# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 20:02:55 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (3S)-3-hydroxy-4-({(2R)-1-[(3-methylbutyl)amino]-1-oxo-4-phenylbutan-2-yl}amino)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCNC(=O)[C@@H](CCc1ccccc1)NC(=O)[C@@H](O)CC(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
 R99  R99  '(3S)-3-hydroxy-4-({(2R)-1-[(3-methylbutyl)amino]-1-oxo-4-phenylbutan-2-yl}amino)-4-oxobutanoic acid'  peptide  54  26  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R99
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
 R99  C4    C  C     0   0.506  -1.6431  -1.6015   1.0404
 R99  O9    O  O     0  -0.482  -1.5289  -1.3508   2.2312
 R99  C3    C  CH1   0  -0.064  -2.9280  -2.2381   0.5110
 R99  O8    O  OH1   0  -0.657  -3.5947  -2.9098   1.5365
 R99  C2    C  CH2   0  -0.615  -3.7927  -1.1306  -0.0955
 R99  C1    C  C     0   0.564  -5.0723  -1.6719  -0.6761
 R99  O6    O  OH1   0  -0.590  -6.0351  -0.7597  -0.6858
 R99  O7    O  O     0  -0.441  -5.2060  -2.7848  -1.1176
 R99  N5    N  NH1   0  -0.622  -0.7307  -1.3066   0.1078
 R99  C10   C  CH1   0  -0.237   0.4768  -0.5557   0.3531
 R99  C11   C  C     0   0.569   1.6479  -1.2561  -0.3298
 R99  O26   O  O     0  -0.494   1.4992  -1.8589  -1.3837
 R99  C12   C  CH2   0  -0.405   0.3641   0.8760  -0.1886
 R99  C13   C  CH2   0  -0.519  -0.7001   1.7021   0.5334
 R99  C14   C  CR6   0   0.141  -0.8273   3.0754  -0.0639
 R99  C15   C  CR16  0  -0.311  -1.7427   3.3267  -1.0834
 R99  C19   C  CR16  0  -0.310  -0.0043   4.1161   0.3611
 R99  C16   C  CR16  0  -0.239  -1.8349   4.5844  -1.6648
 R99  C18   C  CR16  0  -0.239  -0.0925   5.3756  -0.2166
 R99  C17   C  CR16  0  -0.274  -1.0088   5.6141  -1.2330
 R99  C25   C  CH3   0  -0.659   6.8694  -1.0881  -1.5078
 R99  C23   C  CH1   0  -0.238   6.6179  -1.3934  -0.0335
 R99  C24   C  CH3   0  -0.652   7.7146  -0.7775   0.8297
 R99  C22   C  CH2   0  -0.456   5.2486  -0.8983   0.4327
 R99  C21   C  CH2   0  -0.242   4.0811  -1.5823  -0.2613
 R99  N20   N  NH1   0  -0.638   2.8259  -1.0984   0.2791
 R99  H31   H  HCH1  0   0.269  -2.6850  -2.9678  -0.2661
 R99  HO8   H  HOH1  0   0.445  -3.4360  -2.4216   2.3553
 R99  H21   H  HCH2  0   0.287  -4.0087  -0.3614   0.6499
 R99  H22   H  HCH2  0   0.295  -3.2596  -0.6307  -0.9118
 R99  HO6   H  HOH1  0   0.482  -6.8282  -1.1163  -1.1147
 R99  HN5   H  HNH1  0   0.405  -0.8974  -1.5961  -0.8451
 R99  H101  H  HCH1  0   0.283   0.6363  -0.5218   1.4324
 R99  H121  H  HCH2  0   0.253   1.3334   1.3702  -0.0884
 R99  H122  H  HCH2  0   0.246   0.1407   0.8340  -1.2587
 R99  H131  H  HCH2  0   0.243  -1.6657   1.1936   0.4797
 R99  H132  H  HCH2  0   0.252  -0.4410   1.7779   1.5923
 R99  H151  H  HCR6  0   0.242  -2.3957   2.5306  -1.4237
 R99  H191  H  HCR6  0   0.247   0.7106   3.9414   1.1571
 R99  H161  H  HCR6  0   0.254  -2.5553   4.7596  -2.4538
 R99  H181  H  HCR6  0   0.253   0.5538   6.1721   0.1297
 R99  H171  H  HCR6  0   0.253  -1.0808   6.5959  -1.6827
 R99  H251  H  HCH3  0   0.215   6.8050  -0.0132  -1.6947
