# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:22:43 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: 4-(5-{[(2'-methylbiphenyl-2-yl)methyl]amino}pyrazin-2-yl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2ccccc2CNc3cnc(cn3)c4ccc(C[C@H](N)C(O)=O)cc4
#
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
 ML4  ML4  4-(5-{[(2'-methylbiphenyl-2-yl)methyl]amino}pyrazin-2-yl)-L-phenylalanine  ligand  58  33  .  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_ML4
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
 ML4  O3    O  OC    -1  -0.619  -8.5842  -1.9199  -1.0224
 ML4  C2    C  C      0   0.403  -8.3202  -1.2733   0.0111
 ML4  O1    O  O      0  -0.602  -9.0282  -1.1779   1.0319
 ML4  C4    C  CH1    0  -0.198  -6.9465  -0.5638   0.0279
 ML4  N5    N  NH2    0  -0.795  -6.8947   0.4552   1.0559
 ML4  C6    C  CH2    0  -0.525  -5.8487  -1.6518   0.1376
 ML4  C7    C  C      0   0.116  -4.4663  -1.0732   0.1054
 ML4  C12   C  C1     0  -0.288  -3.8425  -0.7742  -1.1062
 ML4  C11   C  C1     0  -0.281  -2.5925  -0.1812  -1.1473
 ML4  C10   C  C      0   0.067  -1.9151   0.1497   0.0292
 ML4  C9    C  C1     0  -0.319  -2.5289  -0.1615   1.2427
 ML4  C8    C  C1     0  -0.305  -3.7814  -0.7572   1.2767
 ML4  C13   C  CR6    0   0.165  -0.5930   0.7928  -0.0228
 ML4  N18   N  N      0  -0.368   0.1363   0.6571  -1.1351
 ML4  C17   C  CR16   0  -0.151   1.3285   1.1939  -1.1911
 ML4  C16   C  CR6    0   0.475   1.8676   1.9087  -0.0973
 ML4  N15   N  N      0  -0.424   1.1171   2.1110   0.9836
 ML4  C14   C  CR16   0  -0.121  -0.0860   1.5631   1.0165
 ML4  N19   N  NH1    0  -0.651   3.1065   2.4503  -0.0852
 ML4  C20   C  CH2    0  -0.401   4.1959   2.1436  -0.9817
 ML4  C21   C  CR6    0   0.085   5.3487   1.4749  -0.2705
 ML4  C26   C  CR6    0   0.038   5.2430   0.1771   0.2460
 ML4  C25   C  CR16   0  -0.279   6.3243  -0.3720   0.9290
 ML4  C24   C  CR16   0  -0.253   7.5029   0.3422   1.1022
 ML4  C23   C  CR16   0  -0.253   7.6096   1.6241   0.5863
 ML4  C22   C  CR16   0  -0.300   6.5337   2.1811  -0.0921
 ML4  C27   C  CR6    0   0.004   4.0080  -0.6338   0.0809
 ML4  C32   C  CR16   0  -0.271   3.0876  -0.7034   1.1231
 ML4  C31   C  CR16   0  -0.249   1.9358  -1.4671   1.0094
 ML4  C30   C  CR16   0  -0.236   1.7010  -2.1762  -0.1583
 ML4  C29   C  CR16   0  -0.289   2.6195  -2.1196  -1.1961
 ML4  C28   C  CR6    0   0.070   3.7792  -1.3543  -1.0981
 ML4  C33   C  CH3    0  -0.743   4.7639  -1.3172  -2.2320
 ML4  H4    H  HCH1   0   0.212  -6.8126  -0.0757  -0.9447
 ML4  HN5   H  HNH2   0   0.327  -7.2180   0.0600   1.9296
 ML4  HN5A  H  HNH2   0   0.336  -5.9420   0.7666   1.2020
 ML4  H6    H  HCH2   0   0.234  -5.9948  -2.2113   1.0672
 ML4  H6A   H  HCH2   0   0.238  -5.9765  -2.3572  -0.6857
 ML4  H12   H  H      0   0.243  -4.3447  -1.0095  -2.0377
 ML4  H11   H  H      0   0.244  -2.1366   0.0365  -2.1042
 ML4  H9    H  H      0   0.244  -2.0257   0.0425   2.1796
 ML4  H8    H  H      0   0.250  -4.2265  -0.9952   2.2357
 ML4  H17   H  HCR6   0   0.261   1.8816   1.0681  -2.1141
 ML4  H14   H  HCR6   0   0.257  -0.6751   1.7621   1.9053
