# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:12:30 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: D-valyl-N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](N)C(C)C)C(=O)N[C@@H](CCCCN)[C@H](O)CCl
#
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
 2YS  2YS  D-valyl-N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-L-leucinamide  peptide  63  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2YS
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
 2YS  N24  N   NH2   0  -0.780   4.6080   3.0425   0.4689
 2YS  C20  C   CH1   0  -0.215   4.0055   1.7563   0.7331
 2YS  C21  C   CH1   0  -0.228   5.0641   0.6319   0.7430
 2YS  C22  C   CH3   0  -0.668   5.7792   0.4832  -0.5974
 2YS  C23  C   CH3   0  -0.649   6.0642   0.8483   1.8723
 2YS  C19  C   C     0   0.531   2.8830   1.4001  -0.2470
 2YS  O25  O   O     0  -0.490   2.7993   1.9091  -1.3557
 2YS  N18  N   NH1   0  -0.633   2.0161   0.4730   0.2001
 2YS  C5   C   CH1   0  -0.204   0.9870  -0.1142  -0.6248
 2YS  C6   C   C     0   0.558  -0.2296  -0.3795   0.2536
 2YS  O17  O   O     0  -0.486  -0.1008  -0.8300   1.3825
 2YS  C4   C   CH2   0  -0.411   1.4783  -1.4237  -1.2625
 2YS  C2   C   CH1   0  -0.259   0.5537  -2.0576  -2.3037
 2YS  C3   C   CH3   0  -0.655   0.3609  -1.1603  -3.5235
 2YS  C1   C   CH3   0  -0.647   1.1125  -3.4140  -2.7233
 2YS  C14  C   CH1   0   0.080  -3.3750  -1.5920  -0.2701
 2YS  C11  C   CH2   0  -0.427  -3.9019   3.3727   0.6580
 2YS  C8   C   CH1   0  -0.130  -2.7076  -0.3215   0.3075
 2YS  C9   C   CH2   0  -0.450  -3.5686   0.9242   0.1140
 2YS  C10  C   CH2   0  -0.416  -2.9505   2.1838   0.7086
 2YS  C12  C   CH2   0  -0.272  -3.2990   4.6309   1.2628
 2YS  N7   N   NH1   0  -0.635  -1.4146  -0.1277  -0.3212
 2YS  N13  N   NH2   0  -0.801  -4.2417   5.7400   1.2074
 2YS  O16  O   OH1   0  -0.658  -4.6998  -1.7416   0.1663
 2YS  C15  C   CH2   0  -0.479  -2.6199  -2.8242   0.1835
 2YS  CL1  CL  CL    0  -0.167  -3.2234  -4.2908  -0.6597
 2YS  H37  H   HNH2  0   0.343   4.8486   3.1138  -0.5120
 2YS  H38  H   HNH2  0   0.351   3.9330   3.7778   0.6372
 2YS  H29  H   HCH1  0   0.258   3.5722   1.7931   1.7389
 2YS  H30  H   HCH1  0   0.225   4.5364  -0.3060   0.9463
 2YS  H31  H   HCH3  0   0.219   6.3460   1.3812  -0.8520
 2YS  H32  H   HCH3  0   0.234   6.4893  -0.3434  -0.5553
 2YS  H33  H   HCH3  0   0.230   5.0902   0.2800  -1.4185
 2YS  H34  H   HCH3  0   0.223   5.5615   0.9212   2.8386
 2YS  H35  H   HCH3  0   0.225   6.7687   0.0168   1.9264
 2YS  H36  H   HCH3  0   0.222   6.6347   1.7646   1.7232
 2YS  H28  H   HNH1  0   0.397   2.1588   0.0689   1.1135
 2YS  H4   H   HCH1  0   0.273   0.7465   0.6110  -1.4034
 2YS  H1   H   HCH2  0   0.241   2.4418  -1.2117  -1.7373
 2YS  H2   H   HCH2  0   0.238   1.6761  -2.1422  -0.4610
 2YS  H20  H   HCH1  0   0.215  -0.4299  -2.2365  -1.8549
 2YS  H14  H   HCH3  0   0.223   1.3225  -0.9255  -3.9861
 2YS  H15  H   HCH3  0   0.236  -0.2594  -1.6523  -4.2737
 2YS  H16  H   HCH3  0   0.221  -0.1231  -0.2128  -3.2809
 2YS  H17  H   HCH3  0   0.229   1.2041  -4.0879  -1.8701
