# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 18:19:42 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: [(2Z,3aS,4R,6Z,7S,10S,10aS)-10-hydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)OC[C@@H]1NC(=N)N2CC[C@H](O)[C@@]23NC(=N)N[C@@H]13
#
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
 D82  D82  "beta-Saxitoxinol"
  ligand  37  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D82
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
 D82  N    N  NH2   0  -0.831  -5.2703  19.3534  -1.4023
 D82  C    C  C     0   0.715  -4.8907  19.3614  -2.6897
 D82  O    O  O     0  -0.510  -5.4362  19.9804  -3.5792
 D82  C5   C  CH2   0  -0.530   0.3554  20.3406  -6.7397
 D82  N4   N  NR15  0  -0.661   0.7357  17.4801  -5.9568
 D82  N3   N  NR5   0  -0.498  -0.3172  19.2954  -4.7587
 D82  C2   C  CH1   0  -0.187  -2.1674  17.4718  -4.1525
 D82  O1   O  O2    0  -0.481  -3.8222  18.5754  -2.8779
 D82  C6   C  CR15  0   0.039  -0.6334  19.2240  -7.0404
 D82  C7   C  C     0   0.321  -0.4405  18.3127  -5.8094
 D82  C8   C  CR5   0   0.560   0.5039  16.1629  -5.6706
 D82  C9   C  CR15  0  -0.081  -1.5552  17.2655  -5.5390
 D82  C1   C  CH2   0  -0.144  -3.3042  18.4857  -4.1989
 D82  C3   C  C     0   0.566  -0.4295  18.9915  -3.4333
 D82  C4   C  CH2   0  -0.239   0.2359  20.5532  -5.2279
 D82  N1   N  NH1   0  -0.648  -1.1076  17.8076  -3.2221
 D82  N2   N  N     0  -0.706   0.0644  19.7656  -2.5416
 D82  N5   N  N     0  -0.714   1.4298  15.2948  -5.5277
 D82  N6   N  NR15  0  -0.664  -0.8572  16.0067  -5.6461
 D82  O2   O  OH1   0  -0.656  -1.9238  19.7796  -7.0839
 D82  H1   H  HNH2  0   0.406  -6.0323  19.9387  -1.1085
 D82  H2   H  HNH2  0   0.405  -4.7493  18.8650  -0.6948
 D82  H4   H  HCH2  0   0.266   0.1460  21.2427  -7.3127
 D82  H5   H  HNR5  0   0.390   1.6550  17.8581  -5.7938
 D82  H6   H  HCH1  0   0.286  -2.5896  16.5175  -3.8266
 D82  H7   H  HCR5  0   0.241  -0.3909  18.6783  -7.9573
 D82  H8   H  HCR5  0   0.267  -2.3486  17.3186  -6.2896
 D82  H9   H  HCH2  0   0.239  -2.9573  19.4612  -4.5452
 D82  H10  H  HCH2  0   0.242  -4.0716  18.1355  -4.8944
 D82  H11  H  HCH2  0   0.238   1.2028  20.7681  -4.7704
 D82  H12  H  HCH2  0   0.236  -0.4349  21.3783  -4.9780
 D82  H13  H  H     0   0.321  -0.1842  19.4467  -1.6118
 D82  H15  H  H     0   0.319   1.0335  14.3816  -5.3402
 D82  H17  H  HOH1  0   0.458  -2.5220  19.1591  -7.5104
 D82  H18  H  HNH1  0   0.390  -1.3109  17.6124  -2.2536
 D82  H14  H  HNR5  0   0.394  -1.2468  15.1860  -5.2102
 D82  H3   H  HCH2  0   0.253   1.3630  20.0134  -7.0005

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
 D82  C6  O2   single  1.406  0.020  1.406
 D82  C6  C5   single  1.521  0.020  1.521
 D82  C6  C7   single  1.544  0.020  1.544
 D82  C5  C4   single  1.531  0.020  1.531
 D82  N4  C7   single  1.449  0.020  1.449
 D82  N4  C8   single  1.368  0.020  1.368
 D82  C7  C9   single  1.553  0.020  1.553
 D82  C7  N3   single  1.444  0.020  1.444
 D82  N5  C8   double  1.277  0.020  1.277
