# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 28 20:12:23 2021
#   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  51  27  .  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_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  -0.634  25.5518   7.2284  83.8482
 485  C2    C  CR6   0   0.340  26.6856   7.7269  83.3132
 485  C3    C  CR16  0  -0.323  27.6685   8.1921  84.1857
 485  C4    C  CR16  0  -0.286  28.8502   8.7077  83.6819
 485  C5    C  CR6   0   0.087  29.0915   8.7771  82.3099
 485  C6    C  CR16  0  -0.297  28.0991   8.3095  81.4548
 485  C7    C  CR16  0  -0.371  26.9074   7.7884  81.9414
 485  C8    C  CH2   0  -0.506  30.3689   9.3694  81.7839
 485  C9    C  CH1   0  -0.208  30.3512  10.9088  81.8190
 485  N10   N  NH2   0  -0.795  29.3129  11.4101  80.9489
 485  C11   C  C     0   0.557  31.7110  11.4046  81.3422
 485  O12   O  O     0  -0.479  31.9704  11.6143  80.1702
 485  N13   N  NH1   0  -0.643  32.6146  11.5605  82.3312
 485  C14   C  CH1   0  -0.217  33.9963  11.8464  82.0765
 485  C15   C  C     0   0.556  34.8331  10.6094  81.7665
 485  O16   O  OH1   0  -0.572  34.1550   9.4801  81.8423
 485  O17   O  O     0  -0.445  36.0006  10.6780  81.4742
 485  C18   C  CH1   0  -0.000  34.6306  12.5729  83.2611
 485  C19   C  CH1   0   0.046  33.9591  13.9111  83.5678
 485  C20   C  CH1   0   0.010  34.5775  14.4886  84.8364
 485  C21   C  CH1   0  -0.012  34.4923  13.4832  85.9823
 485  C22   C  CH1   0   0.022  35.1560  12.1780  85.5347
 485  O23   O  O2    0  -0.497  34.5446  11.6930  84.3525
 485  O24   O  OH1   0  -0.675  34.1756  14.7414  82.4538
 485  O25   O  OH1   0  -0.671  33.9192  15.7001  85.1104
 485  O26   O  OH1   0  -0.668  33.1394  13.3130  86.3227
 485  C27   C  CH3   0  -0.705  35.0884  11.0817  86.5770
 485  H1    H  HOH1  0   0.473  24.9501   6.9452  83.1510
 485  H3    H  HCR6  0   0.262  27.5035   8.1443  85.2551
 485  H4    H  HCR6  0   0.248  29.6044   9.0621  84.3757
 485  H6    H  HCR6  0   0.255  28.2552   8.3458  80.3830
 485  H7    H  HCR6  0   0.269  26.1542   7.4293  81.2486
 485  H81   H  HCH2  0   0.258  31.2151   9.0091  82.3733
 485  H82   H  HCH2  0   0.255  30.5371   9.0467  80.7538
 485  H9    H  HCH1  0   0.240  30.2250  11.2157  82.8698
 485  H101  H  HNH2  0   0.351  29.2390  12.4157  81.0391
 485  H102  H  HNH2  0   0.356  28.4209  11.0406  81.2541
 485  H13   H  HNH1  0   0.400  32.3573  11.2912  83.2686
 485  H14   H  HCH1  0   0.320  34.0691  12.4957  81.2011
 485  H16   H  HOH1  0   0.486  34.7340   8.7321  81.6298
 485  H18   H  HCH1  0   0.245  35.6824  12.7746  83.0075
 485  H19   H  HCH1  0   0.222  32.8859  13.7511  83.7379
 485  H20   H  HCH1  0   0.217  35.6468  14.6602  84.6399
 485  H21   H  HCH1  0   0.227  35.0726  13.8717  86.8335
 485  H2    H  HCH1  0   0.215  36.2149  12.4021  85.3328
 485  H24   H  HOH1  0   0.456  33.7265  15.5780  82.6105
 485  H25   H  HOH1  0   0.456  34.4307  16.1925  85.7596
 485  H26   H  HOH1  0   0.455  33.0882  12.7971  87.1327
 485  H271  H  HCH3  0   0.252  35.6300  10.1966  86.2444
 485  H272  H  HCH3  0   0.239  35.5476  11.4202  87.5061
 485  H273  H  HCH3  0   0.229  34.0615  10.7824  86.7917

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    1.349  0.020  1.349
 485  O1   H1    single    0.850  0.020  0.980
 485  C2   C3    aromatic  1.394  0.020  1.394
 485  C2   C7    aromatic  1.391  0.020  1.391
 485  C3   C4    aromatic  1.384  0.020  1.384
 485  C3   H3    single    0.930  0.020  1.080
 485  C4   C5    aromatic  1.395  0.020  1.395
 485  C4   H4    single    0.930  0.020  1.080
 485  C5   C6    aromatic  1.391  0.020  1.391
 485  C5   C8    single    1.503  0.020  1.503
 485  C6   C7    aromatic  1.389  0.020  1.389
 485  C6   H6    single    0.930  0.020  1.080
 485  C7   H7    single    0.930  0.020  1.080
 485  C8   C9    single    1.540  0.020  1.540
 485  C8   H81   single    0.970  0.020  1.090
 485  C8   H82   single    0.970  0.020  1.090
 485  C9   N10   single    1.445  0.020  1.445
 485  C9   C11   single    1.524  0.020  1.524
 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    1.218  0.020  1.218
 485  C11  N13   single    1.349  0.020  1.349
 485  N13  C14   single    1.434  0.020  1.434
 485  N13  H13   single    0.860  0.020  1.020
 485  C14  C15   single    1.525  0.020  1.525
 485  C14  C18   single    1.528  0.020  1.528
 485  C14  H14   single    0.970  0.020  1.090
