# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:52:48 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-(prop-2-enylamino)-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: OC[C@H]1O[C@@H]2SC(=N[C@@H]2[C@@H](O)[C@@H]1O)NCC=C
#
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
 DV1  DV1  (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-(prop-2-enylamino)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol  ligand  33  17  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DV1
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
 DV1  O1   O  OH1   0  -0.667   1.2825   2.8837  -0.3701
 DV1  C1   C  CH1   0   0.068   1.1980   1.4835  -0.3169
 DV1  C2   C  CH1   0  -0.009   2.5733   0.8300  -0.2950
 DV1  O2   O  OH1   0  -0.672   3.2060   1.1622  -1.5109
 DV1  C3   C  CR15  0  -0.182   0.3897   1.1160   0.9277
 DV1  C4   C  CR15  0  -0.086   0.5052  -0.3797   1.2571
 DV1  O3   O  O2    0  -0.458   1.7392  -0.9562   1.0852
 DV1  C5   C  CH1   0  -0.020   2.4047  -0.6832  -0.1389
 DV1  C6   C  CH2   0  -0.161   3.7302  -1.4107  -0.1008
 DV1  O4   O  OH1   0  -0.668   3.4915  -2.7951  -0.0284
 DV1  N1   N  N     0  -0.424  -1.0031   1.4360   0.7442
 DV1  C7   C  CR5   0   0.337  -1.6746   0.4322   0.3260
 DV1  S1   S  S2    0  -0.047  -0.8404  -1.1346   0.2136
 DV1  N2   N  NH1   0  -0.639  -2.9790   0.4956  -0.0023
 DV1  C8   C  CH2   0  -0.337  -3.7513  -0.5528  -0.6344
 DV1  C9   C  C1    0  -0.179  -5.1801  -0.4811  -0.1950
 DV1  C10  C  C2    0  -0.520  -6.2033  -0.3456  -1.0281
 DV1  H1   H  HOH1  0   0.449   1.7809   3.1183  -1.1602
 DV1  H2   H  HCH1  0   0.205   0.6665   1.0892  -1.1984
 DV1  H3   H  HCH1  0   0.227   3.1417   1.2134   0.5648
 DV1  H4   H  HOH1  0   0.464   4.1578   1.1818  -1.3783
 DV1  H5   H  HCR5  0   0.263   0.7985   1.6765   1.7756
 DV1  H6   H  HCR5  0   0.311   0.2208  -0.5587   2.2948
 DV1  H7   H  HCH1  0   0.231   1.8109  -1.0665  -0.9828
 DV1  H8   H  HCH2  0   0.209   4.2875  -1.1467  -1.0062
 DV1  H9   H  HCH2  0   0.200   4.3150  -1.0487   0.7566
 DV1  H10  H  HOH1  0   0.458   4.3333  -3.2469  -0.1336
 DV1  H11  H  HNH1  0   0.394  -3.3454   1.4333  -0.0793
 DV1  H12  H  HCH2  0   0.249  -3.6843  -0.5019  -1.7261
 DV1  H13  H  HCH2  0   0.261  -3.3381  -1.5183  -0.3313
 DV1  H14  H  H     0   0.256  -5.3512  -0.5553   0.8745
 DV1  H15  H  H     0   0.243  -6.0589  -0.2644  -2.0991
 DV1  H16  H  H     0   0.246  -7.2241  -0.3158  -0.6711

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
 DV1  O1   C1   single  1.404  0.020  1.404
 DV1  C1   C2   single  1.523  0.020  1.523
 DV1  C1   C3   single  1.529  0.020  1.529
 DV1  C2   O2   single  1.410  0.020  1.410
 DV1  C2   C5   single  1.531  0.020  1.531
 DV1  C3   C4   single  1.536  0.020  1.536
 DV1  C3   N1   single  1.441  0.020  1.441
 DV1  C4   O3   single  1.373  0.020  1.373
 DV1  C4   S1   single  1.863  0.020  1.863
 DV1  O3   C5   single  1.420  0.020  1.420
 DV1  C5   C6   single  1.512  0.020  1.512
 DV1  C6   O4   single  1.407  0.020  1.407
 DV1  N1   C7   double  1.278  0.020  1.278
 DV1  C7   S1   single  1.779  0.020  1.779
 DV1  C7   N2   single  1.347  0.020  1.347
 DV1  N2   C8   single  1.447  0.020  1.447
 DV1  C8   C9   single  1.497  0.020  1.497
 DV1  C9   C10  double  1.326  0.020  1.326
 DV1  O1   H1   single  0.850  0.020  0.980
 DV1  C1   H2   single  0.970  0.020  1.090
 DV1  C2   H3   single  0.970  0.020  1.090
 DV1  O2   H4   single  0.850  0.020  0.980
 DV1  C3   H5   single  0.970  0.020  1.090
 DV1  C4   H6   single  0.970  0.020  1.090
 DV1  C5   H7   single  0.970  0.020  1.090
