# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 02:40:13 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-[[(3~{S})-3-acetamido-4-[[(2~{R})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(phenylmethyl)amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@H](CCN(CC(O)=O)Cc1ccccc1)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
 HXF  HXF  "2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(phenylmethyl)amino]ethanoic acid"  ligand  53  28  .  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_HXF
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
 HXF  C4   C  C      0   0.545  37.1395  -29.9542   2.7974
 HXF  C5   C  CH1    0  -0.206  37.0403  -31.9928   4.0869
 HXF  C11  C  CH3    0  -0.686  36.0861  -33.1615   4.3004
 HXF  C7   C  CH2    0  -0.342  32.8932  -28.0192   4.4203
 HXF  C8   C  CH2    0  -0.432  33.4663  -26.3663   2.7913
 HXF  C9   C  C      0   0.405  32.2759  -26.4317   1.8078
 HXF  C10  C  CH3    0  -0.799  33.5856  -30.4777   0.0556
 HXF  C12  C  C      0   0.523  37.4688  -31.4225   5.4420
 HXF  N1   N  NH1    0  -0.671  35.1189  -29.2950   1.4910
 HXF  N2   N  NH1    0  -0.623  36.4184  -30.9714   3.2874
 HXF  C3   C  C      0   0.502  35.0006  -30.1616   0.4676
 HXF  C1   C  CH2    0  -0.494  36.2776  -27.6022   2.8271
 HXF  C2   C  CH1    0  -0.169  36.4045  -28.8843   1.9938
 HXF  O2   O  O      0  -0.494  35.9707  -30.6799  -0.0698
 HXF  O3   O  O      0  -0.494  38.3436  -29.8541   2.9901
 HXF  N4   N  NH1    0  -0.375  38.5432  -32.0501   5.9577
 HXF  O4   O  OC    -1  -0.608  31.8359  -25.3199   1.4585
 HXF  N5   N  NT     0  -0.431  33.8463  -27.6316   3.3921
 HXF  O5   O  O      0  -0.584  31.8813  -27.5499   1.4231
 HXF  O8   O  O      0  -0.457  36.8853  -30.5114   5.9947
 HXF  O9   O  OH1    0  -0.540  38.8741  -31.8605   7.2670
 HXF  C21  C  CR16   0  -0.311  33.1432  -30.0095   5.9572
 HXF  C23  C  CR6    0   0.111  32.8734  -29.5001   4.6925
 HXF  C31  C  CR16   0  -0.305  32.5200  -30.3866   3.6755
 HXF  C41  C  CR16   0  -0.245  32.4243  -31.7472   3.9221
 HXF  C51  C  CR16   0  -0.273  32.6798  -32.2447   5.1960
 HXF  C61  C  CR16   0  -0.242  33.0452  -31.3735   6.2113
 HXF  H1   H  HCH1   0   0.275  37.9247  -32.3599   3.5576
 HXF  H2   H  HCH2   0   0.241  35.3420  -28.5228   4.5295
 HXF  H3   H  HCH3   0   0.252  36.5726  -33.9517   4.8698
 HXF  H4   H  HCH3   0   0.257  35.1936  -32.8487   4.8407
 HXF  H5   H  HCH3   0   0.255  35.7806  -33.5772   3.3406
 HXF  H6   H  HCH2   0   0.217  33.0739  -27.4719   5.3590
 HXF  H7   H  HCH2   0   0.254  31.8976  -27.7278   4.0838
 HXF  H8   H  HCH2   0   0.244  34.3108  -25.9762   2.2181
 HXF  H9   H  HCH2   0   0.208  33.2602  -25.6016   3.5569
 HXF  H10  H  HCH3   0   0.264  33.2487  -31.3712   0.5855
 HXF  H11  H  HCH3   0   0.258  32.8922  -29.6698   0.2830
