# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:02:41 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: 5-[(3S)-3-(2,5-dimethoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c(OC)cc1[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
 18G  18G  5-[(3S)-3-(2,5-dimethoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  53  29  .  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_18G
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
 18G  N2   N  NH2   0  -0.819   7.2266  -2.3792   0.0356
 18G  C14  C  CR6   0   0.536   6.1099  -1.6258   0.0477
 18G  N1   N  N     0  -0.503   6.2320  -0.3752   0.4879
 18G  C13  C  CR6   0   0.461   5.1405   0.3806   0.4712
 18G  N    N  NH2   0  -0.824   5.2518   1.6464   0.8916
 18G  N3   N  N     0  -0.501   4.9923  -2.2011  -0.4099
 18G  C15  C  CR6   0   0.243   3.8972  -1.4513  -0.4249
 18G  C16  C  CH3   0  -0.758   2.6378  -2.1005  -0.9019
 18G  C12  C  CR6   0  -0.352   3.8976  -0.1261   0.0067
 18G  C11  C  CSP   0   0.100   2.7409   0.6908  -0.0012
 18G  C10  C  CSP   0   0.161   1.7686   1.4071  -0.0009
 18G  C8   C  CH1   0  -0.485   0.5937   2.2739   0.0055
 18G  C9   C  CH3   0  -0.645   0.6259   3.2128   1.2230
 18G  C7   C  CR6   0   0.039  -0.6984   1.4794  -0.0275
 18G  C1   C  CR6   0   0.349  -1.8562   2.0518  -0.5616
 18G  O    O  O2    0  -0.476  -1.7440   3.3045  -1.0578
 18G  C    C  CH3   0  -0.436  -2.8800   3.9098  -1.6382
 18G  C6   C  CR16  0  -0.423  -0.7710   0.2015   0.5101
 18G  C4   C  CR6   0   0.350  -1.9572  -0.5258   0.5191
 18G  O1   O  O2    0  -0.468  -2.0718  -1.7597   1.0567
 18G  C5   C  CH3   0  -0.440  -0.9319  -2.3552   1.6363
 18G  C3   C  CR6   0  -0.030  -3.1111   0.0363  -0.0354
 18G  C2   C  CR16  0  -0.422  -3.0398   1.3237  -0.5637
 18G  C17  C  CR6   0   0.092  -4.4056  -0.6797  -0.0572
 18G  C22  C  CR16  0  -0.303  -5.5537  -0.0477   0.4215
 18G  C21  C  CR16  0  -0.242  -6.7887  -0.6799   0.3730
 18G  C20  C  CR16  0  -0.268  -6.8959  -1.9573  -0.1583
 18G  C19  C  CR16  0  -0.242  -5.7597  -2.5955  -0.6410
 18G  C18  C  CR16  0  -0.290  -4.5255  -1.9649  -0.5891
 18G  H1   H  HNH2  0   0.394   8.0327  -2.0625   0.5459
 18G  H2   H  HNH2  0   0.394   7.1370  -3.3699  -0.1084
 18G  H3   H  HNH2  0   0.398   6.1133   1.9563   1.3068
 18G  H4   H  HNH2  0   0.403   4.4369   2.2212   1.0173
 18G  H5   H  HCH3  0   0.260   2.0817  -2.5013  -0.0512
 18G  H6   H  HCH3  0   0.251   1.9818  -1.3962  -1.4108
 18G  H7   H  HCH3  0   0.257   2.8620  -2.9310  -1.5681
 18G  H8   H  HCH1  0   0.281   0.6398   2.8951  -0.8939
 18G  H9   H  HCH3  0   0.240   1.5317   3.8189   1.2170
 18G  H10  H  HCH3  0   0.245  -0.2326   3.8820   1.2049
 18G  H11  H  HCH3  0   0.232   0.5997   2.6407   2.1499
 18G  H12  H  HCH3  0   0.227  -3.2464   3.3485  -2.5018
 18G  H13  H  HCH3  0   0.226  -3.6967   4.0229  -0.9201
 18G  H14  H  HCH3  0   0.260  -2.5683   4.8971  -1.9698
 18G  H15  H  HCR6  0   0.274   0.1328  -0.2212   0.9290
 18G  H16  H  HCH3  0   0.262  -1.2442  -3.3303   2.0020
 18G  H17  H  HCH3  0   0.220  -0.1276  -2.4985   0.9086
 18G  H18  H  HCH3  0   0.228  -0.5443  -1.7723   2.4762
 18G  H19  H  HCR6  0   0.279  -3.9404   1.7395  -0.9960
 18G  H20  H  HCR6  0   0.252  -5.4785   0.9467   0.8450
 18G  H21  H  HCR6  0   0.256  -7.6666  -0.1731   0.7526
