# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 03:09:24 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5-[(3S)-3-(2-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(ccc1c2ccccc2)[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
 11F  11F  5-[(3S)-3-(2-methoxybiphenyl-4-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine  ligand  49  27  .  2021-08-03  2022-07-21
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_11F
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
 11F  C1K   C  CR16  0  -0.302  -4.8244   1.2372   1.3475
 11F  C1I   C  CR16  0  -0.242  -5.9704   2.0190   1.4065
 11F  C1H   C  CR16  0  -0.268  -6.6056   2.4135   0.2374
 11F  C1J   C  CR16  0  -0.243  -6.0835   2.0231  -0.9899
 11F  C1L   C  CR16  0  -0.289  -4.9402   1.2402  -1.0480
 11F  C1V   C  CR6   0   0.093  -4.2944   0.8350   0.1214
 11F  C1Z   C  CR6   0  -0.059  -3.0517   0.0331   0.0838
 11F  C1Y   C  CR6   0   0.377  -2.9733  -1.1827  -0.6167
 11F  C1O   C  CR16  0  -0.450  -1.7852  -1.9076  -0.6253
 11F  O1R   O  O2    0  -0.464  -4.0928  -1.5881  -1.2415
 11F  C1A   C  CH3   0  -0.439  -4.0817  -2.8154  -1.9428
 11F  C1N   C  CR16  0  -0.267  -1.9229   0.4642   0.7702
 11F  C1M   C  CR16  0  -0.325  -0.7390  -0.2603   0.7673
 11F  C1W   C  CR6   0   0.164  -0.6638  -1.4520   0.0615
 11F  C2A   C  CH1   0  -0.510   0.5847  -2.3124   0.0673
 11F  C1C   C  CH3   0  -0.640   0.5663  -3.2817   1.2598
 11F  C1G   C  CSP   0   0.150   1.7975  -1.5001   0.0697
 11F  C1F   C  CSP   0   0.099   2.8004  -0.8276   0.0900
 11F  C5    C  CR6   0  -0.343   3.9346   0.0189   0.1151
 11F  C6    C  CR6   0   0.248   5.2438  -0.4589   0.1421
 11F  C1B   C  CH3   0  -0.754   5.5120  -1.9297   0.1262
 11F  N1    N  N     0  -0.501   6.2923   0.3525   0.1739
 11F  C2    C  CR6   0   0.542   6.0365   1.6672   0.1799
 11F  N1D   N  NH2   0  -0.820   7.0997   2.4877   0.2438
 11F  N3    N  N     0  -0.503   4.8341   2.2386   0.1516
 11F  C4    C  CR6   0   0.454   3.7816   1.4296   0.1213
 11F  N1E   N  NH2   0  -0.826   2.5646   1.9900   0.1170
 11F  H1K   H  HCR6  0   0.252  -4.3425   0.9267   2.2666
 11F  H1I   H  HCR6  0   0.256  -6.3693   2.3125   2.3689
 11F  H1H   H  HCR6  0   0.256  -7.4995   3.0222   0.2805
 11F  H1J   H  HCR6  0   0.255  -6.5678   2.3305  -1.9079
 11F  H1L   H  HCR6  0   0.248  -4.5382   0.9590  -2.0124
 11F  H1O   H  HCR6  0   0.277  -1.7148  -2.8409  -1.1694
 11F  H1A   H  HCH3  0   0.230  -3.3615  -2.8116  -2.7648
 11F  H1AA  H  HCH3  0   0.230  -3.8617  -3.6602  -1.2850
