# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:33:16 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2R)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(C)C)CC(=O)NO
#
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
 PLH  PLH  (2R)-N~1~-[(1S)-1-benzyl-2-(methylamino)-2-oxoethyl]-N~4~-hydroxy-2-(2-methylpropyl)butanediamide  ligand  52  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PLH
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
 PLH  C1    C  C     0   0.527  -1.6586   0.5893   2.6188
 PLH  C2    C  CH2   0  -0.588  -1.0439  -0.2424   1.5136
 PLH  C3    C  CH1   0  -0.395   0.4295   0.1269   1.2849
 PLH  C4    C  CH2   0  -0.401   1.3118  -0.3749   2.4279
 PLH  C5    C  CH1   0  -0.228   2.6104   0.4037   2.6376
 PLH  C6    C  CH3   0  -0.654   3.3817  -0.1897   3.8119
 PLH  C7    C  CH3   0  -0.673   3.4901   0.4520   1.3923
 PLH  C8    C  C     0   0.569   0.8027  -0.4701  -0.0610
 PLH  C9    C  CH1   0  -0.183   0.6392  -0.0540  -2.4800
 PLH  C10   C  C     0   0.553   1.8976   0.2502  -3.2905
 PLH  C11   C  CH3   0  -0.515   4.1243   1.2380  -3.2948
 PLH  C12   C  CH2   0  -0.538  -0.5980   0.5391  -3.1724
 PLH  C13   C  CR6   0   0.136  -1.8536   0.2247  -2.4062
 PLH  C14   C  CR16  0  -0.326  -2.5574   1.2257  -1.7432
 PLH  C15   C  CR16  0  -0.242  -3.6919   0.9269  -0.9975
 PLH  C16   C  CR16  0  -0.269  -4.1349  -0.3843  -0.9006
 PLH  C17   C  CR16  0  -0.239  -3.4403  -1.3921  -1.5596
 PLH  C18   C  CR16  0  -0.294  -2.3117  -1.0883  -2.3066
 PLH  N1    N  NH1   0  -0.373  -2.4278  -0.1245   3.4573
 PLH  N2    N  NH1   0  -0.659   0.6936   0.3838  -1.1068
 PLH  O1    O  OH1   0  -0.543  -2.9983   0.4642   4.5428
 PLH  O2    O  O     0  -0.474  -1.5045   1.7947   2.7078
 PLH  O3    O  O     0  -0.469   1.1095  -1.6415  -0.1976
 PLH  O4    O  O     0  -0.503   1.9663  -0.0897  -4.4647
 PLH  H21   H  HCH2  0   0.304  -1.6326  -0.0477   0.6118
 PLH  H22   H  HCH2  0   0.267  -1.1319  -1.3122   1.7181
 PLH  H3    H  HCH1  0   0.266   0.4957   1.2183   1.2283
 PLH  H41   H  HCH2  0   0.234   0.7390  -0.3275   3.3597
 PLH  H42   H  HCH2  0   0.229   1.5327  -1.4352   2.2717
 PLH  H5    H  HCH1  0   0.219   2.3393   1.4341   2.8964
 PLH  H61   H  HCH3  0   0.227   4.2743   0.3955   4.0381
 PLH  H62   H  HCH3  0   0.225   2.7697  -0.2253   4.7152
 PLH  H63   H  HCH3  0   0.215   3.7036  -1.2101   3.5901
 PLH  H71   H  HCH3  0   0.221   3.7264  -0.5509   1.0306
 PLH  H72   H  HCH3  0   0.217   3.0143   1.0016   0.5785
 PLH  H73   H  HCH3  0   0.237   4.4322   0.9598   1.6058
 PLH  H9    H  HCH1  0   0.291   0.5458  -1.1424  -2.4760
 PLH  H111  H  HCH3  0   0.251   4.7701   1.7087  -2.5594
 PLH  H112  H  HCH3  0   0.242   4.6345   0.3589  -3.6880
 PLH  H113  H  HCH3  0   0.241   3.9683   1.9395  -4.1149
 PLH  H121  H  HCH2  0   0.267  -0.4798   1.6220  -3.2667
 PLH  H122  H  HCH2  0   0.276  -0.6541   0.1387  -4.1851
 PLH  H14   H  HCR6  0   0.251  -2.2163   2.2524  -1.8085
