# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:26:57 2022
#   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  51  29  .  2022-03-10  2022-03-10
;
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  -0.307   0.5613   0.3796  -5.3619
 383  C7    C  CR16   0  -0.371  -0.1267   0.0384  -6.5189
 383  C12   C  CR6    0   0.337  -1.0268  -1.0220  -6.5045
 383  C11   C  CR16   0  -0.323  -1.2238  -1.7334  -5.3222
 383  C10   C  CR16   0  -0.290  -0.5275  -1.3783  -4.1790
 383  C9    C  CR6    0   0.108   0.3800  -0.3191  -4.1721
 383  C14   C  CH2    0  -0.524   1.0880   0.0833  -2.9122
 383  C15   C  CH1    0  -0.230   0.2278   1.0320  -2.0456
 383  C17   C  C      0   0.574   1.0059   1.3185  -0.7705
 383  N19   N  NH1    0  -0.618   0.6567   0.5794   0.2867
 383  C20   C  CH1    0  -0.216   1.4682   0.4583   1.4677
 383  C21   C  C      0   0.434   2.7200  -0.4437   1.2651
 383  O23   O  OC    -1  -0.581   2.9398  -0.8774   0.1249
 383  O18   O  O      0  -0.515   1.8979   2.1582  -0.7515
 383  N16   N  NH2    0  -0.787  -0.1294   2.2861  -2.6769
 383  O22   O  O      0  -0.617   3.4190  -0.5975   2.2872
 383  C6    C  CH1    0  -0.145   0.5837   0.0164   2.6363
 383  N5    N  NT     0  -0.188  -0.1529  -1.1936   2.2745
 383  C4    C  CH1    0   0.076  -1.2336  -1.5066   3.1654
 383  C3    C  CH1    0   0.004  -2.2742  -0.3933   3.0942
 383  C2    C  CT     0   0.132  -1.5272   0.6573   3.9134
 383  C1    C  CH1    0   0.042  -0.3544   1.1659   3.0736
 383  O28   O  OH1    0  -0.561   0.7172  -2.2766   2.1560
 383  O29   O  OH1    0  -0.666  -2.2798   1.7667   4.3020
 383  C30   C  CH2    0  -0.195  -1.0463  -0.2187   5.0803
 383  O31   O  O2     0  -0.496  -0.8516  -1.5209   4.5326
 383  O32   O  OH1    0  -0.651  -2.6084   0.0640   1.8224
 383  O64   O  OH1    0  -0.667   0.3747   2.0855   3.8500
 383  O13   O  OH1    0  -0.635  -1.7255  -1.4025  -7.5952
 383  H8    H  HCR6   0   0.254   1.2621   1.2056  -5.3956
 383  H7    H  HCR6   0   0.267   0.0427   0.5995  -7.4313
 383  H11   H  HCR6   0   0.260  -1.9198  -2.5630  -5.3035
 383  H10   H  HCR6   0   0.247  -0.6930  -1.9442  -3.2692
 383  H141  H  HCH2   0   0.246   2.0254   0.5915  -3.1545
 383  H142  H  HCH2   0   0.254   1.3522  -0.7977  -2.3217
 383  H15   H  HCH1   0   0.250  -0.7002   0.5080  -1.7943
 383  H19   H  HNH1   0   0.386  -0.0667  -0.1156   0.1770
 383  H20   H  HCH1   0   0.241   1.8630   1.4491   1.7165
 383  H161  H  HNH2   0   0.340   0.7150   2.7854  -2.9319
 383  H162  H  HNH2   0   0.352  -0.6159   2.0975  -3.5450
 383  H6    H  HCH1   0   0.248   1.2464  -0.1814   3.4914
 383  H4    H  HCH1   0   0.271  -1.6160  -2.4949   2.9047
 383  H3    H  HCH1   0   0.249  -3.1651  -0.7218   3.6516
 383  H1    H  HCH1   0   0.247  -0.7630   1.6578   2.1845
 383  H28   H  HOH1   0   0.444   1.2123  -2.3508   2.9882
 383  H29   H  HOH1   0   0.451  -3.0656   1.4630   4.7700
 383  H301  H  HCH2   0   0.243  -0.1203   0.1408   5.5367
 383  H302  H  HCH2   0   0.236  -1.8113  -0.2576   5.8644
