# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:19:48 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-amino-1,2,4-trideoxy-4-methyl-1-phenyl-D-xylitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CO)[C@H](O)[C@@H](N)Cc1ccccc1
#
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
 04B  04B  2-amino-1,2,4-trideoxy-4-methyl-1-phenyl-D-xylitol  ligand  34  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_04B
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
 04B  N22  N  NH2   0  -0.786   0.1946  -0.2938  -1.5073
 04B  C8   C  CH1   0  -0.125   0.3752  -0.2307  -0.0676
 04B  C9   C  CH1   0   0.066   1.7346  -0.7488   0.4442
 04B  H3   H  HCH1  0   0.215   1.7472  -0.6134   1.5330
 04B  O20  O  OH1   0  -0.666   1.8456  -2.1446   0.2416
 04B  C10  C  CH1   0  -0.323   2.9530  -0.0086  -0.1336
 04B  C11  C  CH3   0  -0.649   4.2503  -0.5750   0.4405
 04B  C12  C  CH2   0  -0.135   2.8520   1.4912   0.1291
 04B  O13  O  OH1   0  -0.672   4.0000   2.1335  -0.3787
 04B  C7   C  CH2   0  -0.514  -0.7720  -0.9719   0.6290
 04B  C6   C  CR6   0   0.169  -2.1134  -0.3608   0.3434
 04B  C5   C  CR16  0  -0.314  -2.5407   0.7653   1.0448
 04B  C4   C  CR16  0  -0.240  -3.7713   1.3510   0.7790
 04B  C3   C  CR16  0  -0.277  -4.6013   0.8143  -0.1971
 04B  C2   C  CR16  0  -0.244  -4.1887  -0.3092  -0.9017
 04B  C1   C  CR16  0  -0.315  -2.9548  -0.8873  -0.6333
 04B  H28  H  HNH2  0   0.351   0.9242   0.2148  -1.9905
 04B  H29  H  HCH1  0   0.236   0.2927   0.8218   0.2249
 04B  H35  H  HCH3  0   0.233   5.1221  -0.0973  -0.0027
 04B  H36  H  HCH3  0   0.211   4.2988  -0.4190   1.5216
 04B  H37  H  HCH3  0   0.230   4.3345  -1.6448   0.2563
 04B  H38  H  HCH2  0   0.203   1.9496   1.9003  -0.3413
 04B  H39  H  HCH2  0   0.189   2.7454   1.6537   1.2121
 04B  H40  H  HOH1  0   0.454   3.9102   3.0759  -0.2122
 04B  H45  H  HCH2  0   0.242  -0.7676  -2.0216   0.3252
 04B  H46  H  HCH2  0   0.244  -0.5871  -0.9597   1.7069
 04B  H47  H  HCR6  0   0.241  -1.9030   1.1880   1.8133
 04B  H48  H  HCR6  0   0.250  -4.0848   2.2240   1.3375
 04B  H49  H  HCR6  0   0.251  -5.5639   1.2646  -0.4035
 04B  H50  H  HCR6  0   0.250  -4.8292  -0.7380  -1.6622
 04B  H51  H  HCR6  0   0.239  -2.6452  -1.7671  -1.1849
 04B  H2   H  HNH2  0   0.334   0.2357  -1.2498  -1.8397
 04B  H1   H  HOH1  0   0.436   1.9215  -2.3089  -0.7047
 04B  H32  H  HCH1  0   0.214   2.9630  -0.1620  -1.2218

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
 04B  C4   C3   aromatic  1.389  0.020  1.389
 04B  C4   C5   aromatic  1.389  0.020  1.389
 04B  C3   C2   aromatic  1.389  0.020  1.389
 04B  C5   C6   aromatic  1.394  0.020  1.394
 04B  N22  C8   single    1.452  0.020  1.452
 04B  O13  C12  single    1.410  0.020  1.410
 04B  C11  C10  single    1.527  0.020  1.527
 04B  C8   C7   single    1.533  0.020  1.533
 04B  C8   C9   single    1.542  0.020  1.542
 04B  C12  C10  single    1.526  0.020  1.526
 04B  C6   C7   single    1.502  0.020  1.502
 04B  C6   C1   aromatic  1.392  0.020  1.392
 04B  C2   C1   aromatic  1.389  0.020  1.389
 04B  C10  C9   single    1.538  0.020  1.538
 04B  C9   O20  single    1.415  0.020  1.415
 04B  N22  H28  single    0.890  0.020  1.040
 04B  C8   H29  single    0.970  0.020  1.090
 04B  C9   H3   single    0.970  0.020  1.090
 04B  O20  H1   single    0.850  0.020  0.980
 04B  C10  H32  single    0.970  0.020  1.090
 04B  C11  H35  single    0.970  0.020  1.090
 04B  C11  H36  single    0.970  0.020  1.090
 04B  C11  H37  single    0.970  0.020  1.090
 04B  C12  H38  single    0.970  0.020  1.090
 04B  C12  H39  single    0.970  0.020  1.090
 04B  O13  H40  single    0.850  0.020  0.980
 04B  C7   H45  single    0.970  0.020  1.090