 HXF  H12  H  HCH3   0   0.259  33.5482  -30.6937  -1.0104
 HXF  H13  H  HNH1   0   0.434  34.3020  -28.8582   1.9256
 HXF  H14  H  HNH1   0   0.406  35.4147  -30.9717   3.1805
 HXF  H15  H  HCH2   0   0.261  37.2442  -27.4050   3.2929
 HXF  H16  H  HCH1   0   0.276  37.0703  -28.6607   1.1548
 HXF  H17  H  HNH1   0   0.415  38.9178  -32.8961   5.5503
 HXF  H19  H  HOH1   0   0.476  39.6059  -31.2298   7.2679
 HXF  H21  H  HCR6   0   0.255  32.2880  -29.9936   2.6936
 HXF  H22  H  HCR6   0   0.251  32.1405  -32.4214   3.1236
 HXF  H23  H  HCR6   0   0.256  32.5999  -33.3065   5.3912
 HXF  H24  H  HCR6   0   0.252  33.2551  -31.7535   7.2031
 HXF  H26  H  HCH2   0   0.258  36.1108  -26.7683   2.1425
 HXF  C6   C  CH2    0  -0.294  35.2093  -27.6272   3.9157
 HXF  H20  H  HCR6   0   0.247  33.4255  -29.3332   6.7558
 HXF  H25  H  HCH2   0   0.220  35.3711  -26.7732   4.5923

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
 HXF  C10  C3   single    1.507  0.020  1.507
 HXF  C3   O2   double    1.224  0.020  1.224
 HXF  C3   N1   single    1.346  0.020  1.346
 HXF  O5   C9   deloc     1.247  0.020  1.247
 HXF  N1   C2   single    1.440  0.020  1.440
 HXF  C11  C5   single    1.524  0.020  1.524
 HXF  C9   O4   deloc     1.246  0.020  1.246
 HXF  C9   C8   single    1.546  0.020  1.546
 HXF  N2   C4   single    1.340  0.020  1.340
 HXF  N2   C5   single    1.438  0.020  1.438
 HXF  C2   C4   single    1.527  0.020  1.527
 HXF  C2   C1   single    1.534  0.020  1.534
 HXF  C4   O3   double    1.223  0.020  1.223
 HXF  C5   C12  single    1.531  0.020  1.531
 HXF  C8   N5   single    1.451  0.020  1.451
 HXF  C1   C6   single    1.525  0.020  1.525
 HXF  N5   C6   single    1.460  0.020  1.460
 HXF  N5   C7   single    1.455  0.020  1.455
 HXF  C12  O8   double    1.215  0.020  1.215
 HXF  C12  N4   single    1.347  0.020  1.347
 HXF  N4   O9   single    1.364  0.020  1.364
 HXF  C7   C23  single    1.506  0.020  1.506
 HXF  C23  C21  aromatic  1.390  0.020  1.390
 HXF  C23  C31  aromatic  1.395  0.020  1.395
 HXF  C21  C61  aromatic  1.391  0.020  1.391
 HXF  C31  C41  aromatic  1.386  0.020  1.386
 HXF  C61  C51  aromatic  1.387  0.020  1.387
 HXF  C41  C51  aromatic  1.391  0.020  1.391
 HXF  C5   H1   single    0.970  0.020  1.090
 HXF  C6   H2   single    0.970  0.020  1.090
 HXF  C11  H3   single    0.970  0.020  1.090
 HXF  C11  H4   single    0.970  0.020  1.090
 HXF  C11  H5   single    0.970  0.020  1.090
 HXF  C7   H6   single    0.970  0.020  1.090
 HXF  C7   H7   single    0.970  0.020  1.090
 HXF  C8   H8   single    0.970  0.020  1.090
 HXF  C8   H9   single    0.970  0.020  1.090
 HXF  C10  H10  single    0.970  0.020  1.090
 HXF  C10  H11  single    0.970  0.020  1.090
 HXF  C10  H12  single    0.970  0.020  1.090
 HXF  N1   H13  single    0.860  0.020  1.020
 HXF  N2   H14  single    0.860  0.020  1.020