 11F  H1AB  H  HCH3  0   0.262  -5.0799  -2.9415  -2.3542
 11F  H1N   H  HCR6  0   0.255  -1.9679   1.4015   1.3115
 11F  H1M   H  HCR6  0   0.243   0.1196   0.1138   1.3115
 11F  H2A   H  HCH1  0   0.283   0.5820  -2.9135  -0.8481
 11F  H1C   H  HCH3  0   0.242   1.4448  -3.9260   1.2441
 11F  H1CA  H  HCH3  0   0.233   0.5547  -2.7353   2.2024
 11F  H1CB  H  HCH3  0   0.243  -0.3219  -3.9115   1.2145
 11F  H1B   H  HCH3  0   0.257   5.2260  -2.3614  -0.8350
 11F  H1BA  H  HCH3  0   0.254   6.5678  -2.1290   0.2937
 11F  H1BB  H  HCH3  0   0.252   4.9276  -2.4449   0.8888
 11F  HN1D  H  HNH2  0   0.396   8.0220   2.1111   0.1144
 11F  HN1A  H  HNH2  0   0.395   6.9728   3.4747   0.1061
 11F  HN1E  H  HNH2  0   0.398   2.4805   2.9876   0.0238
 11F  HN1B  H  HNH2  0   0.402   1.7412   1.4351  -0.0422

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
 11F  C1V  C1K   aromatic  1.395  0.020  1.395
 11F  C1K  C1I   aromatic  1.389  0.020  1.389
 11F  C1K  H1K   single    0.930  0.020  1.080
 11F  C1I  C1H   aromatic  1.388  0.020  1.388
 11F  C1I  H1I   single    0.930  0.020  1.080
 11F  C1J  C1H   aromatic  1.390  0.020  1.390
 11F  C1H  H1H   single    0.930  0.020  1.080
 11F  C1L  C1J   aromatic  1.387  0.020  1.387
 11F  C1J  H1J   single    0.930  0.020  1.080
 11F  C1V  C1L   aromatic  1.396  0.020  1.396
 11F  C1L  H1L   single    0.930  0.020  1.080
 11F  C1Z  C1V   single    1.479  0.020  1.479
 11F  C1Y  C1Z   aromatic  1.405  0.020  1.405
 11F  C1N  C1Z   aromatic  1.390  0.020  1.390
 11F  C1O  C1Y   aromatic  1.392  0.020  1.392
 11F  C1Y  O1R   single    1.345  0.020  1.345
 11F  C1W  C1O   aromatic  1.392  0.020  1.392
 11F  C1O  H1O   single    0.930  0.020  1.080
 11F  C1A  O1R   single    1.414  0.020  1.414
 11F  C1A  H1A   single    0.970  0.020  1.090
 11F  C1A  H1AA  single    0.970  0.020  1.090
 11F  C1A  H1AB  single    0.970  0.020  1.090
 11F  C1M  C1N   aromatic  1.388  0.020  1.388
 11F  C1N  H1N   single    0.930  0.020  1.080
 11F  C1W  C1M   aromatic  1.387  0.020  1.387
 11F  C1M  H1M   single    0.930  0.020  1.080
 11F  C2A  C1W   single    1.516  0.020  1.516
 11F  C1G  C2A   single    1.460  0.020  1.460
 11F  C2A  C1C   single    1.537  0.020  1.537
 11F  C2A  H2A   single    0.970  0.020  1.090
 11F  C1C  H1C   single    0.970  0.020  1.090
 11F  C1C  H1CA  single    0.970  0.020  1.090
 11F  C1C  H1CB  single    0.970  0.020  1.090
 11F  C1F  C1G   triple    1.208  0.020  1.208
 11F  C5   C1F   single    1.415  0.020  1.415
 11F  C4   C5    aromatic  1.419  0.020  1.419
