# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 09:49:24 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@H](C)c2cc(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
 06U  06U  6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  51  28  .  2021-08-03  2022-07-21
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_06U
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
 06U  N1    N  N     0  -0.505   4.6464  -1.5746  -1.2629
 06U  C2    C  CR6   0   0.537   5.7601  -0.8749  -1.0508
 06U  N3    N  N     0  -0.499   5.8638   0.2572  -0.3454
 06U  C4    C  CR6   0   0.266   4.7453   0.7354   0.1858
 06U  C5    C  CR6   0  -0.342   3.5157   0.1014   0.0255
 06U  C6    C  CR6   0   0.457   3.5250  -1.0991  -0.7351
 06U  CAA   C  CR16  0  -0.378  -5.2993  -0.0015  -1.4893
 06U  NAH   N  NH2   0  -0.820   6.8878  -1.3398  -1.6171
 06U  CAI   C  CH2   0  -0.520   4.8535   2.0298   0.9332
 06U  NAJ   N  NH2   0  -0.827   2.3950  -1.7829  -0.9506
 06U  CAK   C  CSP   0   0.092   2.3018   0.5883   0.5684
 06U  CAL   C  CSP   0   0.143   1.2276   0.9371   0.9960
 06U  CAM   C  CH1   0  -0.510  -0.0762   1.3379   1.5181
 06U  CAN   C  CH3   0  -0.641  -0.0649   1.4149   3.0514
 06U  CAO   C  CR6   0   0.195  -1.1621   0.3986   1.0289
 06U  CAP   C  CR16  0  -0.410  -0.9974  -0.9747   1.1118
 06U  CAQ   C  CR6   0   0.432  -2.0110  -1.8357   0.6907
 06U  CAR   C  CR16  0  -0.469  -3.1962  -1.3122   0.1833
 06U  CAS   C  CR6   0   0.147  -3.3649   0.0702   0.1004
 06U  CAT   C  CR16  0  -0.418  -2.3482   0.9197   0.5252
 06U  CAU   C  CR6   0   0.169  -4.6177   0.6252  -0.4479
 06U  CAV   C  CR16  0  -0.377  -5.1713   1.8031   0.0500
 06U  CAW   C  CR16  0  -0.060  -6.3476   2.2847  -0.5013
 06U  NAX   N  N     0  -0.407  -6.9957   1.6862  -1.4943
 06U  CAY   C  CR16  0  -0.060  -6.4692   0.5635  -1.9704
 06U  CAZ   C  CH3   0  -0.665   4.6409   3.2224   0.0011
 06U  OBA   O  O2    0  -0.471  -1.7595  -3.1502   0.8161
 06U  CBB   C  CH3   0  -0.440  -2.7414  -4.0742   0.3888
 06U  HNAH  H  HNH2  0   0.395   6.8972  -2.2571  -2.0267
 06U  HNAA  H  HNH2  0   0.395   7.7690  -0.9292  -1.3646
 06U  HAI   H  HCH2  0   0.243   4.1206   2.0627   1.7411
 06U  HAIA  H  HCH2  0   0.249   5.8443   2.0887   1.3861
 06U  HNAJ  H  HNH2  0   0.400   2.4266  -2.6636  -1.4341
 06U  HNAB  H  HNH2  0   0.401   1.5315  -1.5114  -0.5136
 06U  HAM   H  HCH1  0   0.286  -0.3033   2.3380   1.1350
 06U  HAN   H  HCH3  0   0.243  -1.0409   1.7327   3.4175
 06U  HANA  H  HCH3  0   0.234   0.1684   0.4448   3.4897
 06U  HANB  H  HCH3  0   0.244   0.6793   2.1338   3.3926
