# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 21:57:38 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: (2S)-[(1S,3S,4S,5R,8R)-2,4,5,8-tetrahydroxy-7-oxa-2-azabicyclo[3.2.1]oct-3-yl](L-tyrosylamino)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H]([C@H]2[C@H](O)[C@]3(O)CO[C@@H]([C@@H]3O)N2O)C(O)=O
#
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
 383  383  '(2S)-[(1S,3S,4S,5R,8R)-2,4,5,8-tetrahydroxy-7-oxa-2-azabicyclo[3.2.1]oct-3-yl](L-tyrosylamino)ethanoic acid'  ligand  52  29  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_383
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
 383  C8    C  CR16  0  -0.296   -9.5084  10.4588  83.3951
 383  C7    C  CR16  0  -0.325   -9.4536   9.1096  83.7089
 383  C12   C  CR6   0   0.340   -9.7182   8.6886  85.0092
 383  C11   C  CR16  0  -0.369  -10.0319   9.6346  85.9824
 383  C10   C  CR16  0  -0.290  -10.0829  10.9797  85.6493
 383  C9    C  CR6   0   0.092   -9.8241  11.4193  84.3538
 383  C14   C  CH2   0  -0.507   -9.9186  12.8763  84.0003
 383  C15   C  CH1   0  -0.200  -11.3674  13.3144  83.7126
 383  C17   C  C     0   0.555  -11.3577  14.8118  83.4332
 383  N19   N  NH1   0  -0.647  -11.4338  15.5736  84.5398
 383  C20   C  CH1   0  -0.189  -11.3185  17.0013  84.5083
 383  C21   C  C     0   0.555   -9.9075  17.5133  84.2511
 383  O23   O  OH1   0  -0.579   -8.9869  16.5662  84.2485
 383  O18   O  O     0  -0.480  -11.2565  15.2864  82.3148
 383  N16   N  NH2   0  -0.796  -11.8855  12.6039  82.5667
 383  O22   O  O     0  -0.446   -9.6812  18.6774  84.0343
 383  C6    C  CH1   0  -0.131  -11.8970  17.5818  85.8079
 383  N5    N  NT    0  -0.222  -11.2767  16.9150  86.9454
 383  C4    C  CH1   0   0.114  -11.9682  17.1287  88.1896
 383  C3    C  CH1   0   0.002  -13.3417  16.4753  88.0997
 383  C2    C  CT    0   0.129  -14.0203  17.5242  87.2195
 383  C1    C  CH1   0   0.012  -13.4299  17.4089  85.8105
 383  O28   O  OH1   0  -0.556   -9.9608  17.3918  87.0478
 383  O29   O  OH1   0  -0.667  -15.4062  17.3594  87.1975
 383  C30   C  CH2   0  -0.195  -13.5520  18.7964  87.9366
 383  O31   O  O2    0  -0.490  -12.2548  18.4885  88.4469
 383  O32   O  OH1   0  -0.652  -13.2712  15.1804  87.5845
 383  O64   O  OH1   0  -0.670  -14.0003  18.4052  84.9915
 383  O13   O  OH1   0  -0.634   -9.6535   7.3666  85.2711
 383  H8    H  HCR6  0   0.253   -9.2945  10.7699  82.3793
 383  H7    H  HCR6  0   0.261   -9.2045   8.3808  82.9472
 383  H11   H  HCR6  0   0.269  -10.2347   9.3242  87.0015
 383  H10   H  HCR6  0   0.250  -10.3224  11.7008  86.4228
 383  H141  H  HCH2  0   0.255   -9.5210  13.4837  84.8164
 383  H142  H  HCH2  0   0.256   -9.3111  13.0891  83.1177
 383  H15   H  HCH1  0   0.235  -11.9541  13.1446  84.6297
 383  H19   H  HNH1  0   0.396  -11.5067  15.1450  85.4525
 383  H20   H  HCH1  0   0.302  -11.9129  17.4037  83.6818
 383  H23   H  HOH1  0   0.484   -8.1174  16.9529  84.0644
 383  H161  H  HNH2  0   0.351  -12.8504  12.8627  82.4037