 R99  H252  H  HCH3  0   0.229   7.8653  -1.4170  -1.8085
 R99  H253  H  HCH3  0   0.229   6.1539  -1.5829  -2.1655
 R99  H231  H  HCH1  0   0.218   6.6482  -2.4812   0.1027
 R99  H241  H  HCH3  0   0.214   7.7213   0.3109   0.7308
 R99  H242  H  HCH3  0   0.226   7.5734  -1.0131   1.8859
 R99  H243  H  HCH3  0   0.227   8.7002  -1.1420   0.5366
 R99  H221  H  HCH2  0   0.234   5.1640  -1.0624   1.5123
 R99  H222  H  HCH2  0   0.226   5.1805   0.1838   0.2754
 R99  H211  H  HCH2  0   0.241   4.1001  -1.3847  -1.3339
 R99  H212  H  HCH2  0   0.233   4.1570  -2.6673  -0.1352
 R99  H20   H  HNH1  0   0.404   2.8468  -0.6446   1.1789

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
 R99  C1   O7    double    1.205  0.020  1.205
 R99  C1   O6    single    1.326  0.020  1.326
 R99  C1   C2    single    1.506  0.020  1.506
 R99  O6   HO6   single    0.850  0.020  0.980
 R99  C2   C3    single    1.530  0.020  1.530
 R99  C2   H21   single    0.970  0.020  1.090
 R99  C2   H22   single    0.970  0.020  1.090
 R99  C3   O8    single    1.395  0.020  1.395
 R99  C3   C4    single    1.529  0.020  1.529
 R99  C3   H31   single    0.970  0.020  1.090
 R99  O8   HO8   single    0.850  0.020  0.980
 R99  C4   O9    double    1.222  0.020  1.222
 R99  C4   N5    single    1.338  0.020  1.338
 R99  N5   C10   single    1.443  0.020  1.443
 R99  N5   HN5   single    0.860  0.020  1.020
 R99  C10  C12   single    1.535  0.020  1.535
 R99  C10  C11   single    1.526  0.020  1.526
 R99  C10  H101  single    0.970  0.020  1.090
 R99  C12  C13   single    1.528  0.020  1.528
 R99  C12  H121  single    0.970  0.020  1.090
 R99  C12  H122  single    0.970  0.020  1.090
 R99  C13  C14   single    1.503  0.020  1.503
 R99  C13  H131  single    0.970  0.020  1.090
 R99  C13  H132  single    0.970  0.020  1.090
 R99  C14  C15   aromatic  1.393  0.020  1.393
 R99  C14  C19   aromatic  1.393  0.020  1.393
 R99  C15  C16   aromatic  1.389  0.020  1.389
 R99  C15  H151  single    0.930  0.020  1.080
 R99  C16  C17   aromatic  1.389  0.020  1.389
 R99  C16  H161  single    0.930  0.020  1.080
 R99  C17  C18   aromatic  1.389  0.020  1.389
 R99  C17  H171  single    0.930  0.020  1.080
 R99  C18  C19   aromatic  1.388  0.020  1.388
 R99  C18  H181  single    0.930  0.020  1.080
 R99  C19  H191  single    0.930  0.020  1.080
 R99  C11  N20   single    1.335  0.020  1.335
 R99  C11  O26   double    1.223  0.020  1.223
 R99  N20  C21   single    1.450  0.020  1.450
 R99  N20  H20   single    0.860  0.020  1.020
 R99  C21  C22   single    1.521  0.020  1.521
 R99  C21  H211  single    0.970  0.020  1.090
 R99  C21  H212  single    0.970  0.020  1.090
 R99  C22  C23   single    1.529  0.020  1.529
 R99  C22  H221  single    0.970  0.020  1.090
 R99  C22  H222  single    0.970  0.020  1.090
 R99  C23  C25   single    1.526  0.020  1.526
 R99  C23  C24   single    1.525  0.020  1.525
 R99  C23  H231  single    0.970  0.020  1.090
 R99  C25  H251  single    0.970  0.020  1.090
 R99  C25  H252  single    0.970  0.020  1.090
 R99  C25  H253  single    0.970  0.020  1.090
