# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 00:53:52 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-ethyl-5-{(3S)-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
 06W  06W  6-ethyl-5-{(3S)-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_06W
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
 06W  N1    N  N     0  -0.504  -4.7293  -1.5175  -1.4256
 06W  C2    C  CR6   0   0.540  -5.8522  -0.8762  -1.1048
 06W  N3    N  N     0  -0.499  -5.9430   0.2739  -0.4254
 06W  C4    C  CR6   0   0.268  -4.8033   0.8250  -0.0286
 06W  C5    C  CR6   0  -0.337  -3.5642   0.2491  -0.3023
 06W  C6    C  CR6   0   0.453  -3.5868  -0.9706  -1.0291
 06W  CAA   C  CR16  0  -0.379   5.8952  -0.1355   0.0303
 06W  NAH   N  NH2   0  -0.820  -7.0084  -1.4459  -1.4843
 06W  CAI   C  CH2   0  -0.525  -4.9025   2.0875   0.7733
 06W  NAJ   N  NH2   0  -0.825  -2.4505  -1.6197  -1.3183
 06W  CAK   C  CSP   0   0.100  -2.3331   0.8020   0.1254
 06W  CAL   C  CSP   0   0.135  -1.2472   1.2180   0.4513
 06W  CAM   C  CH1   0  -0.509   0.0603   1.6731   0.9137
 06W  CAN   C  CH3   0  -0.637   0.0111   2.0500   2.4020
 06W  CAO   C  CR6   0   0.189   1.1251   0.6222   0.6619
 06W  CAP   C  CR16  0  -0.405   0.8730  -0.7181   0.9024
 06W  CAQ   C  CR6   0   0.433   1.8784  -1.6689   0.7226
 06W  CAR   C  CR16  0  -0.471   3.1413  -1.2700   0.2969
 06W  CAS   C  CR6   0   0.150   3.3982   0.0803   0.0542
 06W  CAT   C  CR16  0  -0.418   2.3890   1.0194   0.2384
 06W  CAU   C  CR6   0   0.171   4.7355   0.5050  -0.4029
 06W  CAV   C  CR16  0  -0.379   4.8973   1.5678  -1.2902
 06W  CAW   C  CR16  0  -0.060   6.1735   1.9286  -1.6912
 06W  NAX   N  N     0  -0.407   7.2771   1.3146  -1.2795
 06W  CAY   C  CR16  0  -0.060   7.1253   0.3018  -0.4334
 06W  CAZ   C  CH3   0  -0.666  -4.8175   1.8043   2.2734
 06W  OBA   O  O2    0  -0.471   1.5363  -2.9443   0.9759
 06W  CBB   C  CH3   0  -0.441   2.5240  -3.9499   0.8548
 06W  HNAH  H  HNH2  0   0.396  -6.9972  -2.2386  -2.1012
 06W  HNAA  H  HNH2  0   0.396  -7.8683  -0.9373  -1.3808
 06W  HAI   H  HCH2  0   0.244  -4.1039   2.7757   0.4890
 06W  HAIA  H  HCH2  0   0.249  -5.8528   2.5696   0.5421
 06W  HNAJ  H  HNH2  0   0.401  -1.5584  -1.1788  -1.1738
 06W  HNAB  H  HNH2  0   0.398  -2.4818  -2.4147  -1.9333
 06W  HAM   H  HCH1  0   0.285   0.3380   2.5692   0.3492
 06W  HAN   H  HCH3  0   0.243  -0.7222   2.8373   2.5747
 06W  HANA  H  HCH3  0   0.233  -0.2631   1.1880   3.0099
 06W  HANB  H  HCH3  0   0.243   0.9858   2.4100   2.7307
 06W  HAP   H  HCR6  0   0.261  -0.1078  -1.0429   1.2316
