# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 14:40:37 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(acetylamino)-4,5-anhydro-1,2-dideoxy-4-methyl-1-phenyl-D-xylitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)[C@@]2(C)CO2
#
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
 049  049  2-(acetylamino)-4,5-anhydro-1,2-dideoxy-4-methyl-1-phenyl-D-xylitol  ligand  37  18  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_049
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
 049  C4    C  CR16  0  -0.240   3.8627  -0.0097   1.3178
 049  C5    C  CR16  0  -0.326   2.4978  -0.2677   1.3554
 049  C6    C  CR6   0   0.171   1.8391  -0.7948   0.2489
 049  C7    C  CH1   0  -0.096  -0.4167   0.0152  -0.5061
 049  C8    C  CH2   0  -0.578   0.3570  -1.0481   0.2784
 049  C10   C  CT    0   0.198  -2.7240  -0.6828   0.4813
 049  C9    C  CH1   0   0.032  -1.9003  -0.3417  -0.7582
 049  C12   C  CH2   0  -0.253  -3.8909  -1.5486   0.3200
 049  O13   O  O2    0  -0.497  -2.6736  -2.0523   0.8650
 049  C11   C  CH3   0  -0.704  -2.7228   0.3046   1.6195
 049  N22   N  NH1   0  -0.633  -0.2455   1.3106   0.1130
 049  C23   C  C     0   0.528  -0.2463   2.4662  -0.5773
 049  C18   C  CH3   0  -0.780  -0.0148   3.7110   0.2410
 049  O49   O  O     0  -0.505  -0.4229   2.5126  -1.7873
 049  C3    C  CR16  0  -0.272   4.5894  -0.2771   0.1662
 049  C2    C  CR16  0  -0.240   3.9424  -0.8052  -0.9449
 049  C1    C  CR16  0  -0.301   2.5794  -1.0606  -0.9018
 049  H4    H  HCR6  0   0.254   4.3563   0.3987   2.1902
 049  H5    H  HCR6  0   0.247   1.9392  -0.0643   2.2621
 049  H7    H  HCH1  0   0.269   0.0265   0.0832  -1.5032
 049  H8    H  HCH2  0   0.263   0.1475  -2.0280  -0.1557
 049  H8A   H  HCH2  0   0.262   0.0133  -1.0941   1.3153
 049  H9    H  HCH1  0   0.259  -2.3626   0.5388  -1.2161
 049  H12   H  HCH2  0   0.242  -4.7136  -1.4521   1.0234
 049  H12A  H  HCH2  0   0.244  -4.1721  -1.9342  -0.6546
 049  H11   H  HCH3  0   0.232  -1.7689   0.3316   2.1463
 049  H11A  H  HCH3  0   0.244  -2.9371   1.3103   1.2585
 049  H11B  H  HCH3  0   0.253  -3.4856   0.0459   2.3537
 049  HN22  H  HNH1  0   0.397  -0.0854   1.3543   1.1057
 049  H18   H  HCH3  0   0.268   0.8630   4.2334  -0.1390
 049  H18A  H  HCH3  0   0.267  -0.8662   4.3814   0.1262
 049  H18B  H  HCH3  0   0.249   0.1307   3.5196   1.3024
 049  H3    H  HCR6  0   0.254   5.6532  -0.0801   0.1339
 049  H2    H  HCR6  0   0.254   4.5021  -1.0232  -1.8455
 049  H1    H  HCR6  0   0.247   2.0877  -1.4775  -1.7735
 049  O21   O  OH1   0  -0.658  -1.9700  -1.3626  -1.7217
 049  HO21  H  HOH1  0   0.448  -1.7520  -2.2031  -1.3020

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
 049  C3   C4    aromatic  1.388  0.020  1.388
 049  C4   C5    aromatic  1.390  0.020  1.390
 049  C4   H4    single    0.930  0.020  1.080
 049  C6   C5    aromatic  1.391  0.020  1.391
 049  C5   H5    single    0.930  0.020  1.080
 049  C1   C6    aromatic  1.394  0.020  1.394
