# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:23:02 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 6-[{(2S)-2-amino-3-[4-(benzyloxy)phenyl]propyl}(hydroxy)amino]-6-oxohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CN(O)C(=O)CCCCC(O)=O)Cc1ccc(OCc2ccccc2)cc1
#
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
 HA2  HA2  '6-[{(2S)-2-amino-3-[4-(benzyloxy)phenyl]propyl}(hydroxy)amino]-6-oxohexanoic acid'  ligand  56  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HA2
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
 HA2  C3    C  CR16   0  -0.278   7.3708  39.9577  66.9584
 HA2  C2    C  CR16   0  -0.241   7.2257  38.6345  66.5663
 HA2  C1    C  CR16   0  -0.267   7.4887  37.6052  67.4621
 HA2  C6    C  CR16   0  -0.241   7.9023  37.9074  68.7520
 HA2  C5    C  CR16   0  -0.296   8.0558  39.2325  69.1397
 HA2  C4    C  CR6    0   0.043   7.7883  40.2676  68.2503
 HA2  C7    C  CH2    0  -0.252   7.9099  41.7007  68.7010
 HA2  O1    O  O2     0  -0.485   8.4038  42.5623  67.6967
 HA2  C8    C  CR6    0   0.375   9.6938  42.4394  67.3007
 HA2  C13   C  CR16   0  -0.340  10.0696  43.1956  66.1915
 HA2  C12   C  CR16   0  -0.297  11.3737  43.1525  65.7287
 HA2  C9    C  CR16   0  -0.345  10.6442  41.6415  67.9304
 HA2  C10   C  CR16   0  -0.298  11.9471  41.6118  67.4466
 HA2  C11   C  CR6    0   0.154  12.3407  42.3598  66.3451
 HA2  C14   C  CH2    0  -0.533  13.7430  42.2972  65.8129
 HA2  C15   C  CH1    0  -0.087  13.9055  41.2729  64.6850
 HA2  N2    N  NH2    0  -0.778  13.6106  39.9389  65.1763
 HA2  C16   C  CH2    0  -0.325  15.2588  41.4436  63.9730
 HA2  N3    N  NT     0  -0.204  16.4091  41.5064  64.8456
 HA2  O2    O  OH1    0  -0.546  16.6734  40.3729  65.5698
 HA2  C17   C  C      0   0.556  17.1370  42.6215  65.1002
 HA2  O3    O  O      0  -0.492  16.8975  43.6695  64.5187
 HA2  C18   C  CH2    0  -0.573  18.2627  42.4741  66.1029
 HA2  C19   C  CH2    0  -0.418  19.0208  43.7689  66.3618
 HA2  C20   C  CH2    0  -0.406  18.2708  44.7812  67.2212
 HA2  C21   C  CH2    0  -0.579  19.1083  46.0211  67.4908
 HA2  C22   C  C      0   0.408  18.4500  47.1189  68.3439
 HA2  O5    O  O      0  -0.634  19.2132  48.0130  68.7687
 HA2  O4    O  OC    -1  -0.611  17.2190  47.0528  68.5316
 HA2  H3    H  HCR6   0   0.253   7.1604  40.7491  66.2496
 HA2  H2    H  HCR6   0   0.256   6.9039  38.4048  65.5586
 HA2  H1    H  HCR6   0   0.257   7.3736  36.5740  67.1545
 HA2  H6    H  HCR6   0   0.256   8.1141  37.1124  69.4554
 HA2  H5    H  HCR6   0   0.254   8.3912  39.4622  70.1449
 HA2  H7C1  H  HCH2   0   0.274   6.9237  42.0968  68.9495
 HA2  H7C2  H  HCH2   0   0.239   8.5124  41.7622  69.6139
 HA2  H13   H  HCR6   0   0.257   9.3369  43.8227  65.6986
 HA2  H9    H  HCR6   0   0.270  10.4004  41.0390  68.7945
 HA2  H12   H  HCR6   0   0.244  11.6418  43.7510  64.8653
 HA2  H10   H  HCR6   0   0.242  12.6707  40.9832  67.9511
 HA2  H141  H  HCH2   0   0.247  14.0461  43.2806  65.4439
 HA2  H142  H  HCH2   0   0.240  14.4337  42.0500  66.6252
 HA2  H15   H  HCH1   0   0.239  13.1563  41.5005  63.9176
 HA2  H2N1  H  HNH2   0   0.343  13.7047  39.2698  64.4220
 HA2  H2N2  H  HNH2   0   0.336  14.2911  39.6682  65.8744
 HA2  H161  H  HCH2   0   0.254  15.3998  40.6270  63.2572
 HA2  H162  H  HCH2   0   0.257  15.2517  42.3669  63.3964
 HA2  HA    H  HOH1   0   0.475  17.2199  39.8071  65.0058
