# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:41:13 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (3S)-3-hydroxy-4-({(2S)-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
 RL2  RL2  '(3S)-3-hydroxy-4-({(2S)-1-[(3-methylbutyl)amino]-1-oxo-4-phenylbutan-2-yl}amino)-4-oxobutanoic acid'  peptide  53  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RL2
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
 RL2  C4    C  C      0   0.520  -2.0815   0.7118   0.8682
 RL2  O9    O  O      0  -0.500  -1.9509   0.4470   2.0561
 RL2  C3    C  CH1    0  -0.076  -3.3780   1.3180   0.3417
 RL2  O8    O  OH1    0  -0.662  -4.4662   0.8396   1.0872
 RL2  C2    C  CH2    0  -0.594  -3.2794   2.8391   0.3799
 RL2  C1    C  C      0   0.416  -4.5297   3.5300  -0.2016
 RL2  O6    O  OC    -1  -0.613  -4.9298   4.5528   0.3864
 RL2  O7    O  O      0  -0.612  -5.0140   3.0254  -1.2335
 RL2  N5    N  NH1    0  -0.625  -1.1182   0.5404  -0.0488
 RL2  C10   C  CH1    0  -0.230   0.2098   0.0646   0.2459
 RL2  C11   C  C      0   0.568   1.2258   0.9434  -0.4798
 RL2  O26   O  O      0  -0.495   0.9626   1.4709  -1.5518
 RL2  C12   C  CH2    0  -0.406   0.4143  -1.3944  -0.1851
 RL2  C13   C  CH2    0  -0.516  -0.5255  -2.3677   0.5259
 RL2  C14   C  C      0   0.140  -0.2668  -3.7836   0.0917
 RL2  C15   C  C1     0  -0.315   0.6081  -4.6042   0.7998
 RL2  C19   C  C1     0  -0.310  -0.8670  -4.2910  -1.0596
 RL2  C16   C  C1     0  -0.239   0.8765  -5.8979   0.3711
 RL2  C18   C  C1     0  -0.239  -0.6024  -5.5831  -1.4925
 RL2  C17   C  C1     0  -0.274   0.2718  -6.3920  -0.7772
 RL2  C25   C  CH3    0  -0.659   6.0277   3.5857  -0.1766
 RL2  C23   C  CH1    0  -0.237   6.0747   2.0632  -0.2732
 RL2  C24   C  CH3    0  -0.652   7.3127   1.5218   0.4343
 RL2  C22   C  CH2    0  -0.458   4.8191   1.4032   0.2973
 RL2  C21   C  CH2    0  -0.240   3.5449   1.7457  -0.4592
 RL2  N20   N  NH1    0  -0.640   2.4190   1.0324   0.1136
 RL2  H31   H  HCH1   0   0.244  -3.5424   1.0031  -0.6920
 RL2  HO8   H  HOH1   0   0.439  -4.2491   0.9429   2.0212
 RL2  H21   H  HCH2   0   0.221  -3.0945   3.1731   1.4055
 RL2  H22   H  HCH2   0   0.239  -2.4116   3.1596  -0.2083
 RL2  HN5   H  HNH1   0   0.398  -1.3159   0.7723  -1.0106
 RL2  H101  H  HCH1   0   0.278   0.3577   0.1377   1.3254
 RL2  H121  H  HCH2   0   0.243   0.2770  -1.4751  -1.2678
 RL2  H122  H  HCH2   0   0.249   1.4500  -1.6766   0.0222
 RL2  H131  H  HCH2   0   0.246  -0.3958  -2.2749   1.6066
 RL2  H132  H  HCH2   0   0.249  -1.5619  -2.1038   0.3052
 RL2  H151  H  H      0   0.246   1.0826  -4.2300   1.6999
 RL2  H191  H  H      0   0.246  -1.5523  -3.6660  -1.6209
 RL2  H161  H  H      0   0.253   1.5579  -6.5212   0.9359
 RL2  H181  H  H      0   0.253  -1.0818  -5.9598  -2.3871
 RL2  H171  H  H      0   0.253   0.4773  -7.4013  -1.1098
 RL2  H251  H  HCH3   0   0.214   5.9106   3.9065   0.8618
 RL2  H252  H  HCH3   0   0.229   6.9516   4.0266  -0.5548
 RL2  H253  H  HCH3   0   0.230   5.2057   4.0140  -0.7511
