# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 15:20:34 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 4-{2-amino-6-[(1R)-2,2,2-trifluoro-1-(3'-fluorobiphenyl-4-yl)ethoxy]pyrimidin-4-yl}-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)c2cc(O[C@H](c3ccc(cc3)c4cccc(F)c4)C(F)(F)F)nc(N)n2)C(O)=O
#
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
 ML0  ML0  4-{2-amino-6-[(1R)-2,2,2-trifluoro-1-(3'-fluorobiphenyl-4-yl)ethoxy]pyrimidin-4-yl}-L-phenylalanine  ligand  59  38  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ML0
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
 ML0  O38   O  OC    -1  -0.622  -10.5177   1.3683   0.4602
 ML0  C36   C  C      0   0.383   -9.7599   2.0036  -0.3020
 ML0  O37   O  O      0  -0.604  -10.0317   3.0520  -0.9189
 ML0  C34   C  CH1    0  -0.205   -8.3272   1.4323  -0.4637
 ML0  N35   N  NH2    0  -0.775   -7.5583   1.9729  -1.5691
 ML0  C33   C  CH2    0  -0.523   -7.5658   1.6419   0.8567
 ML0  C30   C  C      0   0.162   -6.2288   0.9659   0.8620
 ML0  C29   C  C1     0  -0.285   -5.0737   1.6321   0.4600
 ML0  C28   C  C1     0  -0.305   -3.8485   0.9869   0.4313
 ML0  C31   C  C1     0  -0.298   -6.1130  -0.3704   1.2407
 ML0  C32   C  C1     0  -0.266   -4.8907  -1.0209   1.2192
 ML0  C27   C  C      0   0.037   -3.7381  -0.3535   0.8032
 ML0  C22   C  CR6    0   0.298   -2.4437  -1.0620   0.7642
 ML0  C21   C  CR16   0  -0.499   -1.3874  -0.6042  -0.0114
 ML0  N23   N  N      0  -0.505   -2.3462  -2.1721   1.4960
 ML0  C24   C  CR6    0   0.560   -1.1894  -2.8269   1.4608
 ML0  N26   N  NH2    0  -0.822   -1.0927  -3.9606   2.1740
 ML0  N25   N  N      0  -0.516   -0.1099  -2.4627   0.7545
 ML0  C20   C  CR6    0   0.599   -0.2288  -1.3738   0.0386
 ML0  O16   O  O2     0  -0.491    0.8082  -0.9455  -0.6965
 ML0  C14   C  CH1    0  -0.244    2.0024  -1.6986  -0.7476
 ML0  C15   C  CT     0   0.990    2.0565  -2.3445  -2.1275
 ML0  F19   F  F      0  -0.298    2.0641  -1.4416  -3.1118
 ML0  F18   F  F      0  -0.297    3.1595  -3.0872  -2.2548
 ML0  F17   F  F      0  -0.301    1.0033  -3.1415  -2.3332
 ML0  C11   C  C      0   0.077    3.1881  -0.8045  -0.5094
 ML0  C10   C  C1     0  -0.272    4.2777  -1.2979   0.1976
 ML0  C9    C  C1     0  -0.293    5.3950  -0.5082   0.4154
 ML0  C12   C  C1     0  -0.268    3.2321   0.4989  -0.9953
 ML0  C13   C  C1     0  -0.293    4.3479   1.2879  -0.7730
 ML0  C8    C  C      0   0.083    5.4487   0.7979  -0.0686
 ML0  C3    C  C      0   0.107    6.6360   1.6450   0.1597
 ML0  C2    C  C1     0  -0.319    7.0894   2.5195  -0.8293
 ML0  C4    C  C1     0  -0.475    7.3251   1.5799   1.3709
 ML0  C5    C  C      0   0.550    8.4342   2.3797   1.5585
 ML0  F7    F  F      0  -0.315    9.0825   2.3109   2.7322
 ML0  C6    C  C1     0  -0.420    8.8969   3.2504   0.5911
 ML0  C1    C  C1     0  -0.225    8.2071   3.3106  -0.6118
 ML0  H34   H  HCH1   0   0.221   -8.4169   0.3509  -0.6173
 ML0  HN35  H  HNH2   0   0.335   -7.9984   1.6912  -2.4368
 ML0  HN3A  H  HNH2   0   0.323   -7.6578   2.9819  -1.5523
 ML0  H33   H  HCH2   0   0.236   -7.4411   2.7157   1.0288