 18G  H22  H  HCR6  0   0.256  -7.8577  -2.4518  -0.2014
 18G  H23  H  HCR6  0   0.255  -5.8361  -3.5878  -1.0669
 18G  H24  H  HCR6  0   0.249  -3.6542  -2.4690  -0.9857

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
 18G  N2   C14  single    1.347  0.020  1.347
 18G  C14  N1   aromatic  1.331  0.020  1.331
 18G  C14  N3   aromatic  1.338  0.020  1.338
 18G  N1   C13  aromatic  1.328  0.020  1.328
 18G  N3   C15  aromatic  1.327  0.020  1.327
 18G  C13  N    single    1.339  0.020  1.339
 18G  C13  C12  aromatic  1.420  0.020  1.420
 18G  C15  C12  aromatic  1.394  0.020  1.394
 18G  C15  C16  single    1.495  0.020  1.495
 18G  C12  C11  single    1.416  0.020  1.416
 18G  C11  C10  triple    1.208  0.020  1.208
 18G  C10  C8   single    1.460  0.020  1.460
 18G  C8   C9   single    1.538  0.020  1.538
 18G  C8   C7   single    1.517  0.020  1.517
 18G  O    C1   single    1.352  0.020  1.352
 18G  O    C    single    1.412  0.020  1.412
 18G  C7   C6   aromatic  1.388  0.020  1.388
 18G  C7   C1   aromatic  1.398  0.020  1.398
 18G  C6   C4   aromatic  1.392  0.020  1.392
 18G  C1   C2   aromatic  1.390  0.020  1.390
 18G  C4   O1   single    1.351  0.020  1.351
 18G  C4   C3   aromatic  1.398  0.020  1.398
 18G  C5   O1   single    1.411  0.020  1.411
 18G  C2   C3   aromatic  1.393  0.020  1.393
 18G  C3   C17  single    1.480  0.020  1.480
 18G  C17  C22  aromatic  1.395  0.020  1.395
 18G  C17  C18  aromatic  1.396  0.020  1.396
 18G  C22  C21  aromatic  1.388  0.020  1.388
 18G  C18  C19  aromatic  1.387  0.020  1.387
 18G  C21  C20  aromatic  1.388  0.020  1.388
 18G  C19  C20  aromatic  1.390  0.020  1.390
 18G  N2   H1   single    0.890  0.020  1.040
 18G  N2   H2   single    0.890  0.020  1.040
 18G  N    H3   single    0.860  0.020  1.020
 18G  N    H4   single    0.860  0.020  1.020
 18G  C16  H5   single    0.970  0.020  1.090
 18G  C16  H6   single    0.970  0.020  1.090
 18G  C16  H7   single    0.970  0.020  1.090
 18G  C8   H8   single    0.970  0.020  1.090
 18G  C9   H9   single    0.970  0.020  1.090
 18G  C9   H10  single    0.970  0.020  1.090
 18G  C9   H11  single    0.970  0.020  1.090
 18G  C    H12  single    0.970  0.020  1.090
 18G  C    H13  single    0.970  0.020  1.090
 18G  C    H14  single    0.970  0.020  1.090
 18G  C6   H15  single    0.930  0.020  1.080
 18G  C5   H16  single    0.970  0.020  1.090
 18G  C5   H17  single    0.970  0.020  1.090
 18G  C5   H18  single    0.970  0.020  1.090
 18G  C2   H19  single    0.930  0.020  1.080
 18G  C22  H20  single    0.930  0.020  1.080
 18G  C21  H21  single    0.930  0.020  1.080
 18G  C20  H22  single    0.930  0.020  1.080
 18G  C19  H23  single    0.930  0.020  1.080
 18G  C18  H24  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
 18G  H2   N2   H1   117.05  3.000
 18G  H2   N2   C14  118.60  3.000
 18G  H1   N2   C14  118.94  3.000
 18G  N3   C14  N1   126.42  3.000
 18G  N3   C14  N2   116.67  3.000
 18G  N1   C14  N2   116.89  3.000
 18G  C13  N1   C14  117.07  3.000
 18G  C12  C13  N    120.86  3.000
 18G  C12  C13  N1   121.37  3.000
 18G  N    C13  N1   117.77  3.000
 18G  H4   N    H3   117.83  3.000
 18G  H4   N    C13  120.84  3.000
 18G  H3   N    C13  119.51  3.000
 18G  C15  N3   C14  116.76  3.000
 18G  C12  C15  C16  120.79  3.000
 18G  C16  C15  N3   116.96  3.000
