# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:19:20 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CCl)[C@H](Cc1ccccc1)NC(=O)CNC(=O)CNC(=O)OCc2ccccc2
#
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
 Y3A  Y3A  N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide  ligand  57  31  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y3A
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
 Y3A  C23   C   C     0   0.768   4.5503   0.1624   1.3363
 Y3A  O41   O   O     0  -0.525   4.5335   0.0141   2.5425
 Y3A  O5    O   O2    0  -0.481   5.6677   0.2544   0.6064
 Y3A  C16   C   CH2   0  -0.239   6.9116   0.1329   1.3051
 Y3A  C20   C   CR6   0   0.075   7.9958   0.1575   0.2709
 Y3A  C19   C   CR16  0  -0.284   8.2754  -0.9834  -0.4780
 Y3A  C18   C   CR16  0  -0.242   9.2611  -0.9615  -1.4536
 Y3A  C17   C   CR16  0  -0.262   9.9801   0.2045  -1.6900
 Y3A  C22   C   CR16  0  -0.242   9.7091   1.3451  -0.9471
 Y3A  C21   C   CR16  0  -0.296   8.7189   1.3202   0.0273
 Y3A  N31   N   NH1   0  -0.672   3.4602   0.2542   0.5616
 Y3A  C14   C   CH2   0  -0.366   2.1370   0.1734   1.1091
 Y3A  C13   C   C     0   0.531   1.1237   0.2123  -0.0221
 Y3A  O31   O   O     0  -0.491   1.4534   0.3881  -1.1861
 Y3A  N3    N   NH1   0  -0.645  -0.1442   0.0427   0.3623
 Y3A  CA3   C   CH2   0  -0.379  -1.2315   0.0522  -0.5755
 Y3A  C3    C   C     0   0.530  -2.5304  -0.2848   0.1353
 Y3A  O3    O   O     0  -0.467  -2.6080  -0.3392   1.3495
 Y3A  C4    C   CH1   0   0.075  -5.5078  -1.9325  -0.8870
 Y3A  O4    O   OH1   0  -0.656  -4.7390  -3.0324  -0.4833
 Y3A  CA4   C   CH1   0  -0.109  -4.9410  -0.6263  -0.2980
 Y3A  N4    N   NH1   0  -0.655  -3.5562  -0.5117  -0.7058
 Y3A  CB4   C   CH2   0  -0.557  -5.7199   0.6269  -0.7226
 Y3A  CG4   C   CR6   0   0.157  -5.0932   1.8757  -0.1705
 Y3A  CD1   C   CR16  0  -0.318  -4.1855   2.6159  -0.9238
 Y3A  CD2   C   CR16  0  -0.295  -5.3699   2.2878   1.1308
 Y3A  CE1   C   CR16  0  -0.240  -3.5643   3.7376  -0.3897
 Y3A  CE2   C   CR16  0  -0.241  -4.7552   3.4099   1.6678
 Y3A  CZ4   C   CR16  0  -0.271  -3.8471   4.1379   0.9091
 Y3A  H21   H   HCH2  0   0.248   7.0307   0.9566   2.0120
 Y3A  H22   H   HCH2  0   0.247   6.9352  -0.8021   1.8689
 Y3A  H25   H   HCR6  0   0.255   7.7227  -1.8971  -0.2927
 Y3A  H24   H   HCR6  0   0.258   9.4715  -1.8543  -2.0282
 Y3A  H23   H   HCR6  0   0.259  10.7516   0.2213  -2.4487
 Y3A  H27   H   HCR6  0   0.258  10.2681   2.2549  -1.1241
 Y3A  H26   H   HCR6  0   0.255   8.5110   2.2128   0.6055
 Y3A  H20   H   HNH1  0   0.402   3.5474   0.3705  -0.4371
 Y3A  H18   H   HCH2  0   0.278   1.9995  -0.7472   1.6833
 Y3A  H19   H   HCH2  0   0.281   1.9316   1.0036   1.7928
