# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:54:53 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  57  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  -0.279   7.4335  39.9228  67.0221
 HA2  C2    C  CR16  0  -0.241   7.2733  38.5866  66.6828
 HA2  C1    C  CR16  0  -0.267   7.5057  37.5914  67.6242
 HA2  C6    C  CR16  0  -0.242   7.9038  37.9408  68.9073
 HA2  C5    C  CR16  0  -0.295   8.0727  39.2780  69.2422
 HA2  C4    C  CR6   0   0.040   7.8365  40.2795  68.3062
 HA2  C7    C  CH2   0  -0.251   7.9744  41.7267  68.7044
 HA2  O1    O  O2    0  -0.485   8.4468  42.5544  67.6631
 HA2  C8    C  CR6   0   0.375   9.7324  42.4290  67.2544
 HA2  C13   C  CR16  0  -0.340  10.0992  43.1875  66.1437
 HA2  C12   C  CR16  0  -0.297  11.3985  43.1426  65.6683
 HA2  C9    C  CR16  0  -0.345  10.6866  41.6257  67.8714
 HA2  C10   C  CR16  0  -0.298  11.9845  41.5935  67.3743
 HA2  C11   C  CR6   0   0.154  12.3696  42.3453  66.2724
 HA2  C14   C  CH2   0  -0.535  13.7676  42.2872  65.7285
 HA2  C15   C  CH1   0  -0.086  13.9277  41.2617  64.6014
 HA2  N2    N  NH2   0  -0.778  13.6429  39.9277  65.0974
 HA2  C16   C  CH2   0  -0.327  15.2756  41.4366  63.8797
 HA2  N3    N  NT    0  -0.204  16.4342  41.4895  64.7433
 HA2  O2    O  OH1   0  -0.546  16.7176  40.3411  65.4364
 HA2  C17   C  C     0   0.559  17.1314  42.6119  65.0429
 HA2  O3    O  O     0  -0.493  16.8696  43.6755  64.5006
 HA2  C18   C  CH2   0  -0.577  18.2564  42.4573  66.0461
 HA2  C19   C  CH2   0  -0.424  18.9580  43.7676  66.3732
 HA2  C20   C  CH2   0  -0.433  18.1373  44.7076  67.2482
 HA2  C21   C  CH2   0  -0.548  18.9328  45.9694  67.5908
 HA2  C22   C  C     0   0.530  18.1924  46.9238  68.4849
 HA2  O5    O  O     0  -0.449  18.5737  47.2986  69.5671
 HA2  O4    O  OH1   0  -0.593  17.0450  47.3286  67.9473
 HA2  H3    H  HCR6  0   0.253   7.2473  40.6868  66.2775
 HA2  H2    H  HCR6  0   0.256   6.9631  38.3209  65.6804
 HA2  H1    H  HCR6  0   0.257   7.3800  36.5502  67.3571
 HA2  H6    H  HCR6  0   0.256   8.0927  37.1727  69.6460
 HA2  H5    H  HCR6  0   0.254   8.3975  39.5440  70.2419
 HA2  H7C1  H  HCH2  0   0.275   6.9956  42.1338  68.9644
 HA2  H7C2  H  HCH2  0   0.239   8.5999  41.8157  69.5995
 HA2  H13   H  HCR6  0   0.257   9.3634  43.8186  65.6604
 HA2  H9    H  HCR6  0   0.272  10.4490  41.0205  68.7354
 HA2  H12   H  HCR6  0   0.244  11.6598  43.7447  64.8053
 HA2  H10   H  HCR6  0   0.242  12.7109  40.9610  67.8695
 HA2  H141  H  HCH2  0   0.248  14.0617  43.2712  65.3542
 HA2  H142  H  HCH2  0   0.239  14.4665  42.0469  66.5359
 HA2  H15   H  HCH1  0   0.239  13.1727  41.4847  63.8384
 HA2  H2N1  H  HNH2  0   0.344  13.7363  39.2563  64.3452
 HA2  H2N2  H  HNH2  0   0.336  14.3270  39.6625  65.7940
 HA2  H161  H  HCH2  0   0.256  15.4113  40.6254  63.1574
 HA2  H162  H  HCH2  0   0.257  15.2655  42.3640  63.3095
