# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:18:11 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-propyl-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: CCCC1=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
 NB1  NB1  (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-propyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  33  16  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NB1
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
 NB1  C1    C  CR15  0  -0.084   1.9934  -1.1352  -1.9481
 NB1  C2    C  CR15  0  -0.194   1.9866  -1.0877  -0.4101
 NB1  C3    C  CH1   0   0.065   1.2948   0.1661   0.1310
 NB1  C4    C  CH1   0  -0.005   1.7076   1.4030  -0.6565
 NB1  C5    C  CH1   0  -0.036   1.4160   1.1650  -2.1372
 NB1  C6    C  CH2   0  -0.174   1.7894   2.3442  -3.0173
 NB1  C7    C  CR5   0   0.132   0.4644  -2.7268  -0.7422
 NB1  C8    C  CH2   0  -0.504  -0.4421  -3.8776  -0.4618
 NB1  CM    C  CH3   0  -0.661  -2.8058  -4.7577  -0.4016
 NB1  N2    N  N     0  -0.343   1.3000  -2.2608   0.0873
 NB1  O3    O  OH1   0  -0.665   1.6166   0.2716   1.4925
 NB1  O4    O  OH1   0  -0.671   0.9603   2.4841  -0.1471
 NB1  O5    O  O2    0  -0.468   2.1919   0.0642  -2.5896
 NB1  O6    O  OH1   0  -0.663   1.4549   2.1420  -4.3677
 NB1  S1    S  S2    0  -0.020   0.3825  -1.9687  -2.3452
 NB1  C9    C  CH2   0  -0.438  -1.9146  -3.5699  -0.7329
 NB1  H1    H  HCR5  0   0.312   2.7801  -1.8044  -2.2998
 NB1  H2    H  HCR5  0   0.277   3.0237  -1.0859  -0.0611
 NB1  H3    H  HCH1  0   0.211   0.2076   0.0454  -0.0058
 NB1  H4    H  HCH1  0   0.230   2.7868   1.5699  -0.5288
 NB1  HA    H  HOH1  0   0.451   1.1644   1.0465   1.8437
 NB1  H5    H  HCH1  0   0.232   0.3448   0.9463  -2.2673
 NB1  HB    H  HOH1  0   0.465   1.4700   3.2938  -0.2418
 NB1  H6C1  H  HCH2  0   0.206   2.8578   2.5675  -2.8894
 NB1  H6C2  H  HCH2  0   0.232   1.2333   3.2204  -2.6815
 NB1  H6    H  HOH1  0   0.449   1.9784   1.4072  -4.7023
 NB1  H8C1  H  HCH2  0   0.256  -0.3009  -4.1684   0.5808
 NB1  H8C2  H  HCH2  0   0.261  -0.1289  -4.7239  -1.0814
 NB1  H9C1  H  HCH2  0   0.229  -2.0500  -3.2978  -1.7833
 NB1  H9C2  H  HCH2  0   0.236  -2.2193  -2.6997  -0.1461
 NB1  HMC1  H  HCH3  0   0.224  -2.7338  -5.0240   0.6541
 NB1  HMC2  H  HCH3  0   0.223  -2.5220  -5.6357  -0.9845
 NB1  HMC3  H  HCH3  0   0.235  -3.8509  -4.5375  -0.6190

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
 NB1  C1  C2    single  1.539  0.020  1.539
 NB1  C1  O5    single  1.375  0.020  1.375
 NB1  C1  S1    single  1.857  0.020  1.857
 NB1  C1  H1    single  0.970  0.020  1.090
 NB1  C2  C3    single  1.531  0.020  1.531
 NB1  C2  N2    single  1.447  0.020  1.447
 NB1  C2  H2    single  0.970  0.020  1.090
 NB1  C3  C4    single  1.523  0.020  1.523
 NB1  C3  O3    single  1.403  0.020  1.403
 NB1  C3  H3    single  0.970  0.020  1.090
 NB1  C4  C5    single  1.528  0.020  1.528
 NB1  C4  O4    single  1.410  0.020  1.410
 NB1  C4  H4    single  0.970  0.020  1.090
 NB1  C5  C6    single  1.518  0.020  1.518
 NB1  C5  O5    single  1.421  0.020  1.421
 NB1  C5  H5    single  0.970  0.020  1.090
 NB1  C6  O6    single  1.406  0.020  1.406
 NB1  C6  H6C1  single  0.970  0.020  1.090
 NB1  C6  H6C2  single  0.970  0.020  1.090
 NB1  C7  C8    single  1.492  0.020  1.492
 NB1  C7  N2    double  1.266  0.020  1.266
 NB1  C7  S1    single  1.775  0.020  1.775