 383  H162  H  HNH2  0   0.356  -11.8967  11.6122  82.7698
 383  H6    H  HCH1  0   0.278  -11.6889  18.6597  85.8243
 383  H4    H  HCH1  0   0.276  -11.3459  16.7412  88.9970
 383  H3    H  HCH1  0   0.261  -13.8038  16.4878  89.0970
 383  H1    H  HCH1  0   0.257  -13.6869  16.4155  85.4287
 383  H28   H  HOH1  0   0.469   -9.4150  16.5973  87.0657
 383  H29   H  HOH1  0   0.450  -15.7701  17.9437  86.5216
 383  H301  H  HCH2  0   0.241  -13.5001  19.6734  87.2856
 383  H302  H  HCH2  0   0.239  -14.2354  19.0276  88.7603
 383  H32   H  HOH1  0   0.461  -14.1582  14.8055  87.5862
 383  H64   H  HOH1  0   0.469  -14.3434  17.9995  84.1913
 383  H13   H  HOH1  0   0.473   -9.8590   7.1973  86.1970

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
 383  C8   C7    aromatic  1.386  0.020  1.386
 383  C8   C9    aromatic  1.393  0.020  1.393
 383  C8   H8    single    0.930  0.020  1.080
 383  C7   C12   aromatic  1.392  0.020  1.392
 383  C7   H7    single    0.930  0.020  1.080
 383  C12  C11   aromatic  1.393  0.020  1.393
 383  C12  O13   single    1.349  0.020  1.349
 383  C11  C10   aromatic  1.387  0.020  1.387
 383  C11  H11   single    0.930  0.020  1.080
 383  C10  C9    aromatic  1.392  0.020  1.392
 383  C10  H10   single    0.930  0.020  1.080
 383  C9   C14   single    1.502  0.020  1.502
 383  C14  C15   single    1.541  0.020  1.541
 383  C14  H141  single    0.970  0.020  1.090
 383  C14  H142  single    0.970  0.020  1.090
 383  C15  C17   single    1.523  0.020  1.523
 383  C15  N16   single    1.444  0.020  1.444
 383  C15  H15   single    0.970  0.020  1.090
 383  C17  N19   single    1.346  0.020  1.346
 383  C17  O18   double    1.219  0.020  1.219
 383  N19  C20   single    1.433  0.020  1.433
 383  N19  H19   single    0.860  0.020  1.020
 383  C20  C21   single    1.523  0.020  1.523
 383  C20  C6    single    1.536  0.020  1.536
 383  C20  H20   single    0.970  0.020  1.090
 383  C21  O23   single    1.321  0.020  1.321
 383  C21  O22   double    1.206  0.020  1.206
 383  O23  H23   single    0.850  0.020  0.980
 383  N16  H161  single    0.890  0.020  1.040
 383  N16  H162  single    0.890  0.020  1.040
 383  C6   N5    single    1.457  0.020  1.457
 383  C6   C1    single    1.543  0.020  1.543
 383  C6   H6    single    0.970  0.020  1.090
 383  N5   C4    single    1.439  0.020  1.439
 383  N5   O28   single    1.403  0.020  1.403
 383  C4   C3    single    1.524  0.020  1.524
 383  C4   O31   single    1.413  0.020  1.413
 383  C4   H4    single    0.970  0.020  1.090
 383  C3   C2    single    1.528  0.020  1.528
 383  C3   O32   single    1.395  0.020  1.395
 383  C3   H3    single    0.970  0.020  1.090
 383  C2   C1    single    1.532  0.020  1.532
 383  C2   O29   single    1.396  0.020  1.396
 383  C2   C30   single    1.534  0.020  1.534
 383  C1   O64   single    1.410  0.020  1.410
 383  C1   H1    single    0.970  0.020  1.090
 383  O28  H28   single    0.850  0.020  0.980