 ML0  H33A  H  HCH2   0   0.245   -8.1759   1.2554   1.6746
 ML0  H29   H  H      0   0.242   -5.1318   2.6746   0.1738
 ML0  H28   H  H      0   0.250   -2.9710   1.5458   0.1320
 ML0  H31   H  H      0   0.245   -6.9969  -0.9115   1.5593
 ML0  H32   H  H      0   0.250   -4.8273  -2.0579   1.5201
 ML0  H21   H  HCR6   0   0.274   -1.4492   0.2722  -0.6383
 ML0  HN26  H  HNH2   0   0.399   -1.8192  -4.1911   2.8286
 ML0  HN2A  H  HNH2   0   0.400   -0.1958  -4.3964   2.2967
 ML0  H14   H  HCH1   0   0.323    1.9904  -2.5054  -0.0097
 ML0  H10   H  H      0   0.265    4.2581  -2.3079   0.5884
 ML0  H9    H  H      0   0.262    6.2366  -0.9242   0.9542
 ML0  H12   H  H      0   0.265    2.3941   0.9199  -1.5344
 ML0  H13   H  H      0   0.262    4.3517   2.3066  -1.1389
 ML0  H2    H  H      0   0.262    6.5804   2.5677  -1.7831
 ML0  H4    H  H      0   0.277    6.9920   0.9304   2.1709
 ML0  H6    H  H      0   0.282    9.7708   3.8627   0.7693
 ML0  H1    H  H      0   0.272    8.5526   3.9778  -1.3899

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
 ML0  C36  O38   deloc     1.248  0.020  1.248
 ML0  O37  C36   deloc     1.246  0.020  1.246
 ML0  C36  C34   single    1.551  0.020  1.551
 ML0  C33  C34   single    1.539  0.020  1.539
 ML0  C34  N35   single    1.451  0.020  1.451
 ML0  C34  H34   single    0.970  0.020  1.090
 ML0  N35  HN35  single    0.890  0.020  1.040
 ML0  N35  HN3A  single    0.890  0.020  1.040
 ML0  C33  C30   single    1.498  0.020  1.498
 ML0  C33  H33   single    0.970  0.020  1.090
 ML0  C33  H33A  single    0.970  0.020  1.090
 ML0  C31  C30   aromatic  1.394  0.020  1.394
 ML0  C30  C29   aromatic  1.393  0.020  1.393
 ML0  C29  C28   aromatic  1.385  0.020  1.385
 ML0  C29  H29   single    0.930  0.020  1.080
 ML0  C27  C28   aromatic  1.395  0.020  1.395
 ML0  C28  H28   single    0.930  0.020  1.080
 ML0  C31  C32   aromatic  1.385  0.020  1.385
 ML0  C31  H31   single    0.930  0.020  1.080
 ML0  C32  C27   aromatic  1.395  0.020  1.395
 ML0  C32  H32   single    0.930  0.020  1.080
 ML0  C27  C22   single    1.476  0.020  1.476
 ML0  N23  C22   aromatic  1.333  0.020  1.333
 ML0  C22  C21   aromatic  1.388  0.020  1.388
 ML0  C21  C20   aromatic  1.392  0.020  1.392
 ML0  C21  H21   single    0.930  0.020  1.080
 ML0  N23  C24   aromatic  1.330  0.020  1.330
 ML0  N26  C24   single    1.343  0.020  1.343
 ML0  C24  N25   aromatic  1.340  0.020  1.340
 ML0  N26  HN26  single    0.890  0.020  1.040
 ML0  N26  HN2A  single    0.890  0.020  1.040
 ML0  N25  C20   aromatic  1.309  0.020  1.309
 ML0  C20  O16   single    1.341  0.020  1.341
 ML0  O16  C14   single    1.413  0.020  1.413
 ML0  C11  C14   single    1.504  0.020  1.504
 ML0  C14  C15   single    1.525  0.020  1.525
 ML0  C14  H14   single    0.970  0.020  1.090
 ML0  C15  F19   single    1.336  0.020  1.336
 ML0  C15  F17   single    1.337  0.020  1.337
 ML0  C15  F18   single    1.336  0.020  1.336
 ML0  C12  C11   aromatic  1.392  0.020  1.392
 ML0  C11  C10   aromatic  1.389  0.020  1.389
 ML0  C9   C10   aromatic  1.385  0.020  1.385
 ML0  C10  H10   single    0.930  0.020  1.080
