# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:01:55 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 5-[(3S)-3-(3-methoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1[C@@H](C)C#Cc2c(C)nc(N)nc2N)c3ccccc3
#
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
 18H  18H  5-[(3S)-3-(3-methoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  49  27  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_18H
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
 18H  CAB  C  CH3   0  -0.754   5.1601   1.5459   1.2052
 18H  C6   C  CR6   0   0.248   5.0162   0.2221   0.5256
 18H  N1   N  N     0  -0.501   6.0852  -0.5622   0.4823
 18H  C2   C  CR6   0   0.540   5.9417  -1.7416  -0.1353
 18H  NAD  N  NH2   0  -0.819   7.0381  -2.5187  -0.2120
 18H  N3   N  N     0  -0.503   4.8303  -2.2085  -0.7002
 18H  C4   C  CR6   0   0.456   3.7570  -1.4270  -0.6570
 18H  NAE  N  NH2   0  -0.825   2.6246  -1.8930  -1.1988
 18H  C5   C  CR6   0  -0.349   3.7975  -0.1502  -0.0391
 18H  CAF  C  CSP   0   0.097   2.6472   0.6743  -0.0049
 18H  CAG  C  CSP   0   0.160   1.6419   1.3433  -0.0011
 18H  CBA  C  CH1   0  -0.485   0.4363   2.1663   0.0229
 18H  CAC  C  CH3   0  -0.644   0.4719   3.1233   1.2265
 18H  CAZ  C  CR6   0   0.013  -0.8254   1.3241   0.0377
 18H  CAY  C  CR6   0   0.387  -2.0301   1.8589  -0.4470
 18H  CAO  C  CR16  0  -0.456  -3.2006   1.1099  -0.4029
 18H  OAR  O  O2    0  -0.471  -1.9710   3.1135  -0.9331
 18H  CAA  C  CH3   0  -0.438  -3.1374   3.6970  -1.4782
 18H  CAN  C  CR16  0  -0.273  -0.8499   0.0413   0.5617
 18H  CAM  C  CR16  0  -0.331  -2.0162  -0.7093   0.6148
 18H  CAW  C  CR6   0   0.105  -3.2070  -0.1810   0.1296
 18H  CAV  C  CR6   0   0.087  -4.4594  -0.9625   0.1768
 18H  CAK  C  CR16  0  -0.311  -4.7431  -1.7835   1.2700
 18H  CAI  C  CR16  0  -0.239  -5.9160  -2.5223   1.3193
 18H  CAH  C  CR16  0  -0.267  -6.8297  -2.4541   0.2756
 18H  CAJ  C  CR16  0  -0.240  -6.5596  -1.6408  -0.8173
 18H  CAL  C  CR16  0  -0.312  -5.3862  -0.9024  -0.8659
 18H  H1   H  HCH3  0   0.254   4.4099   1.6686   1.9873
 18H  H2   H  HCH3  0   0.254   6.1492   1.6452   1.6459
 18H  H3   H  HCH3  0   0.256   5.0106   2.3613   0.4951
 18H  H4   H  HNH2  0   0.395   7.8385  -2.2878   0.3501
 18H  H5   H  HNH2  0   0.394   6.9436  -3.4725  -0.5141
 18H  H6   H  HNH2  0   0.398   2.6415  -2.7529  -1.7196
 18H  H7   H  HNH2  0   0.402   1.8161  -1.3029  -1.2933
 18H  H8   H  HCH1  0   0.279   0.4367   2.7756  -0.8862
 18H  H9   H  HCH3  0   0.240   1.3587   3.7553   1.1887
 18H  H10  H  HCH3  0   0.244  -0.4064   3.7665   1.2233
 18H  H11  H  HCH3  0   0.231   0.4870   2.5632   2.1609
 18H  H12  H  HCR6  0   0.278  -4.1317   1.5312  -0.7573
 18H  H13  H  HCH3  0   0.229  -3.5245   3.1205  -2.3220
 18H  H14  H  HCH3  0   0.230  -3.9281   3.8064  -0.7315
 18H  H15  H  HCH3  0   0.262  -2.8510   4.6848  -1.8300
 18H  H16  H  HCR6  0   0.252   0.0709  -0.3927   0.9317
 18H  H17  H  HCR6  0   0.250  -1.9846  -1.7145   1.0150
 18H  H18  H  HCR6  0   0.255  -4.0502  -1.8309   2.1007
 18H  H19  H  HCR6  0   0.257  -6.1197  -3.1470   2.1795