 ML4  HN19  H  HNH1   0   0.384   3.3512   2.9239   0.7713
 ML4  H20   H  HCH2   0   0.260   3.8318   1.5173  -1.7946
 ML4  H20A  H  HCH2   0   0.268   4.5549   3.0628  -1.4518
 ML4  H25   H  HCR6   0   0.249   6.2410  -1.3768   1.3252
 ML4  H24   H  HCR6   0   0.257   8.3312  -0.1040   1.6371
 ML4  H23   H  HCR6   0   0.256   8.5223   2.1921   0.7127
 ML4  H22   H  HCR6   0   0.254   6.6156   3.1868  -0.4877
 ML4  H32   H  HCR6   0   0.246   3.2738  -0.1419   2.0306
 ML4  H31   H  HCR6   0   0.248   1.2235  -1.4984   1.8235
 ML4  H30   H  HCR6   0   0.247   0.8031  -2.7713  -0.2639
 ML4  H29   H  HCR6   0   0.243   2.4348  -2.6833  -2.1031
 ML4  H33   H  HCH3   0   0.246   5.7688  -1.5831  -1.9011
 ML4  H33A  H  HCH3   0   0.249   4.4773  -2.0080  -3.0239
 ML4  H33B  H  HCH3   0   0.243   4.8341  -0.3223  -2.6774

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
 ML4  C2   O3    deloc     1.247  0.020  1.247
 ML4  O1   C2    deloc     1.246  0.020  1.246
 ML4  C2   C4    single    1.546  0.020  1.546
 ML4  C6   C4    single    1.550  0.020  1.550
 ML4  C4   N5    single    1.448  0.020  1.448
 ML4  C4   H4    single    0.970  0.020  1.090
 ML4  N5   HN5   single    0.890  0.020  1.040
 ML4  N5   HN5A  single    0.890  0.020  1.040
 ML4  C6   C7    single    1.499  0.020  1.499
 ML4  C6   H6    single    0.970  0.020  1.090
 ML4  C6   H6A   single    0.970  0.020  1.090
 ML4  C12  C7    aromatic  1.395  0.020  1.395
 ML4  C7   C8    aromatic  1.393  0.020  1.393
 ML4  C12  C11   aromatic  1.384  0.020  1.384
 ML4  C12  H12   single    0.930  0.020  1.080
 ML4  C11  C10   aromatic  1.397  0.020  1.397
 ML4  C11  H11   single    0.930  0.020  1.080
 ML4  C10  C13   single    1.471  0.020  1.471
 ML4  C10  C9    aromatic  1.395  0.020  1.395
 ML4  C8   C9    aromatic  1.387  0.020  1.387
 ML4  C9   H9    single    0.930  0.020  1.080
 ML4  C8   H8    single    0.930  0.020  1.080
 ML4  N18  C13   aromatic  1.337  0.020  1.337
 ML4  C13  C14   aromatic  1.389  0.020  1.389
 ML4  N18  C17   aromatic  1.309  0.020  1.309
 ML4  C17  C16   aromatic  1.413  0.020  1.413
 ML4  C17  H17   single    0.930  0.020  1.080
 ML4  C16  N19   single    1.352  0.020  1.352
 ML4  C16  N15   aromatic  1.331  0.020  1.331
 ML4  C14  N15   aromatic  1.322  0.020  1.322
 ML4  C14  H14   single    0.930  0.020  1.080
 ML4  N19  C20   single    1.444  0.020  1.444
 ML4  N19  HN19  single    0.860  0.020  1.020
 ML4  C20  C21   single    1.511  0.020  1.511
 ML4  C20  H20   single    0.970  0.020  1.090
 ML4  C20  H20A  single    0.970  0.020  1.090
 ML4  C22  C21   aromatic  1.391  0.020  1.391
 ML4  C21  C26   aromatic  1.401  0.020  1.401
 ML4  C26  C25   aromatic  1.392  0.020  1.392
 ML4  C26  C27   single    1.487  0.020  1.487
 ML4  C24  C25   aromatic  1.389  0.020  1.389
 ML4  C25  H25   single    0.930  0.020  1.080
 ML4  C23  C24   aromatic  1.386  0.020  1.386
 ML4  C24  H24   single    0.930  0.020  1.080
 ML4  C22  C23   aromatic  1.389  0.020  1.389
 ML4  C23  H23   single    0.930  0.020  1.080
 ML4  C22  H22   single    0.930  0.020  1.080
