# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:00:40 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(c1)c2ccc(C)cc2)[C@@H](C)C#Cc3c(C)nc(N)nc3N
#
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
 53S  53S  5-[(3R)-3-(5-methoxy-4'-methylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  52  28  .  2021-08-04  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_53S
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
 53S  C6    C  CR6   0  -0.343  -3.9428  -0.4052   0.1901
 53S  C5    C  CR6   0   0.248  -4.8235  -1.4856   0.1543
 53S  C2    C  CH3   0  -0.440   2.1328   4.2205  -1.0310
 53S  C20   C  CR16  0  -0.297   5.3009   0.2153  -0.2231
 53S  C21   C  CR16  0  -0.282   6.4655  -0.4569  -0.5593
 53S  C22   C  CR6   0   0.085   6.4539  -1.8184  -0.8548
 53S  C26   C  CH3   0  -0.722   7.7188  -2.5518  -1.1910
 53S  C23   C  CR16  0  -0.283   5.2298  -2.4815  -0.8049
 53S  C24   C  CR16  0  -0.296   4.0629  -1.8135  -0.4676
 53S  C25   C  CR6   0   0.067   4.0756  -0.4505  -0.1695
 53S  C18   C  CR6   0   0.144   2.8329   0.2616   0.1904
 53S  C19   C  CR16  0  -0.427   1.8544  -0.3677   0.9568
 53S  C17   C  CR16  0  -0.475   2.6293   1.5749  -0.2357
 53S  C16   C  CR6   0   0.430   1.4604   2.2482   0.1084
 53S  O17   O  O2    0  -0.473   1.1801   3.5108  -0.2643
 53S  C15   C  CR16  0  -0.417   0.4898   1.6063   0.8758
 53S  C14   C  CR6   0   0.202   0.6845   0.3003   1.2972
 53S  C12   C  CH1   0  -0.517  -0.3617  -0.3879   2.1538
 53S  C13   C  CH3   0  -0.640  -0.4793   0.2687   3.5355
 53S  C11   C  CSP   0   0.141  -1.6489  -0.4182   1.4626
 53S  C10   C  CSP   0   0.102  -2.7112  -0.4354   0.8878
 53S  C8    C  CH3   0  -0.755  -4.4960  -2.7515   0.8792
 53S  N4    N  N     0  -0.500  -5.9712  -1.4417  -0.5086
 53S  C3    C  CR6   0   0.539  -6.2526  -0.3007  -1.1504
 53S  N7    N  NH2   0  -0.819  -7.4336  -0.2478  -1.7952
 53S  N2    N  N     0  -0.503  -5.4920   0.7905  -1.1922
 53S  C1    C  CR6   0   0.460  -4.3416   0.7513  -0.5291
 53S  N9    N  NH2   0  -0.825  -3.5739   1.8483  -0.5483
 53S  H2    H  HCH3  0   0.229   3.0794   4.3405  -0.4978
 53S  H2A   H  HCH3  0   0.230   2.3290   3.7361  -1.9909
 53S  H2B   H  HCH3  0   0.262   1.7085   5.2040  -1.2162
 53S  H21   H  HCR6  0   0.248   7.4005   0.0906  -0.5854
 53S  H26   H  HCH3  0   0.250   8.2070  -2.9239  -0.2877
 53S  H26A  H  HCH3  0   0.244   7.5220  -3.4128  -1.8292
 53S  H26B  H  HCH3  0   0.244   8.4331  -1.9070  -1.7022
 53S  H23   H  HCR6  0   0.249   5.1834  -3.5381  -1.0417
 53S  H24   H  HCR6  0   0.252   3.1275  -2.3598  -0.4617
 53S  H19   H  HCR6  0   0.250   2.0125  -1.3789   1.3123
 53S  H17   H  HCR6  0   0.276   3.3776   2.0504  -0.8555
 53S  H15   H  HCR6  0   0.257  -0.4151   2.1420   1.1417
 53S  H12   H  HCH1  0   0.288  -0.0429  -1.4244   2.3021
 53S  H13   H  HCH3  0   0.233  -0.8033   1.3055   3.4506
 53S  H13A  H  HCH3  0   0.243  -1.2007  -0.2652   4.1532
 53S  H13B  H  HCH3  0   0.242   0.4853   0.2507   4.0427
 53S  H8    H  HCH3  0   0.255  -4.4022  -2.5702   1.9513
 53S  H8A   H  HCH3  0   0.254  -5.2718  -3.4962   0.7192
 53S  H8B   H  HCH3  0   0.255  -3.5413  -3.1603   0.5449
 53S  HN7   H  HNH2  0   0.394  -7.9393  -1.1029  -1.9471
 53S  HN7A  H  HNH2  0   0.394  -7.6080   0.5097  -2.4323
 53S  HN9   H  HNH2  0   0.400  -2.6454   1.8322  -0.1643