 383  H32   H  HOH1   0   0.459  -2.9965  -0.6614   1.3233
 383  H64   H  HOH1   0   0.457   0.8246   2.7001   3.2642
 383  H13   H  HOH1   0   0.473  -1.5075  -0.8378  -8.3448

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  1.389  0.020  1.389
 383  C8   C9    aromatic  1.392  0.020  1.392
 383  C8   H8    single    0.930  0.020  1.080
 383  C7   C12   aromatic  1.391  0.020  1.391
 383  C7   H7    single    0.930  0.020  1.080
 383  C12  C11   aromatic  1.394  0.020  1.394
 383  C12  O13   single    1.350  0.020  1.350
 383  C11  C10   aromatic  1.385  0.020  1.385
 383  C11  H11   single    0.930  0.020  1.080
 383  C10  C9    aromatic  1.395  0.020  1.395
 383  C10  H10   single    0.930  0.020  1.080
 383  C9   C14   single    1.500  0.020  1.500
 383  C14  C15   single    1.546  0.020  1.546
 383  C14  H141  single    0.970  0.020  1.090
 383  C14  H142  single    0.970  0.020  1.090
 383  C15  C17   single    1.521  0.020  1.521
 383  C15  N16   single    1.449  0.020  1.449
 383  C15  H15   single    0.970  0.020  1.090
 383  C17  N19   single    1.336  0.020  1.336
 383  C17  O18   double    1.225  0.020  1.225
 383  N19  C20   single    1.438  0.020  1.438
 383  N19  H19   single    0.860  0.020  1.020
 383  C20  C21   single    1.556  0.020  1.556
 383  C20  C6    single    1.531  0.020  1.531
 383  C20  H20   single    0.970  0.020  1.090
 383  C21  O23   deloc     1.240  0.020  1.240
 383  C21  O22   deloc     1.248  0.020  1.248
 383  N16  H161  single    0.890  0.020  1.040
 383  N16  H162  single    0.890  0.020  1.040
 383  C6   N5    single    1.462  0.020  1.462
 383  C6   C1    single    1.547  0.020  1.547
 383  C6   H6    single    0.970  0.020  1.090
 383  N5   C4    single    1.435  0.020  1.435
 383  N5   O28   single    1.394  0.020  1.394
 383  C4   C3    single    1.526  0.020  1.526
 383  C4   O31   single    1.420  0.020  1.420
 383  C4   H4    single    0.970  0.020  1.090
 383  C3   C2    single    1.527  0.020  1.527
 383  C3   O32   single    1.392  0.020  1.392
 383  C3   H3    single    0.970  0.020  1.090
 383  C2   C1    single    1.529  0.020  1.529
 383  C2   O29   single    1.396  0.020  1.396
 383  C2   C30   single    1.536  0.020  1.536
 383  C1   O64   single    1.407  0.020  1.407
 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    1.426  0.020  1.426
 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    119.57  3.000
 383  H8    C8   C7    118.80  3.000
 383  C9    C8   C7    121.63  3.000
 383  H7    C7   C12   120.28  3.000
 383  H7    C7   C8    119.77  3.000
 383  C12   C7   C8    119.96  3.000
 383  O13   C12  C11   117.93  3.000
 383  O13   C12  C7    122.78  3.000
 383  C11   C12  C7    119.29  3.000
 383  H11   C11  C10   120.35  3.000
 383  H11   C11  C12   119.76  3.000
 383  C10   C11  C12   119.89  3.000
 383  H10   C10  C9    119.44  3.000
 383  H10   C10  C11   118.82  3.000
 383  C9    C10  C11   121.73  3.000
 383  C14   C9   C10   120.99  3.000
 383  C14   C9   C8    121.46  3.000
 383  C10   C9   C8    117.50  3.000
 383  H142  C14  H141  106.68  3.000
