# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:11:00 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (3aR,5R,6S,7R,7aR)-2-(ethylamino)-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: CCNC1=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
 NHT  NHT  (3aR,5R,6S,7R,7aR)-2-(ethylamino)-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  32  16  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NHT
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
 NHT  C1    C  CH1   0  -0.086   0.1970  -0.5272   1.1932
 NHT  C2    C  CH1   0  -0.184   0.0255   0.9918   1.0369
 NHT  C3    C  CH1   0   0.066   0.8268   1.5270  -0.1504
 NHT  C4    C  CH1   0  -0.007   2.2286   0.9320  -0.1811
 NHT  C5    C  CH1   0  -0.020   2.1224  -0.5941  -0.1981
 NHT  C6    C  CH2   0  -0.161   3.4758  -1.2692  -0.2212
 NHT  C7    C  C     0   0.337  -2.0005   0.3075   0.3233
 NHT  C10   C  CH3   0  -0.685  -5.4031  -0.3148  -1.0532
 NHT  N2    N  N     0  -0.425  -1.3785   1.2752   0.8817
 NHT  O3    O  OH1   0  -0.667   0.8527   2.9269  -0.0486
 NHT  O4    O  OH1   0  -0.672   2.8596   1.4236  -1.3426
 NHT  O5    O  O2    0  -0.459   1.4560  -1.0309   0.9765
 NHT  N1    N  NH1   0  -0.636  -3.2790   0.3709  -0.0880
 NHT  O6    O  OH1   0  -0.668   3.2907  -2.6606  -0.3173
 NHT  S1    S  S2    0  -0.048  -1.1070  -1.2074   0.0522
 NHT  C9    C  CH2   0  -0.276  -4.1104  -0.7746  -0.4062
 NHT  H6    H  HOH1  0   0.458   4.1531  -3.0661  -0.4418
 NHT  H6C1  H  HCH2  0   0.208   4.0358  -0.8789  -1.0782
 NHT  H6C2  H  HCH2  0   0.200   4.0334  -0.9906   0.6840
 NHT  H5    H  HCH1  0   0.230   1.5555  -0.9028  -1.0898
 NHT  H4    H  HCH1  0   0.226   2.7701   1.2402   0.7250
 NHT  H1    H  HCH1  0   0.309  -0.0898  -0.8353   2.1997
 NHT  HA    H  HOH1  0   0.463   3.8093   1.4563  -1.1976
 NHT  H3    H  HCH1  0   0.206   0.3206   1.2099  -1.0769
 NHT  HB    H  HOH1  0   0.449   1.3317   3.2690  -0.8108
 NHT  H2    H  HCH1  0   0.262   0.4081   1.4673   1.9469
 NHT  H9C1  H  HCH2  0   0.234  -4.3313  -1.3663   0.4880
 NHT  H9C2  H  HCH2  0   0.241  -3.5742  -1.4267  -1.0991
 NHT  H8    H  HCH3  0   0.234  -5.9772   0.3248  -0.3811
 NHT  H11   H  HCH3  0   0.235  -5.2079   0.2396  -1.9711
 NHT  H12   H  HCH3  0   0.245  -6.0220  -1.1758  -1.3011
 NHT  H13   H  HNH1  0   0.390  -3.7574   1.2214   0.1716

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
 NHT  O6   C6    single  1.407  0.020  1.407
 NHT  C6   C5    single  1.513  0.020  1.513
 NHT  C5   O5    single  1.419  0.020  1.419
 NHT  C5   C4    single  1.530  0.020  1.530
 NHT  O5   C1    single  1.373  0.020  1.373
 NHT  C4   O4    single  1.410  0.020  1.410
 NHT  C4   C3    single  1.523  0.020  1.523
 NHT  C3   O3    single  1.404  0.020  1.404
 NHT  C3   C2    single  1.529  0.020  1.529
 NHT  C2   N2    single  1.441  0.020  1.441
 NHT  C2   C1    single  1.537  0.020  1.537
 NHT  N2   C7    double  1.279  0.020  1.279
 NHT  C1   S1    single  1.861  0.020  1.861
 NHT  S1   C7    single  1.780  0.020  1.780
 NHT  C7   N1    single  1.345  0.020  1.345
 NHT  N1   C9    single  1.451  0.020  1.451
 NHT  C9   C10   single  1.517  0.020  1.517
 NHT  O6   H6    single  0.850  0.020  0.980
 NHT  C6   H6C1  single  0.970  0.020  1.090
 NHT  C6   H6C2  single  0.970  0.020  1.090
 NHT  C5   H5    single  0.970  0.020  1.090
 NHT  C4   H4    single  0.970  0.020  1.090
 NHT  C1   H1    single  0.970  0.020  1.090
 NHT  O4   HA    single  0.850  0.020  0.980