 HA2  HA    H  HOH1  0   0.476  17.2739  39.8013  64.8569
 HA2  H181  H  HCH2  0   0.264  17.8774  41.9988  66.9635
 HA2  H182  H  HCH2  0   0.276  18.9829  41.7450  65.6436
 HA2  H191  H  HCH2  0   0.234  19.8875  43.5237  66.8948
 HA2  H192  H  HCH2  0   0.228  19.2506  44.2793  65.4532
 HA2  H201  H  HCH2  0   0.242  17.2112  44.9765  66.7409
 HA2  H202  H  HCH2  0   0.229  17.8559  44.1906  68.1708
 HA2  H211  H  HCH2  0   0.257  19.8688  45.7028  68.0825
 HA2  H212  H  HCH2  0   0.269  19.1923  46.4944  66.6659
 HA2  H4    H  HOH1  0   0.480  16.5949  47.9398  68.5494

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  1.392  0.020  1.392
 HA2  C2   C1    aromatic  1.389  0.020  1.389
 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    1.451  0.020  1.451
 HA2  C15  C16   single    1.539  0.020  1.539
 HA2  C16  N3    single    1.446  0.020  1.446
 HA2  N3   O2    single    1.371  0.020  1.371
 HA2  N3   C17   single    1.355  0.020  1.355
 HA2  C17  O3    double    1.222  0.020  1.222
 HA2  C17  C18   single    1.515  0.020  1.515
 HA2  C18  C19   single    1.522  0.020  1.522
 HA2  C19  C20   single    1.524  0.020  1.524
 HA2  C20  C21   single    1.531  0.020  1.531
 HA2  C21  C22   single    1.503  0.020  1.503
 HA2  C22  O5    double    1.207  0.020  1.207
 HA2  C22  O4    single    1.330  0.020  1.330
 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
 HA2  O4   H4    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
 HA2  H3    C3   C4    120.21  3.000
 HA2  H3    C3   C2    119.43  3.000
 HA2  C4    C3   C2    120.36  3.000
 HA2  H2    C2   C1    119.97  3.000
 HA2  H2    C2   C3    119.72  3.000
 HA2  C1    C2   C3    120.31  3.000
 HA2  H1    C1   C6    120.23  3.000
 HA2  H1    C1   C2    120.17  3.000
 HA2  C6    C1   C2    119.60  3.000
 HA2  H6    C6   C5    119.83  3.000
 HA2  H6    C6   C1    120.15  3.000
 HA2  C5    C6   C1    120.01  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    119.86  3.000
 HA2  C7    C4   C3    121.07  3.000
 HA2  C5    C4   C3    119.04  3.000
 HA2  H7C2  C7   H7C1  106.68  3.000
 HA2  H7C2  C7   O1    111.35  3.000
 HA2  H7C1  C7   O1    104.90  3.000
 HA2  H7C2  C7   C4    110.25  3.000
 HA2  H7C1  C7   C4    109.81  3.000
 HA2  O1    C7   C4    113.50  3.000
 HA2  C8    O1   C7    119.07  3.000
 HA2  C9    C8   C13   119.14  3.000
 HA2  C9    C8   O1    124.77  3.000
 HA2  C13   C8   O1    116.08  3.000
 HA2  H13   C13  C12   120.22  3.000
 HA2  H13   C13  C8    119.59  3.000
 HA2  C12   C13  C8    120.19  3.000
 HA2  H12   C12  C11   119.65  3.000
 HA2  H12   C12  C13   118.78  3.000
 HA2  C11   C12  C13   121.57  3.000
 HA2  H9    C9   C10   118.55  3.000
 HA2  H9    C9   C8    121.79  3.000
 HA2  C10   C9   C8    119.66  3.000
 HA2  H10   C10  C11   119.54  3.000
 HA2  H10   C10  C9    118.44  3.000