 ML0  C8   C9    aromatic  1.394  0.020  1.394
 ML0  C9   H9    single    0.930  0.020  1.080
 ML0  C13  C12   aromatic  1.385  0.020  1.385
 ML0  C12  H12   single    0.930  0.020  1.080
 ML0  C13  C8    aromatic  1.396  0.020  1.396
 ML0  C13  H13   single    0.930  0.020  1.080
 ML0  C3   C8    single    1.476  0.020  1.476
 ML0  C2   C3    aromatic  1.396  0.020  1.396
 ML0  C3   C4    aromatic  1.395  0.020  1.395
 ML0  C1   C2    aromatic  1.387  0.020  1.387
 ML0  C2   H2    single    0.930  0.020  1.080
 ML0  C5   C4    aromatic  1.380  0.020  1.380
 ML0  C4   H4    single    0.930  0.020  1.080
 ML0  C6   C5    aromatic  1.381  0.020  1.381
 ML0  C5   F7    single    1.343  0.020  1.343
 ML0  C1   C6    aromatic  1.388  0.020  1.388
 ML0  C6   H6    single    0.930  0.020  1.080
 ML0  C1   H1    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
 ML0  C34   C36  O37   117.37  3.000
 ML0  C34   C36  O38   115.91  3.000
 ML0  O37   C36  O38   126.71  3.000
 ML0  H34   C34  C33   107.17  3.000
 ML0  H34   C34  N35   107.71  3.000
 ML0  C33   C34  N35   109.93  3.000
 ML0  H34   C34  C36   107.61  3.000
 ML0  N35   C34  C36   115.58  3.000
 ML0  C33   C34  C36   108.51  3.000
 ML0  HN3A  N35  HN35  104.37  3.000
 ML0  HN3A  N35  C34   107.82  3.000
 ML0  HN35  N35  C34   108.59  3.000
 ML0  H33A  C33  H33   107.06  3.000
 ML0  H33A  C33  C30   109.66  3.000
 ML0  H33   C33  C30   109.90  3.000
 ML0  H33A  C33  C34   108.56  3.000
 ML0  H33   C33  C34   108.96  3.000
 ML0  C30   C33  C34   112.53  3.000
 ML0  C31   C30  C29   117.91  3.000
 ML0  C29   C30  C33   121.55  3.000
 ML0  C31   C30  C33   120.51  3.000
 ML0  H29   C29  C28   119.38  3.000
 ML0  H29   C29  C30   119.50  3.000
 ML0  C28   C29  C30   121.12  3.000
 ML0  H28   C28  C27   120.36  3.000
 ML0  H28   C28  C29   118.84  3.000
 ML0  C27   C28  C29   120.79  3.000
 ML0  H31   C31  C32   119.32  3.000
 ML0  H31   C31  C30   119.38  3.000
 ML0  C32   C31  C30   121.30  3.000
 ML0  H32   C32  C27   119.54  3.000
 ML0  H32   C32  C31   119.85  3.000
 ML0  C27   C32  C31   120.60  3.000
 ML0  C22   C27  C32   120.18  3.000
 ML0  C22   C27  C28   121.56  3.000
 ML0  C32   C27  C28   118.26  3.000
 ML0  N23   C22  C21   121.72  3.000
 ML0  C21   C22  C27   121.58  3.000
 ML0  N23   C22  C27   116.69  3.000
 ML0  H21   C21  C20   121.17  3.000
 ML0  H21   C21  C22   123.28  3.000
 ML0  C20   C21  C22   115.53  3.000
 ML0  C24   N23  C22   117.33  3.000
 ML0  N25   C24  N26   116.82  3.000
 ML0  N25   C24  N23   125.50  3.000
 ML0  N26   C24  N23   117.67  3.000
 ML0  HN2A  N26  HN26  117.80  3.000
 ML0  HN2A  N26  C24   119.69  3.000
 ML0  HN26  N26  C24   119.19  3.000
 ML0  C20   N25  C24   116.18  3.000
 ML0  O16   C20  N25   119.69  3.000
 ML0  O16   C20  C21   116.57  3.000
 ML0  N25   C20  C21   123.74  3.000
 ML0  C14   O16  C20   120.21  3.000
 ML0  H14   C14  C11   109.90  3.000
 ML0  H14   C14  C15   107.37  3.000
 ML0  C11   C14  C15   111.54  3.000
 ML0  H14   C14  O16   111.08  3.000
 ML0  C15   C14  O16   106.78  3.000
 ML0  C11   C14  O16   110.11  3.000