 06U  HAP   H  HCR6  0   0.262  -0.0793  -1.3961   1.5068
 06U  HAR   H  HCR6  0   0.282  -4.0034  -1.9610  -0.1297
 06U  HAT   H  HCR6  0   0.255  -2.4645   1.9931   0.4381
 06U  HAV   H  HCR6  0   0.270  -4.7104   2.3379   0.8699
 06U  HAW   H  HCR6  0   0.266  -6.7873   3.1976  -0.1152
 06U  HAY   H  HCR6  0   0.266  -7.0017   0.0844  -2.7845
 06U  HAZ   H  HCH3  0   0.238   4.7342   4.1590   0.5509
 06U  HAZA  H  HCH3  0   0.230   5.3774   3.2291  -0.8028
 06U  HAZB  H  HCH3  0   0.230   3.6485   3.1991  -0.4501
 06U  HBB   H  HCH3  0   0.230  -2.9651  -3.9681  -0.6758
 06U  HBBA  H  HCH3  0   0.263  -2.3288  -5.0648   0.5624
 06U  HBBB  H  HCH3  0   0.231  -3.6699  -3.9754   0.9574
 06U  HAA   H  HCR6  0   0.269  -4.9221  -0.9085  -1.9430

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
 06U  C2   N1    aromatic  1.332  0.020  1.332
 06U  N1   C6    aromatic  1.327  0.020  1.327
 06U  N3   C2    aromatic  1.338  0.020  1.338
 06U  NAH  C2    single    1.345  0.020  1.345
 06U  N3   C4    aromatic  1.327  0.020  1.327
 06U  CAI  C4    single    1.499  0.020  1.499
 06U  C4   C5    aromatic  1.393  0.020  1.393
 06U  C5   CAK   single    1.416  0.020  1.416
 06U  C5   C6    aromatic  1.421  0.020  1.421
 06U  C6   NAJ   single    1.338  0.020  1.338
 06U  CAY  CAA   aromatic  1.385  0.020  1.385
 06U  CAA  CAU   aromatic  1.394  0.020  1.394
 06U  CAA  HAA   single    0.930  0.020  1.080
 06U  NAH  HNAH  single    0.890  0.020  1.040
 06U  NAH  HNAA  single    0.890  0.020  1.040
 06U  CAZ  CAI   single    1.529  0.020  1.529
 06U  CAI  HAI   single    0.970  0.020  1.090
 06U  CAI  HAIA  single    0.970  0.020  1.090
 06U  NAJ  HNAJ  single    0.860  0.020  1.020
 06U  NAJ  HNAB  single    0.860  0.020  1.020
 06U  CAK  CAL   triple    1.208  0.020  1.208
 06U  CAL  CAM   single    1.461  0.020  1.461
 06U  CAO  CAM   single    1.517  0.020  1.517
 06U  CAM  CAN   single    1.535  0.020  1.535
 06U  CAM  HAM   single    0.970  0.020  1.090
 06U  CAN  HAN   single    0.970  0.020  1.090
 06U  CAN  HANA  single    0.970  0.020  1.090
 06U  CAN  HANB  single    0.970  0.020  1.090
 06U  CAP  CAO   aromatic  1.386  0.020  1.386
 06U  CAT  CAO   aromatic  1.390  0.020  1.390
 06U  CAQ  CAP   aromatic  1.395  0.020  1.395
 06U  CAP  HAP   single    0.930  0.020  1.080
 06U  OBA  CAQ   single    1.344  0.020  1.344
 06U  CAR  CAQ   aromatic  1.391  0.020  1.391
 06U  CAR  CAS   aromatic  1.395  0.020  1.395
 06U  CAR  HAR   single    0.930  0.020  1.080
 06U  CAU  CAS   single    1.476  0.020  1.476
 06U  CAS  CAT   aromatic  1.391  0.020  1.391
 06U  CAT  HAT   single    0.930  0.020  1.080