 HA2  C11   C10  C9    122.02  3.000
 HA2  C14   C11  C10   121.66  3.000
 HA2  C14   C11  C12   120.92  3.000
 HA2  C10   C11  C12   117.41  3.000
 HA2  H142  C14  H141  106.17  3.000
 HA2  H142  C14  C15   109.20  3.000
 HA2  H141  C14  C15   108.81  3.000
 HA2  H142  C14  C11   109.62  3.000
 HA2  H141  C14  C11   109.86  3.000
 HA2  C15   C14  C11   112.94  3.000
 HA2  H15   C15  C16   104.70  3.000
 HA2  H15   C15  N2    106.83  3.000
 HA2  C16   C15  N2    115.89  3.000
 HA2  H15   C15  C14   107.69  3.000
 HA2  C16   C15  C14   111.13  3.000
 HA2  N2    C15  C14   110.07  3.000
 HA2  H2N2  N2   H2N1  105.98  3.000
 HA2  H2N2  N2   C15   110.09  3.000
 HA2  H2N1  N2   C15   109.72  3.000
 HA2  H162  C16  H161  106.67  3.000
 HA2  H162  C16  N3    106.80  3.000
 HA2  H161  C16  N3    108.78  3.000
 HA2  H162  C16  C15   109.53  3.000
 HA2  H161  C16  C15   109.50  3.000
 HA2  N3    C16  C15   115.20  3.000
 HA2  C17   N3   O2    118.41  3.000
 HA2  C17   N3   C16   125.07  3.000
 HA2  O2    N3   C16   115.91  3.000
 HA2  HA    O2   N3    106.46  3.000
 HA2  C18   C17  O3    122.79  3.000
 HA2  C18   C17  N3    116.35  3.000
 HA2  O3    C17  N3    120.83  3.000
 HA2  H182  C18  H181  105.41  3.000
 HA2  H182  C18  C19   109.48  3.000
 HA2  H181  C18  C19   109.91  3.000
 HA2  H182  C18  C17   108.41  3.000
 HA2  H181  C18  C17   109.93  3.000
 HA2  C19   C18  C17   113.37  3.000
 HA2  H192  C19  H191  106.17  3.000
 HA2  H192  C19  C20   109.80  3.000
 HA2  H191  C19  C20   108.75  3.000
 HA2  H192  C19  C18   110.22  3.000
 HA2  H191  C19  C18   107.60  3.000
 HA2  C20   C19  C18   113.96  3.000
 HA2  H202  C20  H201  106.89  3.000
 HA2  H202  C20  C21   109.54  3.000
 HA2  H201  C20  C21   110.03  3.000
 HA2  H202  C20  C19   109.34  3.000
 HA2  H201  C20  C19   110.04  3.000
 HA2  C21   C20  C19   110.93  3.000
 HA2  H212  C21  H211  107.14  3.000
 HA2  H212  C21  C22   108.36  3.000
 HA2  H211  C21  C22   108.06  3.000
 HA2  H212  C21  C20   109.23  3.000
 HA2  H211  C21  C20   110.21  3.000
 HA2  C22   C21  C20   113.62  3.000
 HA2  O4    C22  O5    122.70  3.000
 HA2  O4    C22  C21   112.20  3.000
 HA2  O5    C22  C21   125.10  3.000
 HA2  H4    O4   C22   109.97  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  CONST_32  H4   O4   C22  C21   180.00   0.0  0
 HA2  Var_01    O1   C7   C4   C3    -35.55  30.0  2
 HA2  Var_02    C13  C8   O1   C7    174.33  30.0  2
 HA2  Var_03    C15  C14  C11  C12   -85.39  30.0  2
 HA2  Var_04    O2   N3   C16  C15    65.51  30.0  3
 HA2  Var_05    C19  C18  C17  N3   -177.76  30.0  3
 HA2  Var_06    C20  C19  C18  C17    73.10  30.0  3
 HA2  Var_07    C21  C20  C19  C18   177.19  30.0  3
 HA2  Var_08    C22  C21  C20  C19  -178.42  30.0  3
 HA2  Var_09    O5   C22  C21  C20   121.40  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
 HA2  plan-4  H4   0.020

