBA  CAX  CAB   180.00   0.0  0
 D2R  CONST_33  CAX   C5   C6   NAD     0.00   0.0  0
 D2R  CONST_34  CAI   CAJ  CAZ  CAH   180.00   0.0  0
 D2R  CONST_35  CAL   CBB  CAZ  CAH   180.00   0.0  0
 D2R  CONST_36  OAT   CAY  CAI  CAJ   180.00   0.0  0
 D2R  CONST_37  CAP   CBB  CAZ  CAJ   180.00   0.0  0
 D2R  CONST_38  NAQ   CAK  CBA  CAP   180.00   0.0  0
 D2R  CONST_39  CAY   CAL  CBB  CAP   180.00   0.0  0
 D2R  CONST_40  CBB   CAL  CAY  OAT   180.00   0.0  0
 D2R  CONST_41  HAK   CAK  NAQ  C4    180.00   0.0  0
 D2R  CONST_42  HAL   CAL  CAY  CAI   180.00   0.0  0
 D2R  CONST_43  HAI   CAI  CAY  CAL   180.00   0.0  0
 D2R  CONST_44  HAJ   CAJ  CAI  CAY   180.00   0.0  0
 D2R  CONST_45  HNAC  NAC  C2   N1      0.00   0.0  0
 D2R  CONST_46  HNAA  NAC  C2   N1    180.00   0.0  0
 D2R  CONST_48  HNAB  NAD  C6   N1      0.00   0.0  0
 D2R  Var_01    CBB   CAP  CBA  CAK  -115.70  30.0  2
 D2R  Var_02    CBA   CAP  CBB  CAL  -113.92  30.0  3
 D2R  Var_03    CAI   CAY  OAT  CAA     1.71  30.0  3
 D2R  Var_04    HAB   CAB  CAX  C5     88.56  30.0  2
 D2R  Var_05    HAA   CAA  OAT  CAY   -62.49  30.0  3
 D2R  Var_06    CAN   CAO  CAU  OAE     3.64  30.0  1
 D2R  Var_07    CAO   CAN  CAM  CAG   177.12  30.0  3
 D2R  Var_08    CAN   CAM  CAG  CAH  -128.53  30.0  1
 D2R  Var_09    CAU   CAO  CAN  CAM   179.29  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
 D2R  plan-1  CAG   0.020
 D2R  plan-1  CAI   0.020
 D2R  plan-1  CAJ   0.020
 D2R  plan-1  CAL   0.020
 D2R  plan-1  CAY   0.020
 D2R  plan-1  CAZ   0.020
 D2R  plan-1  CBB   0.020
 D2R  plan-1  HAI   0.020
 D2R  plan-1  HAJ   0.020
 D2R  plan-1  HAL   0.020
 D2R  plan-1  CAP   0.020
 D2R  plan-1  OAT   0.020
 D2R  plan-1  CAH   0.020
 D2R  plan-2  N1    0.020
 D2R  plan-2  C2    0.020
 D2R  plan-2  N3    0.020
 D2R  plan-2  C4    0.020
 D2R  plan-2  C5    0.020
 D2R  plan-2  C6    0.020
 D2R  plan-2  NAC   0.020
 D2R  plan-2  NAD   0.020
 D2R  plan-2  CAK   0.020
 D2R  plan-2  NAQ   0.020
 D2R  plan-2  CAX   0.020
 D2R  plan-2  CBA   0.020
 D2R  plan-2  HAK   0.020
 D2R  plan-2  CAB   0.020
 D2R  plan-2  CAP   0.020
 D2R  plan-3  C2    0.020
 D2R  plan-3  NAC   0.020
 D2R  plan-3  HNAC  0.020
 D2R  plan-3  HNAA  0.020
 D2R  plan-4  C6    0.020
 D2R  plan-4  NAD   0.020
 D2R  plan-4  HNAD  0.020
 D2R  plan-4  HNAB  0.020
 D2R  plan-5  OAE   0.020
 D2R  plan-5  OAF   0.020
 D2R  plan-5  CAO   0.020
 D2R  plan-5  CAU   0.020

