# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:38:16 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]-(cyclopentylmethyl)amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@H](CCN(CC1CCCC1)CC(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
 HY9  HY9  "2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(cyclopentylmethyl)amino]ethanoic acid"  ligand  56  27  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HY9
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
 HY9  C3   C  C      0   0.515  30.2962  12.8992  -17.9091
 HY9  C4   C  C      0   0.553  30.1730  11.0751  -20.6054
 HY9  C5   C  CH1    0  -0.190  32.3667  11.0498  -21.6621
 HY9  C6   C  CH2    0  -0.270  26.7205  12.6964  -20.0098
 HY9  C7   C  CH2    0  -0.249  24.3917  12.2275  -19.6916
 HY9  C8   C  CH2    0  -0.421  25.9679  10.4321  -19.7050
 HY9  C9   C  C      0   0.389  25.0834   9.2583  -20.1894
 HY9  C10  C  CH3    0  -0.776  30.7613  14.1993  -17.3045
 HY9  O3   O  O      0  -0.490  29.9012   9.9532  -21.0115
 HY9  N2   N  NH1    0  -0.629  31.3415  11.6737  -20.8563
 HY9  C11  C  CH3    0  -0.704  32.0433  11.1146  -23.1514
 HY9  C12  C  C      0   0.520  32.6901   9.6686  -21.0758
 HY9  C27  C  CH2    0  -0.416  22.3815  13.7618  -19.9741
 HY9  C23  C  CH1    0  -0.272  23.7966  13.4137  -20.4352
 HY9  C24  C  CH2    0  -0.425  23.6164  13.1904  -21.9396
 HY9  C25  C  CH2    0  -0.442  22.4924  14.1566  -22.3723
 HY9  C26  C  CH2    0  -0.448  21.8772  14.7028  -21.0669
 HY9  O2   O  O      0  -0.481  30.4855  11.8222  -17.3668
 HY9  N1   N  NH1    0  -0.649  29.6755  13.0052  -19.1051
 HY9  C1   C  CH2    0  -0.511  28.0159  12.3297  -20.7472
 HY9  C2   C  CH1    0  -0.170  29.1391  11.8692  -19.8125
 HY9  N4   N  NH1    0  -0.386  32.8697   8.6933  -21.9881
 HY9  O4   O  OC    -1  -0.615  25.1905   8.2194  -19.5067
 HY9  N5   N  NT     0  -0.410  25.6486  11.7423  -20.2353
 HY9  O5   O  O      0  -0.598  24.4013   9.4121  -21.2190
 HY9  O8   O  O      0  -0.466  32.8679   9.5162  -19.8842
 HY9  O9   O  OH1    0  -0.540  33.0451   7.4103  -21.5572
 HY9  H1   H  HCH1   0   0.298  33.2749  11.6347  -21.4951
 HY9  H2   H  HCH2   0   0.194  26.9266  12.8253  -18.9308
 HY9  H3   H  HCH2   0   0.242  26.3838  13.6715  -20.3616
 HY9  H4   H  HCH2   0   0.184  24.4927  12.4813  -18.6197
 HY9  H5   H  HCH2   0   0.221  23.6687  11.4115  -19.7464
 HY9  H6   H  HCH2   0   0.234  26.9829  10.1642  -20.0152
 HY9  H7   H  HCH2   0   0.180  25.9906  10.4327  -18.6007
 HY9  H8   H  HCH3   0   0.269  31.8496  14.2500  -17.3603
 HY9  H9   H  HCH3   0   0.251  30.3552  15.0800  -17.7981
 HY9  H10  H  HCH3   0   0.265  30.4883  14.2308  -16.2507
 HY9  H11  H  HNH1   0   0.407  31.5117  12.6003  -20.5002
 HY9  H12  H  HCH3   0   0.261  31.8582  12.1506  -23.4308
