# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 08:42:09 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-bromo-2'-deoxycytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1Br)[C@H]2C[C@H](O)[C@@H](CO)O2
#
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
 5BT  5BT  '5-bromo-2'-deoxycytidine '  ligand  29  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5BT
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
 5BT  N1    N   NR6   0  -0.552   0.2480  -0.1635  -0.2011
 5BT  C2    C   CR6   0   0.614   0.3676   1.1837  -0.5843
 5BT  O2    O   O     0  -0.497   1.4609   1.6234  -0.9012
 5BT  N3    N   N     0  -0.534  -0.7485   1.9387  -0.5917
 5BT  C4    C   CR6   0   0.543  -1.9282   1.4653  -0.2486
 5BT  N4    N   NH2   0  -0.802  -2.9702   2.2879  -0.2942
 5BT  C5    C   CR6   0  -0.332  -2.0679   0.0984   0.1644
 5BT  BR5   BR  BR    0  -0.005  -3.7156  -0.6323   0.6866
 5BT  C6    C   CR16  0   0.130  -0.9502  -0.6596   0.1708
 5BT  C1'   C   CH1   0   0.221   1.4165  -1.0447  -0.1574
 5BT  C2'   C   CH2   0  -0.557   2.2006  -1.1768  -1.4652
 5BT  C3'   C   CH1   0   0.022   3.5542  -0.5257  -1.1814
 5BT  O3'   O   OH1   0  -0.670   4.6592  -1.2097  -1.7191
 5BT  C4'   C   CH1   0   0.023   3.6374  -0.5760   0.3449
 5BT  O4'   O   O2    0  -0.491   2.3024  -0.5943   0.8249
 5BT  C5'   C   CH2   0  -0.165   4.3819   0.5969   0.9325
 5BT  O5'   O   OH1   0  -0.673   4.5144   0.4168   2.3231
 5BT  HN4   H   HNH2  0   0.412  -2.8312   3.2364  -0.6004
 5BT  HN4A  H   HNH2  0   0.417  -3.9080   2.0033  -0.0723
 5BT  H6    H   HCR6  0   0.335  -0.9675  -1.6987   0.4702
 5BT  H1'   H   HCH1  0   0.249   1.0099  -2.0191   0.1274
 5BT  H2'   H   HCH2  0   0.265   2.3518  -2.2380  -1.6706
 5BT  H2'A  H   HCH2  0   0.273   1.6809  -0.7474  -2.3200
 5BT  H3'   H   HCH1  0   0.233   3.5428   0.5140  -1.5189
 5BT  HO3'  H   HOH1  0   0.456   4.7229  -0.9903  -2.6530
 5BT  H4'   H   HCH1  0   0.225   4.1412  -1.5111   0.6330
 5BT  H5'   H   HCH2  0   0.200   5.3597   0.6525   0.4354
 5BT  H5'A  H   HCH2  0   0.204   3.8382   1.5174   0.6860
 5BT  HO5'  H   HOH1  0   0.456   4.9366   1.1998   2.6874

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
 5BT  C1'  N1    single  1.464  0.020  1.464
 5BT  N1   C6    single  1.349  0.020  1.349
 5BT  N1   C2    single  1.406  0.020  1.406
 5BT  O2   C2    double  1.220  0.020  1.220
 5BT  C2   N3    single  1.348  0.020  1.348
 5BT  N3   C4    double  1.317  0.020  1.317
 5BT  C5   C4    single  1.435  0.020  1.435
 5BT  C4   N4    single  1.328  0.020  1.328
 5BT  N4   HN4   single  0.860  0.020  1.020
 5BT  N4   HN4A  single  0.860  0.020  1.020
 5BT  C6   C5    double  1.351  0.020  1.351
 5BT  C5   BR5   single  1.877  0.020  1.877
 5BT  C6   H6    single  0.930  0.020  1.080
 5BT  C2'  C1'   single  1.531  0.020  1.531
 5BT  C1'  O4'   single  1.397  0.020  1.397
 5BT  C1'  H1'   single  0.970  0.020  1.090