 PLH  H15   H  HCR6  0   0.256  -4.2226   1.7193  -0.4857
 PLH  H16   H  HCR6  0   0.255  -5.0146  -0.6211  -0.3162
 PLH  H17   H  HCR6  0   0.255  -3.7792  -2.4179  -1.4914
 PLH  H18   H  HCR6  0   0.252  -1.7803  -1.8843  -2.8161
 PLH  HN1   H  HNH1  0   0.417  -2.4643  -1.1331   3.4456
 PLH  HN2   H  HNH1  0   0.406   0.3888   1.3261  -0.9116
 PLH  HN3   H  HNH1  0   0.411   2.7343   1.1580  -1.6951
 PLH  HO1   H  HOH1  0   0.478  -3.8857   0.7343   4.2719
 PLH  N3    N  NH1   0  -0.631   2.8816   0.8836  -2.6513

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
 PLH  C1   C2    single    1.514  0.020  1.514
 PLH  C1   N1    single    1.343  0.020  1.343
 PLH  C1   O2    double    1.218  0.020  1.218
 PLH  C2   C3    single    1.536  0.020  1.536
 PLH  C2   H21   single    0.970  0.020  1.090
 PLH  C2   H22   single    0.970  0.020  1.090
 PLH  C3   C4    single    1.529  0.020  1.529
 PLH  C3   C8    single    1.519  0.020  1.519
 PLH  C3   H3    single    0.970  0.020  1.090
 PLH  C4   C5    single    1.529  0.020  1.529
 PLH  C4   H41   single    0.970  0.020  1.090
 PLH  C4   H42   single    0.970  0.020  1.090
 PLH  C5   C6    single    1.525  0.020  1.525
 PLH  C5   C7    single    1.525  0.020  1.525
 PLH  C5   H5    single    0.970  0.020  1.090
 PLH  C6   H61   single    0.970  0.020  1.090
 PLH  C6   H62   single    0.970  0.020  1.090
 PLH  C6   H63   single    0.970  0.020  1.090
 PLH  C7   H71   single    0.970  0.020  1.090
 PLH  C7   H72   single    0.970  0.020  1.090
 PLH  C7   H73   single    0.970  0.020  1.090
 PLH  C8   N2    single    1.355  0.020  1.355
 PLH  C8   O3    double    1.219  0.020  1.219
 PLH  C9   C10   single    1.527  0.020  1.527
 PLH  C9   C12   single    1.537  0.020  1.537
 PLH  C9   N2    single    1.442  0.020  1.442
 PLH  C9   H9    single    0.970  0.020  1.090
 PLH  C10  N3    single    1.333  0.020  1.333
 PLH  C10  O4    double    1.224  0.020  1.224
 PLH  C11  N3    single    1.444  0.020  1.444
 PLH  C11  H111  single    0.970  0.020  1.090
 PLH  C11  H112  single    0.970  0.020  1.090
 PLH  C11  H113  single    0.970  0.020  1.090
 PLH  C12  C13   single    1.504  0.020  1.504
 PLH  C12  H121  single    0.970  0.020  1.090
 PLH  C12  H122  single    0.970  0.020  1.090
 PLH  C13  C14   aromatic  1.392  0.020  1.392
 PLH  C13  C18   aromatic  1.394  0.020  1.394
 PLH  C14  C15   aromatic  1.390  0.020  1.390
 PLH  C14  H14   single    0.930  0.020  1.080
 PLH  C15  C16   aromatic  1.387  0.020  1.387
 PLH  C15  H15   single    0.930  0.020  1.080
 PLH  C16  C17   aromatic  1.390  0.020  1.390
 PLH  C16  H16   single    0.930  0.020  1.080
 PLH  C17  C18   aromatic  1.387  0.020  1.387
 PLH  C17  H17   single    0.930  0.020  1.080
 PLH  C18  H18   single    0.930  0.020  1.080
 PLH  N1   O1    single    1.360  0.020  1.360
 PLH  N1   HN1   single    0.860  0.020  1.020
 PLH  N2   HN2   single    0.860  0.020  1.020
 PLH  N3   HN3   single    0.860  0.020  1.020