 HY9  H13  H  HCH3   0   0.245  32.8811  10.7647  -23.7549
 HY9  H14  H  HCH3   0   0.246  31.1572  10.5351  -23.4100
 HY9  H17  H  HCH1   0   0.219  24.4149  14.3071  -20.2857
 HY9  H18  H  HCH2   0   0.210  23.3177  12.1532  -22.1140
 HY9  H19  H  HCH2   0   0.224  24.5411  13.3450  -22.4966
 HY9  H20  H  HCH2   0   0.222  22.8739  14.9664  -22.9956
 HY9  H21  H  HCH2   0   0.222  21.7443  13.6344  -22.9705
 HY9  H22  H  HCH2   0   0.217  22.2410  15.7145  -20.8727
 HY9  H23  H  HCH2   0   0.225  20.7885  14.7613  -21.1060
 HY9  H24  H  HNH1   0   0.408  29.5214  13.9222  -19.4952
 HY9  H25  H  HCH2   0   0.269  27.8054  11.5467  -21.4762
 HY9  H26  H  HCH2   0   0.261  28.3779  13.1841  -21.3259
 HY9  H27  H  HCH1   0   0.279  28.7260  11.1688  -19.0821
 HY9  H28  H  HNH1   0   0.422  32.5015   8.7575  -22.9255
 HY9  H31  H  HOH1   0   0.475  33.9925   7.2351  -21.6243
 HY9  H15  H  HCH2   0   0.225  22.3472  14.2047  -18.9766
 HY9  H16  H  HCH2   0   0.208  21.7754  12.8496  -19.9496

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
 HY9  C11  C5   single  1.525  0.020  1.525
 HY9  O3   C4   double  1.224  0.020  1.224
 HY9  O9   N4   single  1.365  0.020  1.365
 HY9  N4   C12  single  1.347  0.020  1.347
 HY9  C25  C24  single  1.544  0.020  1.544
 HY9  C25  C26  single  1.543  0.020  1.543
 HY9  C12  C5   single  1.535  0.020  1.535
 HY9  C12  O8   double  1.214  0.020  1.214
 HY9  C5   N2   single  1.446  0.020  1.446
 HY9  C24  C23  single  1.532  0.020  1.532
 HY9  C4   N2   single  1.337  0.020  1.337
 HY9  C4   C2   single  1.526  0.020  1.526
 HY9  C26  C27  single  1.528  0.020  1.528
 HY9  C1   C6   single  1.535  0.020  1.535
 HY9  C1   C2   single  1.532  0.020  1.532
 HY9  C6   N5   single  1.453  0.020  1.453
 HY9  C23  C27  single  1.528  0.020  1.528
 HY9  C23  C7   single  1.521  0.020  1.521
 HY9  C2   N1   single  1.442  0.020  1.442
 HY9  N5   C7   single  1.453  0.020  1.453
 HY9  N5   C8   single  1.449  0.020  1.449
 HY9  N1   C3   single  1.352  0.020  1.352
 HY9  O5   C9   deloc   1.245  0.020  1.245
 HY9  C8   C9   single  1.548  0.020  1.548
 HY9  C9   O4   deloc   1.248  0.020  1.248
 HY9  C3   C10  single  1.507  0.020  1.507
 HY9  C3   O2   double  1.221  0.020  1.221
 HY9  C5   H1   single  0.970  0.020  1.090
 HY9  C6   H2   single  0.970  0.020  1.090
 HY9  C6   H3   single  0.970  0.020  1.090
 HY9  C7   H4   single  0.970  0.020  1.090
 HY9  C7   H5   single  0.970  0.020  1.090
 HY9  C8   H6   single  0.970  0.020  1.090
 HY9  C8   H7   single  0.970  0.020  1.090
 HY9  C10  H8   single  0.970  0.020  1.090
 HY9  C10  H9   single  0.970  0.020  1.090
 HY9  C10  H10  single  0.970  0.020  1.090
 HY9  N2   H11  single  0.860  0.020  1.020
 HY9  C11  H12  single  0.970  0.020  1.090
