# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:39:32 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 3,7-anhydro-2,8-dideoxy-2-(L-tyrosylamino)-D-threo-L-galacto-octonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@H]1O)[C@H](NC(=O)[C@@H](N)Cc2ccc(O)cc2)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
 485  485  '3,7-anhydro-2,8-dideoxy-2-(L-tyrosylamino)-D-threo-L-galacto-octonic acid'  ligand  50  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_485
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
 485  O1    O  OH1    0  -0.635  -2.0399   1.1523   7.2060
 485  C2    C  CR6    0   0.337  -1.2600   0.8981   6.1340
 485  C3    C  CR16   0  -0.371  -0.1527   0.0581   6.1896
 485  C4    C  CR16   0  -0.307   0.6111  -0.1580   5.0500
 485  C5    C  CR6    0   0.107   0.3008   0.4503   3.8373
 485  C6    C  CR16   0  -0.290  -0.8144   1.2872   3.8029
 485  C7    C  CR16   0  -0.323  -1.5882   1.5154   4.9282
 485  C8    C  CH2    0  -0.527   1.0909   0.1737   2.5924
 485  C9    C  CH1    0  -0.228   0.4661  -0.9741   1.7638
 485  N10   N  NH2    0  -0.788   0.4150  -2.2587   2.4295
 485  C11   C  C      0   0.566   1.2712  -1.1090   0.4805
 485  O12   O  O      0  -0.512   2.3159  -1.7481   0.4551
 485  N13   N  NH1    0  -0.616   0.7663  -0.4630  -0.5772
 485  C14   C  CH1    0  -0.242   1.5333  -0.1904  -1.7666
 485  C15   C  C      0   0.425   2.4406   1.0647  -1.6166
 485  O16   O  OC    -1  -0.582   2.4411   1.6466  -0.5204
 485  O17   O  O      0  -0.612   3.1079   1.3507  -2.6296
 485  C18   C  CH1    0   0.012   0.6020  -0.0404  -2.9619
 485  C19   C  CH1    0   0.046  -0.2085  -1.3028  -3.2587
 485  C20   C  CH1    0   0.009  -1.2262  -1.0088  -4.3549
 485  C21   C  CH1    0  -0.008  -2.0917   0.1905  -3.9815
 485  C22   C  CH1    0   0.029  -1.1652   1.3738  -3.6933
 485  O23   O  O2     0  -0.499  -0.2464   1.0476  -2.6718
 485  O24   O  OH1    0  -0.678   0.7041  -2.2976  -3.6621
 485  O25   O  OH1    0  -0.674  -1.9703  -2.1840  -4.5725
 485  O26   O  OH1    0  -0.670  -2.8887  -0.1607  -2.8782
 485  C27   C  CH3    0  -0.705  -1.9043   2.6256  -3.2664
 485  H1    H  HOH1   0   0.473  -1.7220   0.6650   7.9739
 485  H3    H  HCR6   0   0.268   0.1186  -0.4293   7.1197
 485  H4    H  HCR6   0   0.253   1.4729  -0.8119   5.1168
 485  H6    H  HCR6   0   0.247  -1.0856   1.7779   2.8747
 485  H7    H  HCR6   0   0.260  -2.4468   2.1738   4.8781
 485  H81   H  HCH2   0   0.247   2.1184  -0.1007   2.8466
 485  H82   H  HCH2   0   0.255   1.1496   1.0700   1.9698
 485  H9    H  HCH1   0   0.253  -0.5609  -0.6848   1.5176
 485  H101  H  HNH2   0   0.340   1.3556  -2.5630   2.6519
 485  H102  H  HNH2   0   0.353  -0.0674  -2.1611   3.3148
 485  H13   H  HNH1   0   0.385  -0.0349   0.1286  -0.4194
 485  H14   H  HCH1   0   0.264   2.1863  -1.0456  -1.9511
 485  H18   H  HCH1   0   0.221   1.2227   0.1824  -3.8421
 485  H19   H  HCH1   0   0.212  -0.7444  -1.6084  -2.3497
 485  H20   H  HCH1   0   0.212  -0.6696  -0.7271  -5.2619
 485  H21   H  HCH1   0   0.220  -2.7118   0.4571  -4.8520
 485  H2    H  HCH1   0   0.205  -0.6224   1.5915  -4.6277
 485  H24   H  HOH1   0   0.451   0.2055  -3.1020  -3.8360
 485  H25   H  HOH1   0   0.454  -2.4434  -2.1007  -5.4062
 485  H26   H  HOH1   0   0.453  -3.5290   0.5397  -2.7224
 485  H271  H  HCH3   0   0.248  -1.2181   3.4669  -3.1716
 485  H272  H  HCH3   0   0.235  -2.6570   2.8944  -4.0080
 485  H273  H  HCH3   0   0.228  -2.4020   2.4953  -2.3041

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
 485  O1   C2    single    1.350  0.020  1.350
 485  O1   H1    single    0.850  0.020  0.980
 485  C2   C3    aromatic  1.391  0.020  1.391
 485  C2   C7    aromatic  1.394  0.020  1.394