 53S  HN9A  H  HNH2  0   0.399  -3.8199   2.6169  -1.1479
 53S  H20   H  HCR6  0   0.251   5.3553   1.2702   0.0171

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
 53S  C6   C5    aromatic  1.394  0.020  1.394
 53S  C6   C10   single    1.416  0.020  1.416
 53S  C6   C1    aromatic  1.419  0.020  1.419
 53S  C5   C8    single    1.495  0.020  1.495
 53S  C5   N4    aromatic  1.326  0.020  1.326
 53S  C2   O17   single    1.414  0.020  1.414
 53S  C20  C21   aromatic  1.386  0.020  1.386
 53S  C20  C25   aromatic  1.395  0.020  1.395
 53S  C21  C22   aromatic  1.393  0.020  1.393
 53S  C22  C26   single    1.500  0.020  1.500
 53S  C22  C23   aromatic  1.393  0.020  1.393
 53S  C23  C24   aromatic  1.386  0.020  1.386
 53S  C24  C25   aromatic  1.395  0.020  1.395
 53S  C25  C18   single    1.477  0.020  1.477
 53S  C18  C19   aromatic  1.393  0.020  1.393
 53S  C18  C17   aromatic  1.396  0.020  1.396
 53S  C19  C14   aromatic  1.390  0.020  1.390
 53S  C17  C16   aromatic  1.392  0.020  1.392
 53S  C16  O17   single    1.346  0.020  1.346
 53S  C16  C15   aromatic  1.394  0.020  1.394
 53S  C15  C14   aromatic  1.386  0.020  1.386
 53S  C14  C12   single    1.517  0.020  1.517
 53S  C12  C13   single    1.534  0.020  1.534
 53S  C12  C11   single    1.461  0.020  1.461
 53S  C11  C10   triple    1.208  0.020  1.208
 53S  N4   C3    aromatic  1.339  0.020  1.339
 53S  C3   N7    single    1.347  0.020  1.347
 53S  C3   N2    aromatic  1.331  0.020  1.331
 53S  N2   C1    aromatic  1.328  0.020  1.328
 53S  C1   N9    single    1.339  0.020  1.339
 53S  C2   H2    single    0.970  0.020  1.090
 53S  C2   H2A   single    0.970  0.020  1.090
 53S  C2   H2B   single    0.970  0.020  1.090
 53S  C20  H20   single    0.930  0.020  1.080
 53S  C21  H21   single    0.930  0.020  1.080
 53S  C26  H26   single    0.970  0.020  1.090
 53S  C26  H26A  single    0.970  0.020  1.090
 53S  C26  H26B  single    0.970  0.020  1.090
 53S  C23  H23   single    0.930  0.020  1.080
 53S  C24  H24   single    0.930  0.020  1.080
 53S  C19  H19   single    0.930  0.020  1.080
 53S  C17  H17   single    0.930  0.020  1.080
 53S  C15  H15   single    0.930  0.020  1.080
 53S  C12  H12   single    0.970  0.020  1.090
 53S  C13  H13   single    0.970  0.020  1.090
 53S  C13  H13A  single    0.970  0.020  1.090
 53S  C13  H13B  single    0.970  0.020  1.090
 53S  C8   H8    single    0.970  0.020  1.090
 53S  C8   H8A   single    0.970  0.020  1.090
 53S  C8   H8B   single    0.970  0.020  1.090
 53S  N7   HN7   single    0.890  0.020  1.040
 53S  N7   HN7A  single    0.890  0.020  1.040
 53S  N9   HN9   single    0.860  0.020  1.020
 53S  N9   HN9A  single    0.860  0.020  1.020

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
 53S  C1    C6   C10   120.77  3.000
 53S  C1    C6   C5    116.17  3.000
 53S  C10   C6   C5    123.07  3.000
 53S  N4    C5   C8    117.39  3.000
 53S  N4    C5   C6    122.26  3.000
 53S  C8    C5   C6    120.35  3.000
 53S  H2B   C2   H2A   108.75  3.000
 53S  H2B   C2   H2    108.77  3.000
 53S  H2A   C2   H2    108.77  3.000
 53S  H2B   C2   O17   106.47  3.000
 53S  H2A   C2   O17   112.01  3.000
 53S  H2    C2   O17   111.97  3.000
 53S  H20   C20  C25   120.01  3.000
 53S  H20   C20  C21   118.94  3.000
 53S  C25   C20  C21   121.04  3.000
 53S  H21   C21  C22   119.72  3.000