 18H  H20  H  HCR6  0   0.258  -7.7451  -3.0302   0.3131
 18H  H21  H  HCR6  0   0.258  -7.2616  -1.5853  -1.6391
 18H  H22  H  HCR6  0   0.252  -5.1808  -0.2890  -1.7347

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
 18H  NAD  C2   single    1.346  0.020  1.346
 18H  C2   N1   aromatic  1.339  0.020  1.339
 18H  C2   N3   aromatic  1.331  0.020  1.331
 18H  N1   C6   aromatic  1.327  0.020  1.327
 18H  N3   C4   aromatic  1.328  0.020  1.328
 18H  C6   CAB  single    1.495  0.020  1.495
 18H  C6   C5   aromatic  1.394  0.020  1.394
 18H  C4   C5   aromatic  1.419  0.020  1.419
 18H  C4   NAE  single    1.339  0.020  1.339
 18H  C5   CAF  single    1.416  0.020  1.416
 18H  CAF  CAG  triple    1.208  0.020  1.208
 18H  CAG  CBA  single    1.460  0.020  1.460
 18H  OAR  CAA  single    1.414  0.020  1.414
 18H  OAR  CAY  single    1.347  0.020  1.347
 18H  CBA  CAZ  single    1.517  0.020  1.517
 18H  CBA  CAC  single    1.538  0.020  1.538
 18H  CAY  CAZ  aromatic  1.404  0.020  1.404
 18H  CAY  CAO  aromatic  1.390  0.020  1.390
 18H  CAZ  CAN  aromatic  1.386  0.020  1.386
 18H  CAO  CAW  aromatic  1.396  0.020  1.396
 18H  CAN  CAM  aromatic  1.388  0.020  1.388
 18H  CAW  CAM  aromatic  1.390  0.020  1.390
 18H  CAW  CAV  single    1.477  0.020  1.477
 18H  CAL  CAV  aromatic  1.396  0.020  1.396
 18H  CAL  CAJ  aromatic  1.387  0.020  1.387
 18H  CAV  CAK  aromatic  1.396  0.020  1.396
 18H  CAJ  CAH  aromatic  1.389  0.020  1.389
 18H  CAK  CAI  aromatic  1.387  0.020  1.387
 18H  CAH  CAI  aromatic  1.389  0.020  1.389
 18H  CAB  H1   single    0.970  0.020  1.090
 18H  CAB  H2   single    0.970  0.020  1.090
 18H  CAB  H3   single    0.970  0.020  1.090
 18H  NAD  H4   single    0.890  0.020  1.040
 18H  NAD  H5   single    0.890  0.020  1.040
 18H  NAE  H6   single    0.860  0.020  1.020
 18H  NAE  H7   single    0.860  0.020  1.020
 18H  CBA  H8   single    0.970  0.020  1.090
 18H  CAC  H9   single    0.970  0.020  1.090
 18H  CAC  H10  single    0.970  0.020  1.090
 18H  CAC  H11  single    0.970  0.020  1.090
 18H  CAO  H12  single    0.930  0.020  1.080
 18H  CAA  H13  single    0.970  0.020  1.090
 18H  CAA  H14  single    0.970  0.020  1.090
 18H  CAA  H15  single    0.970  0.020  1.090
 18H  CAN  H16  single    0.930  0.020  1.080
 18H  CAM  H17  single    0.930  0.020  1.080
 18H  CAK  H18  single    0.930  0.020  1.080
 18H  CAI  H19  single    0.930  0.020  1.080
 18H  CAH  H20  single    0.930  0.020  1.080
 18H  CAJ  H21  single    0.930  0.020  1.080
 18H  CAL  H22  single    0.930  0.020  1.080

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
 18H  H3   CAB  H2   108.66  3.000
 18H  H3   CAB  H1   106.76  3.000
 18H  H2   CAB  H1   108.95  3.000
 18H  H3   CAB  C6   110.64  3.000
 18H  H2   CAB  C6   110.65  3.000
 18H  H1   CAB  C6   111.06  3.000
 18H  C5   C6   N1   122.24  3.000
 18H  C5   C6   CAB  120.32  3.000
 18H  N1   C6   CAB  117.44  3.000
 18H  C2   N1   C6   116.71  3.000
 18H  N3   C2   NAD  116.96  3.000
 18H  N3   C2   N1   126.45  3.000
 18H  NAD  C2   N1   116.58  3.000
 18H  H5   NAD  H4   117.46  3.000