 06W  HAR   H  HCR6  0   0.280   3.9230  -1.9978   0.1253
 06W  HAT   H  HCR6  0   0.254   2.5866   2.0713   0.0719
 06W  HAV   H  HCR6  0   0.270   4.0451   2.1044  -1.6854
 06W  HAW   H  HCR6  0   0.266   6.3049   2.7519  -2.3846
 06W  HAY   H  HCR6  0   0.266   8.0314  -0.1914  -0.0991
 06W  HAZ   H  HCH3  0   0.238  -4.9439   2.7255   2.8420
 06W  HAZA  H  HCH3  0   0.229  -5.5956   1.1080   2.5875
 06W  HAZB  H  HCH3  0   0.232  -3.8512   1.3764   2.5414
 06W  HBB   H  HCH3  0   0.230   3.3662  -3.7765   1.5295
 06W  HBBA  H  HCH3  0   0.263   2.0446  -4.8871   1.1254
 06W  HBBB  H  HCH3  0   0.230   2.9011  -4.0319  -0.1678
 06W  HAA   H  HCR6  0   0.268   5.8547  -0.9539   0.7367

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
 06W  C2   N1    aromatic  1.332  0.020  1.332
 06W  C6   N1    aromatic  1.327  0.020  1.327
 06W  N3   C2    aromatic  1.339  0.020  1.339
 06W  C2   NAH   single    1.344  0.020  1.344
 06W  C4   N3    aromatic  1.327  0.020  1.327
 06W  CAI  C4    single    1.499  0.020  1.499
 06W  C4   C5    aromatic  1.394  0.020  1.394
 06W  CAK  C5    single    1.416  0.020  1.416
 06W  C5   C6    aromatic  1.420  0.020  1.420
 06W  C6   NAJ   single    1.340  0.020  1.340
 06W  CAU  CAA   aromatic  1.394  0.020  1.394
 06W  CAY  CAA   aromatic  1.385  0.020  1.385
 06W  CAA  HAA   single    0.930  0.020  1.080
 06W  NAH  HNAH  single    0.860  0.020  1.020
 06W  NAH  HNAA  single    0.860  0.020  1.020
 06W  CAI  CAZ   single    1.529  0.020  1.529
 06W  CAI  HAI   single    0.970  0.020  1.090
 06W  CAI  HAIA  single    0.970  0.020  1.090
 06W  NAJ  HNAJ  single    0.860  0.020  1.020
 06W  NAJ  HNAB  single    0.860  0.020  1.020
 06W  CAL  CAK   triple    1.208  0.020  1.208
 06W  CAM  CAL   single    1.460  0.020  1.460
 06W  CAN  CAM   single    1.536  0.020  1.536
 06W  CAM  CAO   single    1.517  0.020  1.517
 06W  CAM  HAM   single    0.970  0.020  1.090
 06W  CAN  HAN   single    0.970  0.020  1.090
 06W  CAN  HANA  single    0.970  0.020  1.090
 06W  CAN  HANB  single    0.970  0.020  1.090
 06W  CAT  CAO   aromatic  1.391  0.020  1.391
 06W  CAO  CAP   aromatic  1.385  0.020  1.385
 06W  CAP  CAQ   aromatic  1.395  0.020  1.395
 06W  CAP  HAP   single    0.930  0.020  1.080
 06W  CAR  CAQ   aromatic  1.391  0.020  1.391
 06W  CAQ  OBA   single    1.345  0.020  1.345
 06W  CAS  CAR   aromatic  1.396  0.020  1.396
 06W  CAR  HAR   single    0.930  0.020  1.080
 06W  CAU  CAS   single    1.476  0.020  1.476
 06W  CAT  CAS   aromatic  1.391  0.020  1.391
 06W  CAT  HAT   single    0.930  0.020  1.080
