# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:24:21 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-beta-D-ribofuranosyl-1,3-dihydro-2H-1,3-diazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC=CNC2=O
#
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
 BRD  BRD  1-beta-D-ribofuranosyl-1,3-dihydro-2H-1,3-diazepin-2-one  ligand  31  17  .  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_BRD
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
 BRD  C4    C  C1    0  -0.054   1.3711   0.0814  -3.4803
 BRD  N3    N  NH1   0  -0.681   1.2023  -0.9668  -2.5743
 BRD  C2    C  C     0   0.695   0.6695  -0.8942  -1.3074
 BRD  N1    N  NT    0  -0.567  -0.2886   0.0779  -1.0992
 BRD  C7    C  C1    0  -0.075  -1.2251   0.4481  -2.0932
 BRD  C6    C  C1    0  -0.270  -0.9230   0.8904  -3.3129
 BRD  O2    O  O     0  -0.470   1.0482  -1.6544  -0.4402
 BRD  C1'   C  CR15  0   0.227  -0.6411   0.4617   0.2561
 BRD  O4'   O  O     0  -0.498   0.5045   0.8762   0.9458
 BRD  C4'   C  CR15  0  -0.024   0.4163   0.5228   2.3260
 BRD  C3'   C  CR15  0  -0.051  -0.9964  -0.0352   2.5387
 BRD  C2'   C  CR15  0  -0.013  -1.3216  -0.5797   1.1467
 BRD  O2'   O  OH1   0  -0.662  -2.6781  -0.6470   0.8160
 BRD  O3'   O  OH1   0  -0.670  -1.9292   0.9715   2.8411
 BRD  C5'   C  CH2   0  -0.153   1.5062  -0.4550   2.7134
 BRD  O5'   O  OH1   0  -0.673   2.7537   0.1581   2.4880
 BRD  C5    C  C1    0  -0.303   0.4236   0.9503  -3.8390
 BRD  HC4   H  H     0   0.284   2.3537   0.1132  -3.9341
 BRD  HN3   H  HNH1  0   0.408   1.8966  -1.6955  -2.6438
 BRD  HC7   H  H     0   0.280  -2.2602   0.3801  -1.7805
 BRD  HC6   H  H     0   0.262  -1.7430   1.1859  -3.9561
 BRD  H1'   H  HCR5  0   0.239  -1.3362   1.3031   0.1338
 BRD  H4'   H  HCR5  0   0.241   0.5498   1.4338   2.9229
 BRD  H3'1  H  HCR5  0   0.241  -1.0032  -0.8254   3.3007
 BRD  H2'   H  HCR5  0   0.251  -0.8350  -1.5512   1.0341
 BRD  H2'1  H  HOH1  0   0.459  -3.0639  -1.4135   1.2506
 BRD  H3'   H  HOH1  0   0.454  -1.6993   1.3462   3.6971
 BRD  H5'1  H  HCH2  0   0.209   1.4047  -1.3861   2.1455
 BRD  H5'2  H  HCH2  0   0.196   1.3638  -0.7020   3.7742
 BRD  H5'   H  HOH1  0   0.455   3.4403  -0.4914   2.6624
 BRD  HC5   H  H     0   0.263   0.6653   1.6923  -4.5881

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
 BRD  C4   N3    single  1.396  0.020  1.396
 BRD  C4   C5    double  1.335  0.020  1.335
 BRD  C4   HC4   single  0.930  0.020  1.080
 BRD  N3   C2    single  1.376  0.020  1.376
 BRD  N3   HN3   single  0.890  0.020  1.040
 BRD  C2   N1    single  1.381  0.020  1.381
 BRD  C2   O2    double  1.214  0.020  1.214
 BRD  N1   C7    single  1.415  0.020  1.415
 BRD  N1   C1'   single  1.452  0.020  1.452
 BRD  C7   C6    double  1.332  0.020  1.332
 BRD  C7   HC7   single  0.930  0.020  1.080
 BRD  C6   C5    single  1.447  0.020  1.447
 BRD  C6   HC6   single  0.930  0.020  1.080
 BRD  C1'  O4'   single  1.400  0.020  1.400
 BRD  C1'  C2'   single  1.530  0.020  1.530
 BRD  C1'  H1'   single  0.970  0.020  1.090
 BRD  O4'  C4'   single  1.427  0.020  1.427
 BRD  C4'  C3'   single  1.534  0.020  1.534
