# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 03:07:15 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-ethyl-5-{(3R)-3-[3-methoxy-5-(morpholin-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)N3CCOCC3
#
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
 06V  06V  6-ethyl-5-{(3R)-3-[3-methoxy-5-(morpholin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  55  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_06V
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
 06V  N1    N  N     0  -0.498   4.4873  -0.8363  -1.7838
 06V  C2    C  CR6   0   0.545   5.6456  -0.3798  -1.3113
 06V  N3    N  N     0  -0.493   5.8268   0.3106  -0.1820
 06V  C4    C  CR6   0   0.276   4.7442   0.5734   0.5386
 06V  C5    C  CR6   0  -0.328   3.4755   0.1506   0.1490
 06V  C6    C  CR6   0   0.451   3.4045  -0.5797  -1.0641
 06V  CAA   C  CH2   0  -0.313  -5.5203  -0.1812  -0.8935
 06V  NAH   N  NH2   0  -0.802   6.7413  -0.6107  -2.0622
 06V  CAI   C  CH2   0  -0.514   4.9314   1.3929   1.7783
 06V  NAJ   N  NH2   0  -0.816   2.2284  -1.0656  -1.5069
 06V  CAK   C  CSP   0   0.098   2.2927   0.4016   0.8851
 06V  CAL   C  CSP   0   0.144   1.2212   0.5528   1.4203
 06V  CAM   C  CH1   0  -0.501  -0.0972   0.6465   2.0411
 06V  CAN   C  CH3   0  -0.612  -0.0910   0.0721   3.4635
 06V  CAO   C  CR6   0   0.204  -1.1205  -0.0555   1.1660
 06V  CAP   C  CR16  0  -0.467  -0.8525  -1.3439   0.6994
 06V  CAQ   C  CR6   0   0.434  -1.8059  -1.9847  -0.0759
 06V  CAR   C  CR16  0  -0.469  -3.0118  -1.3534  -0.3881
 06V  CAS   C  CR6   0   0.428  -3.2931  -0.0764   0.0909
 06V  CAT   C  CR16  0  -0.423  -2.3155   0.5667   0.8744
 06V  NAU   N  NT    0  -0.528  -4.5082   0.5512  -0.1607
 06V  CAV   C  CH2   0  -0.301  -4.4864   1.9597  -0.5291
 06V  CAW   C  CH2   0  -0.174  -5.8717   2.5613  -0.4057
 06V  OAX   O  O2    0  -0.482  -6.8180   1.8532  -1.1725
 06V  CAY   C  CH2   0  -0.170  -6.8659   0.5081  -0.7612
 06V  CAZ   C  CH3   0  -0.643   4.6959   2.8772   1.5007
 06V  OBA   O  O2    0  -0.464  -1.6499  -3.2193  -0.5958
 06V  CBB   C  CH3   0  -0.418  -0.4325  -3.8912  -0.3730
 06V  HAAA  H  HCH2  0   0.249  -5.6278  -1.1846  -0.4788
 06V  HNAH  H  HNH2  0   0.377   6.6870  -1.2774  -2.8103
 06V  HNAA  H  HNH2  0   0.378   7.6452  -0.4604  -1.6533
 06V  HAI   H  HCH2  0   0.242   4.2470   1.0544   2.5581
 06V  HAIA  H  HCH2  0   0.239   5.9480   1.2442   2.1432
 06V  HNAJ  H  HNH2  0   0.371   2.1852  -1.3982  -2.4538
 06V  HNAB  H  HNH2  0   0.397   1.3696  -0.7055  -1.1250
 06V  HAM   H  HCH1  0   0.265  -0.3758   1.7025   2.1110
 06V  HAN   H  HCH3  0   0.222   0.1805  -0.9827   3.4602