 D82  C8  N6   single  1.370  0.020  1.370
 D82  C9  N6   single  1.443  0.020  1.443
 D82  C9  C2   single  1.530  0.020  1.530
 D82  C4  N3   single  1.452  0.020  1.452
 D82  N3  C3   single  1.364  0.020  1.364
 D82  C1  C2   single  1.524  0.020  1.524
 D82  C1  O1   single  1.422  0.020  1.422
 D82  C2  N1   single  1.450  0.020  1.450
 D82  O   C    double  1.213  0.020  1.213
 D82  C3  N1   single  1.381  0.020  1.381
 D82  C3  N2   double  1.280  0.020  1.280
 D82  O1  C    single  1.340  0.020  1.340
 D82  C   N    single  1.342  0.020  1.342
 D82  N   H1   single  0.860  0.020  1.020
 D82  N   H2   single  0.860  0.020  1.020
 D82  C5  H3   single  0.970  0.020  1.090
 D82  C5  H4   single  0.970  0.020  1.090
 D82  N4  H5   single  0.890  0.020  1.040
 D82  C2  H6   single  0.970  0.020  1.090
 D82  C6  H7   single  0.970  0.020  1.090
 D82  C9  H8   single  0.970  0.020  1.090
 D82  C1  H9   single  0.970  0.020  1.090
 D82  C1  H10  single  0.970  0.020  1.090
 D82  C4  H11  single  0.970  0.020  1.090
 D82  C4  H12  single  0.970  0.020  1.090
 D82  N2  H13  single  0.890  0.020  1.040
 D82  N5  H15  single  0.890  0.020  1.040
 D82  O2  H17  single  0.850  0.020  0.980
 D82  N1  H18  single  0.890  0.020  1.040
 D82  N6  H14  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
 D82  H2   N   H1   118.05  3.000
 D82  H2   N   C    122.10  3.000
 D82  H1   N   C    119.44  3.000
 D82  O1   C   O    123.71  3.000
 D82  O1   C   N    110.90  3.000
 D82  O    C   N    125.39  3.000
 D82  H4   C5  H3   107.47  3.000
 D82  H4   C5  C4   112.92  3.000
 D82  H3   C5  C4   110.47  3.000
 D82  H4   C5  C6   112.27  3.000
 D82  H3   C5  C6   109.44  3.000
 D82  C4   C5  C6   104.26  3.000
 D82  H5   N4  C8   118.83  3.000
 D82  H5   N4  C7   120.58  3.000
 D82  C8   N4  C7   113.25  3.000
 D82  C4   N3  C3   122.56  3.000
 D82  C3   N3  C7   123.25  3.000
 D82  C4   N3  C7   112.77  3.000
 D82  H6   C2  N1   107.05  3.000
 D82  H6   C2  C1   107.57  3.000
 D82  N1   C2  C1   114.25  3.000
 D82  H6   C2  C9   107.88  3.000
 D82  N1   C2  C9   108.69  3.000
 D82  C1   C2  C9   111.14  3.000
 D82  C1   O1  C    117.26  3.000
 D82  H7   C6  O2   112.00  3.000
 D82  H7   C6  C7   110.25  3.000
 D82  O2   C6  C7   111.88  3.000
 D82  H7   C6  C5   112.81  3.000
 D82  C7   C6  C5   101.21  3.000
 D82  O2   C6  C5   108.22  3.000
 D82  C9   C7  C6   116.57  3.000
 D82  C9   C7  N3   113.17  3.000
 D82  C6   C7  N3   100.90  3.000
 D82  N3   C7  N4   113.32  3.000
 D82  C9   C7  N4   102.29  3.000
 D82  C6   C7  N4   111.07  3.000
 D82  N6   C8  N5   129.83  3.000
 D82  N6   C8  N4   106.37  3.000
 D82  N5   C8  N4   123.72  3.000
 D82  H8   C9  N6   110.01  3.000
 D82  H8   C9  C7   111.62  3.000
 D82  N6   C9  C7   103.18  3.000
 D82  H8   C9  C2   108.98  3.000
 D82  N6   C9  C2   112.24  3.000
 D82  C7   C9  C2   110.74  3.000
 D82  H10  C1  H9   107.91  3.000
 D82  H10  C1  O1   110.83  3.000
 D82  H9   C1  O1   110.75  3.000
 D82  H10  C1  C2   109.26  3.000
 D82  H9   C1  C2   111.54  3.000