 Y3A  HN3   H   HNH1  0   0.409  -0.3724  -0.0926   1.3364
 Y3A  HA3   H   HCH2  0   0.281  -1.3410   1.0357  -1.0463
 Y3A  HA3A  H   HCH2  0   0.282  -1.0587  -0.6653  -1.3812
 Y3A  HO4   H   HOH1  0   0.454  -3.8370  -2.8975  -0.7927
 Y3A  HA4   H   HCH1  0   0.274  -4.9538  -0.7051   0.7911
 Y3A  HN4   H   HNH1  0   0.407  -3.3880  -0.3744  -1.6929
 Y3A  HB4   H   HCH2  0   0.259  -5.7615   0.6751  -1.8147
 Y3A  HB4A  H   HCH2  0   0.268  -6.7506   0.5468  -0.3730
 Y3A  HD1   H   HCR6  0   0.249  -3.9648   2.3184  -1.9426
 Y3A  HD2   H   HCR6  0   0.246  -6.0752   1.7254   1.7322
 Y3A  HE1   H   HCR6  0   0.254  -2.8616   4.2996  -0.9914
 Y3A  HE2   H   HCR6  0   0.254  -4.9852   3.7162   2.6803
 Y3A  HZ4   H   HCR6  0   0.253  -3.3662   5.0131   1.3266
 Y3A  H4    H   HCH1  0   0.222  -5.5224  -1.8347  -1.9834
 Y3A  C15   C   CH2   0  -0.485  -6.9254  -2.1697  -0.4119
 Y3A  CL1   CL  CL    0  -0.160  -7.5868  -3.6856  -1.1105
 Y3A  H15   H   HCH2  0   0.289  -6.9718  -2.2664   0.6723
 Y3A  H15A  H   HCH2  0   0.298  -7.5904  -1.3705  -0.7255

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
 Y3A  N3   CA3   single    1.436  0.020  1.436
 Y3A  CA3  C3    single    1.519  0.020  1.519
 Y3A  C3   O3    double    1.218  0.020  1.218
 Y3A  C3   N4    single    1.346  0.020  1.346
 Y3A  C4   O4    single    1.401  0.020  1.401
 Y3A  C4   CA4   single    1.541  0.020  1.541
 Y3A  C4   C15   single    1.514  0.020  1.514
 Y3A  CA4  N4    single    1.448  0.020  1.448
 Y3A  CA4  CB4   single    1.535  0.020  1.535
 Y3A  CB4  CG4   single    1.502  0.020  1.502
 Y3A  CG4  CD1   aromatic  1.393  0.020  1.393
 Y3A  CG4  CD2   aromatic  1.393  0.020  1.393
 Y3A  CD1  CE1   aromatic  1.389  0.020  1.389
 Y3A  CD2  CE2   aromatic  1.388  0.020  1.388
 Y3A  CE1  CZ4   aromatic  1.388  0.020  1.388
 Y3A  CE2  CZ4   aromatic  1.389  0.020  1.389
 Y3A  N3   C13   single    1.336  0.020  1.336
 Y3A  C13  C14   single    1.519  0.020  1.519
 Y3A  C13  O31   double    1.222  0.020  1.222
 Y3A  C14  N31   single    1.434  0.020  1.434
 Y3A  N31  C23   single    1.341  0.020  1.341
 Y3A  C23  O41   double    1.215  0.020  1.215
 Y3A  C23  O5    single    1.338  0.020  1.338
 Y3A  O5   C16   single    1.432  0.020  1.432
 Y3A  C17  C18   aromatic  1.390  0.020  1.390
 Y3A  C18  C19   aromatic  1.387  0.020  1.387
 Y3A  C19  C20   aromatic  1.393  0.020  1.393
 Y3A  C20  C21   aromatic  1.391  0.020  1.391
 Y3A  C21  C22   aromatic  1.389  0.020  1.389
 Y3A  C17  C22   aromatic  1.388  0.020  1.388
 Y3A  C20  C16   single    1.499  0.020  1.499
 Y3A  N3   HN3   single    0.860  0.020  1.020
 Y3A  CA3  HA3   single    0.970  0.020  1.090
 Y3A  CA3  HA3A  single    0.970  0.020  1.090