 PLH  O1   HO1   single    0.850  0.020  0.980

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
 PLH  O2    C1   N1    123.54  3.000
 PLH  O2    C1   C2    123.06  3.000
 PLH  N1    C1   C2    113.35  3.000
 PLH  H22   C2   H21   106.56  3.000
 PLH  H22   C2   C3    109.91  3.000
 PLH  H21   C2   C3    110.52  3.000
 PLH  H22   C2   C1    111.63  3.000
 PLH  H21   C2   C1    106.59  3.000
 PLH  C3    C2   C1    111.48  3.000
 PLH  H3    C3   C8    109.33  3.000
 PLH  H3    C3   C4    109.33  3.000
 PLH  C8    C3   C4    113.06  3.000
 PLH  H3    C3   C2    107.78  3.000
 PLH  C8    C3   C2    105.85  3.000
 PLH  C4    C3   C2    111.31  3.000
 PLH  H42   C4   H41   105.60  3.000
 PLH  H42   C4   C5    109.97  3.000
 PLH  H41   C4   C5    107.80  3.000
 PLH  H42   C4   C3    109.14  3.000
 PLH  H41   C4   C3    108.68  3.000
 PLH  C5    C4   C3    115.20  3.000
 PLH  H5    C5   C7    107.79  3.000
 PLH  H5    C5   C6    108.00  3.000
 PLH  C7    C5   C6    110.44  3.000
 PLH  H5    C5   C4    107.51  3.000
 PLH  C7    C5   C4    113.20  3.000
 PLH  C6    C5   C4    109.70  3.000
 PLH  H63   C6   H62   107.62  3.000
 PLH  H63   C6   H61   107.57  3.000
 PLH  H62   C6   H61   107.72  3.000
 PLH  H63   C6   C5    110.86  3.000
 PLH  H62   C6   C5    111.49  3.000
 PLH  H61   C6   C5    111.39  3.000
 PLH  H73   C7   H72   106.73  3.000
 PLH  H73   C7   H71   107.78  3.000
 PLH  H72   C7   H71   108.05  3.000
 PLH  H73   C7   C5    110.66  3.000
 PLH  H72   C7   C5    111.93  3.000
 PLH  H71   C7   C5    111.48  3.000
 PLH  O3    C8   N2    122.66  3.000
 PLH  O3    C8   C3    122.61  3.000
 PLH  N2    C8   C3    114.62  3.000
 PLH  H9    C9   N2    107.59  3.000
 PLH  H9    C9   C12   108.50  3.000
 PLH  N2    C9   C12   110.01  3.000
 PLH  H9    C9   C10   105.71  3.000
 PLH  N2    C9   C10   114.44  3.000
 PLH  C12   C9   C10   110.32  3.000
 PLH  O4    C10  N3    123.38  3.000
 PLH  O4    C10  C9    119.99  3.000
 PLH  N3    C10  C9    116.63  3.000
 PLH  H113  C11  H112  108.33  3.000
 PLH  H113  C11  H111  108.39  3.000
 PLH  H112  C11  H111  108.39  3.000
 PLH  H113  C11  N3    111.72  3.000
 PLH  H112  C11  N3    111.46  3.000
 PLH  H111  C11  N3    108.45  3.000
 PLH  H122  C12  H121  106.81  3.000
 PLH  H122  C12  C13   110.69  3.000
 PLH  H121  C12  C13   109.95  3.000
 PLH  H122  C12  C9    108.55  3.000
 PLH  H121  C12  C9    109.51  3.000
 PLH  C13   C12  C9    111.22  3.000
 PLH  C18   C13  C14   118.50  3.000
 PLH  C18   C13  C12   120.50  3.000
 PLH  C14   C13  C12   120.96  3.000
 PLH  H14   C14  C15   119.52  3.000
 PLH  H14   C14  C13   119.57  3.000
 PLH  C15   C14  C13   120.91  3.000
 PLH  H15   C15  C16   120.15  3.000
 PLH  H15   C15  C14   119.76  3.000
 PLH  C16   C15  C14   120.08  3.000
 PLH  H16   C16  C17   120.23  3.000
 PLH  H16   C16  C15   120.27  3.000
 PLH  C17   C16  C15   119.50  3.000
 PLH  H17   C17  C18   119.75  3.000
 PLH  H17   C17  C16   120.05  3.000