 2YS  H18  H   HCH3  0   0.230   0.4647  -3.8933  -3.4586
 2YS  H19  H   HCH3  0   0.217   2.1035  -3.3076  -3.1710
 2YS  H3   H   HCH1  0   0.225  -3.3214  -1.5254  -1.3663
 2YS  H5   H   HCH2  0   0.215  -4.1899   3.5770  -0.3778
 2YS  H6   H   HCH2  0   0.213  -4.8247   3.1190   1.1924
 2YS  H7   H   HCH1  0   0.260  -2.5379  -0.4622   1.3779
 2YS  H9   H   HCH2  0   0.240  -4.5351   0.7539   0.5934
 2YS  H10  H   HCH2  0   0.220  -2.0263   2.4400   0.1829
 2YS  H11  H   HCH2  0   0.218  -2.6676   1.9875   1.7482
 2YS  H12  H   HCH2  0   0.187  -2.9506   4.4040   2.2810
 2YS  H13  H   HCH2  0   0.212  -2.4083   4.9093   0.6924
 2YS  H21  H   HNH1  0   0.401  -1.4154   0.2794  -1.2442
 2YS  H22  H   HNH2  0   0.337  -5.0254   5.5370   1.8162
 2YS  H23  H   HNH2  0   0.345  -3.8091   6.5690   1.5948
 2YS  H27  H   HOH1  0   0.463  -5.2645  -1.1420  -0.3298
 2YS  H25  H   HCH2  0   0.283  -1.5589  -2.7538  -0.0345
 2YS  H26  H   HCH2  0   0.295  -2.7470  -2.9879   1.2529
 2YS  H8   H   HCH2  0   0.231  -3.7719   1.0742  -0.9530

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
 2YS  C3   C2   single  1.527  0.020  1.527
 2YS  C15  C14  single  1.515  0.020  1.515
 2YS  O16  C14  single  1.403  0.020  1.403
 2YS  C2   C4   single  1.530  0.020  1.530
 2YS  C2   C1   single  1.526  0.020  1.526
 2YS  C4   C5   single  1.537  0.020  1.537
 2YS  O17  C6   double  1.222  0.020  1.222
 2YS  C14  C8   single  1.547  0.020  1.547
 2YS  C6   C5   single  1.524  0.020  1.524
 2YS  C6   N7   single  1.341  0.020  1.341
 2YS  C22  C21  single  1.526  0.020  1.526
 2YS  C5   N18  single  1.444  0.020  1.444
 2YS  C8   N7   single  1.451  0.020  1.451
 2YS  C8   C9   single  1.527  0.020  1.527
 2YS  N18  C19  single  1.346  0.020  1.346
 2YS  C23  C21  single  1.524  0.020  1.524
 2YS  C21  C20  single  1.544  0.020  1.544
 2YS  C9   C10  single  1.524  0.020  1.524
 2YS  C19  C20  single  1.532  0.020  1.532
 2YS  C19  O25  double  1.223  0.020  1.223
 2YS  C20  N24  single  1.445  0.020  1.445
 2YS  C11  C10  single  1.524  0.020  1.524
 2YS  C11  C12  single  1.521  0.020  1.521
 2YS  C12  N13  single  1.457  0.020  1.457
 2YS  C15  CL1  single  1.796  0.020  1.796
 2YS  C4   H1   single  0.970  0.020  1.090
 2YS  C4   H2   single  0.970  0.020  1.090
 2YS  C14  H3   single  0.970  0.020  1.090
 2YS  C5   H4   single  0.970  0.020  1.090
 2YS  C11  H5   single  0.970  0.020  1.090
 2YS  C11  H6   single  0.970  0.020  1.090
 2YS  C8   H7   single  0.970  0.020  1.090
 2YS  C9   H8   single  0.970  0.020  1.090
 2YS  C9   H9   single  0.970  0.020  1.090
 2YS  C10  H10  single  0.970  0.020  1.090
 2YS  C10  H11  single  0.970  0.020  1.090
 2YS  C12  H12  single  0.970  0.020  1.090
 2YS  C12  H13  single  0.970  0.020  1.090
 2YS  C3   H14  single  0.970  0.020  1.090
 2YS  C3   H15  single  0.970  0.020  1.090
 2YS  C3   H16  single  0.970  0.020  1.090
 2YS  C1   H17  single  0.970  0.020  1.090
 2YS  C1   H18  single  0.970  0.020  1.090
 2YS  C1   H19  single  0.970  0.020  1.090
 2YS  C2   H20  single  0.970  0.020  1.090
 2YS  N7   H21  single  0.860  0.020  1.020
