# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:42:19 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2~{R},4~{R},5~{R},6~{S})-4-(hydroxymethyl)-5-oxidanyl-3,7-dioxa-1,9-diazatricyclo[6.4.0.0^{2,6}]dodeca-8,11-dien-10-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H]2[C@@H](OC3=NC(=O)C=CN23)[C@@H]1O
#
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
 ANU  ANU  (2~{R},4~{R},5~{R},6~{S})-4-(hydroxymethyl)-5-oxidanyl-3,7-dioxa-1,9-diazatricyclo[6.4.0.0^{2,6}]dodeca-8,11-dien-10-one  ligand  26  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ANU
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
 ANU  O3'  O  OH1   0  -0.655  -2.7583  -2.1522   0.2168
 ANU  C3'  C  CH1   0   0.015  -1.8640  -1.0813   0.2489
 ANU  C2'  C  CR15  0  -0.102  -0.7446  -1.2747  -0.7677
 ANU  O2   O  O     0  -0.446   0.4550  -1.7798  -0.1741
 ANU  C2   C  CR56  0   0.742   1.3476  -0.8062  -0.0824
 ANU  N3   N  N     0  -0.516   2.4777  -0.9644   0.4951
 ANU  C4   C  CR6   0   0.461   3.3555   0.1069   0.5177
 ANU  O4   O  O     0  -0.477   4.4418  -0.0002   1.0660
 ANU  C5   C  CR16  0  -0.512   2.9248   1.3403  -0.1371
 ANU  C6   C  CR16  0   0.097   1.7169   1.4141  -0.7186
 ANU  N1   N  N     0  -0.574   0.9017   0.3188  -0.6829
 ANU  C1'  C  CR15  0   0.229  -0.4213   0.1543  -1.2369
 ANU  O4'  O  O2    0  -0.481  -1.3454   1.0152  -0.6520
 ANU  C4'  C  CH1   0  -0.030  -2.4622   0.2598  -0.1890
 ANU  C5'  C  CH2   0  -0.153  -3.1523   0.9946   0.9315
 ANU  O5'  O  OH1   0  -0.666  -3.7255   2.1727   0.4256
 ANU  H1   H  HOH1  0   0.466  -3.2549  -2.1708   1.0404
 ANU  H2   H  HCH1  0   0.253  -1.4159  -0.9575   1.2450
 ANU  H3   H  HCR5  0   0.318  -1.0376  -1.9425  -1.5775
 ANU  H4   H  HCR6  0   0.287   3.5856   2.1943  -0.1469
 ANU  H5   H  HCR6  0   0.328   1.3351   2.2926  -1.2178
 ANU  H6   H  HCR5  0   0.293  -0.3968   0.2822  -2.3215
 ANU  H7   H  HCH1  0   0.251  -3.1685   0.0892  -1.0132
 ANU  H8   H  HCH2  0   0.206  -3.9098   0.3200   1.3532
 ANU  H9   H  HCH2  0   0.209  -2.4217   1.1944   1.7267
 ANU  H10  H  HOH1  0   0.460  -4.1352   2.6445   1.1564

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
 ANU  O4   C4   double  1.222  0.020  1.222
 ANU  N3   C4   single  1.385  0.020  1.385
 ANU  N3   C2   double  1.279  0.020  1.279
 ANU  C4   C5   single  1.461  0.020  1.461
 ANU  O2   C2   single  1.324  0.020  1.324
 ANU  O2   C2'  single  1.431  0.020  1.431
 ANU  C2   N1   single  1.351  0.020  1.351
 ANU  C2'  C3'  single  1.524  0.020  1.524
 ANU  C2'  C1'  single  1.538  0.020  1.538
 ANU  C5   C6   double  1.343  0.020  1.343
 ANU  C3'  O3'  single  1.396  0.020  1.396
 ANU  C3'  C4'  single  1.532  0.020  1.532
 ANU  C5'  C4'  single  1.507  0.020  1.507
 ANU  C5'  O5'  single  1.404  0.020  1.404
 ANU  N1   C6   single  1.366  0.020  1.366
 ANU  N1   C1'  single  1.444  0.020  1.444
 ANU  C1'  O4'  single  1.392  0.020  1.392
 ANU  C4'  O4'  single  1.426  0.020  1.426
 ANU  O3'  H1   single  0.850  0.020  0.980
 ANU  C3'  H2   single  0.970  0.020  1.090
 ANU  C2'  H3   single  0.970  0.020  1.090