 06V  HANA  H  HCH3  0   0.235   0.6216   0.6058   4.0910
 06V  HANB  H  HCH3  0   0.234  -1.0801   0.1716   3.9085
 06V  HAP   H  HCR6  0   0.254   0.0871  -1.8142   0.9569
 06V  HAR   H  HCR6  0   0.255  -3.7038  -1.8845  -1.0264
 06V  HAT   H  HCR6  0   0.227  -2.4994   1.5527   1.2793
 06V  HAV   H  HCH2  0   0.245  -3.8249   2.5224   0.1250
 06V  HAVA  H  HCH2  0   0.217  -4.1134   2.0903  -1.5552
 06V  HAW   H  HCH2  0   0.202  -6.1672   2.5782   0.6525
 06V  HAWA  H  HCH2  0   0.233  -5.8538   3.5903  -0.7657
 06V  HAY   H  HCH2  0   0.231  -7.5987  -0.0044  -1.3855
 06V  HAYA  H  HCH2  0   0.199  -7.2046   0.4369   0.2821
 06V  HAZ   H  HCH3  0   0.225   5.3689   3.2419   0.7253
 06V  HAZA  H  HCH3  0   0.228   3.6725   3.0618   1.1750
 06V  HAZB  H  HCH3  0   0.230   4.8723   3.4655   2.4004
 06V  HBB   H  HCH3  0   0.243  -0.5027  -4.8418  -0.8967
 06V  HBBA  H  HCH3  0   0.216   0.4249  -3.3358  -0.7657
 06V  HBBB  H  HCH3  0   0.213  -0.2600  -4.0898   0.6887
 06V  HAA   H  HCH2  0   0.213  -5.2588  -0.2915  -1.9572

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
 06V  C2   N1    aromatic  1.332  0.020  1.332
 06V  N1   C6    aromatic  1.325  0.020  1.325
 06V  N3   C2    aromatic  1.336  0.020  1.336
 06V  NAH  C2    single    1.348  0.020  1.348
 06V  N3   C4    aromatic  1.327  0.020  1.327
 06V  CAI  C4    single    1.498  0.020  1.498
 06V  C4   C5    aromatic  1.393  0.020  1.393
 06V  C5   CAK   single    1.416  0.020  1.416
 06V  C5   C6    aromatic  1.418  0.020  1.418
 06V  C6   NAJ   single    1.347  0.020  1.347
 06V  NAU  CAA   single    1.448  0.020  1.448
 06V  CAY  CAA   single    1.518  0.020  1.518
 06V  CAA  HAA   single    0.970  0.020  1.090
 06V  CAA  HAAA  single    0.970  0.020  1.090
 06V  NAH  HNAH  single    0.890  0.020  1.040
 06V  NAH  HNAA  single    0.890  0.020  1.040
 06V  CAZ  CAI   single    1.528  0.020  1.528
 06V  CAI  HAI   single    0.970  0.020  1.090
 06V  CAI  HAIA  single    0.970  0.020  1.090
 06V  NAJ  HNAJ  single    0.890  0.020  1.040
 06V  NAJ  HNAB  single    0.890  0.020  1.040
 06V  CAL  CAK   triple    1.207  0.020  1.207
 06V  CAM  CAL   single    1.460  0.020  1.460
 06V  CAO  CAM   single    1.518  0.020  1.518
 06V  CAM  CAN   single    1.534  0.020  1.534
 06V  CAM  HAM   single    0.970  0.020  1.090
 06V  CAN  HAN   single    0.970  0.020  1.090
 06V  CAN  HANA  single    0.970  0.020  1.090
 06V  CAN  HANB  single    0.970  0.020  1.090
 06V  CAP  CAO   aromatic  1.396  0.020  1.396
 06V  CAT  CAO   aromatic  1.379  0.020  1.379
 06V  CAQ  CAP   aromatic  1.386  0.020  1.386
 06V  CAP  HAP   single    0.930  0.020  1.080