 06U  CAU  CAV   aromatic  1.393  0.020  1.393
 06U  CAW  CAV   aromatic  1.386  0.020  1.386
 06U  CAV  HAV   single    0.930  0.020  1.080
 06U  NAX  CAW   aromatic  1.328  0.020  1.328
 06U  CAW  HAW   single    0.930  0.020  1.080
 06U  CAY  NAX   aromatic  1.328  0.020  1.328
 06U  CAY  HAY   single    0.930  0.020  1.080
 06U  CAZ  HAZ   single    0.970  0.020  1.090
 06U  CAZ  HAZA  single    0.970  0.020  1.090
 06U  CAZ  HAZB  single    0.970  0.020  1.090
 06U  OBA  CBB   single    1.414  0.020  1.414
 06U  CBB  HBB   single    0.970  0.020  1.090
 06U  CBB  HBBA  single    0.970  0.020  1.090
 06U  CBB  HBBB  single    0.970  0.020  1.090

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
 06U  C6    N1   C2    117.05  3.000
 06U  NAH   C2   N3    116.71  3.000
 06U  NAH   C2   N1    116.90  3.000
 06U  N3    C2   N1    126.38  3.000
 06U  C4    N3   C2    116.78  3.000
 06U  CAI   C4   C5    120.95  3.000
 06U  C5    C4   N3    122.27  3.000
 06U  CAI   C4   N3    116.74  3.000
 06U  CAK   C5   C6    120.08  3.000
 06U  C6    C5   C4    116.13  3.000
 06U  CAK   C5   C4    123.79  3.000
 06U  NAJ   C6   C5    120.81  3.000
 06U  NAJ   C6   N1    117.79  3.000
 06U  C5    C6   N1    121.39  3.000
 06U  HAA   CAA  CAY   119.38  3.000
 06U  HAA   CAA  CAU   121.32  3.000
 06U  CAY   CAA  CAU   119.28  3.000
 06U  HNAA  NAH  HNAH  117.88  3.000
 06U  HNAA  NAH  C2    119.24  3.000
 06U  HNAH  NAH  C2    119.68  3.000
 06U  HAIA  CAI  HAI   107.52  3.000
 06U  HAIA  CAI  CAZ   109.71  3.000
 06U  HAI   CAI  CAZ   109.55  3.000
 06U  HAIA  CAI  C4    108.61  3.000
 06U  HAI   CAI  C4    110.29  3.000
 06U  CAZ   CAI  C4    111.08  3.000
 06U  HNAB  NAJ  HNAJ  118.22  3.000
 06U  HNAB  NAJ  C6    121.16  3.000
 06U  HNAJ  NAJ  C6    119.91  3.000
 06U  CAL   CAK  C5    180.00  3.000
 06U  CAM   CAL  CAK   180.00  3.000
 06U  HAM   CAM  CAO   107.72  3.000
 06U  HAM   CAM  CAN   107.77  3.000
 06U  CAO   CAM  CAN   111.00  3.000
 06U  HAM   CAM  CAL   108.11  3.000
 06U  CAN   CAM  CAL   111.36  3.000
 06U  CAO   CAM  CAL   110.72  3.000
 06U  HANB  CAN  HANA  108.37  3.000
 06U  HANB  CAN  HAN   108.31  3.000
 06U  HANA  CAN  HAN   108.44  3.000
 06U  HANB  CAN  CAM   110.54  3.000
 06U  HANA  CAN  CAM   111.01  3.000
 06U  HAN   CAN  CAM   110.09  3.000
 06U  CAT   CAO  CAP   119.65  3.000
 06U  CAT   CAO  CAM   119.71  3.000
 06U  CAP   CAO  CAM   120.62  3.000
 06U  HAP   CAP  CAQ   119.03  3.000
 06U  HAP   CAP  CAO   120.49  3.000
 06U  CAQ   CAP  CAO   120.48  3.000
 06U  OBA   CAQ  CAR   124.15  3.000
 06U  CAR   CAQ  CAP   119.79  3.000