 383  O29  H29   single    0.850  0.020  0.980
 383  C30  O31   single    1.428  0.020  1.428
 383  C30  H301  single    0.970  0.020  1.090
 383  C30  H302  single    0.970  0.020  1.090
 383  O32  H32   single    0.850  0.020  0.980
 383  O64  H64   single    0.850  0.020  0.980
 383  O13  H13   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
 383  H8    C8   C9    119.46  3.000
 383  H8    C8   C7    118.93  3.000
 383  C9    C8   C7    121.61  3.000
 383  H7    C7   C12   119.80  3.000
 383  H7    C7   C8    120.32  3.000
 383  C12   C7   C8    119.88  3.000
 383  O13   C12  C11   122.73  3.000
 383  O13   C12  C7    117.93  3.000
 383  C11   C12  C7    119.34  3.000
 383  H11   C11  C10   119.77  3.000
 383  H11   C11  C12   120.28  3.000
 383  C10   C11  C12   119.95  3.000
 383  H10   C10  C9    119.65  3.000
 383  H10   C10  C11   118.81  3.000
 383  C9    C10  C11   121.53  3.000
 383  C14   C9   C10   120.90  3.000
 383  C14   C9   C8    121.39  3.000
 383  C10   C9   C8    117.69  3.000
 383  H142  C14  H141  107.03  3.000
 383  H142  C14  C15   108.46  3.000
 383  H141  C14  C15   108.88  3.000
 383  H142  C14  C9    110.13  3.000
 383  H141  C14  C9    109.92  3.000
 383  C15   C14  C9    112.26  3.000
 383  H15   C15  N16   113.17  3.000
 383  H15   C15  C17   107.91  3.000
 383  N16   C15  C17   109.89  3.000
 383  H15   C15  C14   107.55  3.000
 383  N16   C15  C14   110.22  3.000
 383  C17   C15  C14   107.93  3.000
 383  O18   C17  N19   122.60  3.000
 383  O18   C17  C15   123.47  3.000
 383  N19   C17  C15   113.91  3.000
 383  H19   N19  C20   116.62  3.000
 383  H19   N19  C17   120.43  3.000
 383  C20   N19  C17   122.79  3.000
 383  H20   C20  C6    107.17  3.000
 383  H20   C20  C21   104.60  3.000
 383  C6    C20  C21   111.39  3.000
 383  H20   C20  N19   109.83  3.000
 383  C6    C20  N19   109.13  3.000
 383  C21   C20  N19   114.41  3.000
 383  O22   C21  O23   124.14  3.000
 383  O22   C21  C20   121.94  3.000
 383  O23   C21  C20   113.89  3.000
 383  H23   O23  C21   109.85  3.000
 383  H162  N16  H161  105.79  3.000
 383  H162  N16  C15   109.07  3.000
 383  H161  N16  C15   110.12  3.000
 383  H6    C6   C1    107.36  3.000
 383  H6    C6   N5    110.90  3.000
 383  C1    C6   N5    111.74  3.000
 383  H6    C6   C20   108.20  3.000
 383  C1    C6   C20   109.47  3.000
 383  N5    C6   C20   109.09  3.000
 383  O28   N5   C4    109.69  3.000
 383  O28   N5   C6    107.50  3.000
 383  C4    N5   C6    113.72  3.000
 383  H4    C4   O31   108.83  3.000
 383  H4    C4   C3    113.93  3.000
 383  O31   C4   C3    103.92  3.000
 383  H4    C4   N5    108.25  3.000
 383  O31   C4   N5    113.43  3.000
 383  C3    C4   N5    108.57  3.000
 383  H3    C3   O32   111.52  3.000
 383  H3    C3   C2    109.15  3.000
 383  O32   C3   C2    116.54  3.000
 383  H3    C3   C4    108.69  3.000
 383  O32   C3   C4    111.97  3.000
 383  C2    C3   C4     98.04  3.000