 RL2  H231  H  HCH1   0   0.218   6.1465   1.7902  -1.3328
 RL2  H241  H  HCH3   0   0.214   7.2851   1.7534   1.5018
 RL2  H242  H  HCH3   0   0.225   7.3876   0.4376   0.3329
 RL2  H243  H  HCH3   0   0.227   8.2243   1.9592   0.0244
 RL2  H221  H  HCH2   0   0.235   4.9521   0.3168   0.2807
 RL2  H222  H  HCH2   0   0.225   4.7091   1.6887   1.3501
 RL2  H211  H  HCH2   0   0.236   3.3541   2.8218  -0.4326
 RL2  H212  H  HCH2   0   0.235   3.6531   1.4669  -1.5101
 RL2  H20   H  HNH1   0   0.404   2.5411   0.6204   1.0253

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
 RL2  C1   O7    deloc     1.247  0.020  1.247
 RL2  C1   O6    deloc     1.246  0.020  1.246
 RL2  C1   C2    single    1.542  0.020  1.542
 RL2  C2   C3    single    1.525  0.020  1.525
 RL2  C2   H21   single    0.970  0.020  1.090
 RL2  C2   H22   single    0.970  0.020  1.090
 RL2  C3   O8    single    1.403  0.020  1.403
 RL2  C3   C4    single    1.525  0.020  1.525
 RL2  C3   H31   single    0.970  0.020  1.090
 RL2  O8   HO8   single    0.850  0.020  0.980
 RL2  C4   O9    double    1.224  0.020  1.224
 RL2  C4   N5    single    1.341  0.020  1.341
 RL2  N5   C10   single    1.441  0.020  1.441
 RL2  N5   HN5   single    0.860  0.020  1.020
 RL2  C10  C12   single    1.535  0.020  1.535
 RL2  C10  C11   single    1.527  0.020  1.527
 RL2  C10  H101  single    0.970  0.020  1.090
 RL2  C12  C13   single    1.528  0.020  1.528
 RL2  C12  H121  single    0.970  0.020  1.090
 RL2  C12  H122  single    0.970  0.020  1.090
 RL2  C13  C14   single    1.503  0.020  1.503
 RL2  C13  H131  single    0.970  0.020  1.090
 RL2  C13  H132  single    0.970  0.020  1.090
 RL2  C14  C15   aromatic  1.393  0.020  1.393
 RL2  C14  C19   aromatic  1.394  0.020  1.394
 RL2  C15  C16   aromatic  1.389  0.020  1.389
 RL2  C15  H151  single    0.930  0.020  1.080
 RL2  C16  C17   aromatic  1.389  0.020  1.389
 RL2  C16  H161  single    0.930  0.020  1.080
 RL2  C17  C18   aromatic  1.389  0.020  1.389
 RL2  C17  H171  single    0.930  0.020  1.080
 RL2  C18  C19   aromatic  1.388  0.020  1.388
 RL2  C18  H181  single    0.930  0.020  1.080
 RL2  C19  H191  single    0.930  0.020  1.080
 RL2  C11  N20   single    1.336  0.020  1.336
 RL2  C11  O26   double    1.223  0.020  1.223
 RL2  N20  C21   single    1.451  0.020  1.451
 RL2  N20  H20   single    0.860  0.020  1.020
 RL2  C21  C22   single    1.521  0.020  1.521
 RL2  C21  H211  single    0.970  0.020  1.090
 RL2  C21  H212  single    0.970  0.020  1.090
 RL2  C22  C23   single    1.529  0.020  1.529
 RL2  C22  H221  single    0.970  0.020  1.090
 RL2  C22  H222  single    0.970  0.020  1.090
 RL2  C23  C25   single    1.526  0.020  1.526
 RL2  C23  C24   single    1.525  0.020  1.525
 RL2  C23  H231  single    0.970  0.020  1.090
 RL2  C25  H251  single    0.970  0.020  1.090
 RL2  C25  H252  single    0.970  0.020  1.090
 RL2  C25  H253  single    0.970  0.020  1.090
 RL2  C24  H241  single    0.970  0.020  1.090