 HXF  C1   H15  single    0.970  0.020  1.090
 HXF  C2   H16  single    0.970  0.020  1.090
 HXF  N4   H17  single    0.890  0.020  1.040
 HXF  O9   H19  single    0.850  0.020  0.980
 HXF  C21  H20  single    0.930  0.020  1.080
 HXF  C31  H21  single    0.930  0.020  1.080
 HXF  C41  H22  single    0.930  0.020  1.080
 HXF  C51  H23  single    0.930  0.020  1.080
 HXF  C61  H24  single    0.930  0.020  1.080
 HXF  C6   H25  single    0.970  0.020  1.090
 HXF  C1   H26  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
 HXF  O3   C4   C2   119.96  3.000
 HXF  O3   C4   N2   122.29  3.000
 HXF  C2   C4   N2   117.74  3.000
 HXF  H1   C5   N2   108.60  3.000
 HXF  H1   C5   C12  109.07  3.000
 HXF  N2   C5   C12  110.39  3.000
 HXF  H1   C5   C11  108.46  3.000
 HXF  C12  C5   C11  109.68  3.000
 HXF  N2   C5   C11  110.59  3.000
 HXF  H5   C11  H4   108.47  3.000
 HXF  H5   C11  H3   108.00  3.000
 HXF  H4   C11  H3   108.37  3.000
 HXF  H5   C11  C5   110.16  3.000
 HXF  H4   C11  C5   111.25  3.000
 HXF  H3   C11  C5   110.49  3.000
 HXF  H7   C7   H6   106.26  3.000
 HXF  H7   C7   C23  107.85  3.000
 HXF  H6   C7   C23  109.68  3.000
 HXF  H7   C7   N5   107.99  3.000
 HXF  H6   C7   N5   111.25  3.000
 HXF  C23  C7   N5   113.48  3.000
 HXF  H9   C8   H8   105.15  3.000
 HXF  H9   C8   N5   111.49  3.000
 HXF  H8   C8   N5   109.03  3.000
 HXF  H9   C8   C9   109.12  3.000
 HXF  H8   C8   C9   106.06  3.000
 HXF  N5   C8   C9   115.36  3.000
 HXF  O5   C9   O4   127.03  3.000
 HXF  O4   C9   C8   114.38  3.000
 HXF  O5   C9   C8   118.56  3.000
 HXF  H12  C10  H11  109.27  3.000
 HXF  H12  C10  H10  107.59  3.000
 HXF  H11  C10  H10  108.02  3.000
 HXF  H12  C10  C3   109.97  3.000
 HXF  H11  C10  C3   112.66  3.000
 HXF  H10  C10  C3   109.18  3.000
 HXF  O8   C12  N4   123.94  3.000
 HXF  N4   C12  C5   112.86  3.000
 HXF  O8   C12  C5   123.19  3.000
 HXF  H13  N1   C2   116.27  3.000
 HXF  H13  N1   C3   121.84  3.000
 HXF  C2   N1   C3   121.83  3.000
 HXF  H14  N2   C5   119.25  3.000
 HXF  H14  N2   C4   119.78  3.000
 HXF  C5   N2   C4   120.64  3.000
 HXF  O2   C3   N1   122.45  3.000
 HXF  N1   C3   C10  115.17  3.000
 HXF  O2   C3   C10  122.36  3.000
 HXF  H26  C1   H15  105.37  3.000
 HXF  H26  C1   C2   108.08  3.000
 HXF  H15  C1   C2   108.04  3.000
 HXF  H26  C1   C6   110.67  3.000
 HXF  H15  C1   C6   108.58  3.000
 HXF  C2   C1   C6   115.58  3.000
 HXF  H16  C2   C1   107.21  3.000
 HXF  H16  C2   N1   109.50  3.000
 HXF  C1   C2   N1   110.73  3.000
 HXF  H16  C2   C4   104.71  3.000
 HXF  C1   C2   C4   109.85  3.000
 HXF  N1   C2   C4   114.44  3.000
 HXF  H17  N4   O9   114.41  3.000
 HXF  H17  N4   C12  122.09  3.000
 HXF  O9   N4   C12  119.76  3.000
 HXF  C8   N5   C7   110.69  3.000
 HXF  C7   N5   C6   111.04  3.000
 HXF  C8   N5   C6   112.97  3.000
