# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:36:22 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5-[(3R)-3-(5-methoxybiphenyl-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)c2ccccc2)[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
 53R  53R  5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  49  27  .  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_53R
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
 53R  C20   C  CR16  0  -0.310  -5.1540  -0.0055  -1.4538
 53R  C21   C  CR16  0  -0.240  -6.3738   0.4771  -1.9050
 53R  C22   C  CR16  0  -0.266  -6.9611   1.5759  -1.2917
 53R  C23   C  CR16  0  -0.239  -6.3180   2.1879  -0.2238
 53R  C24   C  CR16  0  -0.309  -5.0979   1.7052   0.2265
 53R  C25   C  CR6   0   0.082  -4.4977   0.6010  -0.3813
 53R  C18   C  CR6   0   0.140  -3.1974   0.0880   0.0984
 53R  C19   C  CR16  0  -0.419  -2.2026   0.9656   0.5196
 53R  C17   C  CR16  0  -0.472  -2.9571  -1.2871   0.1241
 53R  C16   C  CR6   0   0.429  -1.7303  -1.7717   0.5668
 53R  O17   O  O2    0  -0.472  -1.4129  -3.0777   0.6297
 53R  C2    C  CH3   0  -0.439  -2.3671  -4.0303   0.2042
 53R  C15   C  CR16  0  -0.413  -0.7424  -0.8817   0.9887
 53R  C14   C  CR6   0   0.192  -0.9765   0.4836   0.9647
 53R  C12   C  CH1   0  -0.508   0.0732   1.4601   1.4607
 53R  C13   C  CH3   0  -0.641   0.0729   1.5285   2.9948
 53R  C11   C  CSP   0   0.138   1.3952   1.1130   0.9469
 53R  C10   C  CSP   0   0.105   2.4825   0.7835   0.5372
 53R  C6    C  CR6   0  -0.343   3.7216   0.3334   0.0222
 53R  C5    C  CR6   0   0.250   4.9241   1.0107   0.2195
 53R  C8    C  CH3   0  -0.756   4.9519   2.2840   1.0022
 53R  N4    N  N     0  -0.501   6.0743   0.5673  -0.2681
 53R  C3    C  CR6   0   0.545   6.0314  -0.5750  -0.9671
 53R  N7    N  NH2   0  -0.820   7.1934  -1.0087  -1.4817
 53R  N2    N  N     0  -0.504   4.9487  -1.3097  -1.2152
 53R  C1    C  CR6   0   0.453   3.7953  -0.8683  -0.7281
 53R  N9    N  NH2   0  -0.827   2.7001  -1.6100  -0.9482
 53R  H20   H  HCR6  0   0.253  -4.6999  -0.8503  -1.9572
 53R  H21   H  HCR6  0   0.258  -6.8636  -0.0038  -2.7418
 53R  H22   H  HCR6  0   0.258  -7.9135   1.9516  -1.6423
 53R  H23   H  HCR6  0   0.258  -6.7708   3.0396   0.2672
 53R  H24   H  HCR6  0   0.255  -4.6179   2.1814   1.0725
 53R  H19   H  HCR6  0   0.250  -2.3690   2.0353   0.4764
 53R  H17   H  HCR6  0   0.278  -3.7438  -1.9633  -0.1834
 53R  H2    H  HCH3  0   0.230  -3.2788  -3.9928   0.8063
 53R  H2A   H  HCH3  0   0.228  -2.6335  -3.9001  -0.8479
 53R  H2B   H  HCH3  0   0.261  -1.9053  -5.0064   0.3295
 53R  H15   H  HCR6  0   0.257   0.2072  -1.2732   1.3367
 53R  H12   H  HCH1  0   0.284  -0.1912   2.4531   1.0827
 53R  H13   H  HCH3  0   0.242   0.7947   2.2651   3.3463
 53R  H13A  H  HCH3  0   0.243  -0.9140   1.8171   3.3562
 53R  H13B  H  HCH3  0   0.233   0.3286   0.5617   3.4276
 53R  H8    H  HCH3  0   0.254   4.5565   2.1316   2.0077
 53R  H8A   H  HCH3  0   0.254   5.9669   2.6664   1.0791
 53R  H8B   H  HCH3  0   0.256   4.3269   3.0440   0.5306
 53R  HN7   H  HNH2  0   0.397   8.0496  -0.5442  -1.2388
 53R  HN7A  H  HNH2  0   0.397   7.2440  -1.9091  -1.9232