 Y3A  C4   H4    single    0.970  0.020  1.090
 Y3A  O4   HO4   single    0.850  0.020  0.980
 Y3A  CA4  HA4   single    0.970  0.020  1.090
 Y3A  N4   HN4   single    0.860  0.020  1.020
 Y3A  CB4  HB4   single    0.970  0.020  1.090
 Y3A  CB4  HB4A  single    0.970  0.020  1.090
 Y3A  CD1  HD1   single    0.930  0.020  1.080
 Y3A  CD2  HD2   single    0.930  0.020  1.080
 Y3A  CE1  HE1   single    0.930  0.020  1.080
 Y3A  CE2  HE2   single    0.930  0.020  1.080
 Y3A  CZ4  HZ4   single    0.930  0.020  1.080
 Y3A  C15  H15   single    0.970  0.020  1.090
 Y3A  C15  H15A  single    0.970  0.020  1.090
 Y3A  C15  CL1   single    1.795  0.020  1.795
 Y3A  C14  H18   single    0.970  0.020  1.090
 Y3A  C14  H19   single    0.970  0.020  1.090
 Y3A  N31  H20   single    0.860  0.020  1.020
 Y3A  C16  H21   single    0.970  0.020  1.090
 Y3A  C16  H22   single    0.970  0.020  1.090
 Y3A  C17  H23   single    0.930  0.020  1.080
 Y3A  C18  H24   single    0.930  0.020  1.080
 Y3A  C19  H25   single    0.930  0.020  1.080
 Y3A  C21  H26   single    0.930  0.020  1.080
 Y3A  C22  H27   single    0.930  0.020  1.080

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
 Y3A  N31   C23  O5   111.05  3.000
 Y3A  O5    C23  O41  124.15  3.000
 Y3A  N31   C23  O41  124.80  3.000
 Y3A  C16   O5   C23  116.97  3.000
 Y3A  H22   C16  H21  108.02  3.000
 Y3A  H22   C16  C20  110.77  3.000
 Y3A  H21   C16  C20  110.82  3.000
 Y3A  H22   C16  O5   110.08  3.000
 Y3A  H21   C16  O5   110.29  3.000
 Y3A  C20   C16  O5   106.88  3.000
 Y3A  C21   C20  C19  119.09  3.000
 Y3A  C21   C20  C16  120.72  3.000
 Y3A  C19   C20  C16  120.19  3.000
 Y3A  H25   C19  C18  119.73  3.000
 Y3A  H25   C19  C20  119.74  3.000
 Y3A  C18   C19  C20  120.52  3.000
 Y3A  H24   C18  C17  120.07  3.000
 Y3A  H24   C18  C19  119.90  3.000
 Y3A  C17   C18  C19  120.03  3.000
 Y3A  H23   C17  C22  120.12  3.000
 Y3A  H23   C17  C18  120.06  3.000
 Y3A  C22   C17  C18  119.82  3.000
 Y3A  H27   C22  C21  119.86  3.000
 Y3A  H27   C22  C17  120.15  3.000
 Y3A  C21   C22  C17  119.98  3.000
 Y3A  H26   C21  C22  119.74  3.000
 Y3A  H26   C21  C20  119.70  3.000
 Y3A  C22   C21  C20  120.56  3.000
 Y3A  H20   N31  C14  117.64  3.000
 Y3A  H20   N31  C23  120.64  3.000
 Y3A  C14   N31  C23  121.72  3.000
 Y3A  H19   C14  H18  106.66  3.000
 Y3A  H19   C14  C13  108.69  3.000
 Y3A  H18   C14  C13  109.19  3.000
 Y3A  H19   C14  N31  111.64  3.000
 Y3A  H18   C14  N31  111.34  3.000
 Y3A  C13   C14  N31  109.25  3.000
 Y3A  N3    C13  O31  123.25  3.000
 Y3A  O31   C13  C14  122.19  3.000
 Y3A  N3    C13  C14  114.56  3.000
 Y3A  HN3   N3   CA3  117.38  3.000
 Y3A  HN3   N3   C13  120.62  3.000
