# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 04:57:44 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (3aR,5R,6S,7R,7aR)-2-amino-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=N[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2S1
#
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
 2J4  2J4  (3aR,5R,6S,7R,7aR)-2-amino-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  26  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2J4
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
 2J4  O6    O  OH1   0  -0.668   3.1266   2.2327   0.1712
 2J4  C6    C  CH2   0  -0.161   3.0843   0.8411  -0.0322
 2J4  C5    C  CH1   0  -0.020   1.6528   0.3717   0.0961
 2J4  O5    O  O2    0  -0.458   0.9115   1.0059  -0.9355
 2J4  C4    C  CH1   0  -0.008   1.5113  -1.1460  -0.0461
 2J4  O4    O  OH1   0  -0.672   2.2171  -1.8304   0.9652
 2J4  C3    C  CH1   0   0.067   0.0412  -1.5153   0.1018
 2J4  O3    O  OH1   0  -0.667  -0.1774  -2.8890  -0.0884
 2J4  C2    C  CR15  0  -0.180  -0.8233  -0.7635  -0.9102
 2J4  C1    C  CR15  0  -0.090  -0.4311   0.7216  -0.9947
 2J4  S1    S  S2    0  -0.046  -1.4392   1.4885   0.3689
 2J4  N2    N  N     0  -0.413  -2.2178  -0.8491  -0.5580
 2J4  C7    C  CR5   0   0.313  -2.5948   0.1553   0.1342
 2J4  N1    N  NH2   0  -0.819  -3.8112   0.2961   0.6803
 2J4  H6    H  HOH1  0   0.457   4.0482   2.5058   0.1606
 2J4  H6C1  H  HCH2  0   0.200   3.4694   0.5601  -1.0228
 2J4  H6C2  H  HCH2  0   0.209   3.6872   0.3084   0.7115
 2J4  H5    H  HCH1  0   0.230   1.2606   0.6732   1.0800
 2J4  H4    H  HCH1  0   0.228   1.8639  -1.4428  -1.0446
 2J4  H1    H  HCR5  0   0.308  -0.7972   1.1543  -1.9271
 2J4  HA    H  HOH1  0   0.464   3.0911  -2.0632   0.6401
 2J4  H3    H  HCH1  0   0.204  -0.2696  -1.2057   1.1132
 2J4  HB    H  HOH1  0   0.449   0.3444  -3.3624   0.5684
 2J4  H2    H  HCR5  0   0.262  -0.6515  -1.2068  -1.8972
 2J4  H1N   H  HNH2  0   0.410  -4.0517   1.0922   1.2424
 2J4  H2N   H  HNH2  0   0.402  -4.4341  -0.4937   0.6996

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
 2J4  O6  C6    single  1.407  0.020  1.407
 2J4  C6  C5    single  1.512  0.020  1.512
 2J4  C5  O5    single  1.420  0.020  1.420
 2J4  C5  C4    single  1.531  0.020  1.531
 2J4  O5  C1    single  1.374  0.020  1.374
 2J4  C4  O4    single  1.410  0.020  1.410
 2J4  C4  C3    single  1.523  0.020  1.523
 2J4  C3  O3    single  1.404  0.020  1.404
 2J4  C3  C2    single  1.529  0.020  1.529
 2J4  C2  C1    single  1.538  0.020  1.538
 2J4  C2  N2    single  1.441  0.020  1.441
 2J4  C1  S1    single  1.861  0.020  1.861
 2J4  S1  C7    single  1.780  0.020  1.780
 2J4  N2  C7    double  1.277  0.020  1.277
 2J4  N1  C7    single  1.341  0.020  1.341
 2J4  O6  H6    single  0.850  0.020  0.980
 2J4  C6  H6C1  single  0.970  0.020  1.090
 2J4  C6  H6C2  single  0.970  0.020  1.090
 2J4  C5  H5    single  0.970  0.020  1.090
 2J4  C4  H4    single  0.970  0.020  1.090
 2J4  C1  H1    single  0.970  0.020  1.090
 2J4  O4  HA    single  0.850  0.020  0.980
 2J4  C3  H3    single  0.970  0.020  1.090
 2J4  O3  HB    single  0.850  0.020  0.980
 2J4  C2  H2    single  0.970  0.020  1.090
 2J4  N1  H1N   single  0.860  0.020  1.020
 2J4  N1  H2N   single  0.860  0.020  1.020