 R99  C24  H241  single    0.970  0.020  1.090
 R99  C24  H242  single    0.970  0.020  1.090
 R99  C24  H243  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
 R99  N5    C4   C3    115.07  3.000
 R99  N5    C4   O9    124.77  3.000
 R99  C3    C4   O9    120.09  3.000
 R99  H31   C3   C2    109.08  3.000
 R99  H31   C3   O8    107.89  3.000
 R99  C2    C3   O8    111.70  3.000
 R99  H31   C3   C4    109.71  3.000
 R99  O8    C3   C4    110.34  3.000
 R99  C2    C3   C4    108.11  3.000
 R99  HO8   O8   C3    107.52  3.000
 R99  H22   C2   H21   106.45  3.000
 R99  H22   C2   C1    106.87  3.000
 R99  H21   C2   C1    110.37  3.000
 R99  H22   C2   C3    110.52  3.000
 R99  H21   C2   C3    110.53  3.000
 R99  C1    C2   C3    111.89  3.000
 R99  O7    C1   O6    123.51  3.000
 R99  O6    C1   C2    111.87  3.000
 R99  O7    C1   C2    124.59  3.000
 R99  HO6   O6   C1    110.13  3.000
 R99  HN5   N5   C10   116.60  3.000
 R99  HN5   N5   C4    118.82  3.000
 R99  C10   N5   C4    124.54  3.000
 R99  H101  C10  C12   109.31  3.000
 R99  H101  C10  C11   110.16  3.000
 R99  C12   C10  C11   109.06  3.000
 R99  H101  C10  N5    107.85  3.000
 R99  C11   C10  N5    109.10  3.000
 R99  C12   C10  N5    111.34  3.000
 R99  N20   C11  O26   123.93  3.000
 R99  O26   C11  C10   121.24  3.000
 R99  N20   C11  C10   114.76  3.000
 R99  H122  C12  H121  106.75  3.000
 R99  H122  C12  C13   109.91  3.000
 R99  H121  C12  C13   109.26  3.000
 R99  H122  C12  C10   108.93  3.000
 R99  H121  C12  C10   108.93  3.000
 R99  C13   C12  C10   112.87  3.000
 R99  H132  C13  H131  106.82  3.000
 R99  H132  C13  C14   109.98  3.000
 R99  H131  C13  C14   109.33  3.000
 R99  H132  C13  C12   109.27  3.000
 R99  H131  C13  C12   109.91  3.000
 R99  C14   C13  C12   111.41  3.000
 R99  C19   C14  C15   118.47  3.000
 R99  C19   C14  C13   120.75  3.000
 R99  C15   C14  C13   120.75  3.000
 R99  H151  C15  C16   119.57  3.000
 R99  H151  C15  C14   119.53  3.000
 R99  C16   C15  C14   120.89  3.000
 R99  H191  C19  C18   119.58  3.000
 R99  H191  C19  C14   119.55  3.000
 R99  C18   C19  C14   120.87  3.000
 R99  H161  C16  C17   120.16  3.000
 R99  H161  C16  C15   119.73  3.000
 R99  C17   C16  C15   120.11  3.000
 R99  H181  C18  C17   120.10  3.000
 R99  H181  C18  C19   119.76  3.000
 R99  C17   C18  C19   120.14  3.000
 R99  H171  C17  C18   120.24  3.000
 R99  H171  C17  C16   120.24  3.000
 R99  C18   C17  C16   119.51  3.000
 R99  H253  C25  H252  107.21  3.000
 R99  H253  C25  H251  107.72  3.000
 R99  H252  C25  H251  107.65  3.000
 R99  H253  C25  C23   112.56  3.000
 R99  H252  C25  C23   110.87  3.000
 R99  H251  C25  C23   110.62  3.000
 R99  H231  C23  C22   107.94  3.000
 R99  H231  C23  C24   108.08  3.000
 R99  C22   C23  C24   109.91  3.000
 R99  H231  C23  C25   108.29  3.000
 R99  C24   C23  C25   110.33  3.000
 R99  C22   C23  C25   112.17  3.000
 R99  H243  C24  H242  107.74  3.000
 R99  H243  C24  H241  107.63  3.000
 R99  H242  C24  H241  107.66  3.000
 R99  H243  C24  C23   111.26  3.000
 R99  H242  C24  C23   111.56  3.000