 NHT  C3   H3    single  0.970  0.020  1.090
 NHT  O3   HB    single  0.850  0.020  0.980
 NHT  C2   H2    single  0.970  0.020  1.090
 NHT  C9   H9C1  single  0.970  0.020  1.090
 NHT  C9   H9C2  single  0.970  0.020  1.090
 NHT  C10  H8    single  0.970  0.020  1.090
 NHT  C10  H11   single  0.970  0.020  1.090
 NHT  C10  H12   single  0.970  0.020  1.090
 NHT  N1   H13   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
 NHT  H1    C1   S1    106.15  3.000
 NHT  H1    C1   O5    106.44  3.000
 NHT  S1    C1   O5    114.30  3.000
 NHT  H1    C1   C2    110.10  3.000
 NHT  S1    C1   C2    102.75  3.000
 NHT  O5    C1   C2    116.67  3.000
 NHT  H2    C2   N2    110.15  3.000
 NHT  H2    C2   C3    108.06  3.000
 NHT  N2    C2   C3    110.99  3.000
 NHT  H2    C2   C1    107.79  3.000
 NHT  N2    C2   C1    108.31  3.000
 NHT  C3    C2   C1    111.50  3.000
 NHT  H3    C3   O3    110.87  3.000
 NHT  H3    C3   C4    107.06  3.000
 NHT  O3    C3   C4    111.96  3.000
 NHT  H3    C3   C2    108.14  3.000
 NHT  O3    C3   C2    107.60  3.000
 NHT  C4    C3   C2    111.17  3.000
 NHT  H4    C4   O4    111.13  3.000
 NHT  H4    C4   C5    108.84  3.000
 NHT  O4    C4   C5    111.69  3.000
 NHT  H4    C4   C3    109.10  3.000
 NHT  O4    C4   C3    106.99  3.000
 NHT  C5    C4   C3    109.03  3.000
 NHT  H5    C5   O5    110.01  3.000
 NHT  H5    C5   C6    108.86  3.000
 NHT  O5    C5   C6    107.18  3.000
 NHT  H5    C5   C4    108.94  3.000
 NHT  O5    C5   C4    109.29  3.000
 NHT  C6    C5   C4    112.54  3.000
 NHT  H6C2  C6   H6C1  107.13  3.000
 NHT  H6C2  C6   O6    111.94  3.000
 NHT  H6C1  C6   O6    111.48  3.000
 NHT  H6C2  C6   C5    109.16  3.000
 NHT  H6C1  C6   C5    108.08  3.000
 NHT  O6    C6   C5    108.95  3.000
 NHT  S1    C7   N1    118.10  3.000
 NHT  N1    C7   N2    124.09  3.000
 NHT  S1    C7   N2    117.81  3.000
 NHT  H12   C10  H11   108.19  3.000
 NHT  H12   C10  H8    107.74  3.000
 NHT  H11   C10  H8    108.36  3.000
 NHT  H12   C10  C9    109.98  3.000
 NHT  H11   C10  C9    111.14  3.000
 NHT  H8    C10  C9    111.31  3.000
 NHT  C7    N2   C2    111.85  3.000
 NHT  HB    O3   C3    107.82  3.000
 NHT  HA    O4   C4    109.25  3.000
 NHT  C5    O5   C1    116.63  3.000
 NHT  H13   N1   C9    116.74  3.000
 NHT  H13   N1   C7    114.30  3.000
 NHT  C9    N1   C7    125.09  3.000
 NHT  H6    O6   C6    107.94  3.000
 NHT  C7    S1   C1     86.98  3.000
 NHT  H9C2  C9   H9C1  107.13  3.000
 NHT  H9C2  C9   N1    109.22  3.000
 NHT  H9C1  C9   N1    111.30  3.000
 NHT  H9C2  C9   C10   109.19  3.000
 NHT  H9C1  C9   C10   109.89  3.000
 NHT  N1    C9   C10   110.04  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
 NHT  CONST_01  S1   C7   N2  C2     0.00   0.0  0
 NHT  CONST_02  N1   C7   N2  C2   180.00   0.0  0
 NHT  CONST_05  H13  N1   C7  N2     0.00   0.0  0
 NHT  Var_01    N2   C7   S1  C1    13.08  30.0  1
 NHT  Var_02    C10  C9   N1  C7  -170.48  30.0  3
 NHT  Var_03    H8   C10  C9  N1   -61.26  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
 NHT  chir_01  C1  O5  C2  S1  negativ
 NHT  chir_02  C2  N2  C1  C3  negativ
 NHT  chir_03  C3  O3  C2  C4  positiv
 NHT  chir_04  C4  O4  C5  C3  positiv
 NHT  chir_05  C5  O5  C6  C4  positiv

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
 NHT  plan-1  C2   0.020
 NHT  plan-1  C7   0.020
 NHT  plan-1  N2   0.020
 NHT  plan-1  N1   0.020
 NHT  plan-1  S1   0.020
 NHT  plan-1  C9   0.020
 NHT  plan-1  H13  0.020