 383  H142  C14  C15   109.04  3.000
 383  H141  C14  C15   108.42  3.000
 383  H142  C14  C9    110.59  3.000
 383  H141  C14  C9    110.07  3.000
 383  C15   C14  C9    111.89  3.000
 383  H15   C15  N16   107.78  3.000
 383  H15   C15  C17   109.35  3.000
 383  N16   C15  C17   109.17  3.000
 383  H15   C15  C14   107.85  3.000
 383  N16   C15  C14   115.09  3.000
 383  C17   C15  C14   107.51  3.000
 383  O18   C17  N19   123.85  3.000
 383  O18   C17  C15   120.97  3.000
 383  N19   C17  C15   115.17  3.000
 383  H19   N19  C20   115.83  3.000
 383  H19   N19  C17   118.83  3.000
 383  C20   N19  C17   123.29  3.000
 383  H20   C20  C6    107.22  3.000
 383  H20   C20  C21   105.30  3.000
 383  C6    C20  C21   113.38  3.000
 383  H20   C20  N19   108.29  3.000
 383  C6    C20  N19   108.98  3.000
 383  C21   C20  N19   113.32  3.000
 383  O22   C21  O23   127.66  3.000
 383  O22   C21  C20   114.55  3.000
 383  O23   C21  C20   117.72  3.000
 383  H162  N16  H161  106.04  3.000
 383  H162  N16  C15   109.31  3.000
 383  H161  N16  C15   109.31  3.000
 383  H6    C6   C1    106.22  3.000
 383  H6    C6   N5    110.31  3.000
 383  C1    C6   N5    112.30  3.000
 383  H6    C6   C20   107.29  3.000
 383  C1    C6   C20   110.59  3.000
 383  N5    C6   C20   109.94  3.000
 383  O28   N5   C4    110.69  3.000
 383  O28   N5   C6    110.46  3.000
 383  C4    N5   C6    113.97  3.000
 383  H4    C4   O31   108.37  3.000
 383  H4    C4   C3    114.25  3.000
 383  O31   C4   C3    103.64  3.000
 383  H4    C4   N5    108.25  3.000
 383  O31   C4   N5    113.42  3.000
 383  C3    C4   N5    109.00  3.000
 383  H3    C3   O32   111.48  3.000
 383  H3    C3   C2    109.24  3.000
 383  O32   C3   C2    112.42  3.000
 383  H3    C3   C4    108.09  3.000
 383  O32   C3   C4    116.49  3.000
 383  C2    C3   C4     98.24  3.000
 383  C30   C2   O29   114.24  3.000
 383  C30   C2   C1    111.51  3.000
 383  O29   C2   C1    107.58  3.000
 383  C30   C2   C3     99.69  3.000
 383  O29   C2   C3    115.61  3.000
 383  C1    C2   C3    108.02  3.000
 383  H1    C1   O64   110.35  3.000
 383  H1    C1   C2    108.00  3.000
 383  O64   C1   C2    108.16  3.000
 383  H1    C1   C6    109.30  3.000
 383  O64   C1   C6    109.11  3.000
 383  C2    C1   C6    111.91  3.000
 383  H28   O28  N5    107.74  3.000
 383  H29   O29  C2    108.93  3.000
 383  H302  C30  H301  107.71  3.000
 383  H302  C30  O31   109.73  3.000
 383  H301  C30  O31   110.18  3.000
 383  H302  C30  C2    110.19  3.000
 383  H301  C30  C2    113.25  3.000
 383  O31   C30  C2    105.77  3.000
 383  C30   O31  C4    108.90  3.000
 383  H32   O32  C3    108.84  3.000
 383  H64   O64  C1    108.92  3.000
 383  H13   O13  C12   110.26  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_16  O18  C17  N19  C20    0.00   0.0  0
 383  CONST_17  H19  N19  C17  C15    0.00   0.0  0
 383  Var_01    C2   C30  O31  C4    -2.70  30.0  3
 383  Var_02    C15  C14  C9   C8    93.55  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