 HA2  H181  H  HCH2   0   0.260  17.8677  42.0804  67.0437
 HA2  H182  H  HCH2   0   0.268  18.9533  41.7088  65.7354
 HA2  H191  H  HCH2   0   0.220  19.9558  43.5067  66.8656
 HA2  H192  H  HCH2   0   0.215  19.3098  44.2298  65.4135
 HA2  H201  H  HCH2   0   0.213  17.3369  45.0637  66.7343
 HA2  H202  H  HCH2   0   0.198  17.9907  44.3074  68.1681
 HA2  H211  H  HCH2   0   0.209  20.0557  45.7352  67.9607
 HA2  H212  H  HCH2   0   0.219  19.3966  46.4731  66.5327

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
 HA2  C3   C2    aromatic  1.388  0.020  1.388
 HA2  C3   C4    aromatic  1.393  0.020  1.393
 HA2  C2   C1    aromatic  1.390  0.020  1.390
 HA2  C1   C6    aromatic  1.388  0.020  1.388
 HA2  C6   C5    aromatic  1.389  0.020  1.389
 HA2  C5   C4    aromatic  1.391  0.020  1.391
 HA2  C4   C7    single    1.507  0.020  1.507
 HA2  C7   O1    single    1.412  0.020  1.412
 HA2  O1   C8    single    1.355  0.020  1.355
 HA2  C8   C13   aromatic  1.394  0.020  1.394
 HA2  C8   C9    aromatic  1.392  0.020  1.392
 HA2  C13  C12   aromatic  1.384  0.020  1.384
 HA2  C12  C11   aromatic  1.394  0.020  1.394
 HA2  C9   C10   aromatic  1.390  0.020  1.390
 HA2  C10  C11   aromatic  1.388  0.020  1.388
 HA2  C11  C14   single    1.501  0.020  1.501
 HA2  C14  C15   single    1.532  0.020  1.532
 HA2  C15  N2    single    1.452  0.020  1.452
 HA2  C15  C16   single    1.539  0.020  1.539
 HA2  C16  N3    single    1.445  0.020  1.445
 HA2  N3   O2    single    1.371  0.020  1.371
 HA2  N3   C17   single    1.356  0.020  1.356
 HA2  C17  O3    double    1.222  0.020  1.222
 HA2  C17  C18   single    1.515  0.020  1.515
 HA2  C18  C19   single    1.523  0.020  1.523
 HA2  C19  C20   single    1.525  0.020  1.525
 HA2  C20  C21   single    1.520  0.020  1.520
 HA2  C21  C22   single    1.538  0.020  1.538
 HA2  C22  O5    deloc     1.250  0.020  1.250
 HA2  C22  O4    deloc     1.247  0.020  1.247
 HA2  C3   H3    single    0.930  0.020  1.080
 HA2  C2   H2    single    0.930  0.020  1.080
 HA2  C1   H1    single    0.930  0.020  1.080
 HA2  C6   H6    single    0.930  0.020  1.080
 HA2  C5   H5    single    0.930  0.020  1.080
 HA2  C7   H7C1  single    0.970  0.020  1.090
 HA2  C7   H7C2  single    0.970  0.020  1.090
 HA2  C13  H13   single    0.930  0.020  1.080
 HA2  C9   H9    single    0.930  0.020  1.080
 HA2  C12  H12   single    0.930  0.020  1.080
 HA2  C10  H10   single    0.930  0.020  1.080
 HA2  C14  H141  single    0.970  0.020  1.090
 HA2  C14  H142  single    0.970  0.020  1.090
 HA2  C15  H15   single    0.970  0.020  1.090
 HA2  N2   H2N1  single    0.890  0.020  1.040
 HA2  N2   H2N2  single    0.890  0.020  1.040
 HA2  C16  H161  single    0.970  0.020  1.090
 HA2  C16  H162  single    0.970  0.020  1.090
 HA2  O2   HA    single    0.850  0.020  0.980
 HA2  C18  H181  single    0.970  0.020  1.090
 HA2  C18  H182  single    0.970  0.020  1.090
 HA2  C19  H191  single    0.970  0.020  1.090
 HA2  C19  H192  single    0.970  0.020  1.090
 HA2  C20  H201  single    0.970  0.020  1.090
 HA2  C20  H202  single    0.970  0.020  1.090
 HA2  C21  H211  single    0.970  0.020  1.090
 HA2  C21  H212  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
 HA2  H3    C3   C4    120.18  3.000
 HA2  H3    C3   C2    119.44  3.000
 HA2  C4    C3   C2    120.38  3.000