 11F  C5   C6    aromatic  1.394  0.020  1.394
 11F  N1   C6    aromatic  1.326  0.020  1.326
 11F  C6   C1B   single    1.495  0.020  1.495
 11F  C1B  H1B   single    0.970  0.020  1.090
 11F  C1B  H1BA  single    0.970  0.020  1.090
 11F  C1B  H1BB  single    0.970  0.020  1.090
 11F  C2   N1    aromatic  1.339  0.020  1.339
 11F  N3   C2    aromatic  1.332  0.020  1.332
 11F  N1D  C2    single    1.345  0.020  1.345
 11F  N1D  HN1D  single    0.890  0.020  1.040
 11F  N1D  HN1A  single    0.890  0.020  1.040
 11F  N3   C4    aromatic  1.328  0.020  1.328
 11F  N1E  C4    single    1.340  0.020  1.340
 11F  N1E  HN1E  single    0.860  0.020  1.020
 11F  N1E  HN1B  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
 11F  H1K   C1K  C1V   119.61  3.000
 11F  H1K   C1K  C1I   119.51  3.000
 11F  C1V   C1K  C1I   120.88  3.000
 11F  H1I   C1I  C1H   120.22  3.000
 11F  H1I   C1I  C1K   119.64  3.000
 11F  C1H   C1I  C1K   120.14  3.000
 11F  H1H   C1H  C1J   120.23  3.000
 11F  H1H   C1H  C1I   120.29  3.000
 11F  C1J   C1H  C1I   119.48  3.000
 11F  H1J   C1J  C1L   119.57  3.000
 11F  H1J   C1J  C1H   120.07  3.000
 11F  C1L   C1J  C1H   120.35  3.000
 11F  H1L   C1L  C1V   119.95  3.000
 11F  H1L   C1L  C1J   119.36  3.000
 11F  C1V   C1L  C1J   120.67  3.000
 11F  C1Z   C1V  C1L   121.64  3.000
 11F  C1Z   C1V  C1K   119.86  3.000
 11F  C1L   C1V  C1K   118.48  3.000
 11F  C1N   C1Z  C1Y   117.99  3.000
 11F  C1N   C1Z  C1V   120.11  3.000
 11F  C1Y   C1Z  C1V   121.90  3.000
 11F  O1R   C1Y  C1O   123.42  3.000
 11F  O1R   C1Y  C1Z   116.49  3.000
 11F  C1O   C1Y  C1Z   120.08  3.000
 11F  H1O   C1O  C1W   118.54  3.000
 11F  H1O   C1O  C1Y   120.51  3.000
 11F  C1W   C1O  C1Y   120.95  3.000
 11F  C1A   O1R  C1Y   119.06  3.000
 11F  H1AB  C1A  H1AA  108.84  3.000
 11F  H1AB  C1A  H1A   108.71  3.000
 11F  H1AA  C1A  H1A   108.82  3.000
 11F  H1AB  C1A  O1R   106.34  3.000
 11F  H1AA  C1A  O1R   111.97  3.000
 11F  H1A   C1A  O1R   112.04  3.000
 11F  H1N   C1N  C1M   119.21  3.000
 11F  H1N   C1N  C1Z   118.78  3.000
 11F  C1M   C1N  C1Z   122.00  3.000
 11F  H1M   C1M  C1W   120.62  3.000
 11F  H1M   C1M  C1N   119.66  3.000
 11F  C1W   C1M  C1N   119.72  3.000
 11F  C2A   C1W  C1M   122.02  3.000
 11F  C2A   C1W  C1O   118.66  3.000
 11F  C1M   C1W  C1O   119.26  3.000
 11F  H2A   C2A  C1G   107.99  3.000
 11F  H2A   C2A  C1C   107.60  3.000
 11F  C1G   C2A  C1C   111.08  3.000
 11F  H2A   C2A  C1W   107.83  3.000
 11F  C1C   C2A  C1W   110.55  3.000
 11F  C1G   C2A  C1W   111.62  3.000
 11F  H1CB  C1C  H1CA  108.49  3.000