 HY9  C11  H13  single  0.970  0.020  1.090
 HY9  C11  H14  single  0.970  0.020  1.090
 HY9  C27  H15  single  0.970  0.020  1.090
 HY9  C27  H16  single  0.970  0.020  1.090
 HY9  C23  H17  single  0.970  0.020  1.090
 HY9  C24  H18  single  0.970  0.020  1.090
 HY9  C24  H19  single  0.970  0.020  1.090
 HY9  C25  H20  single  0.970  0.020  1.090
 HY9  C25  H21  single  0.970  0.020  1.090
 HY9  C26  H22  single  0.970  0.020  1.090
 HY9  C26  H23  single  0.970  0.020  1.090
 HY9  N1   H24  single  0.860  0.020  1.020
 HY9  C1   H25  single  0.970  0.020  1.090
 HY9  C1   H26  single  0.970  0.020  1.090
 HY9  C2   H27  single  0.970  0.020  1.090
 HY9  N4   H28  single  0.890  0.020  1.040
 HY9  O9   H31  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
 HY9  N1   C3   O2   122.25  3.000
 HY9  O2   C3   C10  122.34  3.000
 HY9  N1   C3   C10  115.41  3.000
 HY9  C2   C4   N2   117.18  3.000
 HY9  C2   C4   O3   119.94  3.000
 HY9  N2   C4   O3   122.85  3.000
 HY9  H1   C5   C12  104.36  3.000
 HY9  H1   C5   C11  107.62  3.000
 HY9  C12  C5   C11  117.12  3.000
 HY9  H1   C5   N2   105.85  3.000
 HY9  C12  C5   N2   108.96  3.000
 HY9  C11  C5   N2   112.06  3.000
 HY9  H3   C6   H2   105.56  3.000
 HY9  H3   C6   N5   108.03  3.000
 HY9  H2   C6   N5   111.44  3.000
 HY9  H3   C6   C1   108.62  3.000
 HY9  H2   C6   C1   109.83  3.000
 HY9  N5   C6   C1   113.03  3.000
 HY9  H5   C7   H4   106.29  3.000
 HY9  H5   C7   N5   107.73  3.000
 HY9  H4   C7   N5   111.12  3.000
 HY9  H5   C7   C23  107.41  3.000
 HY9  H4   C7   C23  109.30  3.000
 HY9  N5   C7   C23  114.58  3.000
 HY9  H7   C8   H6   105.33  3.000
 HY9  H7   C8   N5   111.72  3.000
 HY9  H6   C8   N5   108.78  3.000
 HY9  H7   C8   C9   108.97  3.000
 HY9  H6   C8   C9   104.81  3.000
 HY9  N5   C8   C9   116.44  3.000
 HY9  O5   C9   O4   127.06  3.000
 HY9  O4   C9   C8   114.28  3.000
 HY9  O5   C9   C8   118.58  3.000
 HY9  H10  C10  H9   108.78  3.000
 HY9  H10  C10  H8   107.35  3.000
 HY9  H9   C10  H8   108.15  3.000
 HY9  H10  C10  C3   109.62  3.000
 HY9  H9   C10  C3   113.63  3.000
 HY9  H8   C10  C3   109.11  3.000
 HY9  H11  N2   C5   118.32  3.000
 HY9  H11  N2   C4   119.56  3.000
 HY9  C5   N2   C4   122.10  3.000
 HY9  H14  C11  H13  108.83  3.000
 HY9  H14  C11  H12  107.87  3.000
 HY9  H13  C11  H12  107.09  3.000
 HY9  H14  C11  C5   112.42  3.000
 HY9  H13  C11  C5   111.34  3.000
 HY9  H12  C11  C5   109.09  3.000
 HY9  O8   C12  N4   123.65  3.000
 HY9  O8   C12  C5   121.23  3.000
 HY9  N4   C12  C5   114.88  3.000
 HY9  H16  C27  H15  107.45  3.000
 HY9  H16  C27  C26  110.26  3.000
 HY9  H15  C27  C26  113.16  3.000
 HY9  H16  C27  C23  109.23  3.000
 HY9  H15  C27  C23  113.39  3.000
 HY9  C26  C27  C23  103.30  3.000