 D82  O1   C1  C2   106.59  3.000
 D82  N2   C3  N1   126.98  3.000
 D82  N2   C3  N3   120.68  3.000
 D82  N1   C3  N3   112.34  3.000
 D82  H12  C4  H11  107.43  3.000
 D82  H12  C4  N3   110.27  3.000
 D82  H11  C4  N3   111.88  3.000
 D82  H12  C4  C5   112.25  3.000
 D82  H11  C4  C5   111.85  3.000
 D82  N3   C4  C5   103.21  3.000
 D82  H18  N1  C3   114.32  3.000
 D82  H18  N1  C2   115.09  3.000
 D82  C3   N1  C2   117.36  3.000
 D82  H13  N2  C3   110.73  3.000
 D82  H15  N5  C8   110.48  3.000
 D82  H14  N6  C9   119.42  3.000
 D82  H14  N6  C8   118.99  3.000
 D82  C9   N6  C8   112.47  3.000
 D82  H17  O2  C6   109.26  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
 D82  CONST_03  N6   C8  N4  C7     0.00   0.0  0
 D82  CONST_05  N1   C3  N3  C4   180.00   0.0  0
 D82  CONST_07  N5   C8  N4  C7   180.00   0.0  0
 D82  CONST_09  N5   C8  N6  C9   180.00   0.0  0
 D82  CONST_10  N2   C3  N3  C4     0.00   0.0  0
 D82  CONST_12  H18  N1  C3  N3   180.00   0.0  0
 D82  CONST_14  H15  N5  C8  N4   180.00   0.0  0
 D82  CONST_15  H13  N2  C3  N3   180.00   0.0  0
 D82  CONST_16  H13  N2  C3  N1     0.00   0.0  0
 D82  CONST_17  H18  N1  C3  N2     0.00   0.0  0
 D82  CONST_20  H15  N5  C8  N6     0.00   0.0  0
 D82  Var_01    C7   N3  C4  C5     4.74  30.0  1
 D82  Var_02    C3   N3  C4  C5   171.51  30.0  1
 D82  Var_03    C6   C5  C4  N3    21.86  30.0  1
 D82  Var_04    H3   C5  C4  N3   -95.62  30.0  1
 D82  Var_05    H4   C5  C4  N3   144.00  30.0  1
 D82  Var_06    H11  C4  C5  C6   142.29  30.0  1
 D82  Var_07    H12  C4  C5  C6   -96.86  30.0  1
 D82  Var_08    H11  C4  N3  C7  -115.67  30.0  1
 D82  Var_09    H12  C4  N3  C7   124.83  30.0  1
 D82  Var_10    H11  C4  N3  C3    51.10  30.0  1
 D82  Var_11    H12  C4  N3  C3   -68.40  30.0  1
 D82  Var_12    C2   C1  O1  C   -176.37  30.0  1
 D82  Var_13    C1   O1  C   N   -179.93  30.0  2
 D82  Var_14    C1   O1  C   O      0.70  30.0  2
 D82  Var_15    H9   C1  O1  C     62.14  30.0  1
 D82  Var_16    H10  C1  O1  C    -57.58  30.0  1
 D82  Var_17    H1   N   C   O     -3.81  30.0  2
 D82  Var_18    H2   N   C   O   -176.30  30.0  2
 D82  Var_19    H1   N   C   O1   176.83  30.0  2
 D82  Var_20    H2   N   C   O1     4.34  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
 D82  chir_01  C2  C9  C1  N1  positiv
 D82  chir_02  C6  O2  C5  C7  negativ
 D82  chir_03  C7  N4  C9  C6  positiv
 D82  chir_04  C9  N6  C2  C7  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
 D82  plan-1  N4   0.020
 D82  plan-1  C7   0.020
 D82  plan-1  C8   0.020
 D82  plan-1  C9   0.020
 D82  plan-1  N5   0.020
 D82  plan-1  N6   0.020
 D82  plan-1  H5   0.020
 D82  plan-1  H15  0.020
 D82  plan-1  H14  0.020
 D82  plan-2  N3   0.020
 D82  plan-2  C2   0.020
 D82  plan-2  C7   0.020
 D82  plan-2  C3   0.020
 D82  plan-2  C4   0.020
 D82  plan-2  N1   0.020
 D82  plan-2  N2   0.020
 D82  plan-2  H13  0.020
 D82  plan-2  H18  0.020
 D82  plan-3  N    0.020
 D82  plan-3  C    0.020
 D82  plan-3  O    0.020
 D82  plan-3  O1   0.020