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
 2J4  H6    O6  C6    107.96  3.000
 2J4  H6C2  C6  H6C1  107.14  3.000
 2J4  H6C2  C6  C5    108.21  3.000
 2J4  H6C1  C6  C5    109.20  3.000
 2J4  H6C2  C6  O6    111.48  3.000
 2J4  H6C1  C6  O6    111.87  3.000
 2J4  C5    C6  O6    108.86  3.000
 2J4  H5    C5  C4    108.75  3.000
 2J4  H5    C5  O5    109.93  3.000
 2J4  C4    C5  O5    109.09  3.000
 2J4  H5    C5  C6    109.15  3.000
 2J4  C4    C5  C6    112.79  3.000
 2J4  O5    C5  C6    107.10  3.000
 2J4  C1    O5  C5    116.70  3.000
 2J4  H4    C4  C3    109.40  3.000
 2J4  H4    C4  O4    111.08  3.000
 2J4  C3    C4  O4    107.21  3.000
 2J4  H4    C4  C5    108.80  3.000
 2J4  C3    C4  C5    108.70  3.000
 2J4  O4    C4  C5    111.60  3.000
 2J4  HA    O4  C4    109.27  3.000
 2J4  H3    C3  C2    108.05  3.000
 2J4  H3    C3  O3    110.81  3.000
 2J4  C2    C3  O3    107.67  3.000
 2J4  H3    C3  C4    107.04  3.000
 2J4  C2    C3  C4    111.25  3.000
 2J4  O3    C3  C4    111.99  3.000
 2J4  HB    O3  C3    107.71  3.000
 2J4  H2    C2  N2    110.36  3.000
 2J4  H2    C2  C1    107.53  3.000
 2J4  N2    C2  C1    108.52  3.000
 2J4  H2    C2  C3    107.98  3.000
 2J4  N2    C2  C3    110.87  3.000
 2J4  C1    C2  C3    111.53  3.000
 2J4  H1    C1  S1    106.32  3.000
 2J4  H1    C1  C2    110.14  3.000
 2J4  S1    C1  C2    102.67  3.000
 2J4  H1    C1  O5    106.42  3.000
 2J4  S1    C1  O5    114.37  3.000
 2J4  C2    C1  O5    116.53  3.000
 2J4  C7    S1  C1     86.93  3.000
 2J4  C7    N2  C2    111.81  3.000
 2J4  N1    C7  N2    124.84  3.000
 2J4  N1    C7  S1    117.18  3.000
 2J4  N2    C7  S1    117.97  3.000
 2J4  H2N   N1  H1N   117.62  3.000
 2J4  H2N   N1  C7    119.15  3.000
 2J4  H1N   N1  C7    121.91  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
 2J4  CONST_01  S1   C7  N2  C2    0.00   0.0  0
 2J4  CONST_02  N1   C7  N2  C2  180.00   0.0  0
 2J4  CONST_03  H1N  N1  C7  S1    0.00   0.0  0
 2J4  CONST_04  H2N  N1  C7  S1  180.00   0.0  0
 2J4  Var_01    N2   C7  S1  C1   13.87  30.0  1

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
 2J4  chir_01  C5  C6  O5  C4  negativ
 2J4  chir_02  C4  O4  C5  C3  positiv
 2J4  chir_03  C3  O3  C2  C4  positiv
 2J4  chir_04  C2  N2  C3  C1  positiv
 2J4  chir_05  C1  S1  O5  C2  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
 2J4  plan-1  C2   0.020
 2J4  plan-1  S1   0.020
 2J4  plan-1  N2   0.020
 2J4  plan-1  C7   0.020
 2J4  plan-1  N1   0.020
 2J4  plan-1  H1N  0.020
 2J4  plan-1  H2N  0.020