 049  C6   C8    single    1.504  0.020  1.504
 049  C9   C7    single    1.547  0.020  1.547
 049  C7   C8    single    1.531  0.020  1.531
 049  C7   N22   single    1.446  0.020  1.446
 049  C7   H7    single    0.970  0.020  1.090
 049  C8   H8    single    0.970  0.020  1.090
 049  C8   H8A   single    0.970  0.020  1.090
 049  C9   C10   single    1.527  0.020  1.527
 049  C12  C10   single    1.462  0.020  1.462
 049  C10  C11   single    1.507  0.020  1.507
 049  C10  O13   single    1.423  0.020  1.423
 049  O21  C9    single    1.405  0.020  1.405
 049  O21  HO21  single    0.850  0.020  0.980
 049  C9   H9    single    0.970  0.020  1.090
 049  C12  O13   single    1.426  0.020  1.426
 049  C12  H12   single    0.970  0.020  1.090
 049  C12  H12A  single    0.970  0.020  1.090
 049  C11  H11   single    0.970  0.020  1.090
 049  C11  H11A  single    0.970  0.020  1.090
 049  C11  H11B  single    0.970  0.020  1.090
 049  N22  C23   single    1.346  0.020  1.346
 049  N22  HN22  single    0.860  0.020  1.020
 049  C23  C18   single    1.508  0.020  1.508
 049  C23  O49   double    1.224  0.020  1.224
 049  C18  H18   single    0.970  0.020  1.090
 049  C18  H18A  single    0.970  0.020  1.090
 049  C18  H18B  single    0.970  0.020  1.090
 049  C2   C3    aromatic  1.390  0.020  1.390
 049  C3   H3    single    0.930  0.020  1.080
 049  C2   C1    aromatic  1.387  0.020  1.387
 049  C2   H2    single    0.930  0.020  1.080
 049  C1   H1    single    0.930  0.020  1.080

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
 049  H4    C4   C3    120.18  3.000
 049  H4    C4   C5    119.75  3.000
 049  C3    C4   C5    120.07  3.000
 049  H5    C5   C6    119.48  3.000
 049  H5    C5   C4    119.60  3.000
 049  C6    C5   C4    120.92  3.000
 049  C1    C6   C8    120.50  3.000
 049  C8    C6   C5    120.98  3.000
 049  C1    C6   C5    118.51  3.000
 049  H7    C7   N22   106.66  3.000
 049  H7    C7   C9    104.75  3.000
 049  N22   C7   C9    112.96  3.000
 049  H7    C7   C8    107.80  3.000
 049  N22   C7   C8    110.06  3.000
 049  C9    C7   C8    114.08  3.000
 049  H8A   C8   H8    106.20  3.000
 049  H8A   C8   C7    110.88  3.000
 049  H8    C8   C7    108.81  3.000
 049  H8A   C8   C6    109.60  3.000
 049  H8    C8   C6    109.41  3.000
 049  C7    C8   C6    111.77  3.000
 049  C11   C10  O13   115.27  3.000
 049  O13   C10  C12    59.21  3.000
 049  C11   C10  C12   118.17  3.000
 049  O13   C10  C9    114.51  3.000
 049  C11   C10  C9    117.80  3.000
 049  C12   C10  C9    118.25  3.000
 049  H9    C9   O21   106.05  3.000
 049  H9    C9   C10   106.95  3.000
 049  O21   C9   C10   111.56  3.000
 049  H9    C9   C7    106.72  3.000
 049  O21   C9   C7    109.08  3.000
 049  C10   C9   C7    115.90  3.000
 049  H12A  C12  H12   114.63  3.000
 049  H12A  C12  O13   116.05  3.000
 049  H12   C12  O13   115.49  3.000
 049  H12A  C12  C10   121.08  3.000
 049  H12   C12  C10   118.70  3.000
 049  O13   C12  C10    59.04  3.000
 049  C12   O13  C10    61.75  3.000