 06W  CAV  CAU   aromatic  1.394  0.020  1.394
 06W  CAW  CAV   aromatic  1.385  0.020  1.385
 06W  CAV  HAV   single    0.930  0.020  1.080
 06W  CAW  NAX   aromatic  1.328  0.020  1.328
 06W  CAW  HAW   single    0.930  0.020  1.080
 06W  NAX  CAY   aromatic  1.328  0.020  1.328
 06W  CAY  HAY   single    0.930  0.020  1.080
 06W  CAZ  HAZ   single    0.970  0.020  1.090
 06W  CAZ  HAZA  single    0.970  0.020  1.090
 06W  CAZ  HAZB  single    0.970  0.020  1.090
 06W  OBA  CBB   single    1.415  0.020  1.415
 06W  CBB  HBB   single    0.970  0.020  1.090
 06W  CBB  HBBA  single    0.970  0.020  1.090
 06W  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
 06W  C6    N1   C2    117.08  3.000
 06W  NAH   C2   N3    116.70  3.000
 06W  NAH   C2   N1    116.94  3.000
 06W  N3    C2   N1    126.36  3.000
 06W  C4    N3   C2    116.77  3.000
 06W  CAI   C4   C5    120.80  3.000
 06W  C5    C4   N3    122.24  3.000
 06W  CAI   C4   N3    116.94  3.000
 06W  CAK   C5   C6    120.26  3.000
 06W  C6    C5   C4    116.19  3.000
 06W  CAK   C5   C4    123.54  3.000
 06W  NAJ   C6   C5    120.86  3.000
 06W  NAJ   C6   N1    117.76  3.000
 06W  C5    C6   N1    121.37  3.000
 06W  HAA   CAA  CAY   119.38  3.000
 06W  HAA   CAA  CAU   121.29  3.000
 06W  CAY   CAA  CAU   119.32  3.000
 06W  HNAA  NAH  HNAH  118.19  3.000
 06W  HNAA  NAH  C2    119.53  3.000
 06W  HNAH  NAH  C2    119.90  3.000
 06W  HAIA  CAI  HAI   107.67  3.000
 06W  HAIA  CAI  CAZ   109.78  3.000
 06W  HAI   CAI  CAZ   109.36  3.000
 06W  HAIA  CAI  C4    108.46  3.000
 06W  HAI   CAI  C4    110.07  3.000
 06W  CAZ   CAI  C4    111.42  3.000
 06W  HNAB  NAJ  HNAJ  117.53  3.000
 06W  HNAB  NAJ  C6    119.24  3.000
 06W  HNAJ  NAJ  C6    120.58  3.000
 06W  CAL   CAK  C5    180.00  3.000
 06W  CAM   CAL  CAK   180.00  3.000
 06W  HAM   CAM  CAO   107.66  3.000
 06W  HAM   CAM  CAN   107.87  3.000
 06W  CAO   CAM  CAN   110.69  3.000
 06W  HAM   CAM  CAL   108.60  3.000
 06W  CAO   CAM  CAL   111.11  3.000
 06W  CAN   CAM  CAL   110.78  3.000
 06W  HANB  CAN  HANA  108.55  3.000
 06W  HANB  CAN  HAN   108.39  3.000
 06W  HANA  CAN  HAN   108.29  3.000
 06W  HANB  CAN  CAM   110.16  3.000
 06W  HANA  CAN  CAM   110.76  3.000
 06W  HAN   CAN  CAM   110.63  3.000
 06W  CAT   CAO  CAP   119.65  3.000
 06W  CAP   CAO  CAM   120.92  3.000
 06W  CAT   CAO  CAM   119.38  3.000
 06W  HAP   CAP  CAQ   119.13  3.000
 06W  HAP   CAP  CAO   120.48  3.000
 06W  CAQ   CAP  CAO   120.39  3.000
 06W  OBA   CAQ  CAR   124.09  3.000
 06W  OBA   CAQ  CAP   116.02  3.000
 06W  CAR   CAQ  CAP   119.88  3.000