 53R  HN9   H  HNH2  0   0.402   1.7864  -1.2449  -0.7406
 53R  HN9A  H  HNH2  0   0.398   2.7553  -2.3899  -1.5804

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
 53R  C20  C21   aromatic  1.387  0.020  1.387
 53R  C20  C25   aromatic  1.396  0.020  1.396
 53R  C21  C22   aromatic  1.389  0.020  1.389
 53R  C22  C23   aromatic  1.389  0.020  1.389
 53R  C23  C24   aromatic  1.387  0.020  1.387
 53R  C24  C25   aromatic  1.396  0.020  1.396
 53R  C25  C18   single    1.478  0.020  1.478
 53R  C18  C19   aromatic  1.392  0.020  1.392
 53R  C18  C17   aromatic  1.396  0.020  1.396
 53R  C19  C14   aromatic  1.391  0.020  1.391
 53R  C17  C16   aromatic  1.391  0.020  1.391
 53R  C16  O17   single    1.346  0.020  1.346
 53R  C16  C15   aromatic  1.395  0.020  1.395
 53R  O17  C2    single    1.414  0.020  1.414
 53R  C15  C14   aromatic  1.385  0.020  1.385
 53R  C14  C12   single    1.517  0.020  1.517
 53R  C12  C13   single    1.536  0.020  1.536
 53R  C12  C11   single    1.460  0.020  1.460
 53R  C11  C10   triple    1.208  0.020  1.208
 53R  C10  C6    single    1.415  0.020  1.415
 53R  C6   C5    aromatic  1.394  0.020  1.394
 53R  C6   C1    aromatic  1.419  0.020  1.419
 53R  C5   C8    single    1.495  0.020  1.495
 53R  C5   N4    aromatic  1.326  0.020  1.326
 53R  N4   C3    aromatic  1.340  0.020  1.340
 53R  C3   N7    single    1.343  0.020  1.343
 53R  C3   N2    aromatic  1.332  0.020  1.332
 53R  N2   C1    aromatic  1.328  0.020  1.328
 53R  C1   N9    single    1.341  0.020  1.341
 53R  C20  H20   single    0.930  0.020  1.080
 53R  C21  H21   single    0.930  0.020  1.080
 53R  C22  H22   single    0.930  0.020  1.080
 53R  C23  H23   single    0.930  0.020  1.080
 53R  C24  H24   single    0.930  0.020  1.080
 53R  C19  H19   single    0.930  0.020  1.080
 53R  C17  H17   single    0.930  0.020  1.080
 53R  C2   H2    single    0.970  0.020  1.090
 53R  C2   H2A   single    0.970  0.020  1.090
 53R  C2   H2B   single    0.970  0.020  1.090
 53R  C15  H15   single    0.930  0.020  1.080
 53R  C12  H12   single    0.970  0.020  1.090
 53R  C13  H13   single    0.970  0.020  1.090
 53R  C13  H13A  single    0.970  0.020  1.090
 53R  C13  H13B  single    0.970  0.020  1.090
 53R  C8   H8    single    0.970  0.020  1.090
 53R  C8   H8A   single    0.970  0.020  1.090
 53R  C8   H8B   single    0.970  0.020  1.090
 53R  N7   HN7   single    0.860  0.020  1.020
 53R  N7   HN7A  single    0.860  0.020  1.020
 53R  N9   HN9   single    0.860  0.020  1.020
 53R  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
 53R  H20   C20  C25   119.91  3.000
 53R  H20   C20  C21   119.26  3.000
 53R  C25   C20  C21   120.81  3.000
 53R  H21   C21  C22   120.11  3.000
 53R  H21   C21  C20   119.66  3.000
 53R  C22   C21  C20   120.23  3.000
 53R  H22   C22  C23   120.24  3.000
 53R  H22   C22  C21   120.26  3.000
 53R  C23   C22  C21   119.50  3.000
 53R  H23   C23  C24   119.64  3.000
 53R  H23   C23  C22   120.12  3.000
 53R  C24   C23  C22   120.23  3.000
 53R  H24   C24  C25   119.83  3.000
 53R  H24   C24  C23   119.36  3.000
 53R  C25   C24  C23   120.80  3.000
 53R  C18   C25  C24   120.76  3.000
 53R  C18   C25  C20   120.82  3.000