 18G  C12  C15  N3   122.24  3.000
 18G  H7   C16  H6   109.38  3.000
 18G  H7   C16  H5   107.56  3.000
 18G  H6   C16  H5   107.13  3.000
 18G  H7   C16  C15  110.68  3.000
 18G  H6   C16  C15  112.07  3.000
 18G  H5   C16  C15  109.86  3.000
 18G  C11  C12  C15  123.13  3.000
 18G  C11  C12  C13  120.72  3.000
 18G  C15  C12  C13  116.15  3.000
 18G  C10  C11  C12  180.00  3.000
 18G  C8   C10  C11  180.00  3.000
 18G  H8   C8   C7   108.38  3.000
 18G  H8   C8   C9   107.65  3.000
 18G  C7   C8   C9   110.78  3.000
 18G  H8   C8   C10  107.43  3.000
 18G  C7   C8   C10  111.98  3.000
 18G  C9   C8   C10  110.43  3.000
 18G  H11  C9   H10  108.54  3.000
 18G  H11  C9   H9   108.46  3.000
 18G  H10  C9   H9   108.27  3.000
 18G  H11  C9   C8   110.63  3.000
 18G  H10  C9   C8   110.22  3.000
 18G  H9   C9   C8   110.64  3.000
 18G  C6   C7   C1   118.80  3.000
 18G  C1   C7   C8   119.96  3.000
 18G  C6   C7   C8   121.20  3.000
 18G  C2   C1   O    123.75  3.000
 18G  C2   C1   C7   119.44  3.000
 18G  O    C1   C7   116.81  3.000
 18G  C    O    C1   118.77  3.000
 18G  H14  C    H13  108.69  3.000
 18G  H14  C    H12  108.75  3.000
 18G  H13  C    H12  108.76  3.000
 18G  H14  C    O    106.50  3.000
 18G  H13  C    O    112.05  3.000
 18G  H12  C    O    111.98  3.000
 18G  H15  C6   C4   120.35  3.000
 18G  H15  C6   C7   117.76  3.000
 18G  C4   C6   C7   121.89  3.000
 18G  C3   C4   O1   117.07  3.000
 18G  C3   C4   C6   119.39  3.000
 18G  O1   C4   C6   123.53  3.000
 18G  C5   O1   C4   118.72  3.000
 18G  H18  C5   H17  108.67  3.000
 18G  H18  C5   H16  108.76  3.000
 18G  H17  C5   H16  108.51  3.000
 18G  H18  C5   O1   112.15  3.000
 18G  H17  C5   O1   112.09  3.000
 18G  H16  C5   O1   106.54  3.000
 18G  C17  C3   C2   119.10  3.000
 18G  C17  C3   C4   122.23  3.000
 18G  C2   C3   C4   118.66  3.000
 18G  H19  C2   C3   117.65  3.000
 18G  H19  C2   C1   120.54  3.000
 18G  C3   C2   C1   121.81  3.000
 18G  C18  C17  C22  118.49  3.000
 18G  C18  C17  C3   121.75  3.000
 18G  C22  C17  C3   119.72  3.000
 18G  H20  C22  C21  119.56  3.000
 18G  H20  C22  C17  119.52  3.000
 18G  C21  C22  C17  120.92  3.000
 18G  H21  C21  C20  120.17  3.000
 18G  H21  C21  C22  119.74  3.000
 18G  C20  C21  C22  120.08  3.000
 18G  H22  C20  C19  120.19  3.000
 18G  H22  C20  C21  120.29  3.000
 18G  C19  C20  C21  119.51  3.000
 18G  H23  C19  C18  119.63  3.000
 18G  H23  C19  C20  119.99  3.000
 18G  C18  C19  C20  120.38  3.000
 18G  H24  C18  C19  119.41  3.000
 18G  H24  C18  C17  119.96  3.000
 18G  C19  C18  C17  120.62  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
 18G  CONST_01  C12  C13  N1   C14     0.00   0.0  0
 18G  CONST_02  C12  C15  N3   C14     0.00   0.0  0
 18G  CONST_03  C15  N3   C14  N1      0.00   0.0  0
 18G  CONST_04  C15  C12  C13  N1      0.00   0.0  0
 18G  CONST_05  N3   C14  N1   C13     0.00   0.0  0
 18G  CONST_06  N3   C15  C12  C13     0.00   0.0  0
 18G  CONST_07  C3   C4   C6   C7      0.00   0.0  0
 18G  CONST_08  C3   C2   C1   C7      0.00   0.0  0
 18G  CONST_09  C4   C6   C7   C1      0.00   0.0  0
 18G  CONST_10  C4   C3   C2   C1      0.00   0.0  0
 18G  CONST_11  C17  C3   C2   C1    180.00   0.0  0
 18G  CONST_12  C2   C1   C7   C6      0.00   0.0  0
 18G  CONST_13  C2   C3   C4   C6      0.00   0.0  0
