# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:08:24 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-[[(3~{S})-3-acetamido-4-[[(2~{R})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@H](CCNCC(O)=O)NC(C)=O)C(=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
 HWX  HWX  "2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]amino]ethanoic acid"  ligand  40  21  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HWX
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
 HWX  C4   C  C      0   0.565  46.9486  149.2896  -1.3459
 HWX  C5   C  CH1    0  -0.203  47.3722  149.7043  -3.7197
 HWX  C11  C  CH3    0  -0.651  46.2199  150.5980  -4.1831
 HWX  C7   C  CH2    0  -0.401  43.3867  146.5999   2.6025
 HWX  C8   C  C      0   0.390  43.5405  146.8791   4.1110
 HWX  C12  C  C      0   0.522  47.8035  148.8037  -4.8705
 HWX  C13  C  CH3    0  -0.782  47.8630  148.3353   3.1268
 HWX  N1   N  NH1    0  -0.617  46.8115  148.6037   0.9811
 HWX  N2   N  NH1    0  -0.643  46.9986  148.8543  -2.6149
 HWX  C3   C  C      0   0.503  47.5902  147.8047   1.7422
 HWX  N3   N  NH1    0  -0.598  43.9615  147.6295   1.7671
 HWX  C1   C  CH2    0  -0.442  44.8427  148.2454  -0.4749
 HWX  O1   O  O      0  -0.485  47.9987  146.7158   1.3683
 HWX  C2   C  CH1    0  -0.224  46.3734  148.2808  -0.3503
 HWX  O3   O  O      0  -0.478  47.3024  150.4059  -1.0033
 HWX  N4   N  NH1    0  -0.372  48.7972  149.3227  -5.6080
 HWX  O8   O  O      0  -0.460  47.2748  147.7294  -5.0881
 HWX  O9   O  OH1    0  -0.537  49.1047  148.7716  -6.8148
 HWX  O2   O  OC    -1  -0.612  42.8057  146.2088   4.8605
 HWX  O4   O  O      0  -0.600  44.4045  147.7124   4.4549
 HWX  H1   H  HCH1   0   0.280  48.2088  150.3332  -3.4068
 HWX  H2   H  HCH2   0   0.222  43.1887  146.9740  -0.0318
 HWX  H3   H  HCH2   0   0.183  44.7400  146.2520   0.3365
 HWX  H4   H  HCH3   0   0.252  45.8955  151.2410  -3.3669
 HWX  H5   H  HCH3   0   0.242  46.5312  151.2360  -5.0104
 HWX  H6   H  HCH3   0   0.237  45.3712  149.9974  -4.5103
 HWX  H7   H  HCH2   0   0.208  42.3246  146.4801   2.3648
 HWX  H8   H  HCH2   0   0.186  43.8412  145.6085   2.4162
 HWX  H9   H  HCH3   0   0.259  48.8288  147.9838   3.4824
 HWX  H10  H  HCH3   0   0.250  47.8389  149.4230   3.1781
 HWX  H11  H  HCH3   0   0.269  47.0943  147.9555   3.8031
 HWX  H12  H  HNH1   0   0.399  46.5644  149.5130   1.3396
 HWX  H13  H  HNH1   0   0.404  46.6497  147.9347  -2.8438
 HWX  H14  H  HNH1   0   0.334  44.8338  147.9164   2.1874
 HWX  H16  H  HCH2   0   0.238  44.4254  149.2326  -0.2545
 HWX  H17  H  HCH2   0   0.247  44.5981  148.0304  -1.5173
 HWX  H18  H  HCH1   0   0.279  46.7590  147.2869  -0.5860
 HWX  H21  H  HNH1   0   0.420  49.1333  150.2666  -5.4744
 HWX  H20  H  HOH1   0   0.478  49.8762  148.2093  -6.6643
 HWX  C6   C  CH2    0  -0.264  44.1685  147.1950   0.4026

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
 HWX  O9   N4   single  1.362  0.020  1.362
 HWX  N4   C12  single  1.342  0.020  1.342
 HWX  O8   C12  double  1.217  0.020  1.217
 HWX  C12  C5   single  1.524  0.020  1.524
 HWX  C5   C11  single  1.530  0.020  1.530
 HWX  C5   N2   single  1.443  0.020  1.443
 HWX  N2   C4   single  1.343  0.020  1.343
 HWX  C4   O3   double  1.220  0.020  1.220