 53R  C24   C25  C20   118.42  3.000
 53R  C17   C18  C19   119.50  3.000
 53R  C17   C18  C25   119.95  3.000
 53R  C19   C18  C25   120.54  3.000
 53R  H19   C19  C14   119.37  3.000
 53R  H19   C19  C18   120.05  3.000
 53R  C14   C19  C18   120.56  3.000
 53R  H17   C17  C16   120.92  3.000
 53R  H17   C17  C18   119.03  3.000
 53R  C16   C17  C18   120.04  3.000
 53R  C15   C16  O17   115.98  3.000
 53R  C15   C16  C17   119.90  3.000
 53R  O17   C16  C17   124.12  3.000
 53R  C2    O17  C16   118.73  3.000
 53R  H2B   C2   H2A   108.74  3.000
 53R  H2B   C2   H2    108.76  3.000
 53R  H2A   C2   H2    108.83  3.000
 53R  H2B   C2   O17   106.48  3.000
 53R  H2A   C2   O17   111.96  3.000
 53R  H2    C2   O17   111.96  3.000
 53R  H15   C15  C14   120.62  3.000
 53R  H15   C15  C16   119.13  3.000
 53R  C14   C15  C16   120.25  3.000
 53R  C12   C14  C15   120.78  3.000
 53R  C12   C14  C19   119.45  3.000
 53R  C15   C14  C19   119.74  3.000
 53R  H12   C12  C11   108.22  3.000
 53R  H12   C12  C13   107.73  3.000
 53R  C11   C12  C13   111.24  3.000
 53R  H12   C12  C14   107.69  3.000
 53R  C11   C12  C14   111.00  3.000
 53R  C13   C12  C14   110.80  3.000
 53R  H13B  C13  H13A  108.40  3.000
 53R  H13B  C13  H13   108.43  3.000
 53R  H13A  C13  H13   108.30  3.000
 53R  H13B  C13  C12   110.93  3.000
 53R  H13A  C13  C12   110.07  3.000
 53R  H13   C13  C12   110.63  3.000
 53R  C10   C11  C12   180.00  3.000
 53R  C6    C10  C11   180.00  3.000
 53R  C1    C6   C5    116.21  3.000
 53R  C1    C6   C10   120.49  3.000
 53R  C5    C6   C10   123.31  3.000
 53R  N4    C5   C8    117.48  3.000
 53R  N4    C5   C6    122.26  3.000
 53R  C8    C5   C6    120.26  3.000
 53R  H8B   C8   H8A   108.68  3.000
 53R  H8B   C8   H8    106.74  3.000
 53R  H8A   C8   H8    108.80  3.000
 53R  H8B   C8   C5    110.88  3.000
 53R  H8A   C8   C5    110.73  3.000
 53R  H8    C8   C5    110.91  3.000
 53R  C3    N4   C5    116.69  3.000
 53R  N2    C3   N7    116.99  3.000
 53R  N2    C3   N4    126.41  3.000
 53R  N7    C3   N4    116.59  3.000
 53R  HN7A  N7   HN7   118.58  3.000
 53R  HN7A  N7   C3    120.11  3.000
 53R  HN7   N7   C3    119.72  3.000
 53R  C1    N2   C3    117.03  3.000
 53R  N9    C1   N2    117.74  3.000
 53R  N9    C1   C6    120.86  3.000
 53R  N2    C1   C6    121.39  3.000
 53R  HN9A  N9   HN9   117.47  3.000
 53R  HN9A  N9   C1    119.17  3.000
 53R  HN9   N9   C1    120.49  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
 53R  CONST_01  C23   C22  C21  C20     0.00   0.0  0
 53R  CONST_02  C23   C24  C25  C20     0.00   0.0  0
 53R  CONST_05  C24   C25  C20  C21     0.00   0.0  0
 53R  CONST_06  C18   C25  C20  C21   180.00   0.0  0
 53R  CONST_07  C24   C23  C22  C21     0.00   0.0  0
 53R  CONST_08  C25   C20  C21  C22     0.00   0.0  0
 53R  CONST_09  C25   C24  C23  C22     0.00   0.0  0
 53R  CONST_10  C18   C25  C24  C23   180.00   0.0  0
 53R  CONST_13  C14   C19  C18  C25   180.00   0.0  0
 53R  CONST_14  C16   C17  C18  C25   180.00   0.0  0
 53R  CONST_15  C15   C14  C19  C18     0.00   0.0  0
 53R  CONST_16  C15   C16  C17  C18     0.00   0.0  0
 53R  CONST_17  C16   C17  C18  C19     0.00   0.0  0
