# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:14:17 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 3-amino-2,3-dideoxy-5-O-(5-methylthiophene-2-carbonyl)-D-erythro-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(cc1)C(=O)OC[C@@H](O)[C@@H](N)CC(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
 Y1Y  Y1Y  '3-amino-2,3-dideoxy-5-O-(5-methylthiophene-2-carbonyl)-D-erythro-pentonic acid'  ligand  32  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y1Y
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
 Y1Y  C01  C  CH3    0  -0.714  35.1263  -35.7644  14.4151
 Y1Y  C02  C  CR5    0  -0.152  35.3122  -34.2956  14.5784
 Y1Y  C03  C  CR15   0  -0.206  35.5492  -33.3649  13.6032
 Y1Y  C04  C  CR15   0  -0.175  35.6766  -32.0506  14.1066
 Y1Y  C05  C  CR5    0  -0.330  35.5335  -31.9963  15.4653
 Y1Y  C06  C  C      0   0.589  35.6007  -30.8548  16.3720
 Y1Y  C08  C  CH2    0  -0.179  35.9568  -28.5158  16.4940
 Y1Y  C09  C  CH1    0   0.012  36.3121  -27.4085  15.5149
 Y1Y  C10  C  CH1    0  -0.111  36.4336  -26.0461  16.2192
 Y1Y  C11  C  CH2    0  -0.548  36.8736  -24.9659  15.2384
 Y1Y  C12  C  C      0   0.406  36.8346  -23.5443  15.8304
 Y1Y  N15  N  NH2    0  -0.794  37.3538  -26.0515  17.3483
 Y1Y  O07  O  O2     0  -0.469  35.8587  -29.7256  15.7311
 Y1Y  O13  O  OC    -1  -0.615  35.8074  -23.2347  16.4695
 Y1Y  O14  O  O      0  -0.615  37.8127  -22.8072  15.5921
 Y1Y  O16  O  OH1    0  -0.668  35.3207  -27.2968  14.5170
 Y1Y  O17  O  O      0  -0.451  35.4409  -30.9444  17.5669
 Y1Y  S18  S  S2     0   0.259  35.2412  -33.5588  16.1279
 Y1Y  H1   H  HCH3   0   0.260  35.8536  -36.3295  14.9987
 Y1Y  H2   H  HCH3   0   0.261  34.1331  -36.0813  14.7354
 Y1Y  H3   H  HCH3   0   0.261  35.2461  -36.0397  13.3689
 Y1Y  H4   H  HCR5   0   0.270  35.6304  -33.6217  12.5563
 Y1Y  H5   H  HCR5   0   0.274  35.8665  -31.1850  13.4881
 Y1Y  H6   H  HCH2   0   0.231  36.7252  -28.6306  17.2595
 Y1Y  H7   H  HCH2   0   0.236  35.0021  -28.3043  16.9851
 Y1Y  H8   H  HCH1   0   0.200  37.2915  -27.6481  15.0700
 Y1Y  H9   H  HCH1   0   0.218  35.4452  -25.7788  16.6067
 Y1Y  H10  H  HCH2   0   0.226  36.2234  -24.9830  14.3589
 Y1Y  H11  H  HCH2   0   0.191  37.8809  -25.2010  14.8780
 Y1Y  H12  H  HNH2   0   0.347  37.0125  -26.6272  18.1063
 Y1Y  H13  H  HNH2   0   0.336  38.2506  -26.4338  17.0708
 Y1Y  H16  H  HOH1   0   0.449  35.3521  -28.0790  13.9579

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
 Y1Y  C03  C04  aromatic  1.413  0.020  1.413
 Y1Y  C03  C02  aromatic  1.369  0.020  1.369
 Y1Y  C04  C05  aromatic  1.367  0.020  1.367
 Y1Y  O16  C09  single    1.411  0.020  1.411
 Y1Y  C01  C02  single    1.489  0.020  1.489
 Y1Y  C02  S18  aromatic  1.717  0.020  1.717
 Y1Y  C11  C12  single    1.540  0.020  1.540
 Y1Y  C11  C10  single    1.524  0.020  1.524
 Y1Y  O14  C12  deloc     1.248  0.020  1.248
 Y1Y  C05  S18  aromatic  1.722  0.020  1.722
 Y1Y  C05  C06  single    1.459  0.020  1.459
 Y1Y  C09  C10  single    1.538  0.020  1.538
 Y1Y  C09  C08  single    1.520  0.020  1.520
 Y1Y  O07  C06  single    1.324  0.020  1.324
 Y1Y  O07  C08  single    1.434  0.020  1.434
 Y1Y  C12  O13  deloc     1.249  0.020  1.249
 Y1Y  C10  N15  single    1.457  0.020  1.457
 Y1Y  C06  O17  double    1.209  0.020  1.209
 Y1Y  C01  H1   single    0.970  0.020  1.090
 Y1Y  C01  H2   single    0.970  0.020  1.090
 Y1Y  C01  H3   single    0.970  0.020  1.090
 Y1Y  C03  H4   single    0.930  0.020  1.080
 Y1Y  C04  H5   single    0.930  0.020  1.080
 Y1Y  C08  H6   single    0.970  0.020  1.090
 Y1Y  C08  H7   single    0.970  0.020  1.090