 HWX  C4   C2   single  1.530  0.020  1.530
 HWX  C1   C2   single  1.536  0.020  1.536
 HWX  C1   C6   single  1.526  0.020  1.526
 HWX  C2   N1   single  1.438  0.020  1.438
 HWX  C6   N3   single  1.447  0.020  1.447
 HWX  N1   C3   single  1.351  0.020  1.351
 HWX  N3   C7   single  1.445  0.020  1.445
 HWX  C3   O1   double  1.222  0.020  1.222
 HWX  C3   C13  single  1.508  0.020  1.508
 HWX  C7   C8   single  1.542  0.020  1.542
 HWX  O4   C8   deloc   1.249  0.020  1.249
 HWX  C8   O2   deloc   1.245  0.020  1.245
 HWX  C5   H1   single  0.970  0.020  1.090
 HWX  C6   H2   single  0.970  0.020  1.090
 HWX  C6   H3   single  0.970  0.020  1.090
 HWX  C11  H4   single  0.970  0.020  1.090
 HWX  C11  H5   single  0.970  0.020  1.090
 HWX  C11  H6   single  0.970  0.020  1.090
 HWX  C7   H7   single  0.970  0.020  1.090
 HWX  C7   H8   single  0.970  0.020  1.090
 HWX  C13  H9   single  0.970  0.020  1.090
 HWX  C13  H10  single  0.970  0.020  1.090
 HWX  C13  H11  single  0.970  0.020  1.090
 HWX  N1   H12  single  0.860  0.020  1.020
 HWX  N2   H13  single  0.860  0.020  1.020
 HWX  N3   H14  single  0.890  0.020  1.040
 HWX  C1   H16  single  0.970  0.020  1.090
 HWX  C1   H17  single  0.970  0.020  1.090
 HWX  C2   H18  single  0.970  0.020  1.090
 HWX  N4   H21  single  0.890  0.020  1.040
 HWX  O9   H20  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
 HWX  O3   C4   C2   121.98  3.000
 HWX  C2   C4   N2   114.54  3.000
 HWX  O3   C4   N2   123.46  3.000
 HWX  H1   C5   N2   108.55  3.000
 HWX  H1   C5   C12  109.86  3.000
 HWX  N2   C5   C12  107.66  3.000
 HWX  H1   C5   C11  109.10  3.000
 HWX  N2   C5   C11  112.39  3.000
 HWX  C12  C5   C11  109.25  3.000
 HWX  H6   C11  H5   108.48  3.000
 HWX  H6   C11  H4   108.58  3.000
 HWX  H5   C11  H4   107.97  3.000
 HWX  H6   C11  C5   110.82  3.000
 HWX  H5   C11  C5   110.89  3.000
 HWX  H4   C11  C5   110.02  3.000
 HWX  H8   C7   H7   105.30  3.000
 HWX  H8   C7   N3   112.19  3.000
 HWX  H7   C7   N3   109.77  3.000
 HWX  H8   C7   C8   106.62  3.000
 HWX  H7   C7   C8   109.21  3.000
 HWX  N3   C7   C8   113.38  3.000
 HWX  O4   C8   O2   126.99  3.000
 HWX  O2   C8   C7   115.63  3.000
 HWX  O4   C8   C7   117.34  3.000
 HWX  O8   C12  N4   124.39  3.000
 HWX  O8   C12  C5   122.27  3.000
 HWX  N4   C12  C5   113.34  3.000
 HWX  H11  C13  H10  107.62  3.000
 HWX  H11  C13  H9   108.08  3.000
 HWX  H10  C13  H9   109.09  3.000
 HWX  H11  C13  C3   108.60  3.000
 HWX  H10  C13  C3   112.99  3.000
 HWX  H9   C13  C3   110.31  3.000
 HWX  H12  N1   C2   117.19  3.000
 HWX  H12  N1   C3   118.33  3.000
 HWX  C2   N1   C3   124.36  3.000
 HWX  H13  N2   C5   116.89  3.000
 HWX  H13  N2   C4   119.78  3.000
 HWX  C5   N2   C4   122.84  3.000
 HWX  O1   C3   N1   123.21  3.000
 HWX  O1   C3   C13  122.29  3.000
 HWX  N1   C3   C13  114.43  3.000
 HWX  H14  N3   C7   107.78  3.000
 HWX  H14  N3   C6   110.75  3.000
 HWX  C7   N3   C6   112.84  3.000
 HWX  H17  C1   H16  106.53  3.000
 HWX  H17  C1   C2   107.77  3.000
 HWX  H16  C1   C2   110.05  3.000
 HWX  H17  C1   C6   108.33  3.000
 HWX  H16  C1   C6   109.68  3.000
 HWX  C2   C1   C6   114.17  3.000
 HWX  H18  C2   C1   108.27  3.000
 HWX  H18  C2   N1   107.25  3.000