 NB1  C8  C9    single  1.529  0.020  1.529
 NB1  C8  H8C1  single  0.970  0.020  1.090
 NB1  C8  H8C2  single  0.970  0.020  1.090
 NB1  CM  C9    single  1.521  0.020  1.521
 NB1  CM  HMC1  single  0.970  0.020  1.090
 NB1  CM  HMC2  single  0.970  0.020  1.090
 NB1  CM  HMC3  single  0.970  0.020  1.090
 NB1  O3  HA    single  0.850  0.020  0.980
 NB1  O4  HB    single  0.850  0.020  0.980
 NB1  O6  H6    single  0.850  0.020  0.980
 NB1  C9  H9C1  single  0.970  0.020  1.090
 NB1  C9  H9C2  single  0.970  0.020  1.090

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
 NB1  H1    C1  S1    106.34  3.000
 NB1  H1    C1  O5    106.29  3.000
 NB1  S1    C1  O5    114.66  3.000
 NB1  H1    C1  C2    110.14  3.000
 NB1  S1    C1  C2    102.93  3.000
 NB1  O5    C1  C2    116.11  3.000
 NB1  H2    C2  N2    109.96  3.000
 NB1  H2    C2  C3    108.31  3.000
 NB1  N2    C2  C3    109.15  3.000
 NB1  H2    C2  C1    108.34  3.000
 NB1  N2    C2  C1    108.70  3.000
 NB1  C3    C2  C1    112.37  3.000
 NB1  H3    C3  O3    110.79  3.000
 NB1  H3    C3  C4    106.97  3.000
 NB1  O3    C3  C4    112.24  3.000
 NB1  H3    C3  C2    108.19  3.000
 NB1  O3    C3  C2    107.52  3.000
 NB1  C4    C3  C2    111.09  3.000
 NB1  H4    C4  O4    111.22  3.000
 NB1  H4    C4  C5    108.88  3.000
 NB1  O4    C4  C5    111.63  3.000
 NB1  H4    C4  C3    109.22  3.000
 NB1  O4    C4  C3    107.00  3.000
 NB1  C5    C4  C3    108.84  3.000
 NB1  H5    C5  O5    109.87  3.000
 NB1  H5    C5  C6    108.97  3.000
 NB1  O5    C5  C6    106.43  3.000
 NB1  H5    C5  C4    109.34  3.000
 NB1  O5    C5  C4    108.97  3.000
 NB1  C6    C5  C4    113.20  3.000
 NB1  H6C2  C6  H6C1  107.25  3.000
 NB1  H6C2  C6  O6    106.85  3.000
 NB1  H6C1  C6  O6    111.86  3.000
 NB1  H6C2  C6  C5    108.67  3.000
 NB1  H6C1  C6  C5    109.23  3.000
 NB1  O6    C6  C5    112.75  3.000
 NB1  S1    C7  N2    117.70  3.000
 NB1  S1    C7  C8    118.11  3.000
 NB1  N2    C7  C8    124.19  3.000
 NB1  H8C2  C8  H8C1  107.32  3.000
 NB1  H8C2  C8  C9    109.32  3.000
 NB1  H8C1  C8  C9    110.35  3.000
 NB1  H8C2  C8  C7    108.44  3.000
 NB1  H8C1  C8  C7    107.85  3.000
 NB1  C9    C8  C7    113.38  3.000
 NB1  HMC3  CM  HMC2  107.78  3.000
 NB1  HMC3  CM  HMC1  107.79  3.000
 NB1  HMC2  CM  HMC1  107.65  3.000
 NB1  HMC3  CM  C9    111.13  3.000
 NB1  HMC2  CM  C9    111.07  3.000
 NB1  HMC1  CM  C9    111.26  3.000
 NB1  C7    N2  C2    112.72  3.000
 NB1  HA    O3  C3    107.85  3.000
 NB1  HB    O4  C4    109.23  3.000
 NB1  C5    O5  C1    116.65  3.000
 NB1  H6    O6  C6    108.32  3.000
 NB1  C7    S1  C1     87.63  3.000
 NB1  H9C2  C9  H9C1  106.44  3.000
 NB1  H9C2  C9  CM    109.96  3.000
 NB1  H9C1  C9  CM    109.32  3.000
 NB1  H9C2  C9  C8    109.49  3.000
 NB1  H9C1  C9  C8    109.87  3.000
 NB1  CM    C9  C8    111.62  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
 NB1  Var_01  N2    C7  S1  C1    13.95  30.0  1
 NB1  Var_02  S1    C7  N2  C2     4.59  30.0  1
 NB1  Var_03  C9    C8  C7  N2   126.80  30.0  3
 NB1  Var_04  CM    C9  C8  C7  -178.59  30.0  3
 NB1  Var_05  HMC1  CM  C9  C8    61.16  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
 NB1  chir_01  C1  C2  O5  S1  positiv
 NB1  chir_02  C2  N2  C3  C1  positiv
 NB1  chir_03  C3  O3  C2  C4  positiv
 NB1  chir_04  C4  O4  C5  C3  positiv
 NB1  chir_05  C5  O5  C6  C4  positiv