 HY9  H17  C23  C24  108.60  3.000
 HY9  H17  C23  C27  107.18  3.000
 HY9  C24  C23  C27  102.74  3.000
 HY9  H17  C23  C7   110.36  3.000
 HY9  C27  C23  C7   113.10  3.000
 HY9  C24  C23  C7   114.36  3.000
 HY9  H19  C24  H18  106.53  3.000
 HY9  H19  C24  C25  112.67  3.000
 HY9  H18  C24  C25  110.49  3.000
 HY9  H19  C24  C23  112.41  3.000
 HY9  H18  C24  C23  109.10  3.000
 HY9  C25  C24  C23  105.65  3.000
 HY9  H21  C25  H20  106.37  3.000
 HY9  H21  C25  C26  111.10  3.000
 HY9  H20  C25  C26  111.11  3.000
 HY9  H21  C25  C24  110.69  3.000
 HY9  H20  C25  C24  111.72  3.000
 HY9  C26  C25  C24  105.94  3.000
 HY9  H23  C26  H22  106.80  3.000
 HY9  H23  C26  C25  112.74  3.000
 HY9  H22  C26  C25  110.20  3.000
 HY9  H23  C26  C27  112.84  3.000
 HY9  H22  C26  C27  109.47  3.000
 HY9  C25  C26  C27  104.80  3.000
 HY9  H24  N1   C2   118.02  3.000
 HY9  H24  N1   C3   118.93  3.000
 HY9  C2   N1   C3   122.91  3.000
 HY9  H26  C1   H25  105.74  3.000
 HY9  H26  C1   C2   108.36  3.000
 HY9  H25  C1   C2   109.49  3.000
 HY9  H26  C1   C6   110.30  3.000
 HY9  H25  C1   C6   109.26  3.000
 HY9  C2   C1   C6   113.42  3.000
 HY9  H27  C2   C1   108.86  3.000
 HY9  H27  C2   N1   108.52  3.000
 HY9  C1   C2   N1   109.59  3.000
 HY9  H27  C2   C4   105.65  3.000
 HY9  N1   C2   C4   114.39  3.000
 HY9  C1   C2   C4   109.64  3.000
 HY9  H28  N4   O9   113.57  3.000
 HY9  H28  N4   C12  122.29  3.000
 HY9  O9   N4   C12  118.93  3.000
 HY9  C8   N5   C7   110.83  3.000
 HY9  C8   N5   C6   111.99  3.000
 HY9  C7   N5   C6   111.16  3.000
 HY9  H31  O9   N4   105.94  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
 HY9  CONST_01  O9   N4   C12  C5    180.00   0.0  0
 HY9  CONST_02  O3   C4   N2   C5      0.00   0.0  0
 HY9  CONST_03  C2   C4   N2   C5    180.00   0.0  0
 HY9  CONST_04  C2   N1   C3   C10   180.00   0.0  0
 HY9  CONST_05  C2   N1   C3   O2      0.00   0.0  0
 HY9  CONST_06  O9   N4   C12  O8      0.00   0.0  0
 HY9  CONST_08  H24  N1   C3   C10     0.00   0.0  0
 HY9  CONST_09  H11  N2   C4   O3    180.00   0.0  0
 HY9  CONST_10  H24  N1   C3   O2    180.00   0.0  0
 HY9  CONST_11  H11  N2   C4   C2      0.00   0.0  0
 HY9  Var_01    C24  C25  C26  C27   -15.37  30.0  1
 HY9  Var_02    C26  C25  C24  C23   -10.71  30.0  1
 HY9  Var_03    C25  C26  C27  C23    35.73  30.0  1
 HY9  Var_04    H20  C25  C26  C27  -136.90  30.0  1
 HY9  Var_05    H21  C25  C26  C27   104.89  30.0  1
 HY9  Var_06    H20  C25  C24  C23   110.42  30.0  1
 HY9  Var_07    H21  C25  C24  C23  -131.24  30.0  1
 HY9  Var_08    H22  C26  C27  C23   -82.45  30.0  1
 HY9  Var_09    H23  C26  C27  C23   158.76  30.0  1
 HY9  Var_10    H22  C26  C25  C24   102.31  30.0  1
 HY9  Var_11    H23  C26  C25  C24  -138.47  30.0  1
 HY9  Var_12    H15  C27  C26  C25   158.75  30.0  1