 06W  HAR   CAR  CAS   119.36  3.000
 06W  HAR   CAR  CAQ   120.78  3.000
 06W  CAS   CAR  CAQ   119.85  3.000
 06W  CAU   CAS  CAT   120.28  3.000
 06W  CAT   CAS  CAR   119.78  3.000
 06W  CAU   CAS  CAR   119.94  3.000
 06W  HAT   CAT  CAS   120.20  3.000
 06W  HAT   CAT  CAO   119.33  3.000
 06W  CAS   CAT  CAO   120.46  3.000
 06W  CAV   CAU  CAS   121.45  3.000
 06W  CAV   CAU  CAA   116.85  3.000
 06W  CAS   CAU  CAA   121.70  3.000
 06W  HAV   CAV  CAW   119.39  3.000
 06W  HAV   CAV  CAU   121.28  3.000
 06W  CAW   CAV  CAU   119.32  3.000
 06W  HAW   CAW  NAX   116.64  3.000
 06W  HAW   CAW  CAV   119.63  3.000
 06W  NAX   CAW  CAV   123.72  3.000
 06W  CAY   NAX  CAW   117.06  3.000
 06W  HAY   CAY  NAX   116.60  3.000
 06W  HAY   CAY  CAA   119.67  3.000
 06W  NAX   CAY  CAA   123.73  3.000
 06W  HAZB  CAZ  HAZA  108.12  3.000
 06W  HAZB  CAZ  HAZ   107.84  3.000
 06W  HAZA  CAZ  HAZ   107.86  3.000
 06W  HAZB  CAZ  CAI   111.29  3.000
 06W  HAZA  CAZ  CAI   111.17  3.000
 06W  HAZ   CAZ  CAI   110.42  3.000
 06W  CBB   OBA  CAQ   118.72  3.000
 06W  HBBB  CBB  HBBA  108.69  3.000
 06W  HBBB  CBB  HBB   108.88  3.000
 06W  HBBA  CBB  HBB   108.84  3.000
 06W  HBBB  CBB  OBA   111.98  3.000
 06W  HBBA  CBB  OBA   106.48  3.000
 06W  HBB   CBB  OBA   111.86  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
 06W  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 06W  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 06W  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 06W  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 06W  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 06W  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 06W  CONST_09  CAW   CAV  CAU  CAA     0.00   0.0  0
 06W  CONST_10  CAW   NAX  CAY  CAA     0.00   0.0  0
 06W  CONST_11  CAR   CAS  CAT  CAO     0.00   0.0  0
 06W  CONST_12  CAU   CAS  CAT  CAO   180.00   0.0  0
 06W  CONST_13  CAR   CAQ  CAP  CAO     0.00   0.0  0
 06W  CONST_14  CAS   CAT  CAO  CAP     0.00   0.0  0
 06W  CONST_15  CAS   CAR  CAQ  CAP     0.00   0.0  0
 06W  CONST_16  CAT   CAO  CAP  CAQ     0.00   0.0  0
 06W  CONST_17  CAU   CAS  CAR  CAQ   180.00   0.0  0
 06W  CONST_18  CAT   CAS  CAR  CAQ     0.00   0.0  0
 06W  CONST_20  CAY   CAA  CAU  CAS   180.00   0.0  0
 06W  CONST_21  CAW   CAV  CAU  CAS   180.00   0.0  0
 06W  CONST_23  NAX   CAY  CAA  CAU     0.00   0.0  0
 06W  CONST_24  NAX   CAW  CAV  CAU     0.00   0.0  0
 06W  CONST_25  CAY   CAA  CAU  CAV     0.00   0.0  0
 06W  CONST_26  CAY   NAX  CAW  CAV     0.00   0.0  0
 06W  CONST_27  CAK   C5   C6   N1    180.00   0.0  0