 R99  H241  C24  C23   110.81  3.000
 R99  H222  C22  H221  106.54  3.000
 R99  H222  C22  C21   109.34  3.000
 R99  H221  C22  C21   108.85  3.000
 R99  H222  C22  C23   109.37  3.000
 R99  H221  C22  C23   108.73  3.000
 R99  C21   C22  C23   113.75  3.000
 R99  H212  C21  H211  106.95  3.000
 R99  H212  C21  N20   110.35  3.000
 R99  H211  C21  N20   108.73  3.000
 R99  H212  C21  C22   109.88  3.000
 R99  H211  C21  C22   110.73  3.000
 R99  N20   C21  C22   110.15  3.000
 R99  H20   N20  C21   117.72  3.000
 R99  H20   N20  C11   118.58  3.000
 R99  C21   N20  C11   123.67  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
 R99  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 R99  CONST_02  C17   C18  C19  C14     0.00   0.0  0
 R99  CONST_03  C18   C19  C14  C15     0.00   0.0  0
 R99  CONST_04  C18   C17  C16  C15     0.00   0.0  0
 R99  CONST_05  C16   C15  C14  C19     0.00   0.0  0
 R99  CONST_06  C16   C17  C18  C19     0.00   0.0  0
 R99  CONST_07  C16   C15  C14  C13   180.00   0.0  0
 R99  CONST_08  C18   C19  C14  C13   180.00   0.0  0
 R99  CONST_09  H161  C16  C15  C14   180.00   0.0  0
 R99  CONST_10  H181  C18  C19  C14   180.00   0.0  0
 R99  CONST_11  H191  C19  C14  C15   180.00   0.0  0
 R99  CONST_12  H171  C17  C16  C15   180.00   0.0  0
 R99  CONST_13  H151  C15  C14  C19   180.00   0.0  0
 R99  CONST_14  C10   N5   C4   O9      0.00   0.0  0
 R99  CONST_15  C10   N5   C4   C3    180.00   0.0  0
 R99  CONST_16  C21   N20  C11  C10   180.00   0.0  0
 R99  CONST_17  C21   N20  C11  O26     0.00   0.0  0
 R99  CONST_18  HN5   N5   C4   O9    180.00   0.0  0
 R99  CONST_19  H20   N20  C11  C10     0.00   0.0  0
 R99  CONST_20  HO6   O6   C1   C2    180.00   0.0  0
 R99  Var_01    C15   C14  C13  C12    91.63  30.0  2
 R99  Var_02    C14   C13  C12  C10  -177.36  30.0  3
 R99  Var_03    O7    C1   C2   C3    -28.36  30.0  3
 R99  Var_04    C22   C21  N20  C11   163.07  30.0  3
 R99  Var_05    C21   C22  C23  C25    63.65  30.0  2
 R99  Var_06    N20   C21  C22  C23   177.50  30.0  1
 R99  Var_07    H241  C24  C23  C25    62.04  30.0  3
 R99  Var_08    H251  C25  C23  C24   -64.33  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
 R99  chir_01  C3   C2  O8   C4   positiv
 R99  chir_02  C10  N5  C12  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
 R99  plan-1  C13   0.020
 R99  plan-1  C14   0.020
 R99  plan-1  C15   0.020
 R99  plan-1  C19   0.020
 R99  plan-1  C16   0.020
 R99  plan-1  C18   0.020
 R99  plan-1  C17   0.020
 R99  plan-1  H151  0.020
 R99  plan-1  H191  0.020
 R99  plan-1  H161  0.020
 R99  plan-1  H181  0.020
 R99  plan-1  H171  0.020
 R99  plan-2  C4    0.020
 R99  plan-2  O9    0.020
 R99  plan-2  C3    0.020
 R99  plan-2  N5    0.020
 R99  plan-2  C10   0.020
 R99  plan-2  HN5   0.020
 R99  plan-3  C10   0.020
 R99  plan-3  C11   0.020
 R99  plan-3  O26   0.020
 R99  plan-3  C21   0.020
 R99  plan-3  N20   0.020
 R99  plan-3  H20   0.020
 R99  plan-4  C2    0.020
 R99  plan-4  C1    0.020
 R99  plan-4  O6    0.020
 R99  plan-4  O7    0.020
 R99  plan-4  HO6   0.020

