# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 23:21:05 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-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)c2c(C)cccc2C)[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
 53V  53V  5-[(3R)-3-(5-methoxy-2',6'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  55  29  .  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_53V
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
 53V  C1    C  CR6   0   0.466   5.2223  -0.5198  -1.0464
 53V  C2    C  CH3   0  -0.438  -2.1087   3.4302   2.2520
 53V  C3    C  CR6   0   0.539   6.5264  -0.0444   0.7483
 53V  C6    C  CR6   0  -0.346   4.0692  -0.1689  -0.2968
 53V  C12   C  CH1   0  -0.511   0.3424  -0.2990  -1.9619
 53V  C13   C  CH3   0  -0.639   0.2995   0.5245  -3.2574
 53V  C14   C  CR6   0   0.185  -0.7017   0.1935  -0.9785
 53V  C15   C  CR16  0  -0.401  -0.4831   1.3366  -0.2273
 53V  C16   C  CR6   0   0.415  -1.4684   1.8114   0.6381
 53V  C17   C  CR16  0  -0.428  -2.6810   1.1354   0.7444
 53V  C18   C  CR6   0   0.058  -2.9017  -0.0131  -0.0121
 53V  C20   C  CR6   0   0.087  -5.2825  -0.3452  -0.6821
 53V  C21   C  CR16  0  -0.322  -6.4882  -1.0302  -0.5536
 53V  C22   C  CR16  0  -0.237  -6.6157  -2.0788   0.3444
 53V  C23   C  CR16  0  -0.322  -5.5334  -2.4571   1.1234
 53V  C24   C  CR6   0   0.086  -4.3131  -1.7948   1.0162
 53V  C27   C  CH3   0  -0.739  -3.1428  -2.2264   1.8531
 53V  C25   C  CR6   0   0.003  -4.1959  -0.7347   0.1099
 53V  C19   C  CR16  0  -0.382  -1.9142  -0.4816  -0.8679
 53V  O17   O  O2    0  -0.473  -1.1627   2.9258   1.3306
 53V  C11   C  CSP   0   0.140   1.6777  -0.2789  -1.3705
 53V  C10   C  CSP   0   0.108   2.7756  -0.2305  -0.8695
 53V  C5    C  CR6   0   0.241   4.2921   0.2478   1.0148
 53V  C8    C  CH3   0  -0.752   3.1441   0.6230   1.8959
 53V  N4    N  N     0  -0.501   5.5082   0.3144   1.5405
 53V  N7    N  NH2   0  -0.819   7.7561  -0.0097   1.2943
 53V  N2    N  N     0  -0.505   6.4383  -0.4541  -0.5148
 53V  N9    N  NH2   0  -0.826   5.1209  -0.9162  -2.3196
 53V  H2    H  HCH3  0   0.260  -1.6637   4.3163   2.6976
 53V  H2A   H  HCH3  0   0.228  -3.0448   3.7153   1.7649
 53V  H2B   H  HCH3  0   0.228  -2.3299   2.7109   3.0451
 53V  H12   H  HCH1  0   0.283   0.0961  -1.3349  -2.2172
 53V  H13   H  HCH3  0   0.241   1.0087   0.1347  -3.9872
 53V  H13A  H  HCH3  0   0.241  -0.6981   0.4811  -3.6942
 53V  H13B  H  HCH3  0   0.233   0.5449   1.5685  -3.0630
 53V  H15   H  HCR6  0   0.251   0.4581   1.8699  -0.2980
 53V  H17   H  HCR6  0   0.273  -3.4623   1.4793   1.4093
 53V  H26   H  HCH3  0   0.246  -4.9534   1.7348  -1.1549
 53V  H26A  H  HCH3  0   0.244  -4.3429   0.6263  -2.3648
 53V  H26B  H  HCH3  0   0.246  -6.0775   0.9115  -2.2318
 53V  H21   H  HCR6  0   0.245  -7.3338  -0.7382  -1.1652