 049  H11B  C11  H11A  107.73  3.000
 049  H11B  C11  H11   107.03  3.000
 049  H11A  C11  H11   108.02  3.000
 049  H11B  C11  C10   110.66  3.000
 049  H11A  C11  C10   110.75  3.000
 049  H11   C11  C10   112.46  3.000
 049  HN22  N22  C23   117.94  3.000
 049  HN22  N22  C7    118.69  3.000
 049  C23   N22  C7    123.33  3.000
 049  O49   C23  C18   121.84  3.000
 049  O49   C23  N22   122.67  3.000
 049  C18   C23  N22   115.49  3.000
 049  H18B  C18  H18A  108.39  3.000
 049  H18B  C18  H18   108.46  3.000
 049  H18A  C18  H18   107.31  3.000
 049  H18B  C18  C23   113.88  3.000
 049  H18A  C18  C23   109.32  3.000
 049  H18   C18  C23   109.28  3.000
 049  H3    C3   C2    120.19  3.000
 049  H3    C3   C4    120.29  3.000
 049  C2    C3   C4    119.52  3.000
 049  H2    C2   C1    119.78  3.000
 049  H2    C2   C3    120.06  3.000
 049  C1    C2   C3    120.16  3.000
 049  H1    C1   C2    119.43  3.000
 049  H1    C1   C6    119.75  3.000
 049  C2    C1   C6    120.82  3.000
 049  HO21  O21  C9    108.88  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
 049  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 049  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 049  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 049  CONST_04  C2    C1   C6   C5      0.00   0.0  0
 049  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 049  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 049  CONST_07  C8    C6   C5   C4    180.00   0.0  0
 049  CONST_08  C2    C1   C6   C8    180.00   0.0  0
 049  CONST_09  H2    C2   C3   C4    180.00   0.0  0
 049  CONST_10  H3    C3   C4   C5    180.00   0.0  0
 049  CONST_11  H1    C1   C6   C5    180.00   0.0  0
 049  CONST_12  H4    C4   C5   C6    180.00   0.0  0
 049  CONST_13  H5    C5   C4   C3    180.00   0.0  0
 049  CONST_14  C18   C23  N22  C7    180.00   0.0  0
 049  CONST_15  O49   C23  N22  C7      0.00   0.0  0
 049  CONST_16  HN22  N22  C23  C18     0.00   0.0  0
 049  Var_01    O13   C12  C10  C9    103.17  30.0  1
 049  Var_02    C11   C10  O13  C12   109.05  30.0  1
 049  Var_03    H12   C12  O13  C10  -109.54  30.0  1
 049  Var_04    C7    C8   C6   C5    104.00  30.0  2
 049  Var_05    H11   C11  C10  C12   136.01  30.0  3
 049  Var_06    H18   C18  C23  N22   121.70  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
 049  chir_01  C7   C9   C8   N22  positiv
 049  chir_03  C9   C7   C10  O21  positiv
 049  chir_04  C10  C12  C11  O13  both

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
 049  plan-1  C4    0.020
 049  plan-1  C5    0.020
 049  plan-1  C6    0.020
 049  plan-1  C8    0.020
 049  plan-1  C3    0.020
 049  plan-1  C2    0.020
 049  plan-1  C1    0.020
 049  plan-1  H4    0.020
 049  plan-1  H5    0.020
 049  plan-1  H3    0.020
 049  plan-1  H2    0.020
 049  plan-1  H1    0.020
 049  plan-2  C7    0.020
 049  plan-2  N22   0.020
 049  plan-2  C23   0.020
 049  plan-2  C18   0.020
 049  plan-2  O49   0.020
 049  plan-2  HN22  0.020