 PLH  C18   C17  C16   120.20  3.000
 PLH  H18   C18  C17   119.41  3.000
 PLH  H18   C18  C13   119.79  3.000
 PLH  C17   C18  C13   120.80  3.000
 PLH  HN1   N1   O1    115.24  3.000
 PLH  HN1   N1   C1    122.99  3.000
 PLH  O1    N1   C1    120.55  3.000
 PLH  HN2   N2   C9    117.14  3.000
 PLH  HN2   N2   C8    117.61  3.000
 PLH  C9    N2   C8    123.14  3.000
 PLH  HO1   O1   N1    106.41  3.000
 PLH  HN3   N3   C11   118.88  3.000
 PLH  HN3   N3   C10   118.51  3.000
 PLH  C11   N3   C10   122.56  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
 PLH  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 PLH  CONST_02  C16   C17  C18  C13     0.00   0.0  0
 PLH  CONST_03  C17   C18  C13  C14     0.00   0.0  0
 PLH  CONST_04  C17   C16  C15  C14     0.00   0.0  0
 PLH  CONST_05  C18   C13  C14  C15     0.00   0.0  0
 PLH  CONST_06  C18   C17  C16  C15     0.00   0.0  0
 PLH  CONST_07  C15   C14  C13  C12   180.00   0.0  0
 PLH  CONST_08  C17   C18  C13  C12   180.00   0.0  0
 PLH  CONST_09  H15   C15  C14  C13   180.00   0.0  0
 PLH  CONST_10  H17   C17  C18  C13   180.00   0.0  0
 PLH  CONST_11  H18   C18  C13  C14   180.00   0.0  0
 PLH  CONST_12  H16   C16  C15  C14   180.00   0.0  0
 PLH  CONST_13  H14   C14  C15  C16   180.00   0.0  0
 PLH  CONST_14  O1    N1   C1   C2    180.00   0.0  0
 PLH  CONST_16  C11   N3   C10  C9    180.00   0.0  0
 PLH  CONST_17  O3    C8   N2   C9      0.00   0.0  0
 PLH  CONST_18  O4    C10  N3   C11     0.00   0.0  0
 PLH  CONST_19  O2    C1   N1   O1      0.00   0.0  0
 PLH  CONST_20  HN1   N1   C1   C2      0.00   0.0  0
 PLH  CONST_21  HN2   N2   C8   C3      0.00   0.0  0
 PLH  CONST_22  HN3   N3   C10  C9      0.00   0.0  0
 PLH  Var_01    C14   C13  C12  C9    110.80  30.0  2
 PLH  Var_02    N1    C1   C2   C3   -137.00  30.0  1
 PLH  Var_03    C6    C5   C4   C3    179.37  30.0  3
 PLH  Var_04    H61   C6   C5   C4   -175.35  30.0  3
 PLH  Var_05    H71   C7   C5   C4    -56.38  30.0  3
 PLH  Var_06    H111  C11  N3   C10  -177.94  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
 PLH  chir_01  C3  C2  C4   C8   negativ
 PLH  chir_02  C9  N2  C10  C12  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
 PLH  plan-1  C12  0.020
 PLH  plan-1  C13  0.020
 PLH  plan-1  C14  0.020
 PLH  plan-1  C15  0.020
 PLH  plan-1  C16  0.020
 PLH  plan-1  C17  0.020
 PLH  plan-1  C18  0.020
 PLH  plan-1  H14  0.020
 PLH  plan-1  H15  0.020
 PLH  plan-1  H16  0.020
 PLH  plan-1  H17  0.020
 PLH  plan-1  H18  0.020
 PLH  plan-2  C1   0.020
 PLH  plan-2  C2   0.020
 PLH  plan-2  N1   0.020
 PLH  plan-2  O1   0.020
 PLH  plan-2  O2   0.020
 PLH  plan-2  HN1  0.020
 PLH  plan-3  C3   0.020
 PLH  plan-3  C8   0.020
 PLH  plan-3  C9   0.020
 PLH  plan-3  N2   0.020
 PLH  plan-3  O3   0.020
 PLH  plan-3  HN2  0.020
 PLH  plan-4  C9   0.020
 PLH  plan-4  C10  0.020
 PLH  plan-4  C11  0.020
 PLH  plan-4  O4   0.020
 PLH  plan-4  HN3  0.020
 PLH  plan-4  N3   0.020