 HXF  H19  O9   N4   105.98  3.000
 HXF  H20  C21  C61  119.71  3.000
 HXF  H20  C21  C23  119.49  3.000
 HXF  C61  C21  C23  120.79  3.000
 HXF  C31  C23  C21  118.67  3.000
 HXF  C31  C23  C7   119.77  3.000
 HXF  C21  C23  C7   121.49  3.000
 HXF  H21  C31  C41  120.19  3.000
 HXF  H21  C31  C23  119.01  3.000
 HXF  C41  C31  C23  120.78  3.000
 HXF  H22  C41  C51  120.05  3.000
 HXF  H22  C41  C31  119.87  3.000
 HXF  C51  C41  C31  120.08  3.000
 HXF  H23  C51  C61  120.23  3.000
 HXF  H23  C51  C41  120.15  3.000
 HXF  C61  C51  C41  119.61  3.000
 HXF  H24  C61  C51  120.09  3.000
 HXF  H24  C61  C21  119.86  3.000
 HXF  C51  C61  C21  120.05  3.000
 HXF  H25  C6   H2   105.80  3.000
 HXF  H25  C6   N5   111.08  3.000
 HXF  H2   C6   N5   108.17  3.000
 HXF  H25  C6   C1   108.84  3.000
 HXF  H2   C6   C1   109.20  3.000
 HXF  N5   C6   C1   113.45  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
 HXF  CONST_01  C41  C31  C23  C21     0.00   0.0  0
 HXF  CONST_02  C41  C51  C61  C21     0.00   0.0  0
 HXF  CONST_03  C51  C61  C21  C23     0.00   0.0  0
 HXF  CONST_04  C51  C41  C31  C23     0.00   0.0  0
 HXF  CONST_05  C61  C21  C23  C31     0.00   0.0  0
 HXF  CONST_06  C61  C51  C41  C31     0.00   0.0  0
 HXF  CONST_07  C61  C21  C23  C7    180.00   0.0  0
 HXF  CONST_08  C41  C31  C23  C7    180.00   0.0  0
 HXF  CONST_09  H21  C31  C23  C21   180.00   0.0  0
 HXF  CONST_10  H23  C51  C61  C21   180.00   0.0  0
 HXF  CONST_11  H24  C61  C21  C23   180.00   0.0  0
 HXF  CONST_12  H22  C41  C31  C23   180.00   0.0  0
 HXF  CONST_13  H20  C21  C23  C31   180.00   0.0  0
 HXF  CONST_14  H23  C51  C41  C31   180.00   0.0  0
 HXF  CONST_15  H24  C61  C51  C41   180.00   0.0  0
 HXF  CONST_16  H20  C21  C61  C51   180.00   0.0  0
 HXF  CONST_17  H21  C31  C41  C51   180.00   0.0  0
 HXF  CONST_18  H22  C41  C51  C61   180.00   0.0  0
 HXF  CONST_19  C2   C4   N2   C5    180.00   0.0  0
 HXF  CONST_20  O3   C4   N2   C5      0.00   0.0  0
 HXF  CONST_21  O9   N4   C12  C5    180.00   0.0  0
 HXF  CONST_22  C2   N1   C3   C10   180.00   0.0  0
 HXF  CONST_23  O2   C3   N1   C2      0.00   0.0  0
 HXF  CONST_24  O9   N4   C12  O8      0.00   0.0  0
 HXF  CONST_25  H17  N4   C12  C5      0.00   0.0  0
 HXF  CONST_26  H13  N1   C3   C10     0.00   0.0  0
 HXF  CONST_27  H14  N2   C4   C2      0.00   0.0  0
 HXF  CONST_28  H13  N1   C3   O2    180.00   0.0  0
 HXF  CONST_29  H14  N2   C4   O3    180.00   0.0  0
 HXF  CONST_30  H17  N4   C12  O8    180.00   0.0  0
 HXF  Var_01    C21  C23  C7   N5    121.23  30.0  2
 HXF  Var_02    C31  C23  C7   N5    -61.66  30.0  2
 HXF  Var_03    H6   C7   C23  C21    -3.87  30.0  1
 HXF  Var_04    H7   C7   C23  C21  -119.19  30.0  1
 HXF  Var_05    H6   C7   C23  C31   173.24  30.0  1
 HXF  Var_06    H7   C7   C23  C31    57.92  30.0  1