 ANU  C5   H4   single  0.930  0.020  1.080
 ANU  C6   H5   single  0.930  0.020  1.080
 ANU  C1'  H6   single  0.970  0.020  1.090
 ANU  C4'  H7   single  0.970  0.020  1.090
 ANU  C5'  H8   single  0.970  0.020  1.090
 ANU  C5'  H9   single  0.970  0.020  1.090
 ANU  O5'  H10  single  0.850  0.020  0.980

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
 ANU  H1   O3'  C3'  109.02  3.000
 ANU  H2   C3'  C4'  108.63  3.000
 ANU  H2   C3'  C2'  108.61  3.000
 ANU  C4'  C3'  C2'  101.96  3.000
 ANU  H2   C3'  O3'  111.63  3.000
 ANU  C4'  C3'  O3'  114.51  3.000
 ANU  C2'  C3'  O3'  110.97  3.000
 ANU  H3   C2'  C1'  113.52  3.000
 ANU  H3   C2'  O2   108.51  3.000
 ANU  C1'  C2'  O2   106.16  3.000
 ANU  H3   C2'  C3'  112.08  3.000
 ANU  C1'  C2'  C3'  103.88  3.000
 ANU  O2   C2'  C3'  112.57  3.000
 ANU  C2   O2   C2'  109.54  3.000
 ANU  N1   C2   N3   126.55  3.000
 ANU  N1   C2   O2   111.04  3.000
 ANU  N3   C2   O2   122.41  3.000
 ANU  C4   N3   C2   118.14  3.000
 ANU  C5   C4   O4   122.49  3.000
 ANU  C5   C4   N3   117.31  3.000
 ANU  O4   C4   N3   120.20  3.000
 ANU  H4   C5   C6   120.21  3.000
 ANU  H4   C5   C4   119.42  3.000
 ANU  C6   C5   C4   120.37  3.000
 ANU  H5   C6   N1   116.96  3.000
 ANU  H5   C6   C5   124.25  3.000
 ANU  N1   C6   C5   118.79  3.000
 ANU  C1'  N1   C6   128.92  3.000
 ANU  C1'  N1   C2   112.23  3.000
 ANU  C6   N1   C2   118.84  3.000
 ANU  H6   C1'  O4'  111.08  3.000
 ANU  H6   C1'  N1   110.32  3.000
 ANU  O4'  C1'  N1   112.13  3.000
 ANU  H6   C1'  C2'  114.60  3.000
 ANU  O4'  C1'  C2'  107.87  3.000
 ANU  N1   C1'  C2'  100.45  3.000
 ANU  C4'  O4'  C1'  109.20  3.000
 ANU  H7   C4'  C5'  109.82  3.000
 ANU  H7   C4'  O4'  110.01  3.000
 ANU  C5'  C4'  O4'  109.98  3.000
 ANU  H7   C4'  C3'  109.23  3.000
 ANU  O4'  C4'  C3'  104.52  3.000
 ANU  C5'  C4'  C3'  113.14  3.000
 ANU  H9   C5'  H8   107.01  3.000
 ANU  H9   C5'  O5'  112.32  3.000
 ANU  H8   C5'  O5'  111.83  3.000
 ANU  H9   C5'  C4'  108.81  3.000
 ANU  H8   C5'  C4'  107.56  3.000
 ANU  O5'  C5'  C4'  109.15  3.000
 ANU  H10  O5'  C5'  108.17  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
 ANU  CONST_01  C4   N3  C2  O2   180.00   0.0  0
 ANU  CONST_02  C6   N1  C2  O2   180.00   0.0  0
 ANU  CONST_03  C1'  N1  C2  O2     0.00   0.0  0
 ANU  CONST_04  C6   N1  C2  N3     0.00   0.0  0
 ANU  CONST_05  C1'  N1  C2  N3   180.00   0.0  0
 ANU  CONST_06  N1   C2  N3  C4     0.00   0.0  0
 ANU  Var_01    N3   C2  O2  C2'  175.15  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
 ANU  chir_01  C3'  C2'  O3'  C4'  positiv
 ANU  chir_02  C2'  O2   C1'  C3'  positiv
 ANU  chir_03  C1'  O4'  N1   C2'  negativ
 ANU  chir_04  C4'  O4'  C3'  C5'  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
 ANU  plan-1  O2   0.020
 ANU  plan-1  C2   0.020
 ANU  plan-1  N3   0.020
 ANU  plan-1  C4   0.020
 ANU  plan-1  O4   0.020
 ANU  plan-1  C5   0.020
 ANU  plan-1  C6   0.020
 ANU  plan-1  N1   0.020
 ANU  plan-1  C1'  0.020
 ANU  plan-1  H4   0.020
 ANU  plan-1  H5   0.020