 53S  H21   C21  C20   119.06  3.000
 53S  C22   C21  C20   121.22  3.000
 53S  C23   C22  C26   121.08  3.000
 53S  C23   C22  C21   117.70  3.000
 53S  C26   C22  C21   121.21  3.000
 53S  H26B  C26  H26A  108.13  3.000
 53S  H26B  C26  H26   107.25  3.000
 53S  H26A  C26  H26   107.21  3.000
 53S  H26B  C26  C22   111.63  3.000
 53S  H26A  C26  C22   111.42  3.000
 53S  H26   C26  C22   110.98  3.000
 53S  H23   C23  C24   119.14  3.000
 53S  H23   C23  C22   119.59  3.000
 53S  C24   C23  C22   121.27  3.000
 53S  H24   C24  C25   119.96  3.000
 53S  H24   C24  C23   119.02  3.000
 53S  C25   C24  C23   121.00  3.000
 53S  C18   C25  C24   121.03  3.000
 53S  C18   C25  C20   121.21  3.000
 53S  C24   C25  C20   117.76  3.000
 53S  C17   C18  C19   119.38  3.000
 53S  C17   C18  C25   120.14  3.000
 53S  C19   C18  C25   120.48  3.000
 53S  H19   C19  C14   119.42  3.000
 53S  H19   C19  C18   119.97  3.000
 53S  C14   C19  C18   120.59  3.000
 53S  H17   C17  C16   120.65  3.000
 53S  H17   C17  C18   119.19  3.000
 53S  C16   C17  C18   120.14  3.000
 53S  C15   C16  O17   116.07  3.000
 53S  C15   C16  C17   119.86  3.000
 53S  O17   C16  C17   124.06  3.000
 53S  C16   O17  C2    118.73  3.000
 53S  H15   C15  C14   120.53  3.000
 53S  H15   C15  C16   119.23  3.000
 53S  C14   C15  C16   120.23  3.000
 53S  C12   C14  C15   120.15  3.000
 53S  C12   C14  C19   120.05  3.000
 53S  C15   C14  C19   119.79  3.000
 53S  H12   C12  C11   107.52  3.000
 53S  H12   C12  C13   107.79  3.000
 53S  C11   C12  C13   111.55  3.000
 53S  H12   C12  C14   107.77  3.000
 53S  C11   C12  C14   110.47  3.000
 53S  C13   C12  C14   111.54  3.000
 53S  H13B  C13  H13A  108.30  3.000
 53S  H13B  C13  H13   108.37  3.000
 53S  H13A  C13  H13   108.27  3.000
 53S  H13B  C13  C12   110.13  3.000
 53S  H13A  C13  C12   110.58  3.000
 53S  H13   C13  C12   111.09  3.000
 53S  C10   C11  C12   180.00  3.000
 53S  C11   C10  C6    180.00  3.000
 53S  H8B   C8   H8A   108.82  3.000
 53S  H8B   C8   H8    106.74  3.000
 53S  H8A   C8   H8    108.64  3.000
 53S  H8B   C8   C5    111.13  3.000
 53S  H8A   C8   C5    110.63  3.000
 53S  H8    C8   C5    110.76  3.000
 53S  C3    N4   C5    116.73  3.000
 53S  N2    C3   N7    117.01  3.000
 53S  N2    C3   N4    126.41  3.000
 53S  N7    C3   N4    116.57  3.000
 53S  HN7A  N7   HN7   117.27  3.000
 53S  HN7A  N7   C3    119.03  3.000
 53S  HN7   N7   C3    118.70  3.000
 53S  C1    N2   C3    117.07  3.000
 53S  N9    C1   N2    117.72  3.000
 53S  N9    C1   C6    120.92  3.000
 53S  N2    C1   C6    121.36  3.000
 53S  HN9A  N9   HN9   117.79  3.000
 53S  HN9A  N9   C1    119.64  3.000
 53S  HN9   N9   C1    120.74  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
 53S  CONST_01  C3    N4   C5   C6     0.00   0.0  0
 53S  CONST_02  C3    N2   C1   C6     0.00   0.0  0
 53S  CONST_03  N2    C1   C6   C5     0.00   0.0  0
 53S  CONST_04  N2    C3   N4   C5     0.00   0.0  0
 53S  CONST_05  C23   C22  C21  C20    0.00   0.0  0
 53S  CONST_06  C23   C24  C25  C20    0.00   0.0  0
 53S  CONST_09  C24   C25  C20  C21    0.00   0.0  0
 53S  CONST_10  C18   C25  C20  C21  180.00   0.0  0
 53S  CONST_11  C24   C23  C22  C21    0.00   0.0  0
 53S  CONST_12  C25   C20  C21  C22    0.00   0.0  0
 53S  CONST_13  C25   C24  C23  C22    0.00   0.0  0