 06V  OBA  CAQ   single    1.349  0.020  1.349
 06V  CAR  CAQ   aromatic  1.397  0.020  1.397
 06V  CAR  CAS   aromatic  1.393  0.020  1.393
 06V  CAR  HAR   single    0.930  0.020  1.080
 06V  NAU  CAS   single    1.391  0.020  1.391
 06V  CAS  CAT   aromatic  1.408  0.020  1.408
 06V  CAT  HAT   single    0.930  0.020  1.080
 06V  CAV  NAU   single    1.456  0.020  1.456
 06V  CAW  CAV   single    1.515  0.020  1.515
 06V  CAV  HAV   single    0.970  0.020  1.090
 06V  CAV  HAVA  single    0.970  0.020  1.090
 06V  CAW  OAX   single    1.409  0.020  1.409
 06V  CAW  HAW   single    0.970  0.020  1.090
 06V  CAW  HAWA  single    0.970  0.020  1.090
 06V  OAX  CAY   single    1.407  0.020  1.407
 06V  CAY  HAY   single    0.970  0.020  1.090
 06V  CAY  HAYA  single    0.970  0.020  1.090
 06V  CAZ  HAZ   single    0.970  0.020  1.090
 06V  CAZ  HAZA  single    0.970  0.020  1.090
 06V  CAZ  HAZB  single    0.970  0.020  1.090
 06V  OBA  CBB   single    1.408  0.020  1.408
 06V  CBB  HBB   single    0.970  0.020  1.090
 06V  CBB  HBBA  single    0.970  0.020  1.090
 06V  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
 06V  C6    N1   C2    116.85  3.000
 06V  NAH   C2   N3    116.68  3.000
 06V  NAH   C2   N1    116.78  3.000
 06V  N3    C2   N1    126.52  3.000
 06V  C4    N3   C2    116.79  3.000
 06V  CAI   C4   C5    120.76  3.000
 06V  C5    C4   N3    122.09  3.000
 06V  CAI   C4   N3    117.12  3.000
 06V  CAK   C5   C6    119.63  3.000
 06V  C6    C5   C4    116.19  3.000
 06V  CAK   C5   C4    124.18  3.000
 06V  NAJ   C6   C5    120.71  3.000
 06V  NAJ   C6   N1    117.70  3.000
 06V  C5    C6   N1    121.57  3.000
 06V  HAAA  CAA  HAA   107.37  3.000
 06V  HAAA  CAA  CAY   107.29  3.000
 06V  HAA   CAA  CAY   109.90  3.000
 06V  HAAA  CAA  NAU   109.98  3.000
 06V  HAA   CAA  NAU   111.93  3.000
 06V  CAY   CAA  NAU   110.23  3.000
 06V  HNAA  NAH  HNAH  116.87  3.000
 06V  HNAA  NAH  C2    118.65  3.000
 06V  HNAH  NAH  C2    119.01  3.000
 06V  HAIA  CAI  HAI   107.66  3.000
 06V  HAIA  CAI  CAZ   109.69  3.000
 06V  HAI   CAI  CAZ   109.53  3.000
 06V  HAIA  CAI  C4    108.60  3.000
 06V  HAI   CAI  C4    110.08  3.000
 06V  CAZ   CAI  C4    111.21  3.000
 06V  HNAB  NAJ  HNAJ  116.07  3.000
 06V  HNAB  NAJ  C6    119.41  3.000
 06V  HNAJ  NAJ  C6    117.82  3.000
 06V  CAL   CAK  C5    180.00  3.000
 06V  CAM   CAL  CAK   180.00  3.000
 06V  HAM   CAM  CAO   108.14  3.000
 06V  HAM   CAM  CAN   107.65  3.000
 06V  CAO   CAM  CAN   111.35  3.000
 06V  HAM   CAM  CAL   108.59  3.000
 06V  CAN   CAM  CAL   111.50  3.000
 06V  CAO   CAM  CAL   109.50  3.000
 06V  HANB  CAN  HANA  108.30  3.000