 18H  H5   NAD  C2   119.24  3.000
 18H  H4   NAD  C2   118.96  3.000
 18H  C4   N3   C2   117.03  3.000
 18H  C5   C4   NAE  120.90  3.000
 18H  NAE  C4   N3   117.74  3.000
 18H  C5   C4   N3   121.36  3.000
 18H  H7   NAE  H6   117.83  3.000
 18H  H7   NAE  C4   120.92  3.000
 18H  H6   NAE  C4   119.54  3.000
 18H  CAF  C5   C4   120.75  3.000
 18H  CAF  C5   C6   123.03  3.000
 18H  C4   C5   C6   116.21  3.000
 18H  CAG  CAF  C5   180.00  3.000
 18H  CBA  CAG  CAF  180.00  3.000
 18H  H8   CBA  CAZ  108.51  3.000
 18H  H8   CBA  CAC  107.68  3.000
 18H  CAZ  CBA  CAC  110.91  3.000
 18H  H8   CBA  CAG  107.46  3.000
 18H  CAC  CBA  CAG  110.15  3.000
 18H  CAZ  CBA  CAG  111.96  3.000
 18H  H11  CAC  H10  108.51  3.000
 18H  H11  CAC  H9   108.46  3.000
 18H  H10  CAC  H9   108.29  3.000
 18H  H11  CAC  CBA  110.59  3.000
 18H  H10  CAC  CBA  110.28  3.000
 18H  H9   CAC  CBA  110.64  3.000
 18H  CAN  CAZ  CAY  117.89  3.000
 18H  CAN  CAZ  CBA  122.16  3.000
 18H  CAY  CAZ  CBA  119.91  3.000
 18H  OAR  CAY  CAO  123.38  3.000
 18H  CAO  CAY  CAZ  120.41  3.000
 18H  OAR  CAY  CAZ  116.21  3.000
 18H  H12  CAO  CAW  118.75  3.000
 18H  H12  CAO  CAY  120.30  3.000
 18H  CAW  CAO  CAY  120.93  3.000
 18H  CAA  OAR  CAY  119.18  3.000
 18H  H15  CAA  H14  108.71  3.000
 18H  H15  CAA  H13  108.83  3.000
 18H  H14  CAA  H13  108.91  3.000
 18H  H15  CAA  OAR  106.41  3.000
 18H  H14  CAA  OAR  112.01  3.000
 18H  H13  CAA  OAR  111.86  3.000
 18H  H16  CAN  CAM  118.99  3.000
 18H  H16  CAN  CAZ  119.01  3.000
 18H  CAM  CAN  CAZ  122.00  3.000
 18H  H17  CAM  CAW  120.47  3.000
 18H  H17  CAM  CAN  119.46  3.000
 18H  CAW  CAM  CAN  120.06  3.000
 18H  CAV  CAW  CAM  120.94  3.000
 18H  CAV  CAW  CAO  120.35  3.000
 18H  CAM  CAW  CAO  118.72  3.000
 18H  CAL  CAV  CAK  118.37  3.000
 18H  CAK  CAV  CAW  120.56  3.000
 18H  CAL  CAV  CAW  121.07  3.000
 18H  H18  CAK  CAI  119.38  3.000
 18H  H18  CAK  CAV  119.76  3.000
 18H  CAI  CAK  CAV  120.85  3.000
 18H  H19  CAI  CAH  120.11  3.000
 18H  H19  CAI  CAK  119.66  3.000
 18H  CAH  CAI  CAK  120.23  3.000
 18H  H20  CAH  CAJ  120.24  3.000
 18H  H20  CAH  CAI  120.28  3.000
 18H  CAJ  CAH  CAI  119.48  3.000
 18H  H21  CAJ  CAL  119.65  3.000
 18H  H21  CAJ  CAH  120.10  3.000
 18H  CAL  CAJ  CAH  120.25  3.000
 18H  H22  CAL  CAJ  119.33  3.000
 18H  H22  CAL  CAV  119.84  3.000
 18H  CAJ  CAL  CAV  120.82  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
 18H  CONST_01  N3   C2   N1   C6      0.00   0.0  0
 18H  CONST_02  N3   C4   C5   C6      0.00   0.0  0
 18H  CONST_03  C4   N3   C2   N1      0.00   0.0  0
 18H  CONST_04  C4   C5   C6   N1      0.00   0.0  0
 18H  CONST_05  C5   C6   N1   C2      0.00   0.0  0
 18H  CONST_06  C5   C4   N3   C2      0.00   0.0  0
 18H  CONST_07  CAW  CAO  CAY  CAZ     0.00   0.0  0
 18H  CONST_08  CAW  CAM  CAN  CAZ     0.00   0.0  0
 18H  CONST_09  CAM  CAN  CAZ  CAY     0.00   0.0  0
 18H  CONST_10  CAM  CAW  CAO  CAY     0.00   0.0  0
 18H  CONST_11  CAV  CAW  CAO  CAY   180.00   0.0  0
 18H  CONST_12  CAN  CAZ  CAY  CAO     0.00   0.0  0