 2YS  N13  H22  single  0.890  0.020  1.040
 2YS  N13  H23  single  0.890  0.020  1.040
 2YS  C15  H25  single  0.970  0.020  1.090
 2YS  C15  H26  single  0.970  0.020  1.090
 2YS  O16  H27  single  0.850  0.020  0.980
 2YS  N18  H28  single  0.860  0.020  1.020
 2YS  C20  H29  single  0.970  0.020  1.090
 2YS  C21  H30  single  0.970  0.020  1.090
 2YS  C22  H31  single  0.970  0.020  1.090
 2YS  C22  H32  single  0.970  0.020  1.090
 2YS  C22  H33  single  0.970  0.020  1.090
 2YS  C23  H34  single  0.970  0.020  1.090
 2YS  C23  H35  single  0.970  0.020  1.090
 2YS  C23  H36  single  0.970  0.020  1.090
 2YS  N24  H37  single  0.890  0.020  1.040
 2YS  N24  H38  single  0.890  0.020  1.040

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
 2YS  H38  N24  H37  105.57  3.000
 2YS  H38  N24  C20  109.77  3.000
 2YS  H37  N24  C20  109.81  3.000
 2YS  H29  C20  C19  107.78  3.000
 2YS  H29  C20  C21  106.83  3.000
 2YS  C19  C20  C21  109.70  3.000
 2YS  H29  C20  N24  107.63  3.000
 2YS  C19  C20  N24  113.30  3.000
 2YS  C21  C20  N24  111.32  3.000
 2YS  H30  C21  C23  107.47  3.000
 2YS  H30  C21  C22  107.78  3.000
 2YS  C23  C21  C22  110.92  3.000
 2YS  H30  C21  C20  107.13  3.000
 2YS  C23  C21  C20  110.56  3.000
 2YS  C22  C21  C20  112.73  3.000
 2YS  H33  C22  H32  107.40  3.000
 2YS  H33  C22  H31  107.79  3.000
 2YS  H32  C22  H31  107.12  3.000
 2YS  H33  C22  C21  112.53  3.000
 2YS  H32  C22  C21  110.18  3.000
 2YS  H31  C22  C21  111.58  3.000
 2YS  H36  C23  H35  108.03  3.000
 2YS  H36  C23  H34  107.82  3.000
 2YS  H35  C23  H34  107.71  3.000
 2YS  H36  C23  C21  111.20  3.000
 2YS  H35  C23  C21  110.63  3.000
 2YS  H34  C23  C21  111.30  3.000
 2YS  N18  C19  O25  122.95  3.000
 2YS  O25  C19  C20  122.23  3.000
 2YS  N18  C19  C20  114.81  3.000
 2YS  H28  N18  C5   117.08  3.000
 2YS  H28  N18  C19  119.05  3.000
 2YS  C5   N18  C19  123.33  3.000
 2YS  H4   C5   C4   109.92  3.000
 2YS  H4   C5   C6   110.56  3.000
 2YS  C4   C5   C6   110.24  3.000
 2YS  H4   C5   N18  107.14  3.000
 2YS  C6   C5   N18  108.09  3.000
 2YS  C4   C5   N18  110.83  3.000
 2YS  N7   C6   O17  123.94  3.000
 2YS  N7   C6   C5   115.20  3.000
 2YS  O17  C6   C5   120.82  3.000
 2YS  H2   C4   H1   106.60  3.000
 2YS  H2   C4   C2   109.61  3.000
 2YS  H1   C4   C2   108.47  3.000
 2YS  H2   C4   C5   108.25  3.000
 2YS  H1   C4   C5   107.23  3.000
 2YS  C2   C4   C5   116.24  3.000
 2YS  H20  C2   C1   107.22  3.000
 2YS  H20  C2   C3   108.05  3.000
 2YS  C1   C2   C3   110.43  3.000
 2YS  H20  C2   C4   109.35  3.000
 2YS  C1   C2   C4   109.52  3.000
 2YS  C3   C2   C4   112.13  3.000
 2YS  H16  C3   H15  107.00  3.000
 2YS  H16  C3   H14  107.34  3.000
 2YS  H15  C3   H14  107.83  3.000
 2YS  H16  C3   C2   112.87  3.000
 2YS  H15  C3   C2   110.87  3.000
 2YS  H14  C3   C2   110.70  3.000
 2YS  H19  C1   H18  107.77  3.000
 2YS  H19  C1   H17  107.72  3.000
 2YS  H18  C1   H17  107.79  3.000
 2YS  H19  C1   C2   110.99  3.000
 2YS  H18  C1   C2   111.01  3.000
 2YS  H17  C1   C2   111.39  3.000
 2YS  H3   C14  C15  108.87  3.000