 18G  CONST_14  C17  C3   C4   C6    180.00   0.0  0
 18G  CONST_17  C21  C22  C17  C3    180.00   0.0  0
 18G  CONST_18  C19  C18  C17  C3    180.00   0.0  0
 18G  CONST_21  C20  C21  C22  C17     0.00   0.0  0
 18G  CONST_22  C20  C19  C18  C17     0.00   0.0  0
 18G  CONST_23  C19  C18  C17  C22     0.00   0.0  0
 18G  CONST_24  C19  C20  C21  C22     0.00   0.0  0
 18G  CONST_25  C18  C17  C22  C21     0.00   0.0  0
 18G  CONST_26  C18  C19  C20  C21     0.00   0.0  0
 18G  CONST_27  C13  N1   C14  N2    180.00   0.0  0
 18G  CONST_28  C15  N3   C14  N2    180.00   0.0  0
 18G  CONST_29  N    C13  N1   C14   180.00   0.0  0
 18G  CONST_30  C16  C15  N3   C14   180.00   0.0  0
 18G  CONST_31  C11  C12  C13  N1    180.00   0.0  0
 18G  CONST_32  C16  C15  C12  C13   180.00   0.0  0
 18G  CONST_33  C15  C12  C13  N     180.00   0.0  0
 18G  CONST_34  C11  C12  C15  N3    180.00   0.0  0
 18G  CONST_35  C4   C6   C7   C8    180.00   0.0  0
 18G  CONST_36  C2   C1   C7   C8    180.00   0.0  0
 18G  CONST_37  O1   C4   C6   C7    180.00   0.0  0
 18G  CONST_38  C6   C7   C1   O     180.00   0.0  0
 18G  CONST_39  C3   C2   C1   O     180.00   0.0  0
 18G  CONST_40  C2   C3   C4   O1    180.00   0.0  0
 18G  CONST_41  C17  C3   C4   O1      0.00   0.0  0
 18G  CONST_42  H19  C2   C1   C7    180.00   0.0  0
 18G  CONST_43  H15  C6   C7   C1    180.00   0.0  0
 18G  CONST_44  H20  C22  C17  C3      0.00   0.0  0
 18G  CONST_45  H24  C18  C17  C3      0.00   0.0  0
 18G  CONST_46  H21  C21  C22  C17   180.00   0.0  0
 18G  CONST_47  H23  C19  C18  C17   180.00   0.0  0
 18G  CONST_48  H22  C20  C21  C22   180.00   0.0  0
 18G  CONST_49  H1   N2   C14  N1      0.00   0.0  0
 18G  CONST_50  H2   N2   C14  N1    180.00   0.0  0
 18G  CONST_51  H3   N    C13  N1      0.00   0.0  0
 18G  CONST_52  H4   N    C13  N1    180.00   0.0  0
 18G  Var_01    C2   C1   O    C      -1.30  30.0  2
 18G  Var_02    C3   C4   O1   C5   -179.46  30.0  2
 18G  Var_03    H5   C16  C15  N3     93.41  30.0  2
 18G  Var_04    H12  C    O    C1    -61.03  30.0  3
 18G  Var_05    H16  C5   O1   C4    179.98  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
 18G  chir_01  C8  C10  C9  C7  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
 18G  plan-1  N2   0.020
 18G  plan-1  C14  0.020
 18G  plan-1  N1   0.020
 18G  plan-1  C13  0.020
 18G  plan-1  N    0.020
 18G  plan-1  N3   0.020
 18G  plan-1  C15  0.020
 18G  plan-1  C16  0.020
 18G  plan-1  C12  0.020
 18G  plan-1  C11  0.020
 18G  plan-1  C10  0.020
 18G  plan-2  C8   0.020
 18G  plan-2  C7   0.020
 18G  plan-2  C1   0.020
 18G  plan-2  O    0.020
 18G  plan-2  C6   0.020
 18G  plan-2  C4   0.020
 18G  plan-2  O1   0.020
 18G  plan-2  C3   0.020
 18G  plan-2  C2   0.020
 18G  plan-2  C17  0.020
 18G  plan-2  H15  0.020
 18G  plan-2  H19  0.020
 18G  plan-3  C3   0.020
 18G  plan-3  C17  0.020
 18G  plan-3  C22  0.020
 18G  plan-3  C21  0.020
 18G  plan-3  C20  0.020
 18G  plan-3  C19  0.020
 18G  plan-3  C18  0.020
 18G  plan-3  H20  0.020
 18G  plan-3  H21  0.020
 18G  plan-3  H22  0.020
 18G  plan-3  H23  0.020
 18G  plan-3  H24  0.020
 18G  plan-4  N2   0.020
 18G  plan-4  C14  0.020
 18G  plan-4  H1   0.020
 18G  plan-4  H2   0.020
 18G  plan-5  C13  0.020
 18G  plan-5  N    0.020
 18G  plan-5  H3   0.020
 18G  plan-5  H4   0.020