 06U  OBA   CAQ  CAP   116.06  3.000
 06U  HAR   CAR  CAS   119.13  3.000
 06U  HAR   CAR  CAQ   121.02  3.000
 06U  CAS   CAR  CAQ   119.83  3.000
 06U  CAU   CAS  CAT   120.27  3.000
 06U  CAT   CAS  CAR   119.90  3.000
 06U  CAU   CAS  CAR   119.82  3.000
 06U  HAT   CAT  CAS   120.14  3.000
 06U  HAT   CAT  CAO   119.49  3.000
 06U  CAS   CAT  CAO   120.35  3.000
 06U  CAV   CAU  CAS   121.49  3.000
 06U  CAV   CAU  CAA   116.93  3.000
 06U  CAS   CAU  CAA   121.58  3.000
 06U  HAV   CAV  CAW   119.43  3.000
 06U  HAV   CAV  CAU   121.29  3.000
 06U  CAW   CAV  CAU   119.27  3.000
 06U  HAW   CAW  NAX   116.60  3.000
 06U  HAW   CAW  CAV   119.68  3.000
 06U  NAX   CAW  CAV   123.71  3.000
 06U  CAY   NAX  CAW   117.09  3.000
 06U  HAY   CAY  NAX   116.61  3.000
 06U  HAY   CAY  CAA   119.68  3.000
 06U  NAX   CAY  CAA   123.71  3.000
 06U  HAZB  CAZ  HAZA  108.05  3.000
 06U  HAZB  CAZ  HAZ   107.76  3.000
 06U  HAZA  CAZ  HAZ   107.98  3.000
 06U  HAZB  CAZ  CAI   111.24  3.000
 06U  HAZA  CAZ  CAI   111.13  3.000
 06U  HAZ   CAZ  CAI   110.54  3.000
 06U  CBB   OBA  CAQ   118.73  3.000
 06U  HBBB  CBB  HBBA  108.76  3.000
 06U  HBBB  CBB  HBB   108.91  3.000
 06U  HBBA  CBB  HBB   108.76  3.000
 06U  HBBB  CBB  OBA   111.93  3.000
 06U  HBBA  CBB  OBA   106.47  3.000
 06U  HBB   CBB  OBA   111.90  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
 06U  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 06U  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 06U  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 06U  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 06U  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 06U  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 06U  CONST_07  CAW   NAX  CAY  CAA     0.00   0.0  0
 06U  CONST_10  CAW   CAV  CAU  CAA     0.00   0.0  0
 06U  CONST_11  CAR   CAQ  CAP  CAO     0.00   0.0  0
 06U  CONST_12  CAR   CAS  CAT  CAO     0.00   0.0  0
 06U  CONST_13  CAU   CAS  CAT  CAO   180.00   0.0  0
 06U  CONST_14  CAS   CAT  CAO  CAP     0.00   0.0  0
 06U  CONST_15  CAS   CAR  CAQ  CAP     0.00   0.0  0
 06U  CONST_16  CAT   CAO  CAP  CAQ     0.00   0.0  0
 06U  CONST_17  CAU   CAS  CAR  CAQ   180.00   0.0  0
 06U  CONST_18  CAT   CAS  CAR  CAQ     0.00   0.0  0
 06U  CONST_20  CAY   CAA  CAU  CAS   180.00   0.0  0
 06U  CONST_21  CAW   CAV  CAU  CAS   180.00   0.0  0
 06U  CONST_23  NAX   CAY  CAA  CAU     0.00   0.0  0
 06U  CONST_24  NAX   CAW  CAV  CAU     0.00   0.0  0
 06U  CONST_25  CAY   CAA  CAU  CAV     0.00   0.0  0
 06U  CONST_26  CAY   NAX  CAW  CAV     0.00   0.0  0