 53V  H22   H  HCR6  0   0.250  -7.5590  -2.6021   0.4362
 53V  H23   H  HCR6  0   0.245  -5.6330  -3.2775   1.8241
 53V  H27   H  HCH3  0   0.247  -2.3764  -2.7084   1.2430
 53V  H27A  H  HCH3  0   0.244  -2.6639  -1.3813   2.3484
 53V  H27B  H  HCH3  0   0.246  -3.4483  -2.9370   2.6201
 53V  H19   H  HCR6  0   0.243  -2.0884  -1.3780  -1.4519
 53V  H8    H  HCH3  0   0.259   2.5972  -0.2707   2.2042
 53V  H8A   H  HCH3  0   0.255   3.4963   1.1316   2.7904
 53V  H8B   H  HCH3  0   0.248   2.4323   1.2646   1.3770
 53V  HN7   H  HNH2  0   0.395   7.8850   0.4556   2.1753
 53V  HN7A  H  HNH2  0   0.394   8.5604  -0.1099   0.7004
 53V  HN9   H  HNH2  0   0.405   4.2256  -1.0570  -2.7537
 53V  HN9A  H  HNH2  0   0.398   5.9426  -1.2052  -2.8212
 53V  C26   C  CH3   0  -0.738  -5.1592   0.7891  -1.6592

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
 53V  C1   C6    aromatic  1.419  0.020  1.419
 53V  C1   N2    aromatic  1.329  0.020  1.329
 53V  C1   N9    single    1.337  0.020  1.337
 53V  C2   O17   single    1.414  0.020  1.414
 53V  C3   N4    aromatic  1.339  0.020  1.339
 53V  C3   N7    single    1.346  0.020  1.346
 53V  C3   N2    aromatic  1.331  0.020  1.331
 53V  C6   C10   single    1.416  0.020  1.416
 53V  C6   C5    aromatic  1.394  0.020  1.394
 53V  C12  C13   single    1.536  0.020  1.536
 53V  C12  C14   single    1.517  0.020  1.517
 53V  C12  C11   single    1.461  0.020  1.461
 53V  C14  C15   aromatic  1.385  0.020  1.385
 53V  C14  C19   aromatic  1.392  0.020  1.392
 53V  C15  C16   aromatic  1.395  0.020  1.395
 53V  C16  C17   aromatic  1.392  0.020  1.392
 53V  C16  O17   single    1.347  0.020  1.347
 53V  C17  C18   aromatic  1.393  0.020  1.393
 53V  C18  C25   single    1.487  0.020  1.487
 53V  C18  C19   aromatic  1.388  0.020  1.388
 53V  C26  C20   single    1.502  0.020  1.502
 53V  C20  C21   aromatic  1.393  0.020  1.393
 53V  C20  C25   aromatic  1.400  0.020  1.400
 53V  C21  C22   aromatic  1.386  0.020  1.386
 53V  C22  C23   aromatic  1.386  0.020  1.386
 53V  C23  C24   aromatic  1.393  0.020  1.393
 53V  C24  C27   single    1.502  0.020  1.502
 53V  C24  C25   aromatic  1.400  0.020  1.400
 53V  C11  C10   triple    1.208  0.020  1.208
 53V  C5   C8    single    1.495  0.020  1.495
 53V  C5   N4    aromatic  1.327  0.020  1.327
 53V  C2   H2    single    0.970  0.020  1.090
 53V  C2   H2A   single    0.970  0.020  1.090
 53V  C2   H2B   single    0.970  0.020  1.090
 53V  C12  H12   single    0.970  0.020  1.090
 53V  C13  H13   single    0.970  0.020  1.090
 53V  C13  H13A  single    0.970  0.020  1.090
 53V  C13  H13B  single    0.970  0.020  1.090
 53V  C15  H15   single    0.930  0.020  1.080
 53V  C17  H17   single    0.930  0.020  1.080
 53V  C26  H26   single    0.970  0.020  1.090
 53V  C26  H26A  single    0.970  0.020  1.090