 06V  HANB  CAN  HAN   108.43  3.000
 06V  HANA  CAN  HAN   108.25  3.000
 06V  HANB  CAN  CAM   109.94  3.000
 06V  HANA  CAN  CAM   110.69  3.000
 06V  HAN   CAN  CAM   111.15  3.000
 06V  CAT   CAO  CAP   120.81  3.000
 06V  CAT   CAO  CAM   119.83  3.000
 06V  CAP   CAO  CAM   119.33  3.000
 06V  HAP   CAP  CAQ   121.98  3.000
 06V  HAP   CAP  CAO   119.23  3.000
 06V  CAQ   CAP  CAO   118.79  3.000
 06V  OBA   CAQ  CAR   115.31  3.000
 06V  CAR   CAQ  CAP   120.67  3.000
 06V  OBA   CAQ  CAP   124.01  3.000
 06V  HAR   CAR  CAS   121.63  3.000
 06V  HAR   CAR  CAQ   117.56  3.000
 06V  CAS   CAR  CAQ   120.80  3.000
 06V  NAU   CAS  CAT   120.07  3.000
 06V  CAT   CAS  CAR   118.03  3.000
 06V  NAU   CAS  CAR   121.88  3.000
 06V  HAT   CAT  CAS   120.44  3.000
 06V  HAT   CAT  CAO   118.66  3.000
 06V  CAS   CAT  CAO   120.89  3.000
 06V  CAV   NAU  CAS   117.99  3.000
 06V  CAV   NAU  CAA   111.82  3.000
 06V  CAS   NAU  CAA   118.29  3.000
 06V  HAVA  CAV  HAV   107.07  3.000
 06V  HAVA  CAV  CAW   109.81  3.000
 06V  HAV   CAV  CAW   107.56  3.000
 06V  HAVA  CAV  NAU   110.86  3.000
 06V  HAV   CAV  NAU   110.95  3.000
 06V  CAW   CAV  NAU   110.47  3.000
 06V  HAWA  CAW  HAW   107.93  3.000
 06V  HAWA  CAW  OAX   107.80  3.000
 06V  HAW   CAW  OAX   110.57  3.000
 06V  HAWA  CAW  CAV   109.44  3.000
 06V  HAW   CAW  CAV   109.29  3.000
 06V  OAX   CAW  CAV   111.72  3.000
 06V  CAY   OAX  CAW   110.13  3.000
 06V  HAYA  CAY  HAY   107.81  3.000
 06V  HAYA  CAY  OAX   110.48  3.000
 06V  HAY   CAY  OAX   107.74  3.000
 06V  HAYA  CAY  CAA   109.06  3.000
 06V  HAY   CAY  CAA   109.41  3.000
 06V  OAX   CAY  CAA   112.23  3.000
 06V  HAZB  CAZ  HAZA  107.91  3.000
 06V  HAZB  CAZ  HAZ   107.88  3.000
 06V  HAZA  CAZ  HAZ   108.10  3.000
 06V  HAZB  CAZ  CAI   110.46  3.000
 06V  HAZA  CAZ  CAI   111.32  3.000
 06V  HAZ   CAZ  CAI   111.05  3.000
 06V  CBB   OBA  CAQ   118.41  3.000
 06V  HBBB  CBB  HBBA  108.47  3.000
 06V  HBBB  CBB  HBB   108.59  3.000
 06V  HBBA  CBB  HBB   108.74  3.000
 06V  HBBB  CBB  OBA   112.12  3.000
 06V  HBBA  CBB  OBA   112.23  3.000
 06V  HBB   CBB  OBA   106.56  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
 06V  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 06V  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 06V  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 06V  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 06V  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 06V  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 06V  CONST_07  CAR   CAQ  CAP  CAO     0.00   0.0  0
 06V  CONST_08  CAR   CAS  CAT  CAO     0.00   0.0  0