 HWX  C1   C2   N1   112.57  3.000
 HWX  H18  C2   C4   109.09  3.000
 HWX  N1   C2   C4   109.87  3.000
 HWX  C1   C2   C4   109.70  3.000
 HWX  H21  N4   O9   114.83  3.000
 HWX  H21  N4   C12  122.32  3.000
 HWX  O9   N4   C12  119.85  3.000
 HWX  H20  O9   N4   106.12  3.000
 HWX  H3   C6   H2   105.49  3.000
 HWX  H3   C6   C1   108.95  3.000
 HWX  H2   C6   C1   107.84  3.000
 HWX  H3   C6   N3   112.75  3.000
 HWX  H2   C6   N3   107.87  3.000
 HWX  C1   C6   N3   113.50  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
 HWX  CONST_01  O9   N4   C12  C5    180.00   0.0  0
 HWX  CONST_02  O3   C4   N2   C5      0.00   0.0  0
 HWX  CONST_03  C2   C4   N2   C5    180.00   0.0  0
 HWX  CONST_04  C2   N1   C3   C13   180.00   0.0  0
 HWX  CONST_05  C2   N1   C3   O1      0.00   0.0  0
 HWX  CONST_06  O9   N4   C12  O8      0.00   0.0  0
 HWX  CONST_07  H21  N4   C12  C5      0.00   0.0  0
 HWX  CONST_08  H12  N1   C3   C13     0.00   0.0  0
 HWX  CONST_09  H12  N1   C3   O1    180.00   0.0  0
 HWX  CONST_10  H13  N2   C4   C2      0.00   0.0  0
 HWX  CONST_11  H13  N2   C4   O3    180.00   0.0  0
 HWX  CONST_12  H21  N4   C12  O8    180.00   0.0  0
 HWX  Var_01    C8   C7   N3   C6    162.96  30.0  3
 HWX  Var_02    C1   C6   N3   C7   -176.95  30.0  1
 HWX  Var_03    C2   C1   C6   N3     82.84  30.0  1
 HWX  Var_04    O4   C8   C7   N3    -18.37  30.0  3
 HWX  Var_05    O2   C8   C7   N3    163.73  30.0  3
 HWX  Var_06    H7   C7   N3   C6    -74.61  30.0  3
 HWX  Var_07    H8   C7   N3   C6     42.10  30.0  3
 HWX  Var_08    H2   C6   N3   C7     63.63  30.0  1
 HWX  Var_09    H3   C6   N3   C7    -52.45  30.0  1
 HWX  Var_10    H14  N3   C7   C8     40.36  30.0  1
 HWX  Var_11    H9   C13  C3   N1   -150.60  30.0  3
 HWX  Var_12    H10  C13  C3   N1    -28.20  30.0  3
 HWX  Var_13    H11  C13  C3   N1     91.12  30.0  3
 HWX  Var_14    H16  C1   C6   N3    -41.19  30.0  1
 HWX  Var_15    H17  C1   C6   N3   -157.09  30.0  1
 HWX  Var_16    H14  N3   C6   C1    -56.03  30.0  3
 HWX  Var_17    H9   C13  C3   O1     32.25  30.0  3
 HWX  Var_18    H10  C13  C3   O1    154.65  30.0  3
 HWX  Var_19    H11  C13  C3   O1    -86.03  30.0  3
 HWX  Var_20    H2   C6   C1   C2   -157.71  30.0  3
 HWX  Var_21    H3   C6   C1   C2    -43.68  30.0  3
 HWX  Var_22    H7   C7   C8   O2     40.98  30.0  2
 HWX  Var_23    H8   C7   C8   O2    -72.32  30.0  2
 HWX  Var_24    H7   C7   C8   O4   -141.11  30.0  2
 HWX  Var_25    H8   C7   C8   O4    105.58  30.0  2

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
 HWX  chir_01  C5  C12  C11  N2  negativ
 HWX  chir_02  C2  N1   C4   C1  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
 HWX  plan-1  C4   0.020
 HWX  plan-1  C5   0.020
 HWX  plan-1  N2   0.020
 HWX  plan-1  C2   0.020
 HWX  plan-1  O3   0.020
 HWX  plan-1  H13  0.020
 HWX  plan-2  C5   0.020
 HWX  plan-2  C12  0.020
 HWX  plan-2  N4   0.020
 HWX  plan-2  O8   0.020
 HWX  plan-2  O9   0.020
 HWX  plan-2  H21  0.020
 HWX  plan-3  C13  0.020
 HWX  plan-3  N1   0.020
 HWX  plan-3  C3   0.020
 HWX  plan-3  O1   0.020
 HWX  plan-3  C2   0.020
 HWX  plan-3  H12  0.020
 HWX  plan-4  C7   0.020
 HWX  plan-4  C8   0.020
 HWX  plan-4  O2   0.020
 HWX  plan-4  O4   0.020