 ML0  F17   C15  F18   107.72  3.000
 ML0  F18   C15  F19   107.51  3.000
 ML0  F17   C15  F19   107.10  3.000
 ML0  F18   C15  C14   110.56  3.000
 ML0  F17   C15  C14   111.34  3.000
 ML0  F19   C15  C14   112.39  3.000
 ML0  C12   C11  C10   119.04  3.000
 ML0  C10   C11  C14   119.19  3.000
 ML0  C12   C11  C14   121.75  3.000
 ML0  H10   C10  C9    119.29  3.000
 ML0  H10   C10  C11   120.04  3.000
 ML0  C9    C10  C11   120.67  3.000
 ML0  H9    C9   C8    120.20  3.000
 ML0  H9    C9   C10   119.09  3.000
 ML0  C8    C9   C10   120.70  3.000
 ML0  H12   C12  C13   118.86  3.000
 ML0  H12   C12  C11   120.93  3.000
 ML0  C13   C12  C11   120.20  3.000
 ML0  H13   C13  C8    119.88  3.000
 ML0  H13   C13  C12   119.00  3.000
 ML0  C8    C13  C12   121.10  3.000
 ML0  C3    C8   C13   120.72  3.000
 ML0  C3    C8   C9    120.99  3.000
 ML0  C13   C8   C9    118.28  3.000
 ML0  C4    C3   C2    118.95  3.000
 ML0  C4    C3   C8    120.31  3.000
 ML0  C2    C3   C8    120.74  3.000
 ML0  H2    C2   C1    119.47  3.000
 ML0  H2    C2   C3    119.98  3.000
 ML0  C1    C2   C3    120.54  3.000
 ML0  H4    C4   C5    119.62  3.000
 ML0  H4    C4   C3    121.17  3.000
 ML0  C5    C4   C3    119.20  3.000
 ML0  C6    C5   F7    118.86  3.000
 ML0  F7    C5   C4    118.50  3.000
 ML0  C6    C5   C4    122.64  3.000
 ML0  H6    C6   C1    121.31  3.000
 ML0  H6    C6   C5    120.80  3.000
 ML0  C1    C6   C5    117.89  3.000
 ML0  H1    C1   C6    119.44  3.000
 ML0  H1    C1   C2    119.77  3.000
 ML0  C6    C1   C2    120.79  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
 ML0  CONST_01  C27   C32  C31  C30    0.00   0.0  0
 ML0  CONST_02  C27   C28  C29  C30    0.00   0.0  0
 ML0  CONST_03  C32   C31  C30  C29    0.00   0.0  0
 ML0  CONST_04  C32   C27  C28  C29    0.00   0.0  0
 ML0  CONST_05  C22   C27  C28  C29  180.00   0.0  0
 ML0  CONST_06  C31   C30  C29  C28    0.00   0.0  0
 ML0  CONST_07  C31   C32  C27  C28    0.00   0.0  0
 ML0  CONST_10  C22   C27  C32  C31  180.00   0.0  0
 ML0  CONST_13  C24   N23  C22  C27  180.00   0.0  0
 ML0  CONST_14  C20   C21  C22  C27  180.00   0.0  0
 ML0  CONST_15  N25   C24  N23  C22    0.00   0.0  0
 ML0  CONST_16  N25   C20  C21  C22    0.00   0.0  0
 ML0  CONST_17  C24   N23  C22  C21    0.00   0.0  0
 ML0  CONST_18  C24   N25  C20  C21    0.00   0.0  0
 ML0  CONST_19  C20   C21  C22  N23    0.00   0.0  0
 ML0  CONST_20  C20   N25  C24  N23    0.00   0.0  0
 ML0  CONST_21  C8    C13  C12  C11    0.00   0.0  0
 ML0  CONST_22  C8    C9   C10  C11    0.00   0.0  0
 ML0  CONST_23  C13   C12  C11  C10    0.00   0.0  0
 ML0  CONST_24  C13   C8   C9   C10    0.00   0.0  0
 ML0  CONST_25  C3    C8   C9   C10  180.00   0.0  0
 ML0  CONST_26  C12   C11  C10  C9     0.00   0.0  0
 ML0  CONST_27  C12   C13  C8   C9     0.00   0.0  0
 ML0  CONST_30  C3    C8   C13  C12  180.00   0.0  0
 ML0  CONST_33  C1    C2   C3   C8   180.00   0.0  0
 ML0  CONST_34  C5    C4   C3   C8   180.00   0.0  0
 ML0  CONST_35  C6    C1   C2   C3     0.00   0.0  0
 ML0  CONST_36  C6    C5   C4   C3     0.00   0.0  0
 ML0  CONST_37  C5    C4   C3   C2     0.00   0.0  0