 RL2  C24  H242  single    0.970  0.020  1.090
 RL2  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
 RL2  N5    C4   C3    115.18  3.000
 RL2  N5    C4   O9    124.01  3.000
 RL2  C3    C4   O9    120.78  3.000
 RL2  H31   C3   C2    108.71  3.000
 RL2  H31   C3   O8    106.71  3.000
 RL2  C2    C3   O8    112.15  3.000
 RL2  H31   C3   C4    109.86  3.000
 RL2  O8    C3   C4    109.90  3.000
 RL2  C2    C3   C4    109.45  3.000
 RL2  HO8   O8   C3    107.66  3.000
 RL2  H22   C2   H21   106.25  3.000
 RL2  H22   C2   C1    107.96  3.000
 RL2  H21   C2   C1    110.71  3.000
 RL2  H22   C2   C3    109.24  3.000
 RL2  H21   C2   C3    109.81  3.000
 RL2  C1    C2   C3    112.64  3.000
 RL2  O7    C1   O6    126.74  3.000
 RL2  O6    C1   C2    116.75  3.000
 RL2  O7    C1   C2    116.47  3.000
 RL2  HN5   N5   C10   116.83  3.000
 RL2  HN5   N5   C4    118.80  3.000
 RL2  C10   N5   C4    124.36  3.000
 RL2  H101  C10  C12   108.85  3.000
 RL2  H101  C10  C11   109.95  3.000
 RL2  C12   C10  C11   108.97  3.000
 RL2  H101  C10  N5    107.75  3.000
 RL2  C11   C10  N5    109.03  3.000
 RL2  C12   C10  N5    112.28  3.000
 RL2  N20   C11  O26   123.56  3.000
 RL2  O26   C11  C10   121.43  3.000
 RL2  N20   C11  C10   114.94  3.000
 RL2  H122  C12  H121  106.71  3.000
 RL2  H122  C12  C13   109.26  3.000
 RL2  H121  C12  C13   109.64  3.000
 RL2  H122  C12  C10   108.56  3.000
 RL2  H121  C12  C10   109.34  3.000
 RL2  C13   C12  C10   113.13  3.000
 RL2  H132  C13  H131  106.98  3.000
 RL2  H132  C13  C14   109.42  3.000
 RL2  H131  C13  C14   110.20  3.000
 RL2  H132  C13  C12   109.61  3.000
 RL2  H131  C13  C12   109.46  3.000
 RL2  C14   C13  C12   111.08  3.000
 RL2  C19   C14  C15   118.42  3.000
 RL2  C19   C14  C13   120.48  3.000
 RL2  C15   C14  C13   121.07  3.000
 RL2  H151  C15  C16   119.55  3.000
 RL2  H151  C15  C14   119.58  3.000
 RL2  C16   C15  C14   120.87  3.000
 RL2  H191  C19  C18   119.71  3.000
 RL2  H191  C19  C14   119.34  3.000
 RL2  C18   C19  C14   120.95  3.000
 RL2  H161  C16  C17   120.04  3.000
 RL2  H161  C16  C15   119.79  3.000
 RL2  C17   C16  C15   120.17  3.000
 RL2  H181  C18  C17   120.10  3.000
 RL2  H181  C18  C19   119.81  3.000
 RL2  C17   C18  C19   120.09  3.000
 RL2  H171  C17  C18   120.28  3.000
 RL2  H171  C17  C16   120.22  3.000
 RL2  C18   C17  C16   119.51  3.000
 RL2  H253  C25  H252  107.27  3.000
 RL2  H253  C25  H251  107.72  3.000
 RL2  H252  C25  H251  107.53  3.000
 RL2  H253  C25  C23   112.44  3.000
 RL2  H252  C25  C23   110.80  3.000
 RL2  H251  C25  C23   110.86  3.000
 RL2  H231  C23  C22   107.87  3.000
 RL2  H231  C23  C24   107.86  3.000
 RL2  C22   C23  C24   109.89  3.000
 RL2  H231  C23  C25   108.15  3.000
 RL2  C24   C23  C25   110.47  3.000
 RL2  C22   C23  C25   112.44  3.000
 RL2  H243  C24  H242  107.82  3.000
 RL2  H243  C24  H241  107.65  3.000
 RL2  H242  C24  H241  107.64  3.000
 RL2  H243  C24  C23   111.20  3.000
 RL2  H242  C24  C23   111.42  3.000