 ML4  C32  C27   aromatic  1.392  0.020  1.392
 ML4  C27  C28   aromatic  1.400  0.020  1.400
 ML4  C32  C31   aromatic  1.387  0.020  1.387
 ML4  C32  H32   single    0.930  0.020  1.080
 ML4  C31  C30   aromatic  1.386  0.020  1.386
 ML4  C31  H31   single    0.930  0.020  1.080
 ML4  C30  C29   aromatic  1.387  0.020  1.387
 ML4  C30  H30   single    0.930  0.020  1.080
 ML4  C28  C29   aromatic  1.393  0.020  1.393
 ML4  C29  H29   single    0.930  0.020  1.080
 ML4  C28  C33   single    1.502  0.020  1.502
 ML4  C33  H33   single    0.970  0.020  1.090
 ML4  C33  H33A  single    0.970  0.020  1.090
 ML4  C33  H33B  single    0.970  0.020  1.090

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
 ML4  C4    C2   O1    117.44  3.000
 ML4  C4    C2   O3    115.78  3.000
 ML4  O1    C2   O3    126.74  3.000
 ML4  H4    C4   C6    106.79  3.000
 ML4  H4    C4   N5    108.18  3.000
 ML4  C6    C4   N5    114.73  3.000
 ML4  H4    C4   C2    107.65  3.000
 ML4  N5    C4   C2    111.25  3.000
 ML4  C6    C4   C2    107.94  3.000
 ML4  HN5A  N5   HN5   107.22  3.000
 ML4  HN5A  N5   C4    110.63  3.000
 ML4  HN5   N5   C4    109.06  3.000
 ML4  H6A   C6   H6    107.12  3.000
 ML4  H6A   C6   C7    109.95  3.000
 ML4  H6    C6   C7    109.79  3.000
 ML4  H6A   C6   C4    108.50  3.000
 ML4  H6    C6   C4    108.93  3.000
 ML4  C7    C6   C4    112.39  3.000
 ML4  C8    C7   C12   117.50  3.000
 ML4  C8    C7   C6    121.52  3.000
 ML4  C12   C7   C6    120.92  3.000
 ML4  H12   C12  C11   119.07  3.000
 ML4  H12   C12  C7    119.51  3.000
 ML4  C11   C12  C7    121.42  3.000
 ML4  H11   C11  C10   119.51  3.000
 ML4  H11   C11  C12   119.53  3.000
 ML4  C10   C11  C12   120.95  3.000
 ML4  C13   C10  C9    121.58  3.000
 ML4  C9    C10  C11   117.79  3.000
 ML4  C13   C10  C11   120.62  3.000
 ML4  H9    C9   C8    118.63  3.000
 ML4  H9    C9   C10   120.41  3.000
 ML4  C8    C9   C10   120.95  3.000
 ML4  H8    C8   C9    119.13  3.000
 ML4  H8    C8   C7    119.49  3.000
 ML4  C9    C8   C7    121.37  3.000
 ML4  C14   C13  N18   118.66  3.000
 ML4  C14   C13  C10   122.94  3.000
 ML4  N18   C13  C10   118.38  3.000
 ML4  C17   N18  C13   119.40  3.000
 ML4  H17   C17  C16   121.55  3.000
 ML4  H17   C17  N18   117.00  3.000
 ML4  C16   C17  N18   121.45  3.000
 ML4  N19   C16  N15   116.63  3.000
 ML4  N15   C16  C17   119.35  3.000
 ML4  N19   C16  C17   123.98  3.000
 ML4  C14   N15  C16   118.04  3.000
 ML4  H14   C14  N15   116.01  3.000
 ML4  H14   C14  C13   121.09  3.000
 ML4  N15   C14  C13   122.89  3.000
 ML4  HN19  N19  C20   116.35  3.000
 ML4  HN19  N19  C16   114.71  3.000
 ML4  C20   N19  C16   126.91  3.000
 ML4  H20A  C20  H20   105.81  3.000
 ML4  H20A  C20  C21   108.91  3.000
 ML4  H20   C20  C21   110.62  3.000
 ML4  H20A  C20  N19   109.64  3.000
 ML4  H20   C20  N19   109.48  3.000
 ML4  C21   C20  N19   112.18  3.000
 ML4  C22   C21  C26   119.17  3.000
 ML4  C26   C21  C20   121.74  3.000
 ML4  C22   C21  C20   119.06  3.000
 ML4  C27   C26  C25   118.99  3.000
 ML4  C27   C26  C21   121.81  3.000
 ML4  C25   C26  C21   119.19  3.000
 ML4  H25   C25  C24   119.77  3.000