 53V  C26  H26B  single    0.970  0.020  1.090
 53V  C21  H21   single    0.930  0.020  1.080
 53V  C22  H22   single    0.930  0.020  1.080
 53V  C23  H23   single    0.930  0.020  1.080
 53V  C27  H27   single    0.970  0.020  1.090
 53V  C27  H27A  single    0.970  0.020  1.090
 53V  C27  H27B  single    0.970  0.020  1.090
 53V  C19  H19   single    0.930  0.020  1.080
 53V  C8   H8    single    0.970  0.020  1.090
 53V  C8   H8A   single    0.970  0.020  1.090
 53V  C8   H8B   single    0.970  0.020  1.090
 53V  N7   HN7   single    0.890  0.020  1.040
 53V  N7   HN7A  single    0.890  0.020  1.040
 53V  N9   HN9   single    0.860  0.020  1.020
 53V  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
 53V  N9    C1   N2    117.71  3.000
 53V  N9    C1   C6    120.96  3.000
 53V  N2    C1   C6    121.33  3.000
 53V  H2B   C2   H2A   108.76  3.000
 53V  H2B   C2   H2    108.77  3.000
 53V  H2A   C2   H2    108.71  3.000
 53V  H2B   C2   O17   111.93  3.000
 53V  H2A   C2   O17   112.06  3.000
 53V  H2    C2   O17   106.51  3.000
 53V  N2    C3   N7    116.96  3.000
 53V  N2    C3   N4    126.41  3.000
 53V  N7    C3   N4    116.61  3.000
 53V  C5    C6   C10   122.65  3.000
 53V  C5    C6   C1    116.16  3.000
 53V  C10   C6   C1    121.18  3.000
 53V  H12   C12  C11   108.25  3.000
 53V  H12   C12  C14   107.67  3.000
 53V  C11   C12  C14   111.25  3.000
 53V  H12   C12  C13   107.72  3.000
 53V  C11   C12  C13   111.09  3.000
 53V  C14   C12  C13   110.71  3.000
 53V  H13B  C13  H13A  108.41  3.000
 53V  H13B  C13  H13   108.40  3.000
 53V  H13A  C13  H13   108.25  3.000
 53V  H13B  C13  C12   110.91  3.000
 53V  H13A  C13  C12   110.02  3.000
 53V  H13   C13  C12   110.78  3.000
 53V  C19   C14  C15   119.64  3.000
 53V  C19   C14  C12   119.58  3.000
 53V  C15   C14  C12   120.73  3.000
 53V  H15   C15  C16   119.10  3.000
 53V  H15   C15  C14   120.50  3.000
 53V  C16   C15  C14   120.40  3.000
 53V  O17   C16  C17   124.06  3.000
 53V  O17   C16  C15   116.12  3.000
 53V  C17   C16  C15   119.82  3.000
 53V  H17   C17  C18   118.78  3.000
 53V  H17   C17  C16   121.42  3.000
 53V  C18   C17  C16   119.80  3.000
 53V  C19   C18  C25   120.40  3.000
 53V  C19   C18  C17   120.02  3.000
 53V  C25   C18  C17   119.58  3.000
 53V  C25   C20  C21   118.88  3.000
 53V  C25   C20  C26   120.95  3.000
 53V  C21   C20  C26   120.17  3.000
 53V  H21   C21  C22   119.84  3.000
 53V  H21   C21  C20   119.40  3.000
 53V  C22   C21  C20   120.76  3.000
 53V  H22   C22  C23   120.05  3.000
 53V  H22   C22  C21   120.04  3.000
 53V  C23   C22  C21   119.91  3.000
 53V  H23   C23  C24   119.37  3.000
 53V  H23   C23  C22   119.89  3.000
 53V  C24   C23  C22   120.74  3.000
 53V  C25   C24  C27   120.88  3.000
 53V  C25   C24  C23   118.91  3.000
 53V  C27   C24  C23   120.21  3.000