 06W  CONST_28  NAJ   C6   N1   C2    180.00   0.0  0
 06W  CONST_29  CAI   C4   N3   C2    180.00   0.0  0
 06W  CONST_30  CAK   C5   C4   N3    180.00   0.0  0
 06W  CONST_31  NAH   C2   N3   C4    180.00   0.0  0
 06W  CONST_32  NAJ   C6   C5   C4    180.00   0.0  0
 06W  CONST_33  NAH   C2   N1   C6    180.00   0.0  0
 06W  CONST_34  CAI   C4   C5   C6    180.00   0.0  0
 06W  CONST_35  CAS   CAT  CAO  CAM   180.00   0.0  0
 06W  CONST_36  CAQ   CAP  CAO  CAM   180.00   0.0  0
 06W  CONST_37  OBA   CAQ  CAP  CAO   180.00   0.0  0
 06W  CONST_38  OBA   CAQ  CAR  CAS   180.00   0.0  0
 06W  CONST_39  HAV   CAV  CAU  CAA   180.00   0.0  0
 06W  CONST_40  HAT   CAT  CAO  CAP   180.00   0.0  0
 06W  CONST_41  HAR   CAR  CAQ  CAP   180.00   0.0  0
 06W  CONST_42  HAP   CAP  CAQ  CAR   180.00   0.0  0
 06W  CONST_43  HAA   CAA  CAU  CAS     0.00   0.0  0
 06W  CONST_44  HAY   CAY  CAA  CAU   180.00   0.0  0
 06W  CONST_45  HAW   CAW  CAV  CAU   180.00   0.0  0
 06W  CONST_46  HNAH  NAH  C2   N1      0.00   0.0  0
 06W  CONST_47  HNAA  NAH  C2   N1    180.00   0.0  0
 06W  CONST_48  HNAJ  NAJ  C6   N1    180.00   0.0  0
 06W  CONST_49  HNAB  NAJ  C6   N1      0.00   0.0  0
 06W  Var_01    CAZ   CAI  C4   N3     96.84  30.0  1
 06W  Var_02    HAZ   CAZ  CAI  C4   -177.03  30.0  3
 06W  Var_03    HBB   CBB  OBA  CAQ    59.82  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
 06W  chir_01  CAM  CAL  CAN  CAO  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
 06W  plan-1  N1    0.020
 06W  plan-1  C2    0.020
 06W  plan-1  N3    0.020
 06W  plan-1  C4    0.020
 06W  plan-1  C5    0.020
 06W  plan-1  C6    0.020
 06W  plan-1  NAH   0.020
 06W  plan-1  CAI   0.020
 06W  plan-1  NAJ   0.020
 06W  plan-1  CAK   0.020
 06W  plan-1  CAL   0.020
 06W  plan-2  CAM   0.020
 06W  plan-2  CAO   0.020
 06W  plan-2  CAP   0.020
 06W  plan-2  CAQ   0.020
 06W  plan-2  CAR   0.020
 06W  plan-2  CAS   0.020
 06W  plan-2  CAT   0.020
 06W  plan-2  CAU   0.020
 06W  plan-2  OBA   0.020
 06W  plan-2  HAP   0.020
 06W  plan-2  HAR   0.020
 06W  plan-2  HAT   0.020
 06W  plan-3  CAA   0.020
 06W  plan-3  CAS   0.020
 06W  plan-3  CAU   0.020
 06W  plan-3  CAV   0.020
 06W  plan-3  CAW   0.020
 06W  plan-3  NAX   0.020
 06W  plan-3  CAY   0.020
 06W  plan-3  HAV   0.020
 06W  plan-3  HAW   0.020
 06W  plan-3  HAY   0.020
 06W  plan-3  HAA   0.020
 06W  plan-4  C2    0.020
 06W  plan-4  NAH   0.020
 06W  plan-4  HNAH  0.020
 06W  plan-4  HNAA  0.020
 06W  plan-5  C6    0.020
 06W  plan-5  NAJ   0.020
 06W  plan-5  HNAJ  0.020
 06W  plan-5  HNAB  0.020