 485  C3   C4    aromatic  1.389  0.020  1.389
 485  C3   H3    single    0.930  0.020  1.080
 485  C4   C5    aromatic  1.392  0.020  1.392
 485  C4   H4    single    0.930  0.020  1.080
 485  C5   C6    aromatic  1.395  0.020  1.395
 485  C5   C8    single    1.500  0.020  1.500
 485  C6   C7    aromatic  1.385  0.020  1.385
 485  C6   H6    single    0.930  0.020  1.080
 485  C7   H7    single    0.930  0.020  1.080
 485  C8   C9    single    1.547  0.020  1.547
 485  C8   H81   single    0.970  0.020  1.090
 485  C8   H82   single    0.970  0.020  1.090
 485  C9   N10   single    1.448  0.020  1.448
 485  C9   C11   single    1.521  0.020  1.521
 485  C9   H9    single    0.970  0.020  1.090
 485  N10  H101  single    0.890  0.020  1.040
 485  N10  H102  single    0.890  0.020  1.040
 485  C11  O12   double    1.225  0.020  1.225
 485  C11  N13   single    1.338  0.020  1.338
 485  N13  C14   single    1.441  0.020  1.441
 485  N13  H13   single    0.890  0.020  1.040
 485  C14  C15   single    1.556  0.020  1.556
 485  C14  C18   single    1.523  0.020  1.523
 485  C14  H14   single    0.970  0.020  1.090
 485  C15  O16   deloc     1.241  0.020  1.241
 485  C15  O17   deloc     1.246  0.020  1.246
 485  C18  C19   single    1.529  0.020  1.529
 485  C18  O23   single    1.410  0.020  1.410
 485  C18  H18   single    0.970  0.020  1.090
 485  C19  C20   single    1.524  0.020  1.524
 485  C19  O24   single    1.409  0.020  1.409
 485  C19  H19   single    0.970  0.020  1.090
 485  C20  C21   single    1.525  0.020  1.525
 485  C20  O25   single    1.408  0.020  1.408
 485  C20  H20   single    0.970  0.020  1.090
 485  C21  C22   single    1.530  0.020  1.530
 485  C21  O26   single    1.406  0.020  1.406
 485  C21  H21   single    0.970  0.020  1.090
 485  C22  O23   single    1.412  0.020  1.412
 485  C22  C27   single    1.515  0.020  1.515
 485  C22  H2    single    0.970  0.020  1.090
 485  O24  H24   single    0.850  0.020  0.980
 485  O25  H25   single    0.850  0.020  0.980
 485  O26  H26   single    0.850  0.020  0.980
 485  C27  H271  single    0.970  0.020  1.090
 485  C27  H272  single    0.970  0.020  1.090
 485  C27  H273  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
 485  H1    O1   C2    110.31  3.000
 485  C7    C2   C3    119.31  3.000
 485  C7    C2   O1    117.87  3.000
 485  C3    C2   O1    122.81  3.000
 485  H3    C3   C4    119.75  3.000
 485  H3    C3   C2    120.32  3.000
 485  C4    C3   C2    119.93  3.000
 485  H4    C4   C5    119.64  3.000
 485  H4    C4   C3    118.73  3.000
 485  C5    C4   C3    121.63  3.000
 485  C8    C5   C6    120.75  3.000
 485  C8    C5   C4    121.67  3.000
 485  C6    C5   C4    117.52  3.000
 485  H6    C6   C7    118.77  3.000
 485  H6    C6   C5    119.51  3.000
 485  C7    C6   C5    121.72  3.000
 485  H7    C7   C6    120.37  3.000
 485  H7    C7   C2    119.73  3.000
 485  C6    C7   C2    119.90  3.000
 485  H82   C8   H81   106.73  3.000
 485  H82   C8   C9    108.96  3.000
 485  H81   C8   C9    108.53  3.000
 485  H82   C8   C5    110.47  3.000
 485  H81   C8   C5    110.38  3.000
 485  C9    C8   C5    111.62  3.000
 485  H9    C9   C11   109.28  3.000
 485  H9    C9   N10   107.73  3.000
 485  C11   C9   N10   109.15  3.000
 485  H9    C9   C8    107.65  3.000
 485  C11   C9   C8    107.69  3.000
 485  N10   C9   C8    115.23  3.000
 485  H102  N10  H101  106.21  3.000
 485  H102  N10  C9    109.46  3.000
 485  H101  N10  C9    109.55  3.000
 485  N13   C11  O12   123.86  3.000
 485  N13   C11  C9    115.11  3.000
 485  O12   C11  C9    121.01  3.000
 485  H13   N13  C14   116.17  3.000
 485  H13   N13  C11   117.34  3.000
 485  C14   N13  C11   122.87  3.000