 53V  H27B  C27  H27A  108.00  3.000
 53V  H27B  C27  H27   107.60  3.000
 53V  H27A  C27  H27   106.72  3.000
 53V  H27B  C27  C24   111.18  3.000
 53V  H27A  C27  C24   111.87  3.000
 53V  H27   C27  C24   111.25  3.000
 53V  C24   C25  C20   120.80  3.000
 53V  C24   C25  C18   119.58  3.000
 53V  C20   C25  C18   119.62  3.000
 53V  H19   C19  C18   119.79  3.000
 53V  H19   C19  C14   119.88  3.000
 53V  C18   C19  C14   120.32  3.000
 53V  C16   O17  C2    118.58  3.000
 53V  C10   C11  C12   180.00  3.000
 53V  C11   C10  C6    180.00  3.000
 53V  N4    C5   C8    117.25  3.000
 53V  N4    C5   C6    122.31  3.000
 53V  C8    C5   C6    120.44  3.000
 53V  H8B   C8   H8A   109.14  3.000
 53V  H8B   C8   H8    106.80  3.000
 53V  H8A   C8   H8    108.21  3.000
 53V  H8B   C8   C5    111.64  3.000
 53V  H8A   C8   C5    110.70  3.000
 53V  H8    C8   C5    110.21  3.000
 53V  C5    N4   C3    116.69  3.000
 53V  HN7A  N7   HN7   117.50  3.000
 53V  HN7A  N7   C3    119.27  3.000
 53V  HN7   N7   C3    119.00  3.000
 53V  C3    N2   C1    117.10  3.000
 53V  HN9A  N9   HN9   118.20  3.000
 53V  HN9A  N9   C1    119.89  3.000
 53V  HN9   N9   C1    121.35  3.000
 53V  H26B  C26  H26A  107.91  3.000
 53V  H26B  C26  H26   107.73  3.000
 53V  H26A  C26  H26   106.69  3.000
 53V  H26B  C26  C20   110.95  3.000
 53V  H26A  C26  C20   111.68  3.000
 53V  H26   C26  C20   111.66  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
 53V  CONST_01  N4    C5   C6   C1      0.00   0.0  0
 53V  CONST_02  N4    C3   N2   C1      0.00   0.0  0
 53V  CONST_03  C6    C5   N4   C3      0.00   0.0  0
 53V  CONST_04  C6    C1   N2   C3      0.00   0.0  0
 53V  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 53V  CONST_06  C17   C18  C19  C14     0.00   0.0  0
 53V  CONST_07  C25   C18  C19  C14   180.00   0.0  0
 53V  CONST_08  C18   C19  C14  C15     0.00   0.0  0
 53V  CONST_09  C18   C17  C16  C15     0.00   0.0  0
 53V  CONST_10  C19   C14  C15  C16     0.00   0.0  0
 53V  CONST_11  C25   C18  C17  C16   180.00   0.0  0
 53V  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 53V  CONST_15  C21   C20  C25  C18   180.00   0.0  0
 53V  CONST_16  C23   C24  C25  C18   180.00   0.0  0
 53V  CONST_17  C23   C22  C21  C20     0.00   0.0  0
 53V  CONST_19  C23   C24  C25  C20     0.00   0.0  0
 53V  CONST_20  C24   C25  C20  C21     0.00   0.0  0
 53V  CONST_21  C24   C23  C22  C21     0.00   0.0  0
 53V  CONST_22  C25   C20  C21  C22     0.00   0.0  0
 53V  CONST_23  C25   C24  C23  C22     0.00   0.0  0
 53V  CONST_25  N2    C1   C6   C5      0.00   0.0  0
 53V  CONST_26  N2    C3   N4   C5      0.00   0.0  0
 53V  CONST_27  C8    C5   C6   C1    180.00   0.0  0
 53V  CONST_28  N7    C3   N2   C1    180.00   0.0  0
 53V  CONST_29  C8    C5   N4   C3    180.00   0.0  0
 53V  CONST_30  N9    C1   N2   C3    180.00   0.0  0