 2YS  H3   C14  O16  111.26  3.000
 2YS  C15  C14  O16  106.91  3.000
 2YS  H3   C14  C8   107.54  3.000
 2YS  O16  C14  C8   112.27  3.000
 2YS  C15  C14  C8   109.95  3.000
 2YS  H6   C11  H5   106.45  3.000
 2YS  H6   C11  C12  109.36  3.000
 2YS  H5   C11  C12  109.04  3.000
 2YS  H6   C11  C10  109.21  3.000
 2YS  H5   C11  C10  109.96  3.000
 2YS  C12  C11  C10  112.64  3.000
 2YS  H7   C8   N7   107.65  3.000
 2YS  H7   C8   C9   108.47  3.000
 2YS  N7   C8   C9   109.80  3.000
 2YS  H7   C8   C14  109.08  3.000
 2YS  C9   C8   C14  112.30  3.000
 2YS  N7   C8   C14  109.42  3.000
 2YS  H9   C9   H8   106.52  3.000
 2YS  H9   C9   C10  108.45  3.000
 2YS  H8   C9   C10  109.98  3.000
 2YS  H9   C9   C8   108.44  3.000
 2YS  H8   C9   C8   109.85  3.000
 2YS  C10  C9   C8   113.34  3.000
 2YS  H11  C10  H10  106.26  3.000
 2YS  H11  C10  C9   109.08  3.000
 2YS  H10  C10  C9   110.42  3.000
 2YS  H11  C10  C11  109.43  3.000
 2YS  H10  C10  C11  109.21  3.000
 2YS  C9   C10  C11  112.26  3.000
 2YS  H13  C12  H12  106.10  3.000
 2YS  H13  C12  N13  108.26  3.000
 2YS  H12  C12  N13  113.41  3.000
 2YS  H13  C12  C11  109.03  3.000
 2YS  H12  C12  C11  108.85  3.000
 2YS  N13  C12  C11  111.00  3.000
 2YS  H21  N7   C8   116.73  3.000
 2YS  H21  N7   C6   117.94  3.000
 2YS  C8   N7   C6   125.23  3.000
 2YS  H23  N13  H22  105.35  3.000
 2YS  H23  N13  C12  109.42  3.000
 2YS  H22  N13  C12  108.98  3.000
 2YS  H27  O16  C14  109.12  3.000
 2YS  H26  C15  H25  108.72  3.000
 2YS  H26  C15  CL1  107.39  3.000
 2YS  H25  C15  CL1  106.68  3.000
 2YS  H26  C15  C14  110.98  3.000
 2YS  H25  C15  C14  111.99  3.000
 2YS  CL1  C15  C14  110.87  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
 2YS  CONST_01  C5   N18  C19  C20   180.00   0.0  0
 2YS  CONST_02  C5   N18  C19  O25     0.00   0.0  0
 2YS  CONST_03  C8   N7   C6   C5    180.00   0.0  0
 2YS  CONST_04  C8   N7   C6   O17     0.00   0.0  0
 2YS  CONST_05  H28  N18  C19  C20     0.00   0.0  0
 2YS  CONST_06  H21  N7   C6   C5      0.00   0.0  0
 2YS  Var_01    C3   C2   C4   C5     63.08  30.0  1
 2YS  Var_02    C8   C9   C10  C11  -172.82  30.0  1
 2YS  Var_03    C12  C11  C10  C9    179.39  30.0  1
 2YS  Var_04    N13  C12  C11  C10  -179.46  30.0  3
 2YS  Var_05    H31  C22  C21  C20    63.21  30.0  3
 2YS  Var_06    H34  C23  C21  C20    56.13  30.0  3
 2YS  Var_07    H14  C3   C2   C4     57.48  30.0  3
 2YS  Var_08    H17  C1   C2   C4     59.23  30.0  3
 2YS  Var_09    H22  N13  C12  C11    66.64  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
 2YS  chir_01  C20  C21  C19  N24  positiv
 2YS  chir_02  C5   N18  C6   C4   positiv
 2YS  chir_03  C14  O16  C15  C8   positiv
 2YS  chir_04  C8   N7   C9   C14  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
 2YS  plan-1  C20  0.020
 2YS  plan-1  C19  0.020
 2YS  plan-1  O25  0.020
 2YS  plan-1  N18  0.020
 2YS  plan-1  C5   0.020
 2YS  plan-1  H28  0.020
 2YS  plan-2  C5   0.020
 2YS  plan-2  C6   0.020
 2YS  plan-2  O17  0.020
 2YS  plan-2  C8   0.020
 2YS  plan-2  N7   0.020
 2YS  plan-2  H21  0.020