 11F  H1CB  C1C  H1C   108.35  3.000
 11F  H1CA  C1C  H1C   108.52  3.000
 11F  H1CB  C1C  C2A   110.00  3.000
 11F  H1CA  C1C  C2A   110.80  3.000
 11F  H1C   C1C  C2A   110.62  3.000
 11F  C1F   C1G  C2A   180.00  3.000
 11F  C5    C1F  C1G   180.00  3.000
 11F  C4    C5   C6    116.22  3.000
 11F  C6    C5   C1F   123.23  3.000
 11F  C4    C5   C1F   120.55  3.000
 11F  N1    C6   C1B   117.41  3.000
 11F  C1B   C6   C5    120.36  3.000
 11F  N1    C6   C5    122.23  3.000
 11F  H1BB  C1B  H1BA  109.03  3.000
 11F  H1BB  C1B  H1B   106.77  3.000
 11F  H1BA  C1B  H1B   108.51  3.000
 11F  H1BB  C1B  C6    111.18  3.000
 11F  H1BA  C1B  C6    110.66  3.000
 11F  H1B   C1B  C6    110.57  3.000
 11F  C2    N1   C6    116.72  3.000
 11F  N3    C2   N1D   116.95  3.000
 11F  N1D   C2   N1    116.63  3.000
 11F  N3    C2   N1    126.42  3.000
 11F  HN1A  N1D  HN1D  117.82  3.000
 11F  HN1A  N1D  C2    119.55  3.000
 11F  HN1D  N1D  C2    119.41  3.000
 11F  C4    N3   C2    117.05  3.000
 11F  N1E   C4   N3    117.72  3.000
 11F  N1E   C4   C5    120.91  3.000
 11F  N3    C4   C5    121.36  3.000
 11F  HN1B  N1E  HN1E  117.67  3.000
 11F  HN1B  N1E  C4    120.89  3.000
 11F  HN1E  N1E  C4    119.42  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
 11F  CONST_01  C1J   C1L  C1V  C1K    0.00   0.0  0
 11F  CONST_04  C1J   C1H  C1I  C1K    0.00   0.0  0
 11F  CONST_05  C1L   C1V  C1K  C1I    0.00   0.0  0
 11F  CONST_06  C1Z   C1V  C1K  C1I  180.00   0.0  0
 11F  CONST_07  C1L   C1J  C1H  C1I    0.00   0.0  0
 11F  CONST_08  C1V   C1K  C1I  C1H    0.00   0.0  0
 11F  CONST_09  C1V   C1L  C1J  C1H    0.00   0.0  0
 11F  CONST_10  C1Z   C1V  C1L  C1J  180.00   0.0  0
 11F  CONST_13  C1O   C1Y  C1Z  C1V  180.00   0.0  0
 11F  CONST_14  C1M   C1N  C1Z  C1V  180.00   0.0  0
 11F  CONST_15  C1W   C1O  C1Y  C1Z    0.00   0.0  0
 11F  CONST_16  C1W   C1M  C1N  C1Z    0.00   0.0  0
 11F  CONST_17  C1M   C1N  C1Z  C1Y    0.00   0.0  0
 11F  CONST_18  C1M   C1W  C1O  C1Y    0.00   0.0  0
 11F  CONST_19  C1N   C1Z  C1Y  C1O    0.00   0.0  0
 11F  CONST_20  C1N   C1M  C1W  C1O    0.00   0.0  0
 11F  CONST_21  C2    N3   C4   C5     0.00   0.0  0
 11F  CONST_22  C2    N1   C6   C5     0.00   0.0  0
 11F  CONST_23  N3    C4   C5   C6     0.00   0.0  0
 11F  CONST_24  N3    C2   N1   C6     0.00   0.0  0
 11F  CONST_25  C4    C5   C6   N1     0.00   0.0  0
 11F  CONST_26  C4    N3   C2   N1     0.00   0.0  0
 11F  CONST_27  O1R   C1Y  C1Z  C1V    0.00   0.0  0
 11F  CONST_28  C2A   C1W  C1O  C1Y  180.00   0.0  0