 53V  CONST_31  C16   C15  C14  C12   180.00   0.0  0
 53V  CONST_32  C18   C19  C14  C12   180.00   0.0  0
 53V  CONST_33  O17   C16  C15  C14   180.00   0.0  0
 53V  CONST_34  O17   C16  C17  C18   180.00   0.0  0
 53V  CONST_35  C26   C20  C25  C18     0.00   0.0  0
 53V  CONST_36  C27   C24  C25  C18     0.00   0.0  0
 53V  CONST_37  C22   C21  C20  C26   180.00   0.0  0
 53V  CONST_38  C24   C25  C20  C26   180.00   0.0  0
 53V  CONST_39  C27   C24  C25  C20   180.00   0.0  0
 53V  CONST_40  C27   C24  C23  C22   180.00   0.0  0
 53V  CONST_41  N2    C1   C6   C10   180.00   0.0  0
 53V  CONST_42  N4    C5   C6   C10   180.00   0.0  0
 53V  CONST_43  N9    C1   C6   C5    180.00   0.0  0
 53V  CONST_44  N7    C3   N4   C5    180.00   0.0  0
 53V  CONST_45  H19   C19  C14  C15   180.00   0.0  0
 53V  CONST_46  H17   C17  C16  C15   180.00   0.0  0
 53V  CONST_47  H15   C15  C16  C17   180.00   0.0  0
 53V  CONST_48  H22   C22  C21  C20   180.00   0.0  0
 53V  CONST_49  H23   C23  C22  C21   180.00   0.0  0
 53V  CONST_50  H21   C21  C22  C23   180.00   0.0  0
 53V  CONST_51  HN9   N9   C1   C6      0.00   0.0  0
 53V  CONST_52  HN9A  N9   C1   C6    180.00   0.0  0
 53V  CONST_53  HN7   N7   C3   N4      0.00   0.0  0
 53V  CONST_54  HN7A  N7   C3   N4    180.00   0.0  0
 53V  Var_01    C15   C16  O17  C2   -178.18  30.0  3
 53V  Var_02    H8    C8   C5   C6     73.18  30.0  2
 53V  Var_03    H26   C26  C20  C21   116.72  30.0  2
 53V  Var_04    H27   C27  C24  C23   109.27  30.0  2
 53V  Var_05    H2    C2   O17  C16   179.68  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
 53V  chir_01  C12  C13  C14  C11  positiv

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
 53V  plan-1  C1    0.020
 53V  plan-1  C3    0.020
 53V  plan-1  C6    0.020
 53V  plan-1  C11   0.020
 53V  plan-1  C10   0.020
 53V  plan-1  C5    0.020
 53V  plan-1  C8    0.020
 53V  plan-1  N4    0.020
 53V  plan-1  N7    0.020
 53V  plan-1  N2    0.020
 53V  plan-1  N9    0.020
 53V  plan-2  C12   0.020
 53V  plan-2  C14   0.020
 53V  plan-2  C15   0.020
 53V  plan-2  C16   0.020
 53V  plan-2  C17   0.020
 53V  plan-2  C18   0.020
 53V  plan-2  C25   0.020
 53V  plan-2  C19   0.020
 53V  plan-2  O17   0.020
 53V  plan-2  H15   0.020
 53V  plan-2  H17   0.020
 53V  plan-2  H19   0.020
 53V  plan-3  C18   0.020
 53V  plan-3  C20   0.020
 53V  plan-3  C21   0.020
 53V  plan-3  C22   0.020
 53V  plan-3  C23   0.020
 53V  plan-3  C24   0.020
 53V  plan-3  C27   0.020
 53V  plan-3  C25   0.020
 53V  plan-3  H21   0.020
 53V  plan-3  H22   0.020
 53V  plan-3  H23   0.020
 53V  plan-3  C26   0.020
 53V  plan-4  C3    0.020
 53V  plan-4  N7    0.020
 53V  plan-4  HN7   0.020
 53V  plan-4  HN7A  0.020
 53V  plan-5  C1    0.020
 53V  plan-5  N9    0.020
 53V  plan-5  HN9   0.020
 53V  plan-5  HN9A  0.020

