# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:14:54 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-amino-1,4-anhydro-2,5-dideoxy-5-[(4-fluorobenzene-1-carbonyl)amino]-D-arabinitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CO[C@H](CNC(=O)c2ccc(F)cc2)[C@H]1O
#
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
 D8J  D8J  2-amino-1,4-anhydro-2,5-dideoxy-5-[(4-fluorobenzene-1-carbonyl)amino]-D-arabinitol  ligand  33  18  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8J
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
 D8J  C4   C  CR16  0  -0.271   -5.3894   0.2604   5.8516
 D8J  C5   C  CR6   0  -0.040   -6.7756   0.3178   5.7201
 D8J  C6   C  C     0   0.545   -7.4731   1.4368   5.0222
 D8J  N1   N  NH2   0  -0.801   -9.9827   0.2124   0.5107
 D8J  C7   C  CH2   0  -0.349   -7.2866   3.2160   3.3535
 D8J  C8   C  CH1   0   0.047   -8.0411   2.8929   2.0770
 D8J  C9   C  CH1   0   0.018   -9.1377   1.8366   2.1789
 D8J  C10  C  CH1   0  -0.162   -9.3272   1.4882   0.7133
 D8J  C11  C  CH2   0  -0.145   -7.8688   1.4685   0.2567
 D8J  F    F  F     0  -0.307   -5.0061  -2.7915   7.7183
 D8J  C2   C  CR6   0   0.534   -5.5842  -1.7741   7.0680
 D8J  C1   C  CR16  0  -0.399   -6.9624  -1.7463   6.9616
 D8J  C3   C  CR16  0  -0.397   -4.7834  -0.7854   6.5298
 D8J  C    C  CR16  0  -0.251   -7.5523  -0.6878   6.2920
 D8J  O    O  O     0  -0.501   -8.6228   1.7458   5.3254
 D8J  N    N  NH1   0  -0.633   -6.7788   2.0657   4.0624
 D8J  O1   O  O2    0  -0.503   -7.1605   2.3798   1.0932
 D8J  O2   O  OH1   0  -0.676  -10.3136   2.2735   2.7980
 D8J  H1   H  HCR6  0   0.273   -4.7583   1.0430   5.4510
 D8J  H3   H  HNH2  0   0.350  -10.0373   0.0134  -0.4811
 D8J  H5   H  HCH2  0   0.274   -6.4447   3.8692   3.1191
 D8J  H6   H  HCH2  0   0.259   -7.9441   3.7812   4.0138
 D8J  H7   H  HCH1  0   0.212   -8.4934   3.8371   1.7343
 D8J  H8   H  HCH1  0   0.207   -8.7360   0.9382   2.6704
 D8J  H9   H  HCH1  0   0.221   -9.8484   2.3264   0.2245
 D8J  H10  H  HCH2  0   0.207   -7.4624   0.4584   0.3797
 D8J  H11  H  HCH2  0   0.225   -7.7526   1.7568  -0.7912
 D8J  H12  H  HCR6  0   0.287   -7.5627  -2.5348   7.3958
 D8J  H13  H  HCR6  0   0.289   -3.7082  -0.8252   6.6418
 D8J  H14  H  HCR6  0   0.273   -8.6298  -0.6516   6.2071
 D8J  H15  H  HNH1  0   0.412   -5.8857   1.7004   3.7769
 D8J  H16  H  HOH1  0   0.451  -10.1472   2.2682   3.7489
 D8J  H2   H  HNH2  0   0.349  -10.9445   0.2826   0.8199

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
 D8J  C11  C10  single    1.528  0.020  1.528
 D8J  C11  O1   single    1.425  0.020  1.425
 D8J  C10  N1   single    1.449  0.020  1.449
 D8J  C10  C9   single    1.518  0.020  1.518
 D8J  O1   C8   single    1.417  0.020  1.417
 D8J  C8   C9   single    1.526  0.020  1.526
 D8J  C8   C7   single    1.518  0.020  1.518
 D8J  C9   O2   single    1.399  0.020  1.399
 D8J  C7   N    single    1.443  0.020  1.443
 D8J  N    C6   single    1.341  0.020  1.341
 D8J  C6   O    double    1.229  0.020  1.229
 D8J  C6   C5   single    1.492  0.020  1.492
 D8J  C5   C    aromatic  1.393  0.020  1.393
 D8J  C5   C4   aromatic  1.394  0.020  1.394
 D8J  C    C1   aromatic  1.384  0.020  1.384
 D8J  C4   C3   aromatic  1.386  0.020  1.386
 D8J  C3   C2   aromatic  1.381  0.020  1.381
 D8J  C1   C2   aromatic  1.383  0.020  1.383
 D8J  C2   F    single    1.339  0.020  1.339
 D8J  C4   H1   single    0.930  0.020  1.080
 D8J  N1   H2   single    0.890  0.020  1.040
 D8J  N1   H3   single    0.890  0.020  1.040
 D8J  C7   H5   single    0.970  0.020  1.090
 D8J  C7   H6   single    0.970  0.020  1.090
 D8J  C8   H7   single    0.970  0.020  1.090
 D8J  C9   H8   single    0.970  0.020  1.090
 D8J  C10  H9   single    0.970  0.020  1.090
 D8J  C11  H10  single    0.970  0.020  1.090
 D8J  C11  H11  single    0.970  0.020  1.090
 D8J  C1   H12  single    0.930  0.020  1.080
 D8J  C3   H13  single    0.930  0.020  1.080