 383  C30   C2   O29   114.11  3.000
 383  C30   C2   C1    112.01  3.000
 383  O29   C2   C1    111.05  3.000
 383  C30   C2   C3     99.47  3.000
 383  O29   C2   C3    111.65  3.000
 383  C1    C2   C3    107.87  3.000
 383  H1    C1   O64   110.09  3.000
 383  H1    C1   C2    107.38  3.000
 383  O64   C1   C2    108.97  3.000
 383  H1    C1   C6    109.53  3.000
 383  O64   C1   C6    108.77  3.000
 383  C2    C1   C6    112.09  3.000
 383  H28   O28  N5    104.62  3.000
 383  H29   O29  C2    108.30  3.000
 383  H302  C30  H301  107.95  3.000
 383  H302  C30  O31   110.11  3.000
 383  H301  C30  O31   110.04  3.000
 383  H302  C30  C2    109.65  3.000
 383  H301  C30  C2    113.66  3.000
 383  O31   C30  C2    105.41  3.000
 383  C30   O31  C4    109.07  3.000
 383  H32   O32  C3    108.31  3.000
 383  H64   O64  C1    109.26  3.000
 383  H13   O13  C12   110.39  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
 383  CONST_01  C11  C12  C7   C8     0.00   0.0  0
 383  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 383  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 383  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 383  CONST_05  C9   C8   C7   C12    0.00   0.0  0
 383  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 383  CONST_07  O13  C12  C7   C8   180.00   0.0  0
 383  CONST_08  C14  C9   C8   C7   180.00   0.0  0
 383  CONST_09  C14  C9   C10  C11  180.00   0.0  0
 383  CONST_10  O13  C12  C11  C10  180.00   0.0  0
 383  CONST_11  H10  C10  C9   C8   180.00   0.0  0
 383  CONST_12  H11  C11  C12  C7   180.00   0.0  0
 383  CONST_13  H8   C8   C7   C12  180.00   0.0  0
 383  CONST_14  H7   C7   C12  C11  180.00   0.0  0
 383  CONST_15  C20  N19  C17  C15  180.00   0.0  0
 383  CONST_16  O18  C17  N19  C20    0.00   0.0  0
 383  CONST_17  H19  N19  C17  C15    0.00   0.0  0
 383  CONST_18  H23  O23  C21  C20  180.00   0.0  0
 383  Var_01    C2   C30  O31  C4    -4.66  30.0  3
 383  Var_02    C15  C14  C9   C8    96.05  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
 383  chir_01  C15  C14  C17  N16  negativ
 383  chir_02  C20  N19  C21  C6   positiv
 383  chir_03  C6   N5   C1   C20  positiv
 383  chir_04  C4   O31  N5   C3   positiv
 383  chir_05  C3   O32  C4   C2   negativ
 383  chir_06  C2   C30  C1   C3   negativ
 383  chir_07  C1   O64  C2   C6   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
 383  plan-1  C8   0.020
 383  plan-1  C7   0.020
 383  plan-1  C12  0.020
 383  plan-1  C11  0.020
 383  plan-1  C10  0.020
 383  plan-1  C9   0.020
 383  plan-1  C14  0.020
 383  plan-1  O13  0.020
 383  plan-1  H8   0.020
 383  plan-1  H7   0.020
 383  plan-1  H11  0.020
 383  plan-1  H10  0.020
 383  plan-2  C15  0.020
 383  plan-2  C17  0.020
 383  plan-2  N19  0.020
 383  plan-2  C20  0.020
 383  plan-2  O18  0.020
 383  plan-2  H19  0.020
 383  plan-3  C20  0.020
 383  plan-3  C21  0.020
 383  plan-3  O23  0.020
 383  plan-3  O22  0.020
 383  plan-3  H23  0.020