 HY9  Var_13    H16  C27  C26  C25   -80.88  30.0  1
 HY9  Var_14    H18  C24  C25  C26   107.16  30.0  1
 HY9  Var_15    H19  C24  C25  C26  -133.81  30.0  1
 HY9  Var_16    C23  C7   N5   C6     69.45  30.0  3
 HY9  Var_17    C23  C7   N5   C8   -165.32  30.0  3
 HY9  Var_18    C9   C8   N5   C6   -164.96  30.0  3
 HY9  Var_19    C1   C6   N5   C7   -171.32  30.0  2
 HY9  Var_20    C9   C8   N5   C7     70.28  30.0  3
 HY9  Var_21    C1   C6   N5   C8     64.11  30.0  2
 HY9  Var_22    N5   C6   C1   C2   -109.57  30.0  3
 HY9  Var_23    N5   C8   C9   O4   -165.14  30.0  3
 HY9  Var_24    O5   C9   C8   N5     17.87  30.0  3
 HY9  Var_25    H4   C7   N5   C6    -55.04  30.0  3
 HY9  Var_26    H5   C7   N5   C6   -171.10  30.0  3
 HY9  Var_27    H6   C8   N5   C6    -46.89  30.0  3
 HY9  Var_28    H7   C8   N5   C6     68.96  30.0  3
 HY9  Var_29    H2   C6   N5   C7     64.43  30.0  2
 HY9  Var_30    H3   C6   N5   C7    -51.10  30.0  2
 HY9  Var_31    H6   C8   N5   C7   -171.65  30.0  3
 HY9  Var_32    H7   C8   N5   C7    -55.80  30.0  3
 HY9  Var_33    H2   C6   N5   C8    -60.15  30.0  2
 HY9  Var_34    H3   C6   N5   C8   -175.67  30.0  2
 HY9  Var_35    H4   C7   N5   C8     70.19  30.0  3
 HY9  Var_36    H5   C7   N5   C8    -45.87  30.0  3
 HY9  Var_37    H8   C10  C3   O2     70.53  30.0  3
 HY9  Var_38    H9   C10  C3   O2   -168.72  30.0  3
 HY9  Var_39    H10  C10  C3   O2    -46.77  30.0  3
 HY9  Var_40    H8   C10  C3   N1   -108.35  30.0  3
 HY9  Var_41    H9   C10  C3   N1     12.41  30.0  3
 HY9  Var_42    H10  C10  C3   N1    134.35  30.0  3
 HY9  Var_43    H2   C6   C1   C2     15.57  30.0  3
 HY9  Var_44    H3   C6   C1   C2    130.55  30.0  3
 HY9  Var_45    H6   C8   C9   O4     74.64  30.0  3
 HY9  Var_46    H7   C8   C9   O4    -37.70  30.0  3
 HY9  Var_47    H25  C1   C6   N5     12.87  30.0  1
 HY9  Var_48    H26  C1   C6   N5    128.69  30.0  1
 HY9  Var_49    H6   C8   C9   O5   -102.35  30.0  3
 HY9  Var_50    H7   C8   C9   O5    145.31  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
 HY9  chir_01  C5   C11  C12  N2  positiv
 HY9  chir_02  C23  C24  C27  C7  negativ
 HY9  chir_03  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
 HY9  plan-1  C3   0.020
 HY9  plan-1  C10  0.020
 HY9  plan-1  O2   0.020
 HY9  plan-1  N1   0.020
 HY9  plan-1  C2   0.020
 HY9  plan-1  H24  0.020
 HY9  plan-2  C4   0.020
 HY9  plan-2  C5   0.020
 HY9  plan-2  O3   0.020
 HY9  plan-2  N2   0.020
 HY9  plan-2  C2   0.020
 HY9  plan-2  H11  0.020
 HY9  plan-3  C5   0.020
 HY9  plan-3  C12  0.020
 HY9  plan-3  N4   0.020
 HY9  plan-3  O8   0.020
 HY9  plan-3  O9   0.020
 HY9  plan-3  H28  0.020
 HY9  plan-4  C8   0.020
 HY9  plan-4  C9   0.020
 HY9  plan-4  O4   0.020
 HY9  plan-4  O5   0.020