 06V  CONST_09  CAS   CAT  CAO  CAP     0.00   0.0  0
 06V  CONST_10  CAS   CAR  CAQ  CAP     0.00   0.0  0
 06V  CONST_11  CAT   CAO  CAP  CAQ     0.00   0.0  0
 06V  CONST_12  CAT   CAS  CAR  CAQ     0.00   0.0  0
 06V  CONST_13  NAU   CAS  CAT  CAO   180.00   0.0  0
 06V  CONST_14  NAU   CAS  CAR  CAQ   180.00   0.0  0
 06V  CONST_15  CAK   C5   C6   N1    180.00   0.0  0
 06V  CONST_16  NAJ   C6   N1   C2    180.00   0.0  0
 06V  CONST_17  CAI   C4   N3   C2    180.00   0.0  0
 06V  CONST_18  CAK   C5   C4   N3    180.00   0.0  0
 06V  CONST_19  NAH   C2   N3   C4    180.00   0.0  0
 06V  CONST_20  NAJ   C6   C5   C4    180.00   0.0  0
 06V  CONST_21  NAH   C2   N1   C6    180.00   0.0  0
 06V  CONST_22  CAI   C4   C5   C6    180.00   0.0  0
 06V  CONST_23  CAQ   CAP  CAO  CAM   180.00   0.0  0
 06V  CONST_24  CAS   CAT  CAO  CAM   180.00   0.0  0
 06V  CONST_25  OBA   CAQ  CAP  CAO   180.00   0.0  0
 06V  CONST_26  OBA   CAQ  CAR  CAS   180.00   0.0  0
 06V  CONST_27  HAT   CAT  CAO  CAP   180.00   0.0  0
 06V  CONST_28  HAR   CAR  CAQ  CAP   180.00   0.0  0
 06V  CONST_29  HAP   CAP  CAQ  CAR   180.00   0.0  0
 06V  CONST_30  HNAH  NAH  C2   N1      0.00   0.0  0
 06V  CONST_31  HNAA  NAH  C2   N1    180.00   0.0  0
 06V  CONST_32  HNAJ  NAJ  C6   N1      0.00   0.0  0
 06V  Var_01    CAR   CAS  NAU  CAA     2.73  30.0  2
 06V  Var_02    CAW   CAV  NAU  CAA    52.72  30.0  1
 06V  Var_03    CAY   CAA  NAU  CAS   165.55  30.0  1
 06V  Var_04    OAX   CAY  CAA  NAU    55.65  30.0  1
 06V  Var_05    OAX   CAW  CAV  NAU   -55.89  30.0  1
 06V  Var_06    CAZ   CAI  C4   N3     93.77  30.0  1
 06V  Var_07    HAZ   CAZ  CAI  C4    -58.19  30.0  3
 06V  Var_08    HBB   CBB  OBA  CAQ  -178.23  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
 06V  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
 06V  plan-1  N1    0.020
 06V  plan-1  C2    0.020
 06V  plan-1  N3    0.020
 06V  plan-1  C4    0.020
 06V  plan-1  C5    0.020
 06V  plan-1  C6    0.020
 06V  plan-1  NAH   0.020
 06V  plan-1  CAI   0.020
 06V  plan-1  NAJ   0.020
 06V  plan-1  CAK   0.020
 06V  plan-1  CAL   0.020
 06V  plan-2  CAM   0.020
 06V  plan-2  CAO   0.020
 06V  plan-2  CAP   0.020
 06V  plan-2  CAQ   0.020
 06V  plan-2  CAR   0.020
 06V  plan-2  CAS   0.020
 06V  plan-2  CAT   0.020
 06V  plan-2  NAU   0.020
 06V  plan-2  OBA   0.020
 06V  plan-2  HAP   0.020
 06V  plan-2  HAR   0.020
 06V  plan-2  HAT   0.020
 06V  plan-3  C2    0.020
 06V  plan-3  NAH   0.020
 06V  plan-3  HNAH  0.020
 06V  plan-3  HNAA  0.020
 06V  plan-4  C6    0.020
 06V  plan-4  NAJ   0.020
 06V  plan-4  HNAJ  0.020
 06V  plan-4  HNAB  0.020