 HA2  H2    C2   C1    119.95  3.000
 HA2  H2    C2   C3    119.77  3.000
 HA2  C1    C2   C3    120.28  3.000
 HA2  H1    C1   C6    120.22  3.000
 HA2  H1    C1   C2    120.16  3.000
 HA2  C6    C1   C2    119.62  3.000
 HA2  H6    C6   C5    119.85  3.000
 HA2  H6    C6   C1    120.15  3.000
 HA2  C5    C6   C1    120.00  3.000
 HA2  H5    C5   C4    119.65  3.000
 HA2  H5    C5   C6    119.67  3.000
 HA2  C4    C5   C6    120.68  3.000
 HA2  C7    C4   C5    120.06  3.000
 HA2  C7    C4   C3    120.88  3.000
 HA2  C5    C4   C3    119.03  3.000
 HA2  H7C2  C7   H7C1  106.67  3.000
 HA2  H7C2  C7   O1    111.47  3.000
 HA2  H7C1  C7   O1    104.86  3.000
 HA2  H7C2  C7   C4    110.30  3.000
 HA2  H7C1  C7   C4    109.89  3.000
 HA2  O1    C7   C4    113.30  3.000
 HA2  C8    O1   C7    119.04  3.000
 HA2  C9    C8   C13   119.14  3.000
 HA2  C9    C8   O1    124.75  3.000
 HA2  C13   C8   O1    116.11  3.000
 HA2  H13   C13  C12   120.21  3.000
 HA2  H13   C13  C8    119.59  3.000
 HA2  C12   C13  C8    120.20  3.000
 HA2  H12   C12  C11   119.63  3.000
 HA2  H12   C12  C13   118.81  3.000
 HA2  C11   C12  C13   121.55  3.000
 HA2  H9    C9   C10   118.52  3.000
 HA2  H9    C9   C8    121.81  3.000
 HA2  C10   C9   C8    119.66  3.000
 HA2  H10   C10  C11   119.52  3.000
 HA2  H10   C10  C9    118.46  3.000
 HA2  C11   C10  C9    122.02  3.000
 HA2  C14   C11  C10   121.58  3.000
 HA2  C14   C11  C12   120.99  3.000
 HA2  C10   C11  C12   117.42  3.000
 HA2  H142  C14  H141  106.19  3.000
 HA2  H142  C14  C15   109.17  3.000
 HA2  H141  C14  C15   108.88  3.000
 HA2  H142  C14  C11   109.62  3.000
 HA2  H141  C14  C11   109.95  3.000
 HA2  C15   C14  C11   112.82  3.000
 HA2  H15   C15  C16   104.72  3.000
 HA2  H15   C15  N2    106.79  3.000
 HA2  C16   C15  N2    115.92  3.000
 HA2  H15   C15  C14   107.70  3.000
 HA2  C16   C15  C14   111.08  3.000
 HA2  N2    C15  C14   110.10  3.000
 HA2  H2N2  N2   H2N1  105.95  3.000
 HA2  H2N2  N2   C15   110.04  3.000
 HA2  H2N1  N2   C15   109.65  3.000
 HA2  H162  C16  H161  106.69  3.000
 HA2  H162  C16  N3    106.75  3.000
 HA2  H161  C16  N3    108.93  3.000
 HA2  H162  C16  C15   109.48  3.000
 HA2  H161  C16  C15   109.45  3.000
 HA2  N3    C16  C15   115.18  3.000
 HA2  C17   N3   O2    118.51  3.000
 HA2  C17   N3   C16   125.20  3.000
 HA2  O2    N3   C16   115.89  3.000
 HA2  HA    O2   N3    106.53  3.000
 HA2  C18   C17  O3    122.96  3.000
 HA2  C18   C17  N3    116.31  3.000
 HA2  O3    C17  N3    120.71  3.000
 HA2  H182  C18  H181  105.38  3.000
 HA2  H182  C18  C19   109.72  3.000
 HA2  H181  C18  C19   109.86  3.000
 HA2  H182  C18  C17   108.35  3.000
 HA2  H181  C18  C17   109.64  3.000
 HA2  C19   C18  C17   113.57  3.000
 HA2  H192  C19  H191  105.94  3.000
 HA2  H192  C19  C20   109.81  3.000
 HA2  H191  C19  C20   108.65  3.000
 HA2  H192  C19  C18   110.04  3.000
 HA2  H191  C19  C18   107.46  3.000
 HA2  C20   C19  C18   114.54  3.000
 HA2  H202  C20  H201  106.20  3.000
 HA2  H202  C20  C21   109.90  3.000
 HA2  H201  C20  C21   109.85  3.000
 HA2  H202  C20  C19   109.01  3.000
 HA2  H201  C20  C19   109.97  3.000
 HA2  C21   C20  C19   111.74  3.000
 HA2  H212  C21  H211  104.75  3.000
 HA2  H212  C21  C22   107.61  3.000
 HA2  H211  C21  C22   108.57  3.000
 HA2  H212  C21  C20   109.00  3.000
 HA2  H211  C21  C20   109.85  3.000