 DV1  C6   H8   single  0.970  0.020  1.090
 DV1  C6   H9   single  0.970  0.020  1.090
 DV1  O4   H10  single  0.850  0.020  0.980
 DV1  N2   H11  single  0.890  0.020  1.040
 DV1  C8   H12  single  0.970  0.020  1.090
 DV1  C8   H13  single  0.970  0.020  1.090
 DV1  C9   H14  single  0.930  0.020  1.080
 DV1  C10  H15  single  0.930  0.020  1.080
 DV1  C10  H16  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
 DV1  H1   O1   C1   107.77  3.000
 DV1  H2   C1   C3   108.07  3.000
 DV1  H2   C1   C2   107.07  3.000
 DV1  C3   C1   C2   111.26  3.000
 DV1  H2   C1   O1   110.82  3.000
 DV1  C3   C1   O1   107.61  3.000
 DV1  C2   C1   O1   111.97  3.000
 DV1  H3   C2   C5   108.78  3.000
 DV1  H3   C2   O2   111.10  3.000
 DV1  C5   C2   O2   111.73  3.000
 DV1  H3   C2   C1   109.18  3.000
 DV1  C5   C2   C1   109.04  3.000
 DV1  O2   C2   C1   106.96  3.000
 DV1  H4   O2   C2   109.27  3.000
 DV1  H5   C3   N1   110.22  3.000
 DV1  H5   C3   C4   107.71  3.000
 DV1  N1   C3   C4   108.44  3.000
 DV1  H5   C3   C1   108.04  3.000
 DV1  N1   C3   C1   110.73  3.000
 DV1  C4   C3   C1   111.65  3.000
 DV1  H6   C4   S1   106.15  3.000
 DV1  H6   C4   O3   106.53  3.000
 DV1  S1   C4   O3   114.15  3.000
 DV1  H6   C4   C3   110.14  3.000
 DV1  S1   C4   C3   102.72  3.000
 DV1  O3   C4   C3   116.73  3.000
 DV1  C5   O3   C4   116.65  3.000
 DV1  H7   C5   C6   108.94  3.000
 DV1  H7   C5   O3   109.94  3.000
 DV1  C6   C5   O3   107.25  3.000
 DV1  H7   C5   C2   109.00  3.000
 DV1  C6   C5   C2   112.43  3.000
 DV1  O3   C5   C2   109.25  3.000
 DV1  H9   C6   H8   107.14  3.000
 DV1  H9   C6   O4   111.98  3.000
 DV1  H8   C6   O4   111.47  3.000
 DV1  H9   C6   C5   109.12  3.000
 DV1  H8   C6   C5   108.01  3.000
 DV1  O4   C6   C5   109.02  3.000
 DV1  H10  O4   C6   107.96  3.000
 DV1  C7   N1   C3   112.03  3.000
 DV1  N2   C7   S1   118.71  3.000
 DV1  N2   C7   N1   123.49  3.000
 DV1  S1   C7   N1   117.79  3.000
 DV1  C7   S1   C4    86.93  3.000
 DV1  H11  N2   C8   116.48  3.000
 DV1  H11  N2   C7   114.45  3.000
 DV1  C8   N2   C7   126.10  3.000
 DV1  H13  C8   H12  107.12  3.000
 DV1  H13  C8   C9   108.77  3.000
 DV1  H12  C8   C9   110.42  3.000
 DV1  H13  C8   N2   108.48  3.000
 DV1  H12  C8   N2   111.66  3.000
 DV1  C9   C8   N2   110.27  3.000
 DV1  H14  C9   C10  120.27  3.000
 DV1  H14  C9   C8   115.88  3.000
 DV1  C10  C9   C8   123.84  3.000
 DV1  H16  C10  H15  116.73  3.000
 DV1  H16  C10  C9   121.56  3.000
 DV1  H15  C10  C9   121.71  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
 DV1  CONST_01  S1   C7   N1  C3    0.00   0.0  0
 DV1  CONST_02  N2   C7   N1  C3  180.00   0.0  0
 DV1  CONST_03  C8   N2   C7  N1  180.00   0.0  0
 DV1  CONST_04  C8   N2   C7  S1    0.00   0.0  0
 DV1  CONST_05  H11  N2   C7  N1    0.00   0.0  0
 DV1  Var_01    N1   C7   S1  C4   14.26  30.0  1
 DV1  Var_02    C9   C8   N2  C7  149.24  30.0  3
 DV1  Var_03    C10  C9   C8  N2  122.52  30.0  3
 DV1  Var_04    H15  C10  C9  C8   -0.80   0.0  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
 DV1  chir_01  C1  O1  C2  C3  negativ
 DV1  chir_02  C2  O2  C5  C1  positiv
 DV1  chir_03  C3  N1  C1  C4  positiv
 DV1  chir_04  C4  S1  O3  C3  negativ
 DV1  chir_05  C5  O3  C2  C6  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
 DV1  plan-1  C3   0.020
 DV1  plan-1  N1   0.020
 DV1  plan-1  C7   0.020
 DV1  plan-1  S1   0.020
 DV1  plan-1  N2   0.020
 DV1  plan-1  C8   0.020
 DV1  plan-1  H11  0.020
 DV1  plan-2  C8   0.020
 DV1  plan-2  C9   0.020
 DV1  plan-2  C10  0.020
 DV1  plan-2  H14  0.020
 DV1  plan-2  H15  0.020
 DV1  plan-2  H16  0.020