 18H  CONST_13  CAN  CAM  CAW  CAO     0.00   0.0  0
 18H  CONST_16  CAV  CAW  CAM  CAN   180.00   0.0  0
 18H  CONST_19  CAJ  CAL  CAV  CAW   180.00   0.0  0
 18H  CONST_20  CAI  CAK  CAV  CAW   180.00   0.0  0
 18H  CONST_21  CAH  CAJ  CAL  CAV     0.00   0.0  0
 18H  CONST_22  CAH  CAI  CAK  CAV     0.00   0.0  0
 18H  CONST_23  CAJ  CAL  CAV  CAK     0.00   0.0  0
 18H  CONST_24  CAJ  CAH  CAI  CAK     0.00   0.0  0
 18H  CONST_25  CAL  CAV  CAK  CAI     0.00   0.0  0
 18H  CONST_26  CAL  CAJ  CAH  CAI     0.00   0.0  0
 18H  CONST_27  C2   N1   C6   CAB   180.00   0.0  0
 18H  CONST_28  C4   C5   C6   CAB   180.00   0.0  0
 18H  CONST_29  NAD  C2   N1   C6    180.00   0.0  0
 18H  CONST_30  NAE  C4   C5   C6    180.00   0.0  0
 18H  CONST_31  CAF  C5   C6   N1    180.00   0.0  0
 18H  CONST_32  NAE  C4   N3   C2    180.00   0.0  0
 18H  CONST_33  C4   N3   C2   NAD   180.00   0.0  0
 18H  CONST_34  CAF  C5   C4   N3    180.00   0.0  0
 18H  CONST_35  CAO  CAY  CAZ  CBA   180.00   0.0  0
 18H  CONST_36  CAM  CAN  CAZ  CBA   180.00   0.0  0
 18H  CONST_37  CAN  CAZ  CAY  OAR   180.00   0.0  0
 18H  CONST_38  CAW  CAO  CAY  OAR   180.00   0.0  0
 18H  CONST_39  H12  CAO  CAY  CAZ   180.00   0.0  0
 18H  CONST_40  H17  CAM  CAN  CAZ   180.00   0.0  0
 18H  CONST_41  H16  CAN  CAZ  CAY   180.00   0.0  0
 18H  CONST_42  H22  CAL  CAV  CAW     0.00   0.0  0
 18H  CONST_43  H18  CAK  CAV  CAW     0.00   0.0  0
 18H  CONST_44  H21  CAJ  CAL  CAV   180.00   0.0  0
 18H  CONST_45  H19  CAI  CAK  CAV   180.00   0.0  0
 18H  CONST_46  H20  CAH  CAI  CAK   180.00   0.0  0
 18H  CONST_47  H4   NAD  C2   N1      0.00   0.0  0
 18H  CONST_48  H5   NAD  C2   N1    180.00   0.0  0
 18H  CONST_49  H6   NAE  C4   N3      0.00   0.0  0
 18H  CONST_50  H7   NAE  C4   N3    180.00   0.0  0
 18H  Var_01    H1   CAB  C6   N1   -125.30  30.0  2
 18H  Var_02    H13  CAA  OAR  CAY   -59.63  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
 18H  chir_01  CBA  CAG  CAZ  CAC  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
 18H  plan-1  CAB  0.020
 18H  plan-1  C6   0.020
 18H  plan-1  N1   0.020
 18H  plan-1  C2   0.020
 18H  plan-1  NAD  0.020
 18H  plan-1  N3   0.020
 18H  plan-1  C4   0.020
 18H  plan-1  NAE  0.020
 18H  plan-1  C5   0.020
 18H  plan-1  CAF  0.020
 18H  plan-1  CAG  0.020
 18H  plan-2  CBA  0.020
 18H  plan-2  CAZ  0.020
 18H  plan-2  CAY  0.020
 18H  plan-2  CAO  0.020
 18H  plan-2  OAR  0.020
 18H  plan-2  CAN  0.020
 18H  plan-2  CAM  0.020
 18H  plan-2  CAW  0.020
 18H  plan-2  CAV  0.020
 18H  plan-2  H12  0.020
 18H  plan-2  H16  0.020
 18H  plan-2  H17  0.020
 18H  plan-3  CAW  0.020
 18H  plan-3  CAV  0.020
 18H  plan-3  CAK  0.020
 18H  plan-3  CAI  0.020
 18H  plan-3  CAH  0.020
 18H  plan-3  CAJ  0.020
 18H  plan-3  CAL  0.020
 18H  plan-3  H18  0.020
 18H  plan-3  H19  0.020
 18H  plan-3  H20  0.020
 18H  plan-3  H21  0.020
 18H  plan-3  H22  0.020
 18H  plan-4  C2   0.020
 18H  plan-4  NAD  0.020
 18H  plan-4  H4   0.020
 18H  plan-4  H5   0.020
 18H  plan-5  C4   0.020
 18H  plan-5  NAE  0.020
 18H  plan-5  H6   0.020
 18H  plan-5  H7   0.020