 11F  CONST_29  C1N   C1Z  C1Y  O1R  180.00   0.0  0
 11F  CONST_30  C1W   C1O  C1Y  O1R  180.00   0.0  0
 11F  CONST_31  C2A   C1W  C1M  C1N  180.00   0.0  0
 11F  CONST_32  N3    C4   C5   C1F  180.00   0.0  0
 11F  CONST_33  N1    C6   C5   C1F  180.00   0.0  0
 11F  CONST_34  N1E   C4   C5   C6   180.00   0.0  0
 11F  CONST_35  N1D   C2   N1   C6   180.00   0.0  0
 11F  CONST_36  C4    C5   C6   C1B  180.00   0.0  0
 11F  CONST_37  C2    N1   C6   C1B  180.00   0.0  0
 11F  CONST_38  N1E   C4   N3   C2   180.00   0.0  0
 11F  CONST_39  C4    N3   C2   N1D  180.00   0.0  0
 11F  CONST_40  H1L   C1L  C1V  C1K  180.00   0.0  0
 11F  CONST_41  H1H   C1H  C1I  C1K  180.00   0.0  0
 11F  CONST_42  H1J   C1J  C1H  C1I  180.00   0.0  0
 11F  CONST_43  H1K   C1K  C1I  C1H  180.00   0.0  0
 11F  CONST_44  H1I   C1I  C1H  C1J  180.00   0.0  0
 11F  CONST_45  H1N   C1N  C1Z  C1V    0.00   0.0  0
 11F  CONST_46  H1O   C1O  C1Y  C1Z  180.00   0.0  0
 11F  CONST_47  H1M   C1M  C1N  C1Z  180.00   0.0  0
 11F  CONST_48  HN1E  N1E  C4   C5   180.00   0.0  0
 11F  CONST_49  HN1B  N1E  C4   C5     0.00   0.0  0
 11F  CONST_50  HN1D  N1D  C2   N1     0.00   0.0  0
 11F  CONST_51  HN1A  N1D  C2   N1   180.00   0.0  0
 11F  Var_01    H1B   C1B  C6   C5    67.80  30.0  2
 11F  Var_02    H1A   C1A  O1R  C1Y  -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
 11F  chir_01  C2A  C1W  C1G  C1C  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
 11F  plan-1  C1K   0.020
 11F  plan-1  C1I   0.020
 11F  plan-1  C1H   0.020
 11F  plan-1  C1J   0.020
 11F  plan-1  C1L   0.020
 11F  plan-1  C1V   0.020
 11F  plan-1  C1Z   0.020
 11F  plan-1  H1K   0.020
 11F  plan-1  H1I   0.020
 11F  plan-1  H1H   0.020
 11F  plan-1  H1J   0.020
 11F  plan-1  H1L   0.020
 11F  plan-2  C1V   0.020
 11F  plan-2  C1Z   0.020
 11F  plan-2  C1Y   0.020
 11F  plan-2  C1O   0.020
 11F  plan-2  O1R   0.020
 11F  plan-2  C1N   0.020
 11F  plan-2  C1M   0.020
 11F  plan-2  C1W   0.020
 11F  plan-2  C2A   0.020
 11F  plan-2  H1O   0.020
 11F  plan-2  H1N   0.020
 11F  plan-2  H1M   0.020
 11F  plan-3  C1G   0.020
 11F  plan-3  C1F   0.020
 11F  plan-3  C5    0.020
 11F  plan-3  C6    0.020
 11F  plan-3  C1B   0.020
 11F  plan-3  N1    0.020
 11F  plan-3  C2    0.020
 11F  plan-3  N1D   0.020
 11F  plan-3  N3    0.020
 11F  plan-3  C4    0.020
 11F  plan-3  N1E   0.020
 11F  plan-4  C2    0.020
 11F  plan-4  N1D   0.020
 11F  plan-4  HN1D  0.020
 11F  plan-4  HN1A  0.020
 11F  plan-5  C4    0.020
 11F  plan-5  N1E   0.020
 11F  plan-5  HN1E  0.020
 11F  plan-5  HN1B  0.020