 Y1Y  C09  H8   single    0.970  0.020  1.090
 Y1Y  C10  H9   single    0.970  0.020  1.090
 Y1Y  C11  H10  single    0.970  0.020  1.090
 Y1Y  C11  H11  single    0.970  0.020  1.090
 Y1Y  N15  H12  single    0.890  0.020  1.040
 Y1Y  N15  H13  single    0.890  0.020  1.040
 Y1Y  O16  H16  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
 Y1Y  H3   C01  H2   108.00  3.000
 Y1Y  H3   C01  H1   108.05  3.000
 Y1Y  H2   C01  H1   107.43  3.000
 Y1Y  H3   C01  C02  109.94  3.000
 Y1Y  H2   C01  C02  111.59  3.000
 Y1Y  H1   C01  C02  111.67  3.000
 Y1Y  S18  C02  C03  111.00  3.000
 Y1Y  S18  C02  C01  121.12  3.000
 Y1Y  C03  C02  C01  127.88  3.000
 Y1Y  H4   C03  C04  124.00  3.000
 Y1Y  H4   C03  C02  122.79  3.000
 Y1Y  C04  C03  C02  113.22  3.000
 Y1Y  H5   C04  C05  123.73  3.000
 Y1Y  H5   C04  C03  123.84  3.000
 Y1Y  C05  C04  C03  112.43  3.000
 Y1Y  S18  C05  C06  118.58  3.000
 Y1Y  C06  C05  C04  130.07  3.000
 Y1Y  S18  C05  C04  111.35  3.000
 Y1Y  O17  C06  O07  124.58  3.000
 Y1Y  O17  C06  C05  123.37  3.000
 Y1Y  O07  C06  C05  112.05  3.000
 Y1Y  H7   C08  H6   108.66  3.000
 Y1Y  H7   C08  O07  110.01  3.000
 Y1Y  H6   C08  O07  109.44  3.000
 Y1Y  H7   C08  C09  110.62  3.000
 Y1Y  H6   C08  C09  111.35  3.000
 Y1Y  O07  C08  C09  106.74  3.000
 Y1Y  H8   C09  O16  110.86  3.000
 Y1Y  H8   C09  C10  107.89  3.000
 Y1Y  O16  C09  C10  108.01  3.000
 Y1Y  H8   C09  C08  108.02  3.000
 Y1Y  C10  C09  C08  111.63  3.000
 Y1Y  O16  C09  C08  110.42  3.000
 Y1Y  H9   C10  N15  107.27  3.000
 Y1Y  H9   C10  C11  108.39  3.000
 Y1Y  N15  C10  C11  108.61  3.000
 Y1Y  H9   C10  C09  107.88  3.000
 Y1Y  N15  C10  C09  113.67  3.000
 Y1Y  C11  C10  C09  110.84  3.000
 Y1Y  H11  C11  H10  106.19  3.000
 Y1Y  H11  C11  C12  110.35  3.000
 Y1Y  H10  C11  C12  107.96  3.000
 Y1Y  H11  C11  C10  108.98  3.000
 Y1Y  H10  C11  C10  109.56  3.000
 Y1Y  C12  C11  C10  113.54  3.000
 Y1Y  O14  C12  O13  126.59  3.000
 Y1Y  O13  C12  C11  116.51  3.000
 Y1Y  O14  C12  C11  116.87  3.000
 Y1Y  H13  N15  H12  106.80  3.000
 Y1Y  H13  N15  C10  110.38  3.000
 Y1Y  H12  N15  C10  111.71  3.000
 Y1Y  C08  O07  C06  118.40  3.000
 Y1Y  H16  O16  C09  108.88  3.000
 Y1Y  C05  S18  C02   92.01  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
 Y1Y  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 Y1Y  CONST_02  C04  C05  S18  C02    0.00   0.0  0
 Y1Y  CONST_03  S18  C05  C04  C03    0.00   0.0  0
 Y1Y  CONST_04  C05  S18  C02  C03    0.00   0.0  0
 Y1Y  CONST_05  S18  C02  C03  C04    0.00   0.0  0
 Y1Y  CONST_06  C04  C03  C02  C01  180.00   0.0  0
 Y1Y  CONST_07  C05  S18  C02  C01  180.00   0.0  0
 Y1Y  CONST_08  C06  C05  S18  C02  180.00   0.0  0
 Y1Y  CONST_09  C06  C05  C04  C03  180.00   0.0  0
 Y1Y  CONST_10  H5   C04  C03  C02  180.00   0.0  0
 Y1Y  CONST_11  H4   C03  C04  C05  180.00   0.0  0
 Y1Y  Var_01    O07  C06  C05  C04   -0.94  30.0  2
 Y1Y  Var_02    H1   C01  C02  C03  122.27  30.0  2
 Y1Y  Var_03    C09  C08  O07  C06  177.72  30.0  3
 Y1Y  Var_04    O14  C12  C11  C10  135.92  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
 Y1Y  chir_01  C09  O16  C10  C08  negativ
 Y1Y  chir_02  C10  N15  C11  C09  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
 Y1Y  plan-1  C01  0.020
 Y1Y  plan-1  C02  0.020
 Y1Y  plan-1  C03  0.020
 Y1Y  plan-1  C04  0.020
 Y1Y  plan-1  C05  0.020
 Y1Y  plan-1  C06  0.020
 Y1Y  plan-1  S18  0.020
 Y1Y  plan-1  H4   0.020
 Y1Y  plan-1  H5   0.020
 Y1Y  plan-2  C11  0.020
 Y1Y  plan-2  C12  0.020
 Y1Y  plan-2  O13  0.020
 Y1Y  plan-2  O14  0.020
 Y1Y  plan-3  C05  0.020
 Y1Y  plan-3  C06  0.020
 Y1Y  plan-3  O07  0.020
 Y1Y  plan-3  O17  0.020