 485  H14   C14  C18   108.08  3.000
 485  H14   C14  C15   107.42  3.000
 485  C18   C14  C15   110.66  3.000
 485  H14   C14  N13   108.04  3.000
 485  C18   C14  N13   109.93  3.000
 485  C15   C14  N13   112.54  3.000
 485  O17   C15  O16   127.60  3.000
 485  O17   C15  C14   114.77  3.000
 485  O16   C15  C14   117.62  3.000
 485  H18   C18  O23   110.36  3.000
 485  H18   C18  C19   108.12  3.000
 485  O23   C18  C19   110.97  3.000
 485  H18   C18  C14   107.64  3.000
 485  O23   C18  C14   106.41  3.000
 485  C19   C18  C14   113.28  3.000
 485  H19   C19  O24   110.88  3.000
 485  H19   C19  C20   108.85  3.000
 485  O24   C19  C20   111.27  3.000
 485  H19   C19  C18   109.12  3.000
 485  O24   C19  C18   107.16  3.000
 485  C20   C19  C18   109.53  3.000
 485  H20   C20  O25   110.70  3.000
 485  H20   C20  C21   106.70  3.000
 485  O25   C20  C21   113.22  3.000
 485  H20   C20  C19   107.71  3.000
 485  O25   C20  C19   107.64  3.000
 485  C21   C20  C19   110.76  3.000
 485  H21   C21  O26   111.19  3.000
 485  H21   C21  C22   107.61  3.000
 485  O26   C21  C22   112.87  3.000
 485  H21   C21  C20   108.43  3.000
 485  O26   C21  C20   108.51  3.000
 485  C22   C21  C20   108.09  3.000
 485  H2    C22  C27   108.41  3.000
 485  H2    C22  O23   109.78  3.000
 485  C27   C22  O23   107.72  3.000
 485  H2    C22  C21   106.93  3.000
 485  C27   C22  C21   113.37  3.000
 485  O23   C22  C21   110.58  3.000
 485  C22   O23  C18   114.89  3.000
 485  H24   O24  C19   107.84  3.000
 485  H25   O25  C20   108.75  3.000
 485  H26   O26  C21   108.83  3.000
 485  H273  C27  H272  108.32  3.000
 485  H273  C27  H271  107.61  3.000
 485  H272  C27  H271  107.67  3.000
 485  H273  C27  C22   111.86  3.000
 485  H272  C27  C22   110.42  3.000
 485  H271  C27  C22   110.81  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
 485  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 485  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 485  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 485  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 485  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 485  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 485  CONST_07  C4   C3   C2   O1   180.00   0.0  0
 485  CONST_08  C6   C7   C2   O1   180.00   0.0  0
 485  CONST_09  C8   C5   C4   C3   180.00   0.0  0
 485  CONST_10  C8   C5   C6   C7   180.00   0.0  0
 485  CONST_11  H4   C4   C3   C2   180.00   0.0  0
 485  CONST_12  H6   C6   C7   C2   180.00   0.0  0
 485  CONST_13  H7   C7   C2   C3   180.00   0.0  0
 485  CONST_14  H3   C3   C4   C5   180.00   0.0  0
 485  CONST_16  C14  N13  C11  O12    0.00   0.0  0
 485  CONST_17  H13  N13  C11  C9     0.00   0.0  0
 485  Var_01    C9   C8   C5   C4    92.82  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
 485  chir_01  C9   C8   N10  C11  positiv
 485  chir_02  C14  N13  C15  C18  positiv
 485  chir_03  C18  O23  C19  C14  positiv
 485  chir_04  C19  O24  C18  C20  negativ
 485  chir_05  C20  O25  C19  C21  positiv
 485  chir_06  C21  O26  C22  C20  negativ
 485  chir_07  C22  O23  C21  C27  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
 485  plan-1  O1   0.020
 485  plan-1  C2   0.020
 485  plan-1  C3   0.020
 485  plan-1  C4   0.020
 485  plan-1  C5   0.020
 485  plan-1  C6   0.020
 485  plan-1  C7   0.020
 485  plan-1  C8   0.020
 485  plan-1  H3   0.020
 485  plan-1  H4   0.020
 485  plan-1  H6   0.020
 485  plan-1  H7   0.020
 485  plan-2  C9   0.020
 485  plan-2  C11  0.020
 485  plan-2  O12  0.020
 485  plan-2  N13  0.020
 485  plan-2  C14  0.020
 485  plan-2  H13  0.020
 485  plan-3  C14  0.020
 485  plan-3  C15  0.020
 485  plan-3  O16  0.020
 485  plan-3  O17  0.020