 Y3A  CA3   N3   C13  122.00  3.000
 Y3A  HA3A  CA3  HA3  106.76  3.000
 Y3A  HA3A  CA3  C3   109.55  3.000
 Y3A  HA3   CA3  C3   108.35  3.000
 Y3A  HA3A  CA3  N3   110.95  3.000
 Y3A  HA3   CA3  N3   111.24  3.000
 Y3A  C3    CA3  N3   109.91  3.000
 Y3A  N4    C3   O3   124.54  3.000
 Y3A  N4    C3   CA3  113.38  3.000
 Y3A  O3    C3   CA3  122.07  3.000
 Y3A  H4    C4   C15  108.31  3.000
 Y3A  H4    C4   CA4  108.08  3.000
 Y3A  C15   C4   CA4  110.94  3.000
 Y3A  H4    C4   O4   111.34  3.000
 Y3A  C15   C4   O4   107.48  3.000
 Y3A  CA4   C4   O4   110.70  3.000
 Y3A  HO4   O4   C4   108.14  3.000
 Y3A  HA4   CA4  CB4  109.19  3.000
 Y3A  HA4   CA4  N4   107.32  3.000
 Y3A  CB4   CA4  N4   110.04  3.000
 Y3A  HA4   CA4  C4   108.41  3.000
 Y3A  CB4   CA4  C4   113.55  3.000
 Y3A  N4    CA4  C4   108.13  3.000
 Y3A  HN4   N4   CA4  116.42  3.000
 Y3A  HN4   N4   C3   117.43  3.000
 Y3A  CA4   N4   C3   124.49  3.000
 Y3A  HB4A  CB4  HB4  106.69  3.000
 Y3A  HB4A  CB4  CG4  109.71  3.000
 Y3A  HB4   CB4  CG4  110.25  3.000
 Y3A  HB4A  CB4  CA4  109.31  3.000
 Y3A  HB4   CB4  CA4  109.35  3.000
 Y3A  CG4   CB4  CA4  111.42  3.000
 Y3A  CD2   CG4  CD1  118.54  3.000
 Y3A  CD2   CG4  CB4  120.42  3.000
 Y3A  CD1   CG4  CB4  120.99  3.000
 Y3A  HD1   CD1  CE1  119.47  3.000
 Y3A  HD1   CD1  CG4  119.68  3.000
 Y3A  CE1   CD1  CG4  120.84  3.000
 Y3A  HD2   CD2  CE2  119.54  3.000
 Y3A  HD2   CD2  CG4  119.61  3.000
 Y3A  CE2   CD2  CG4  120.85  3.000
 Y3A  HE1   CE1  CZ4  120.17  3.000
 Y3A  HE1   CE1  CD1  119.72  3.000
 Y3A  CZ4   CE1  CD1  120.10  3.000
 Y3A  HE2   CE2  CZ4  120.10  3.000
 Y3A  HE2   CE2  CD2  119.77  3.000
 Y3A  CZ4   CE2  CD2  120.13  3.000
 Y3A  HZ4   CZ4  CE2  120.23  3.000
 Y3A  HZ4   CZ4  CE1  120.24  3.000
 Y3A  CE2   CZ4  CE1  119.54  3.000
 Y3A  H15A  C15  H15  109.06  3.000
 Y3A  H15A  C15  CL1  106.46  3.000
 Y3A  H15   C15  CL1  107.26  3.000
 Y3A  CL1   C15  C4   110.80  3.000
 Y3A  H15A  C15  C4   111.56  3.000
 Y3A  H15   C15  C4   111.48  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
 Y3A  CONST_01  C17  C18  C19  C20     0.00   0.0  0
 Y3A  CONST_02  C17  C22  C21  C20     0.00   0.0  0
 Y3A  CONST_03  C22  C17  C18  C19     0.00   0.0  0
 Y3A  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 Y3A  CONST_05  C21  C22  C17  C18     0.00   0.0  0
 Y3A  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 Y3A  CONST_07  CZ4  CE1  CD1  CG4     0.00   0.0  0
 Y3A  CONST_08  CZ4  CE2  CD2  CG4     0.00   0.0  0
 Y3A  CONST_09  CE2  CD2  CG4  CD1     0.00   0.0  0
 Y3A  CONST_10  CE2  CZ4  CE1  CD1     0.00   0.0  0
 Y3A  CONST_11  CE1  CD1  CG4  CD2     0.00   0.0  0
 Y3A  CONST_12  CE1  CZ4  CE2  CD2     0.00   0.0  0