 485  C15  O16   single    1.319  0.020  1.319
 485  C15  O17   double    1.205  0.020  1.205
 485  O16  H16   single    0.850  0.020  0.980
 485  C18  C19   single    1.528  0.020  1.528
 485  C18  O23   single    1.405  0.020  1.405
 485  C18  H18   single    0.970  0.020  1.090
 485  C19  C20   single    1.525  0.020  1.525
 485  C19  O24   single    1.406  0.020  1.406
 485  C19  H19   single    0.970  0.020  1.090
 485  C20  C21   single    1.527  0.020  1.527
 485  C20  O25   single    1.406  0.020  1.406
 485  C20  H20   single    0.970  0.020  1.090
 485  C21  C22   single    1.531  0.020  1.531
 485  C21  O26   single    1.405  0.020  1.405
 485  C21  H21   single    0.970  0.020  1.090
 485  C22  O23   single    1.417  0.020  1.417
 485  C22  C27   single    1.514  0.020  1.514
 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    110.27  3.000
 485  C7    C2   C3    119.34  3.000
 485  C7    C2   O1    122.78  3.000
 485  C3    C2   O1    117.88  3.000
 485  H3    C3   C4    120.39  3.000
 485  H3    C3   C2    119.72  3.000
 485  C4    C3   C2    119.89  3.000
 485  H4    C4   C5    119.52  3.000
 485  H4    C4   C3    118.86  3.000
 485  C5    C4   C3    121.62  3.000
 485  C8    C5   C6    121.58  3.000
 485  C8    C5   C4    120.72  3.000
 485  C6    C5   C4    117.68  3.000
 485  H6    C6   C7    118.87  3.000
 485  H6    C6   C5    119.60  3.000
 485  C7    C6   C5    121.53  3.000
 485  H7    C7   C6    119.76  3.000
 485  H7    C7   C2    120.31  3.000
 485  C6    C7   C2    119.94  3.000
 485  H82   C8   H81   106.98  3.000
 485  H82   C8   C9    108.57  3.000
 485  H81   C8   C9    109.05  3.000
 485  H82   C8   C5    110.14  3.000
 485  H81   C8   C5    109.85  3.000
 485  C9    C8   C5    112.10  3.000
 485  H9    C9   C11   108.06  3.000
 485  H9    C9   N10   113.29  3.000
 485  C11   C9   N10   109.88  3.000
 485  H9    C9   C8    107.55  3.000
 485  C11   C9   C8    107.93  3.000
 485  N10   C9   C8    109.97  3.000
 485  H102  N10  H101  105.74  3.000
 485  H102  N10  C9    108.96  3.000
 485  H101  N10  C9    110.09  3.000
 485  N13   C11  O12   122.87  3.000
 485  N13   C11  C9    113.96  3.000
 485  O12   C11  C9    123.15  3.000
 485  H13   N13  C14   117.66  3.000
 485  H13   N13  C11   118.66  3.000
 485  C14   N13  C11   122.58  3.000
 485  H14   C14  C18   108.12  3.000
 485  H14   C14  C15   106.41  3.000
 485  C18   C14  C15   108.39  3.000
 485  H14   C14  N13   108.98  3.000
 485  C18   C14  N13   110.93  3.000
 485  C15   C14  N13   113.77  3.000
 485  O17   C15  O16   124.08  3.000
 485  O17   C15  C14   122.31  3.000
 485  O16   C15  C14   113.61  3.000
 485  H16   O16  C15   109.93  3.000
 485  H18   C18  O23   110.63  3.000
 485  H18   C18  C19   107.79  3.000
 485  O23   C18  C19   111.45  3.000
 485  H18   C18  C14   107.78  3.000
 485  O23   C18  C14   106.22  3.000
 485  C19   C18  C14   112.93  3.000
 485  H19   C19  O24   111.05  3.000
 485  H19   C19  C20   108.82  3.000
 485  O24   C19  C20   111.90  3.000
 485  H19   C19  C18   109.44  3.000
 485  O24   C19  C18   106.88  3.000
 485  C20   C19  C18   108.69  3.000
 485  H20   C20  O25   110.82  3.000
 485  H20   C20  C21   106.91  3.000
 485  O25   C20  C21   113.27  3.000
 485  H20   C20  C19   107.73  3.000
 485  O25   C20  C19   107.38  3.000
 485  C21   C20  C19   110.63  3.000
 485  H21   C21  O26   111.28  3.000
 485  H21   C21  C22   107.35  3.000
 485  O26   C21  C22   112.63  3.000
 485  H21   C21  C20   108.57  3.000
 485  O26   C21  C20   108.38  3.000
 485  C22   C21  C20   108.53  3.000
 485  H2    C22  C27   108.45  3.000
 485  H2    C22  O23   109.38  3.000
 485  C27   C22  O23   107.90  3.000
 485  H2    C22  C21   107.27  3.000
 485  C27   C22  C21   113.36  3.000
 485  O23   C22  C21   110.41  3.000
 485  C22   O23  C18   114.06  3.000
 485  H24   O24  C19   108.21  3.000
 485  H25   O25  C20   108.89  3.000
 485  H26   O26  C21   108.68  3.000
 485  H273  C27  H272  108.29  3.000
 485  H273  C27  H271  107.76  3.000
 485  H272  C27  H271  107.64  3.000
 485  H273  C27  C22   112.09  3.000
 485  H272  C27  C22   110.06  3.000
 485  H271  C27  C22   110.84  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_15  C14  N13  C11  C9   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  CONST_18  H16  O16  C15  C14  180.00   0.0  0
 485  Var_01    C9   C8   C5   C4   -77.91  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
 485  plan-3  H16  0.020