 ML4  H25   C25  C26   119.05  3.000
 ML4  C24   C25  C26   121.17  3.000
 ML4  H24   C24  C23   120.42  3.000
 ML4  H24   C24  C25   119.94  3.000
 ML4  C23   C24  C25   119.64  3.000
 ML4  H23   C23  C22   119.99  3.000
 ML4  H23   C23  C24   120.45  3.000
 ML4  C22   C23  C24   119.55  3.000
 ML4  H22   C22  C23   119.47  3.000
 ML4  H22   C22  C21   119.25  3.000
 ML4  C23   C22  C21   121.27  3.000
 ML4  C28   C27  C32   119.77  3.000
 ML4  C28   C27  C26   120.65  3.000
 ML4  C32   C27  C26   119.56  3.000
 ML4  H32   C32  C31   119.80  3.000
 ML4  H32   C32  C27   119.18  3.000
 ML4  C31   C32  C27   121.01  3.000
 ML4  H31   C31  C30   120.49  3.000
 ML4  H31   C31  C32   120.06  3.000
 ML4  C30   C31  C32   119.44  3.000
 ML4  H30   C30  C29   119.92  3.000
 ML4  H30   C30  C31   120.26  3.000
 ML4  C29   C30  C31   119.82  3.000
 ML4  H29   C29  C28   119.12  3.000
 ML4  H29   C29  C30   119.48  3.000
 ML4  C28   C29  C30   121.41  3.000
 ML4  C33   C28  C29   120.41  3.000
 ML4  C33   C28  C27   121.05  3.000
 ML4  C29   C28  C27   118.54  3.000
 ML4  H33B  C33  H33A  107.35  3.000
 ML4  H33B  C33  H33   106.65  3.000
 ML4  H33A  C33  H33   107.96  3.000
 ML4  H33B  C33  C28   111.86  3.000
 ML4  H33A  C33  C28   111.14  3.000
 ML4  H33   C33  C28   111.64  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
 ML4  CONST_01  C10   C11  C12  C7      0.00   0.0  0
 ML4  CONST_02  C10   C9   C8   C7      0.00   0.0  0
 ML4  CONST_03  C9    C8   C7   C12     0.00   0.0  0
 ML4  CONST_04  C13   C10  C11  C12   180.00   0.0  0
 ML4  CONST_05  C9    C10  C11  C12     0.00   0.0  0
 ML4  CONST_06  C8    C7   C12  C11     0.00   0.0  0
 ML4  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 ML4  CONST_10  C17   N18  C13  C10   180.00   0.0  0
 ML4  CONST_11  N15   C14  C13  C10   180.00   0.0  0
 ML4  CONST_14  C13   C10  C9   C8    180.00   0.0  0
 ML4  CONST_15  C16   C17  N18  C13     0.00   0.0  0
 ML4  CONST_16  C16   N15  C14  C13     0.00   0.0  0
 ML4  CONST_17  N15   C14  C13  N18     0.00   0.0  0
 ML4  CONST_18  N15   C16  C17  N18     0.00   0.0  0
 ML4  CONST_19  C14   C13  N18  C17     0.00   0.0  0
 ML4  CONST_20  C14   N15  C16  C17     0.00   0.0  0
 ML4  CONST_21  C24   C23  C22  C21     0.00   0.0  0
 ML4  CONST_22  C24   C25  C26  C21     0.00   0.0  0
 ML4  CONST_25  C23   C22  C21  C26     0.00   0.0  0
 ML4  CONST_26  C23   C24  C25  C26     0.00   0.0  0
 ML4  CONST_27  C31   C32  C27  C26   180.00   0.0  0
 ML4  CONST_28  C29   C28  C27  C26   180.00   0.0  0
 ML4  CONST_29  C22   C21  C26  C25     0.00   0.0  0
 ML4  CONST_32  C22   C23  C24  C25     0.00   0.0  0
 ML4  CONST_33  C27   C26  C25  C24   180.00   0.0  0
 ML4  CONST_34  C27   C26  C21  C22   180.00   0.0  0
 ML4  CONST_35  C30   C31  C32  C27     0.00   0.0  0
 ML4  CONST_36  C30   C29  C28  C27     0.00   0.0  0
 ML4  CONST_37  C29   C28  C27  C32     0.00   0.0  0
 ML4  CONST_38  C29   C30  C31  C32     0.00   0.0  0
 ML4  CONST_39  C28   C27  C32  C31     0.00   0.0  0
 ML4  CONST_40  C28   C29  C30  C31     0.00   0.0  0
 ML4  CONST_41  C11   C12  C7   C6    180.00   0.0  0