 Y3A  CONST_13  C18  C19  C20  C16   180.00   0.0  0
 Y3A  CONST_14  C22  C21  C20  C16   180.00   0.0  0
 Y3A  CONST_15  CE1  CD1  CG4  CB4   180.00   0.0  0
 Y3A  CONST_16  CE2  CD2  CG4  CB4   180.00   0.0  0
 Y3A  CONST_17  H24  C18  C19  C20   180.00   0.0  0
 Y3A  CONST_18  H27  C22  C21  C20   180.00   0.0  0
 Y3A  CONST_19  H23  C17  C18  C19   180.00   0.0  0
 Y3A  CONST_20  H26  C21  C20  C19   180.00   0.0  0
 Y3A  CONST_21  H25  C19  C18  C17   180.00   0.0  0
 Y3A  CONST_22  HE1  CE1  CD1  CG4   180.00   0.0  0
 Y3A  CONST_23  HE2  CE2  CD2  CG4   180.00   0.0  0
 Y3A  CONST_24  HD2  CD2  CG4  CD1   180.00   0.0  0
 Y3A  CONST_25  HZ4  CZ4  CE1  CD1   180.00   0.0  0
 Y3A  CONST_26  HD1  CD1  CG4  CD2   180.00   0.0  0
 Y3A  CONST_27  CA3  N3   C13  C14   180.00   0.0  0
 Y3A  CONST_28  CA3  N3   C13  O31     0.00   0.0  0
 Y3A  CONST_29  CA4  N4   C3   CA3   180.00   0.0  0
 Y3A  CONST_30  CA4  N4   C3   O3      0.00   0.0  0
 Y3A  CONST_31  HN3  N3   C13  C14     0.00   0.0  0
 Y3A  CONST_32  HN4  N4   C3   CA3     0.00   0.0  0
 Y3A  Var_01    C19  C20  C16  O5    -78.53  30.0  3
 Y3A  Var_02    CD1  CG4  CB4  CA4    94.65  30.0  2
 Y3A  Var_03    C20  C16  O5   C23   175.53  30.0  3
 Y3A  Var_04    C13  C14  N31  C23  -176.06  30.0  1
 Y3A  Var_05    C14  N31  C23  O41    -0.43  30.0  2
 Y3A  Var_06    N31  C23  O5   C16  -178.25  30.0  2
 Y3A  Var_07    N3   C13  C14  N31   175.23  30.0  1
 Y3A  Var_08    C3   CA3  N3   C13   175.06  30.0  3
 Y3A  Var_09    O3   C3   CA3  N3     10.22  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
 Y3A  chir_01  C4   O4  CA4  C15  positiv
 Y3A  chir_02  CA4  N4  CB4  C4   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
 Y3A  plan-1  C16  0.020
 Y3A  plan-1  C20  0.020
 Y3A  plan-1  C19  0.020
 Y3A  plan-1  C18  0.020
 Y3A  plan-1  C17  0.020
 Y3A  plan-1  C22  0.020
 Y3A  plan-1  C21  0.020
 Y3A  plan-1  H25  0.020
 Y3A  plan-1  H24  0.020
 Y3A  plan-1  H23  0.020
 Y3A  plan-1  H27  0.020
 Y3A  plan-1  H26  0.020
 Y3A  plan-2  CB4  0.020
 Y3A  plan-2  CG4  0.020
 Y3A  plan-2  CD1  0.020
 Y3A  plan-2  CD2  0.020
 Y3A  plan-2  CE1  0.020
 Y3A  plan-2  CE2  0.020
 Y3A  plan-2  CZ4  0.020
 Y3A  plan-2  HD1  0.020
 Y3A  plan-2  HD2  0.020
 Y3A  plan-2  HE1  0.020
 Y3A  plan-2  HE2  0.020
 Y3A  plan-2  HZ4  0.020
 Y3A  plan-3  C14  0.020
 Y3A  plan-3  C13  0.020
 Y3A  plan-3  O31  0.020
 Y3A  plan-3  N3   0.020
 Y3A  plan-3  CA3  0.020
 Y3A  plan-3  HN3  0.020
 Y3A  plan-4  CA3  0.020
 Y3A  plan-4  C3   0.020
 Y3A  plan-4  O3   0.020
 Y3A  plan-4  CA4  0.020
 Y3A  plan-4  N4   0.020
 Y3A  plan-4  HN4  0.020
 Y3A  plan-5  C23  0.020
 Y3A  plan-5  O41  0.020
 Y3A  plan-5  O5   0.020
 Y3A  plan-5  N31  0.020