 06U  CONST_27  CAK   C5   C6   N1    180.00   0.0  0
 06U  CONST_28  NAJ   C6   N1   C2    180.00   0.0  0
 06U  CONST_29  CAI   C4   N3   C2    180.00   0.0  0
 06U  CONST_30  CAK   C5   C4   N3    180.00   0.0  0
 06U  CONST_31  NAH   C2   N3   C4    180.00   0.0  0
 06U  CONST_32  NAJ   C6   C5   C4    180.00   0.0  0
 06U  CONST_33  NAH   C2   N1   C6    180.00   0.0  0
 06U  CONST_34  CAI   C4   C5   C6    180.00   0.0  0
 06U  CONST_35  CAQ   CAP  CAO  CAM   180.00   0.0  0
 06U  CONST_36  CAS   CAT  CAO  CAM   180.00   0.0  0
 06U  CONST_37  OBA   CAQ  CAP  CAO   180.00   0.0  0
 06U  CONST_38  OBA   CAQ  CAR  CAS   180.00   0.0  0
 06U  CONST_39  HAV   CAV  CAU  CAA   180.00   0.0  0
 06U  CONST_40  HAT   CAT  CAO  CAP   180.00   0.0  0
 06U  CONST_41  HAR   CAR  CAQ  CAP   180.00   0.0  0
 06U  CONST_42  HAP   CAP  CAQ  CAR   180.00   0.0  0
 06U  CONST_43  HAA   CAA  CAU  CAS     0.00   0.0  0
 06U  CONST_44  HAY   CAY  CAA  CAU   180.00   0.0  0
 06U  CONST_45  HAW   CAW  CAV  CAU   180.00   0.0  0
 06U  CONST_46  HNAH  NAH  C2   N1      0.00   0.0  0
 06U  CONST_47  HNAA  NAH  C2   N1    180.00   0.0  0
 06U  CONST_48  HNAJ  NAJ  C6   N1      0.00   0.0  0
 06U  CONST_49  HNAB  NAJ  C6   N1    180.00   0.0  0
 06U  Var_01    CAZ   CAI  C4   N3     89.47  30.0  1
 06U  Var_02    HAZ   CAZ  CAI  C4   -179.26  30.0  3
 06U  Var_03    HBB   CBB  OBA  CAQ    60.28  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 06U  chir_01  CAM  CAL  CAO  CAN  negativ

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
 06U  plan-1  N1    0.020
 06U  plan-1  C2    0.020
 06U  plan-1  N3    0.020
 06U  plan-1  C4    0.020
 06U  plan-1  C5    0.020
 06U  plan-1  C6    0.020
 06U  plan-1  NAH   0.020
 06U  plan-1  CAI   0.020
 06U  plan-1  NAJ   0.020
 06U  plan-1  CAK   0.020
 06U  plan-1  CAL   0.020
 06U  plan-2  CAM   0.020
 06U  plan-2  CAO   0.020
 06U  plan-2  CAP   0.020
 06U  plan-2  CAQ   0.020
 06U  plan-2  CAR   0.020
 06U  plan-2  CAS   0.020
 06U  plan-2  CAT   0.020
 06U  plan-2  CAU   0.020
 06U  plan-2  OBA   0.020
 06U  plan-2  HAP   0.020
 06U  plan-2  HAR   0.020
 06U  plan-2  HAT   0.020
 06U  plan-3  CAA   0.020
 06U  plan-3  CAS   0.020
 06U  plan-3  CAU   0.020
 06U  plan-3  CAV   0.020
 06U  plan-3  CAW   0.020
 06U  plan-3  NAX   0.020
 06U  plan-3  CAY   0.020
 06U  plan-3  HAV   0.020
 06U  plan-3  HAW   0.020
 06U  plan-3  HAY   0.020
 06U  plan-3  HAA   0.020
 06U  plan-4  C2    0.020
 06U  plan-4  NAH   0.020
 06U  plan-4  HNAH  0.020
 06U  plan-4  HNAA  0.020
 06U  plan-5  C6    0.020
 06U  plan-5  NAJ   0.020
 06U  plan-5  HNAJ  0.020
 06U  plan-5  HNAB  0.020