 HXF  Var_07    C23  C7   N5   C6    -77.00  30.0  3
 HXF  Var_08    C23  C7   N5   C8    156.69  30.0  3
 HXF  Var_09    C9   C8   N5   C6    159.67  30.0  2
 HXF  Var_10    C9   C8   N5   C7    -75.09  30.0  2
 HXF  Var_11    C1   C6   N5   C7    164.43  30.0  3
 HXF  Var_12    C1   C6   N5   C8    -70.53  30.0  3
 HXF  Var_13    N5   C6   C1   C2    -69.34  30.0  3
 HXF  Var_14    N5   C8   C9   O4    169.74  30.0  3
 HXF  Var_15    O5   C9   C8   N5    -12.08  30.0  2
 HXF  Var_16    H8   C8   N5   C6     40.51  30.0  2
 HXF  Var_17    H9   C8   N5   C6    -75.14  30.0  2
 HXF  Var_18    H6   C7   N5   C6     47.26  30.0  3
 HXF  Var_19    H7   C7   N5   C6    163.50  30.0  3
 HXF  Var_20    H8   C8   N5   C7    165.75  30.0  2
 HXF  Var_21    H9   C8   N5   C7     50.09  30.0  2
 HXF  Var_22    H2   C6   N5   C7     43.12  30.0  3
 HXF  Var_23    H25  C6   N5   C7    -72.59  30.0  3
 HXF  Var_24    H2   C6   N5   C8    168.16  30.0  3
 HXF  Var_25    H25  C6   N5   C8     52.46  30.0  3
 HXF  Var_26    H6   C7   N5   C8    -79.06  30.0  3
 HXF  Var_27    H7   C7   N5   C8     37.18  30.0  3
 HXF  Var_28    H10  C10  C3   N1    -93.03  30.0  3
 HXF  Var_29    H11  C10  C3   N1     26.98  30.0  3
 HXF  Var_30    H12  C10  C3   N1    149.13  30.0  3
 HXF  Var_31    H2   C6   C1   C2     51.39  30.0  3
 HXF  Var_32    H25  C6   C1   C2    166.45  30.0  3
 HXF  Var_33    H10  C10  C3   O2     85.35  30.0  3
 HXF  Var_34    H11  C10  C3   O2   -154.65  30.0  3
 HXF  Var_35    H12  C10  C3   O2    -32.49  30.0  3
 HXF  Var_36    H8   C8   C9   O4    -69.48  30.0  3
 HXF  Var_37    H9   C8   C9   O4     43.33  30.0  3
 HXF  Var_38    H15  C1   C6   N5    169.11  30.0  2
 HXF  Var_39    H26  C1   C6   N5     53.91  30.0  2
 HXF  Var_40    H8   C8   C9   O5    108.71  30.0  3
 HXF  Var_41    H9   C8   C9   O5   -138.48  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
 HXF  chir_01  C5  C11  N2  C12  negativ
 HXF  chir_02  C2  N1   C1  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
 HXF  plan-1  C7   0.020
 HXF  plan-1  C21  0.020
 HXF  plan-1  C23  0.020
 HXF  plan-1  C31  0.020
 HXF  plan-1  C41  0.020
 HXF  plan-1  C51  0.020
 HXF  plan-1  C61  0.020
 HXF  plan-1  H21  0.020
 HXF  plan-1  H22  0.020
 HXF  plan-1  H23  0.020
 HXF  plan-1  H24  0.020
 HXF  plan-1  H20  0.020
 HXF  plan-2  C4   0.020
 HXF  plan-2  C5   0.020
 HXF  plan-2  N2   0.020
 HXF  plan-2  C2   0.020
 HXF  plan-2  O3   0.020
 HXF  plan-2  H14  0.020
 HXF  plan-3  C5   0.020
 HXF  plan-3  C12  0.020
 HXF  plan-3  N4   0.020
 HXF  plan-3  O8   0.020
 HXF  plan-3  O9   0.020
 HXF  plan-3  H17  0.020
 HXF  plan-4  C10  0.020
 HXF  plan-4  N1   0.020
 HXF  plan-4  C3   0.020
 HXF  plan-4  C2   0.020
 HXF  plan-4  O2   0.020
 HXF  plan-4  H13  0.020
 HXF  plan-5  C8   0.020
 HXF  plan-5  C9   0.020
 HXF  plan-5  O4   0.020
 HXF  plan-5  O5   0.020