 BRD  C4'  C5'   single  1.515  0.020  1.515
 BRD  C4'  H4'   single  0.970  0.020  1.090
 BRD  C3'  C2'   single  1.530  0.020  1.530
 BRD  C3'  O3'   single  1.405  0.020  1.405
 BRD  C3'  H3'1  single  0.970  0.020  1.090
 BRD  C2'  O2'   single  1.398  0.020  1.398
 BRD  C2'  H2'   single  0.970  0.020  1.090
 BRD  O2'  H2'1  single  0.850  0.020  0.980
 BRD  O3'  H3'   single  0.850  0.020  0.980
 BRD  C5'  O5'   single  1.408  0.020  1.408
 BRD  C5'  H5'1  single  0.970  0.020  1.090
 BRD  C5'  H5'2  single  0.970  0.020  1.090
 BRD  O5'  H5'   single  0.850  0.020  0.980
 BRD  C5   HC5   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
 BRD  HC4   C4   C5    120.83  3.000
 BRD  HC4   C4   N3    113.82  3.000
 BRD  C5    C4   N3    125.27  3.000
 BRD  HN3   N3   C2    111.59  3.000
 BRD  HN3   N3   C4    114.49  3.000
 BRD  C2    N3   C4    127.21  3.000
 BRD  O2    C2   N1    123.35  3.000
 BRD  O2    C2   N3    120.25  3.000
 BRD  N1    C2   N3    116.40  3.000
 BRD  C1'   N1   C7    115.20  3.000
 BRD  C1'   N1   C2    119.69  3.000
 BRD  C7    N1   C2    122.52  3.000
 BRD  HC7   C7   C6    120.12  3.000
 BRD  HC7   C7   N1    114.40  3.000
 BRD  C6    C7   N1    125.45  3.000
 BRD  HC6   C6   C5    118.51  3.000
 BRD  HC6   C6   C7    117.55  3.000
 BRD  C5    C6   C7    123.90  3.000
 BRD  H1'   C1'  C2'   107.75  3.000
 BRD  H1'   C1'  O4'   110.24  3.000
 BRD  C2'   C1'  O4'   106.18  3.000
 BRD  H1'   C1'  N1    104.61  3.000
 BRD  C2'   C1'  N1    118.12  3.000
 BRD  O4'   C1'  N1    109.84  3.000
 BRD  C4'   O4'  C1'   110.64  3.000
 BRD  H4'   C4'  C5'   108.02  3.000
 BRD  H4'   C4'  C3'   109.79  3.000
 BRD  C5'   C4'  C3'   113.11  3.000
 BRD  H4'   C4'  O4'   108.23  3.000
 BRD  C5'   C4'  O4'   111.27  3.000
 BRD  C3'   C4'  O4'   106.32  3.000
 BRD  H3'1  C3'  O3'   111.23  3.000
 BRD  H3'1  C3'  C2'   111.97  3.000
 BRD  O3'   C3'  C2'   108.04  3.000
 BRD  H3'1  C3'  C4'   111.34  3.000
 BRD  O3'   C3'  C4'   112.37  3.000
 BRD  C2'   C3'  C4'   101.49  3.000
 BRD  H2'   C2'  O2'   111.41  3.000
 BRD  H2'   C2'  C3'   108.40  3.000
 BRD  O2'   C2'  C3'   116.02  3.000
 BRD  H2'   C2'  C1'   110.32  3.000
 BRD  O2'   C2'  C1'   109.07  3.000
 BRD  C3'   C2'  C1'   101.12  3.000
 BRD  H2'1  O2'  C2'   108.71  3.000
 BRD  H3'   O3'  C3'   108.17  3.000
 BRD  H5'2  C5'  H5'1  107.31  3.000
 BRD  H5'2  C5'  O5'   111.55  3.000
 BRD  H5'1  C5'  O5'   111.67  3.000
 BRD  H5'2  C5'  C4'   107.39  3.000
 BRD  H5'1  C5'  C4'   110.45  3.000
 BRD  O5'   C5'  C4'   108.39  3.000
 BRD  H5'   O5'  C5'   108.04  3.000
 BRD  HC5   C5   C6    119.21  3.000
 BRD  HC5   C5   C4    118.30  3.000
 BRD  C6    C5   C4    122.41  3.000

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
 BRD  chir_01  C1'  N1   O4'  C2'  positiv
 BRD  chir_02  C4'  O4'  C3'  C5'  negativ
 BRD  chir_03  C3'  O3'  C4'  C2'  positiv
 BRD  chir_04  C2'  O2'  C3'  C1'  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
 BRD  plan-1  C4   0.020
 BRD  plan-1  N3   0.020
 BRD  plan-1  C2   0.020
 BRD  plan-1  N1   0.020
 BRD  plan-1  C7   0.020
 BRD  plan-1  O2   0.020
 BRD  plan-1  C1'  0.020
 BRD  plan-1  HN3  0.020