 ML4  CONST_42  C9    C8   C7   C6    180.00   0.0  0
 ML4  CONST_43  N19   C16  C17  N18   180.00   0.0  0
 ML4  CONST_44  N19   C16  N15  C14   180.00   0.0  0
 ML4  CONST_45  C23   C22  C21  C20   180.00   0.0  0
 ML4  CONST_46  C25   C26  C21  C20   180.00   0.0  0
 ML4  CONST_47  C27   C26  C21  C20     0.00   0.0  0
 ML4  CONST_48  C33   C28  C27  C26     0.00   0.0  0
 ML4  CONST_49  C33   C28  C27  C32   180.00   0.0  0
 ML4  CONST_50  C33   C28  C29  C30   180.00   0.0  0
 ML4  CONST_51  H11   C11  C12  C7    180.00   0.0  0
 ML4  CONST_52  H9    C9   C8   C7    180.00   0.0  0
 ML4  CONST_53  H8    C8   C7   C12   180.00   0.0  0
 ML4  CONST_54  H12   C12  C11  C10   180.00   0.0  0
 ML4  CONST_55  H14   C14  C13  C10     0.00   0.0  0
 ML4  CONST_56  H17   C17  N18  C13   180.00   0.0  0
 ML4  CONST_57  H23   C23  C22  C21   180.00   0.0  0
 ML4  CONST_58  H25   C25  C26  C21   180.00   0.0  0
 ML4  CONST_59  H22   C22  C21  C26   180.00   0.0  0
 ML4  CONST_60  H24   C24  C25  C26   180.00   0.0  0
 ML4  CONST_61  H32   C32  C27  C26     0.00   0.0  0
 ML4  CONST_62  H31   C31  C32  C27   180.00   0.0  0
 ML4  CONST_63  H29   C29  C28  C27   180.00   0.0  0
 ML4  CONST_64  H30   C30  C31  C32   180.00   0.0  0
 ML4  CONST_66  C20   N19  C16  N15   180.00   0.0  0
 ML4  CONST_67  HN19  N19  C16  C17   180.00   0.0  0
 ML4  Var_01    C12   C7   C6   C4    -83.42  30.0  2
 ML4  Var_02    C21   C20  N19  C16  -113.85  30.0  3
 ML4  Var_03    C22   C21  C20  N19  -109.63  30.0  2
 ML4  Var_04    H33   C33  C28  C27    53.77  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
 ML4  chir_01  C4  C2  C6  N5  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
 ML4  plan-1  C6    0.020
 ML4  plan-1  C7    0.020
 ML4  plan-1  C12   0.020
 ML4  plan-1  C11   0.020
 ML4  plan-1  C10   0.020
 ML4  plan-1  C9    0.020
 ML4  plan-1  C8    0.020
 ML4  plan-1  C13   0.020
 ML4  plan-1  H12   0.020
 ML4  plan-1  H11   0.020
 ML4  plan-1  H9    0.020
 ML4  plan-1  H8    0.020
 ML4  plan-2  C10   0.020
 ML4  plan-2  C13   0.020
 ML4  plan-2  N18   0.020
 ML4  plan-2  C17   0.020
 ML4  plan-2  C16   0.020
 ML4  plan-2  N15   0.020
 ML4  plan-2  C14   0.020
 ML4  plan-2  N19   0.020
 ML4  plan-2  H17   0.020
 ML4  plan-2  H14   0.020
 ML4  plan-3  C20   0.020
 ML4  plan-3  C21   0.020
 ML4  plan-3  C26   0.020
 ML4  plan-3  C25   0.020
 ML4  plan-3  C24   0.020
 ML4  plan-3  C23   0.020
 ML4  plan-3  C22   0.020
 ML4  plan-3  C27   0.020
 ML4  plan-3  H25   0.020
 ML4  plan-3  H24   0.020
 ML4  plan-3  H23   0.020
 ML4  plan-3  H22   0.020
 ML4  plan-4  C26   0.020
 ML4  plan-4  C27   0.020
 ML4  plan-4  C32   0.020
 ML4  plan-4  C31   0.020
 ML4  plan-4  C30   0.020
 ML4  plan-4  C29   0.020
 ML4  plan-4  C28   0.020
 ML4  plan-4  C33   0.020
 ML4  plan-4  H32   0.020
 ML4  plan-4  H31   0.020
 ML4  plan-4  H30   0.020
 ML4  plan-4  H29   0.020
 ML4  plan-5  C16   0.020
 ML4  plan-5  N19   0.020
 ML4  plan-5  C20   0.020
 ML4  plan-5  HN19  0.020
 ML4  plan-6  O3    0.020
 ML4  plan-6  C2    0.020
 ML4  plan-6  O1    0.020
 ML4  plan-6  C4    0.020