 04B  C7   H46  single    0.970  0.020  1.090
 04B  C5   H47  single    0.930  0.020  1.080
 04B  C4   H48  single    0.930  0.020  1.080
 04B  C3   H49  single    0.930  0.020  1.080
 04B  C2   H50  single    0.930  0.020  1.080
 04B  C1   H51  single    0.930  0.020  1.080
 04B  N22  H2   single    0.890  0.020  1.040

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
 04B  H2   N22  H28  106.76  3.000
 04B  H2   N22  C8   111.18  3.000
 04B  H28  N22  C8   111.21  3.000
 04B  H29  C8   C7   106.67  3.000
 04B  H29  C8   C9   107.49  3.000
 04B  C7   C8   C9   110.27  3.000
 04B  H29  C8   N22  107.28  3.000
 04B  C9   C8   N22  115.09  3.000
 04B  C7   C8   N22  109.65  3.000
 04B  C10  C9   O20  111.03  3.000
 04B  O20  C9   H3   105.24  3.000
 04B  C10  C9   H3   107.71  3.000
 04B  H3   C9   C8   107.33  3.000
 04B  O20  C9   C8   110.68  3.000
 04B  C10  C9   C8   114.33  3.000
 04B  H1   O20  C9   108.36  3.000
 04B  H32  C10  C12  107.95  3.000
 04B  H32  C10  C11  108.22  3.000
 04B  C12  C10  C11  110.85  3.000
 04B  H32  C10  C9   108.18  3.000
 04B  C12  C10  C9   110.84  3.000
 04B  C11  C10  C9   110.68  3.000
 04B  H37  C11  H36  107.70  3.000
 04B  H37  C11  H35  107.48  3.000
 04B  H36  C11  H35  107.73  3.000
 04B  H37  C11  C10  111.49  3.000
 04B  H36  C11  C10  110.87  3.000
 04B  H35  C11  C10  111.38  3.000
 04B  H39  C12  H38  106.70  3.000
 04B  H39  C12  O13  111.47  3.000
 04B  H38  C12  O13  110.22  3.000
 04B  H39  C12  C10  108.72  3.000
 04B  H38  C12  C10  110.32  3.000
 04B  O13  C12  C10  109.38  3.000
 04B  H40  O13  C12  107.95  3.000
 04B  H46  C7   H45  106.50  3.000
 04B  H46  C7   C6   109.51  3.000
 04B  H45  C7   C6   109.98  3.000
 04B  H46  C7   C8   108.41  3.000
 04B  H45  C7   C8   109.58  3.000
 04B  C6   C7   C8   112.66  3.000
 04B  C1   C6   C5   118.25  3.000
 04B  C1   C6   C7   121.29  3.000
 04B  C5   C6   C7   120.46  3.000
 04B  H47  C5   C4   119.50  3.000
 04B  H47  C5   C6   119.43  3.000
 04B  C4   C5   C6   121.07  3.000
 04B  H48  C4   C3   120.07  3.000
 04B  H48  C4   C5   119.86  3.000
 04B  C3   C4   C5   120.07  3.000
 04B  H49  C3   C2   120.26  3.000
 04B  H49  C3   C4   120.30  3.000
 04B  C2   C3   C4   119.43  3.000
 04B  H50  C2   C1   119.77  3.000
 04B  H50  C2   C3   120.06  3.000
 04B  C1   C2   C3   120.18  3.000
 04B  H51  C1   C2   119.57  3.000
 04B  H51  C1   C6   119.44  3.000
 04B  C2   C1   C6   120.99  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
 04B  CONST_01  C3   C4  C5  C6    0.00   0.0  0
 04B  CONST_02  C3   C2  C1  C6    0.00   0.0  0
 04B  CONST_03  C2   C3  C4  C5    0.00   0.0  0
 04B  CONST_04  C2   C1  C6  C5    0.00   0.0  0
 04B  CONST_05  C1   C2  C3  C4    0.00   0.0  0
 04B  CONST_06  C1   C6  C5  C4    0.00   0.0  0
 04B  CONST_07  C4   C5  C6  C7  180.00   0.0  0
 04B  CONST_08  C2   C1  C6  C7  180.00   0.0  0
 04B  CONST_09  H48  C4  C5  C6  180.00   0.0  0
 04B  CONST_10  H50  C2  C1  C6  180.00   0.0  0
 04B  CONST_11  H49  C3  C4  C5  180.00   0.0  0
 04B  CONST_12  H51  C1  C6  C5  180.00   0.0  0
 04B  CONST_13  H47  C5  C4  C3  180.00   0.0  0
 04B  Var_01    C5   C6  C7  C8  -80.75  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
 04B  chir_01  C8   N22  C7   C9   negativ
 04B  chir_02  C9   O20  C8   C10  positiv
 04B  chir_03  C10  C9   C12  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
 04B  plan-1  C7   0.020
 04B  plan-1  C6   0.020
 04B  plan-1  C5   0.020
 04B  plan-1  C4   0.020
 04B  plan-1  C3   0.020
 04B  plan-1  C2   0.020
 04B  plan-1  C1   0.020
 04B  plan-1  H47  0.020
 04B  plan-1  H48  0.020
 04B  plan-1  H49  0.020
 04B  plan-1  H50  0.020
 04B  plan-1  H51  0.020