 RL2  H241  C24  C23   110.94  3.000
 RL2  H222  C22  H221  106.57  3.000
 RL2  H222  C22  C21   109.57  3.000
 RL2  H221  C22  C21   108.53  3.000
 RL2  H222  C22  C23   109.16  3.000
 RL2  H221  C22  C23   108.84  3.000
 RL2  C21   C22  C23   113.90  3.000
 RL2  H212  C21  H211  106.97  3.000
 RL2  H212  C21  N20   109.34  3.000
 RL2  H211  C21  N20   109.82  3.000
 RL2  H212  C21  C22   109.75  3.000
 RL2  H211  C21  C22   110.84  3.000
 RL2  N20   C21  C22   110.06  3.000
 RL2  H20   N20  C21   117.66  3.000
 RL2  H20   N20  C11   118.87  3.000
 RL2  C21   N20  C11   123.41  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
 RL2  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 RL2  CONST_02  C17   C18  C19  C14     0.00   0.0  0
 RL2  CONST_03  C18   C19  C14  C15     0.00   0.0  0
 RL2  CONST_04  C18   C17  C16  C15     0.00   0.0  0
 RL2  CONST_05  C16   C15  C14  C19     0.00   0.0  0
 RL2  CONST_06  C16   C17  C18  C19     0.00   0.0  0
 RL2  CONST_07  C16   C15  C14  C13   180.00   0.0  0
 RL2  CONST_08  C18   C19  C14  C13   180.00   0.0  0
 RL2  CONST_09  H161  C16  C15  C14   180.00   0.0  0
 RL2  CONST_10  H181  C18  C19  C14   180.00   0.0  0
 RL2  CONST_11  H191  C19  C14  C15   180.00   0.0  0
 RL2  CONST_12  H171  C17  C16  C15   180.00   0.0  0
 RL2  CONST_13  H151  C15  C14  C19   180.00   0.0  0
 RL2  CONST_14  C10   N5   C4   O9      0.00   0.0  0
 RL2  CONST_15  C10   N5   C4   C3    180.00   0.0  0
 RL2  CONST_16  C21   N20  C11  C10   180.00   0.0  0
 RL2  CONST_17  C21   N20  C11  O26     0.00   0.0  0
 RL2  CONST_18  HN5   N5   C4   O9    180.00   0.0  0
 RL2  CONST_19  H20   N20  C11  C10     0.00   0.0  0
 RL2  Var_01    C15   C14  C13  C12    92.86  30.0  2
 RL2  Var_02    C14   C13  C12  C10  -178.81  30.0  3
 RL2  Var_03    O7    C1   C2   C3    -41.24  30.0  3
 RL2  Var_04    C22   C21  N20  C11  -167.53  30.0  3
 RL2  Var_05    C21   C22  C23  C25    63.76  30.0  1
 RL2  Var_06    N20   C21  C22  C23   177.51  30.0  1
 RL2  Var_07    H241  C24  C23  C25    62.87  30.0  3
 RL2  Var_08    H251  C25  C23  C24   -64.70  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
 RL2  chir_01  C3   C2  O8   C4   positiv
 RL2  chir_02  C10  N5  C12  C11  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
 RL2  plan-1  C13   0.020
 RL2  plan-1  C14   0.020
 RL2  plan-1  C15   0.020
 RL2  plan-1  C19   0.020
 RL2  plan-1  C16   0.020
 RL2  plan-1  C18   0.020
 RL2  plan-1  C17   0.020
 RL2  plan-1  H151  0.020
 RL2  plan-1  H191  0.020
 RL2  plan-1  H161  0.020
 RL2  plan-1  H181  0.020
 RL2  plan-1  H171  0.020
 RL2  plan-2  C4    0.020
 RL2  plan-2  O9    0.020
 RL2  plan-2  C3    0.020
 RL2  plan-2  N5    0.020
 RL2  plan-2  C10   0.020
 RL2  plan-2  HN5   0.020
 RL2  plan-3  C10   0.020
 RL2  plan-3  C11   0.020
 RL2  plan-3  O26   0.020
 RL2  plan-3  C21   0.020
 RL2  plan-3  N20   0.020
 RL2  plan-3  H20   0.020
 RL2  plan-4  C2    0.020
 RL2  plan-4  C1    0.020
 RL2  plan-4  O6    0.020
 RL2  plan-4  O7    0.020