 D8J  C    H14  single    0.930  0.020  1.080
 D8J  N    H15  single    0.860  0.020  1.020
 D8J  O2   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
 D8J  H1   C4   C3   118.15  3.000
 D8J  H1   C4   C5   121.02  3.000
 D8J  C3   C4   C5   120.81  3.000
 D8J  C    C5   C6   118.21  3.000
 D8J  C    C5   C4   119.08  3.000
 D8J  C6   C5   C4   122.69  3.000
 D8J  N    C6   O    122.90  3.000
 D8J  O    C6   C5   120.71  3.000
 D8J  N    C6   C5   116.39  3.000
 D8J  H3   N1   H2   105.15  3.000
 D8J  H3   N1   C10  109.53  3.000
 D8J  H2   N1   C10  109.03  3.000
 D8J  H6   C7   H5   106.57  3.000
 D8J  H6   C7   N    109.14  3.000
 D8J  H5   C7   N    108.13  3.000
 D8J  H6   C7   C8   108.67  3.000
 D8J  H5   C7   C8   109.29  3.000
 D8J  N    C7   C8   114.73  3.000
 D8J  H7   C8   O1   110.47  3.000
 D8J  H7   C8   C9   108.60  3.000
 D8J  O1   C8   C9   104.03  3.000
 D8J  H7   C8   C7   106.46  3.000
 D8J  C9   C8   C7   116.64  3.000
 D8J  O1   C8   C7   110.62  3.000
 D8J  H8   C9   O2   111.37  3.000
 D8J  H8   C9   C10  106.82  3.000
 D8J  O2   C9   C10  113.20  3.000
 D8J  H8   C9   C8   109.44  3.000
 D8J  O2   C9   C8   114.67  3.000
 D8J  C10  C9   C8   100.60  3.000
 D8J  H9   C10  C11  109.20  3.000
 D8J  H9   C10  C9   108.23  3.000
 D8J  C11  C10  C9    99.92  3.000
 D8J  H9   C10  N1   113.20  3.000
 D8J  C9   C10  N1   113.17  3.000
 D8J  C11  C10  N1   112.25  3.000
 D8J  H11  C11  H10  108.14  3.000
 D8J  H11  C11  O1   109.95  3.000
 D8J  H10  C11  O1   109.83  3.000
 D8J  H11  C11  C10  112.61  3.000
 D8J  H10  C11  C10  109.41  3.000
 D8J  O1   C11  C10  106.89  3.000
 D8J  C3   C2   C1   122.24  3.000
 D8J  C1   C2   F    118.89  3.000
 D8J  C3   C2   F    118.87  3.000
 D8J  H12  C1   C    120.99  3.000
 D8J  H12  C1   C2   120.50  3.000
 D8J  C    C1   C2   118.51  3.000
 D8J  H13  C3   C2   120.63  3.000
 D8J  H13  C3   C4   120.87  3.000
 D8J  C2   C3   C4   118.50  3.000
 D8J  H14  C    C1   119.21  3.000
 D8J  H14  C    C5   119.93  3.000
 D8J  C1   C    C5   120.85  3.000
 D8J  H15  N    C7   117.53  3.000
 D8J  H15  N    C6   119.49  3.000
 D8J  C7   N    C6   122.89  3.000
 D8J  C11  O1   C8   109.28  3.000
 D8J  H16  O2   C9   106.82  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
 D8J  CONST_01  C1   C    C5  C4    0.00   0.0  0
 D8J  CONST_02  C1   C2   C3  C4    0.00   0.0  0
 D8J  CONST_03  C2   C1   C   C5    0.00   0.0  0
 D8J  CONST_04  C2   C3   C4  C5    0.00   0.0  0
 D8J  CONST_05  C    C5   C4  C3    0.00   0.0  0
 D8J  CONST_06  C    C1   C2  C3    0.00   0.0  0
 D8J  CONST_07  F    C2   C3  C4  180.00   0.0  0
 D8J  CONST_08  C1   C    C5  C6  180.00   0.0  0
 D8J  CONST_09  C3   C4   C5  C6  180.00   0.0  0
 D8J  CONST_10  C    C1   C2  F   180.00   0.0  0
 D8J  CONST_11  H14  C    C5  C4  180.00   0.0  0
 D8J  CONST_12  H12  C1   C   C5  180.00   0.0  0
 D8J  CONST_13  H13  C3   C4  C5  180.00   0.0  0
 D8J  CONST_14  H1   C4   C3  C2  180.00   0.0  0
 D8J  CONST_15  C7   N    C6  C5  180.00   0.0  0
 D8J  CONST_16  H15  N    C6  C5    0.00   0.0  0
 D8J  CONST_17  O    C6   N   C7    0.00   0.0  0
 D8J  Var_01    C10  C11  O1  C8    3.65  30.0  1
 D8J  Var_02    N    C6   C5  C4   27.60  30.0  2
 D8J  Var_03    C8   C7   N   C6  -91.32  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
 D8J  chir_01  C8   O1  C9  C7   negativ
 D8J  chir_02  C9   O2  C8  C10  positiv
 D8J  chir_03  C10  N1  C9  C11  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
 D8J  plan-1  C4   0.020
 D8J  plan-1  C5   0.020
 D8J  plan-1  C6   0.020
 D8J  plan-1  F    0.020
 D8J  plan-1  C2   0.020
 D8J  plan-1  C1   0.020
 D8J  plan-1  C3   0.020
 D8J  plan-1  C    0.020
 D8J  plan-1  H1   0.020
 D8J  plan-1  H12  0.020
 D8J  plan-1  H13  0.020
 D8J  plan-1  H14  0.020
 D8J  plan-2  C5   0.020
 D8J  plan-2  C6   0.020
 D8J  plan-2  C7   0.020
 D8J  plan-2  O    0.020
 D8J  plan-2  N    0.020
 D8J  plan-2  H15  0.020