 HA2  C22   C21  C20   116.40  3.000
 HA2  O4    C22  O5    126.13  3.000
 HA2  O4    C22  C21   117.91  3.000
 HA2  O5    C22  C21   115.96  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
 HA2  CONST_01  C6   C1   C2   C3      0.00   0.0  0
 HA2  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 HA2  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 HA2  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 HA2  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 HA2  CONST_06  C4   C5   C6   C1      0.00   0.0  0
 HA2  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 HA2  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 HA2  CONST_09  C10  C9   C8   C13     0.00   0.0  0
 HA2  CONST_10  C10  C11  C12  C13     0.00   0.0  0
 HA2  CONST_11  C9   C8   C13  C12     0.00   0.0  0
 HA2  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 HA2  CONST_13  C7   C4   C3   C2    180.00   0.0  0
 HA2  CONST_14  C7   C4   C5   C6    180.00   0.0  0
 HA2  CONST_15  C12  C13  C8   O1    180.00   0.0  0
 HA2  CONST_16  C10  C9   C8   O1    180.00   0.0  0
 HA2  CONST_17  C14  C11  C12  C13   180.00   0.0  0
 HA2  CONST_18  C14  C11  C10  C9    180.00   0.0  0
 HA2  CONST_19  H1   C1   C2   C3    180.00   0.0  0
 HA2  CONST_20  H5   C5   C4   C3    180.00   0.0  0
 HA2  CONST_21  H6   C6   C1   C2    180.00   0.0  0
 HA2  CONST_22  H3   C3   C2   C1    180.00   0.0  0
 HA2  CONST_23  H2   C2   C1   C6    180.00   0.0  0
 HA2  CONST_24  H12  C12  C13  C8    180.00   0.0  0
 HA2  CONST_25  H10  C10  C9   C8    180.00   0.0  0
 HA2  CONST_26  H9   C9   C8   C13   180.00   0.0  0
 HA2  CONST_27  H13  C13  C8   C9    180.00   0.0  0
 HA2  CONST_28  O3   C17  N3   C16     0.00   0.0  0
 HA2  CONST_29  C18  C17  N3   C16   180.00   0.0  0
 HA2  CONST_30  O3   C17  N3   O2    180.00   0.0  0
 HA2  CONST_31  C18  C17  N3   O2      0.00   0.0  0
 HA2  Var_01    O1   C7   C4   C3    -37.89  30.0  2
 HA2  Var_02    C13  C8   O1   C7    171.94  30.0  2
 HA2  Var_03    C15  C14  C11  C12   -84.81  30.0  2
 HA2  Var_04    O2   N3   C16  C15    64.35  30.0  3
 HA2  Var_05    C19  C18  C17  N3   -178.88  30.0  3
 HA2  Var_06    C20  C19  C18  C17    74.48  30.0  3
 HA2  Var_07    C21  C20  C19  C18   177.45  30.0  3
 HA2  Var_08    C22  C21  C20  C19   179.66  30.0  3
 HA2  Var_09    O5   C22  C21  C20   167.21  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
 HA2  chir_01  C15  C14  N2  C16  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
 HA2  plan-1  C3   0.020
 HA2  plan-1  C2   0.020
 HA2  plan-1  C1   0.020
 HA2  plan-1  C6   0.020
 HA2  plan-1  C5   0.020
 HA2  plan-1  C4   0.020
 HA2  plan-1  C7   0.020
 HA2  plan-1  H3   0.020
 HA2  plan-1  H2   0.020
 HA2  plan-1  H1   0.020
 HA2  plan-1  H6   0.020
 HA2  plan-1  H5   0.020
 HA2  plan-2  O1   0.020
 HA2  plan-2  C8   0.020
 HA2  plan-2  C13  0.020
 HA2  plan-2  C12  0.020
 HA2  plan-2  C9   0.020
 HA2  plan-2  C10  0.020
 HA2  plan-2  C11  0.020
 HA2  plan-2  C14  0.020
 HA2  plan-2  H13  0.020
 HA2  plan-2  H9   0.020
 HA2  plan-2  H12  0.020
 HA2  plan-2  H10  0.020
 HA2  plan-3  C16  0.020
 HA2  plan-3  N3   0.020
 HA2  plan-3  O2   0.020
 HA2  plan-3  C17  0.020
 HA2  plan-3  O3   0.020
 HA2  plan-3  C18  0.020
 HA2  plan-4  C21  0.020
 HA2  plan-4  C22  0.020
 HA2  plan-4  O5   0.020
 HA2  plan-4  O4   0.020