 ML0  CONST_38  C5    C6   C1   C2     0.00   0.0  0
 ML0  CONST_39  C1    C2   C3   C4     0.00   0.0  0
 ML0  CONST_40  C1    C6   C5   C4     0.00   0.0  0
 ML0  CONST_41  C32   C31  C30  C33  180.00   0.0  0
 ML0  CONST_42  C28   C29  C30  C33  180.00   0.0  0
 ML0  CONST_43  N26   C24  N23  C22  180.00   0.0  0
 ML0  CONST_44  O16   C20  C21  C22  180.00   0.0  0
 ML0  CONST_45  O16   C20  N25  C24  180.00   0.0  0
 ML0  CONST_46  C20   N25  C24  N26  180.00   0.0  0
 ML0  CONST_47  C13   C12  C11  C14  180.00   0.0  0
 ML0  CONST_48  C9    C10  C11  C14  180.00   0.0  0
 ML0  CONST_49  F7    C5   C4   C3   180.00   0.0  0
 ML0  CONST_50  C1    C6   C5   F7   180.00   0.0  0
 ML0  CONST_51  H32   C32  C31  C30  180.00   0.0  0
 ML0  CONST_52  H28   C28  C29  C30  180.00   0.0  0
 ML0  CONST_53  H31   C31  C30  C29  180.00   0.0  0
 ML0  CONST_54  H29   C29  C30  C31  180.00   0.0  0
 ML0  CONST_55  H21   C21  C22  C27    0.00   0.0  0
 ML0  CONST_56  H13   C13  C12  C11  180.00   0.0  0
 ML0  CONST_57  H9    C9   C10  C11  180.00   0.0  0
 ML0  CONST_58  H12   C12  C11  C10  180.00   0.0  0
 ML0  CONST_59  H10   C10  C11  C12  180.00   0.0  0
 ML0  CONST_60  H2    C2   C3   C8     0.00   0.0  0
 ML0  CONST_61  H4    C4   C3   C8     0.00   0.0  0
 ML0  CONST_62  H1    C1   C2   C3   180.00   0.0  0
 ML0  CONST_63  H6    C6   C1   C2   180.00   0.0  0
 ML0  CONST_64  HN26  N26  C24  N23    0.00   0.0  0
 ML0  CONST_65  HN2A  N26  C24  N23  180.00   0.0  0
 ML0  Var_01    C31   C30  C33  C34  -86.34  30.0  2

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
 ML0  chir_01  C34  C36  C33  N35  positiv
 ML0  chir_02  C14  O16  C11  C15  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
 ML0  plan-1  C33   0.020
 ML0  plan-1  C30   0.020
 ML0  plan-1  C29   0.020
 ML0  plan-1  C28   0.020
 ML0  plan-1  C31   0.020
 ML0  plan-1  C32   0.020
 ML0  plan-1  C27   0.020
 ML0  plan-1  C22   0.020
 ML0  plan-1  H29   0.020
 ML0  plan-1  H28   0.020
 ML0  plan-1  H31   0.020
 ML0  plan-1  H32   0.020
 ML0  plan-2  C27   0.020
 ML0  plan-2  C22   0.020
 ML0  plan-2  C21   0.020
 ML0  plan-2  N23   0.020
 ML0  plan-2  C24   0.020
 ML0  plan-2  N26   0.020
 ML0  plan-2  N25   0.020
 ML0  plan-2  C20   0.020
 ML0  plan-2  O16   0.020
 ML0  plan-2  H21   0.020
 ML0  plan-3  C14   0.020
 ML0  plan-3  C11   0.020
 ML0  plan-3  C10   0.020
 ML0  plan-3  C9    0.020
 ML0  plan-3  C12   0.020
 ML0  plan-3  C13   0.020
 ML0  plan-3  C8    0.020
 ML0  plan-3  C3    0.020
 ML0  plan-3  H10   0.020
 ML0  plan-3  H9    0.020
 ML0  plan-3  H12   0.020
 ML0  plan-3  H13   0.020
 ML0  plan-4  C8    0.020
 ML0  plan-4  C3    0.020
 ML0  plan-4  C2    0.020
 ML0  plan-4  C4    0.020
 ML0  plan-4  C5    0.020
 ML0  plan-4  F7    0.020
 ML0  plan-4  C6    0.020
 ML0  plan-4  C1    0.020
 ML0  plan-4  H2    0.020
 ML0  plan-4  H4    0.020
 ML0  plan-4  H6    0.020
 ML0  plan-4  H1    0.020
 ML0  plan-5  C24   0.020
 ML0  plan-5  N26   0.020
 ML0  plan-5  HN26  0.020
 ML0  plan-5  HN2A  0.020
 ML0  plan-6  O38   0.020
 ML0  plan-6  C36   0.020
 ML0  plan-6  O37   0.020
 ML0  plan-6  C34   0.020