 53R  CONST_18  C16   C15  C14  C19     0.00   0.0  0
 53R  CONST_19  C14   C19  C18  C17     0.00   0.0  0
 53R  CONST_20  C14   C15  C16  C17     0.00   0.0  0
 53R  CONST_21  C3    N4   C5   C6      0.00   0.0  0
 53R  CONST_22  C3    N2   C1   C6      0.00   0.0  0
 53R  CONST_23  N2    C1   C6   C5      0.00   0.0  0
 53R  CONST_24  N2    C3   N4   C5      0.00   0.0  0
 53R  CONST_25  C1    C6   C5   N4      0.00   0.0  0
 53R  CONST_26  C1    N2   C3   N4      0.00   0.0  0
 53R  CONST_27  C12   C14  C19  C18   180.00   0.0  0
 53R  CONST_28  O17   C16  C17  C18   180.00   0.0  0
 53R  CONST_29  C12   C14  C15  C16   180.00   0.0  0
 53R  CONST_30  C14   C15  C16  O17   180.00   0.0  0
 53R  CONST_31  N4    C5   C6   C10   180.00   0.0  0
 53R  CONST_32  N2    C1   C6   C10   180.00   0.0  0
 53R  CONST_33  N9    C1   C6   C5    180.00   0.0  0
 53R  CONST_34  N7    C3   N4   C5    180.00   0.0  0
 53R  CONST_35  C1    C6   C5   C8    180.00   0.0  0
 53R  CONST_36  C3    N4   C5   C8    180.00   0.0  0
 53R  CONST_37  N9    C1   N2   C3    180.00   0.0  0
 53R  CONST_38  C1    N2   C3   N7    180.00   0.0  0
 53R  CONST_39  H22   C22  C21  C20   180.00   0.0  0
 53R  CONST_40  H24   C24  C25  C20   180.00   0.0  0
 53R  CONST_41  H23   C23  C22  C21   180.00   0.0  0
 53R  CONST_42  H20   C20  C21  C22   180.00   0.0  0
 53R  CONST_43  H21   C21  C22  C23   180.00   0.0  0
 53R  CONST_44  H19   C19  C18  C25     0.00   0.0  0
 53R  CONST_45  H17   C17  C18  C25     0.00   0.0  0
 53R  CONST_46  H15   C15  C14  C19   180.00   0.0  0
 53R  CONST_47  HN9   N9   C1   C6      0.00   0.0  0
 53R  CONST_48  HN9A  N9   C1   C6    180.00   0.0  0
 53R  CONST_49  HN7   N7   C3   N4      0.00   0.0  0
 53R  CONST_50  HN7A  N7   C3   N4    180.00   0.0  0
 53R  Var_01    C15   C16  O17  C2   -179.41  30.0  3
 53R  Var_02    H8    C8   C5   C6     57.81  30.0  2
 53R  Var_03    H2    C2   O17  C16   -61.82  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
 53R  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
 53R  plan-1  C20   0.020
 53R  plan-1  C21   0.020
 53R  plan-1  C22   0.020
 53R  plan-1  C23   0.020
 53R  plan-1  C24   0.020
 53R  plan-1  C25   0.020
 53R  plan-1  C18   0.020
 53R  plan-1  H20   0.020
 53R  plan-1  H21   0.020
 53R  plan-1  H22   0.020
 53R  plan-1  H23   0.020
 53R  plan-1  H24   0.020
 53R  plan-2  C25   0.020
 53R  plan-2  C18   0.020
 53R  plan-2  C19   0.020
 53R  plan-2  C17   0.020
 53R  plan-2  C16   0.020
 53R  plan-2  O17   0.020
 53R  plan-2  C15   0.020
 53R  plan-2  C14   0.020
 53R  plan-2  C12   0.020
 53R  plan-2  H19   0.020
 53R  plan-2  H17   0.020
 53R  plan-2  H15   0.020
 53R  plan-3  C11   0.020
 53R  plan-3  C10   0.020
 53R  plan-3  C6    0.020
 53R  plan-3  C5    0.020
 53R  plan-3  C8    0.020
 53R  plan-3  N4    0.020
 53R  plan-3  C3    0.020
 53R  plan-3  N7    0.020
 53R  plan-3  N2    0.020
 53R  plan-3  C1    0.020
 53R  plan-3  N9    0.020
 53R  plan-4  C3    0.020
 53R  plan-4  N7    0.020
 53R  plan-4  HN7   0.020
 53R  plan-4  HN7A  0.020
 53R  plan-5  C1    0.020
 53R  plan-5  N9    0.020
 53R  plan-5  HN9   0.020
 53R  plan-5  HN9A  0.020