 53S  CONST_14  C18   C25  C24  C23  180.00   0.0  0
 53S  CONST_17  C14   C19  C18  C25  180.00   0.0  0
 53S  CONST_18  C16   C17  C18  C25  180.00   0.0  0
 53S  CONST_19  C15   C14  C19  C18    0.00   0.0  0
 53S  CONST_20  C15   C16  C17  C18    0.00   0.0  0
 53S  CONST_21  C16   C17  C18  C19    0.00   0.0  0
 53S  CONST_22  C16   C15  C14  C19    0.00   0.0  0
 53S  CONST_23  C14   C19  C18  C17    0.00   0.0  0
 53S  CONST_24  C14   C15  C16  C17    0.00   0.0  0
 53S  CONST_25  C1    C6   C5   N4     0.00   0.0  0
 53S  CONST_26  C1    N2   C3   N4     0.00   0.0  0
 53S  CONST_27  N9    C1   C6   C5   180.00   0.0  0
 53S  CONST_28  N7    C3   N4   C5   180.00   0.0  0
 53S  CONST_29  C26   C22  C21  C20  180.00   0.0  0
 53S  CONST_30  C24   C23  C22  C26  180.00   0.0  0
 53S  CONST_31  C12   C14  C19  C18  180.00   0.0  0
 53S  CONST_32  O17   C16  C17  C18  180.00   0.0  0
 53S  CONST_33  C12   C14  C15  C16  180.00   0.0  0
 53S  CONST_34  C14   C15  C16  O17  180.00   0.0  0
 53S  CONST_35  N4    C5   C6   C10  180.00   0.0  0
 53S  CONST_36  N2    C1   C6   C10  180.00   0.0  0
 53S  CONST_37  C1    C6   C5   C8   180.00   0.0  0
 53S  CONST_38  C3    N4   C5   C8   180.00   0.0  0
 53S  CONST_39  N9    C1   N2   C3   180.00   0.0  0
 53S  CONST_40  C1    N2   C3   N7   180.00   0.0  0
 53S  CONST_41  H24   C24  C25  C20  180.00   0.0  0
 53S  CONST_42  H23   C23  C22  C21  180.00   0.0  0
 53S  CONST_43  H20   C20  C21  C22  180.00   0.0  0
 53S  CONST_44  H21   C21  C22  C23  180.00   0.0  0
 53S  CONST_45  H19   C19  C18  C25    0.00   0.0  0
 53S  CONST_46  H17   C17  C18  C25    0.00   0.0  0
 53S  CONST_47  H15   C15  C14  C19  180.00   0.0  0
 53S  CONST_48  HN9   N9   C1   C6     0.00   0.0  0
 53S  CONST_49  HN9A  N9   C1   C6   180.00   0.0  0
 53S  CONST_50  HN7   N7   C3   N4     0.00   0.0  0
 53S  CONST_51  HN7A  N7   C3   N4   180.00   0.0  0
 53S  Var_01    C17   C16  O17  C2    -1.30  30.0  3
 53S  Var_02    H8    C8   C5   C6    61.32  30.0  2
 53S  Var_03    H26   C26  C22  C21   87.73  30.0  2
 53S  Var_04    H2    C2   O17  C16  -61.16  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
 53S  chir_01  C12  C14  C13  C11  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
 53S  plan-1  C6    0.020
 53S  plan-1  C5    0.020
 53S  plan-1  C11   0.020
 53S  plan-1  C10   0.020
 53S  plan-1  C8    0.020
 53S  plan-1  N4    0.020
 53S  plan-1  C3    0.020
 53S  plan-1  N7    0.020
 53S  plan-1  N2    0.020
 53S  plan-1  C1    0.020
 53S  plan-1  N9    0.020
 53S  plan-2  C20   0.020
 53S  plan-2  C21   0.020
 53S  plan-2  C22   0.020
 53S  plan-2  C26   0.020
 53S  plan-2  C23   0.020
 53S  plan-2  C24   0.020
 53S  plan-2  C25   0.020
 53S  plan-2  C18   0.020
 53S  plan-2  H21   0.020
 53S  plan-2  H23   0.020
 53S  plan-2  H24   0.020
 53S  plan-2  H20   0.020
 53S  plan-3  C25   0.020
 53S  plan-3  C18   0.020
 53S  plan-3  C19   0.020
 53S  plan-3  C17   0.020
 53S  plan-3  C16   0.020
 53S  plan-3  O17   0.020
 53S  plan-3  C15   0.020
 53S  plan-3  C14   0.020
 53S  plan-3  C12   0.020
 53S  plan-3  H19   0.020
 53S  plan-3  H17   0.020
 53S  plan-3  H15   0.020
 53S  plan-4  C3    0.020
 53S  plan-4  N7    0.020
 53S  plan-4  HN7   0.020
 53S  plan-4  HN7A  0.020
 53S  plan-5  C1    0.020
 53S  plan-5  N9    0.020
 53S  plan-5  HN9   0.020
 53S  plan-5  HN9A  0.020