 5BT  C2'  C3'   single  1.529  0.020  1.529
 5BT  C2'  H2'   single  0.970  0.020  1.090
 5BT  C2'  H2'A  single  0.970  0.020  1.090
 5BT  C3'  O3'   single  1.406  0.020  1.406
 5BT  C3'  C4'   single  1.529  0.020  1.529
 5BT  C3'  H3'   single  0.970  0.020  1.090
 5BT  O3'  HO3'  single  0.850  0.020  0.980
 5BT  C5'  C4'   single  1.508  0.020  1.508
 5BT  C4'  O4'   single  1.419  0.020  1.419
 5BT  C4'  H4'   single  0.970  0.020  1.090
 5BT  C5'  O5'   single  1.409  0.020  1.409
 5BT  C5'  H5'   single  0.970  0.020  1.090
 5BT  C5'  H5'A  single  0.970  0.020  1.090
 5BT  O5'  HO5'  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
 5BT  C1'   N1   C6   118.64  3.000
 5BT  C6    N1   C2   120.21  3.000
 5BT  C1'   N1   C2   121.13  3.000
 5BT  N3    C2   O2   122.60  3.000
 5BT  N3    C2   N1   117.90  3.000
 5BT  O2    C2   N1   119.50  3.000
 5BT  C4    N3   C2   122.63  3.000
 5BT  C5    C4   N4   121.57  3.000
 5BT  N4    C4   N3   118.12  3.000
 5BT  C5    C4   N3   120.32  3.000
 5BT  HN4A  N4   HN4  117.58  3.000
 5BT  HN4A  N4   C4   123.31  3.000
 5BT  HN4   N4   C4   119.06  3.000
 5BT  C6    C5   BR5  120.45  3.000
 5BT  BR5   C5   C4   122.45  3.000
 5BT  C6    C5   C4   117.10  3.000
 5BT  H6    C6   C5   121.82  3.000
 5BT  H6    C6   N1   116.35  3.000
 5BT  C5    C6   N1   121.83  3.000
 5BT  H1'   C1'  O4'  109.87  3.000
 5BT  H1'   C1'  C2'  109.64  3.000
 5BT  O4'   C1'  C2'  107.68  3.000
 5BT  H1'   C1'  N1   104.31  3.000
 5BT  O4'   C1'  N1   109.45  3.000
 5BT  C2'   C1'  N1   115.80  3.000
 5BT  H2'A  C2'  H2'  107.57  3.000
 5BT  H2'A  C2'  C3'  113.61  3.000
 5BT  H2'   C2'  C3'  109.05  3.000
 5BT  H2'A  C2'  C1'  113.11  3.000
 5BT  H2'   C2'  C1'  108.40  3.000
 5BT  C3'   C2'  C1'  104.96  3.000
 5BT  H3'   C3'  C4'  109.88  3.000
 5BT  H3'   C3'  O3'  110.65  3.000
 5BT  C4'   C3'  O3'  108.83  3.000
 5BT  H3'   C3'  C2'  109.79  3.000
 5BT  C4'   C3'  C2'  102.68  3.000
 5BT  O3'   C3'  C2'  114.68  3.000
 5BT  HO3'  O3'  C3'  108.20  3.000
 5BT  H4'   C4'  C5'  109.44  3.000
 5BT  H4'   C4'  O4'  109.34  3.000
 5BT  C5'   C4'  O4'  110.03  3.000
 5BT  H4'   C4'  C3'  108.31  3.000
 5BT  O4'   C4'  C3'  106.67  3.000
 5BT  C5'   C4'  C3'  112.96  3.000
 5BT  C4'   O4'  C1'  111.28  3.000
 5BT  H5'A  C5'  H5'  107.27  3.000
 5BT  H5'A  C5'  O5'  112.07  3.000
 5BT  H5'   C5'  O5'  111.69  3.000
 5BT  H5'A  C5'  C4'  108.69  3.000
 5BT  H5'   C5'  C4'  107.61  3.000
 5BT  O5'   C5'  C4'  109.37  3.000
 5BT  HO5'  O5'  C5'  108.14  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
 5BT  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 5BT  CONST_02  C5    C4  N3  C2    0.00  0.0  0
 5BT  CONST_03  C1'   N1  C2  N3  180.00  0.0  0
 5BT  CONST_04  C6    N1  C2  N3    0.00  0.0  0
 5BT  CONST_05  N4    C4  N3  C2  180.00  0.0  0
 5BT  CONST_06  C1'   N1  C2  O2    0.00  0.0  0
 5BT  CONST_07  C6    N1  C2  O2  180.00  0.0  0
 5BT  CONST_08  C4    N3  C2  O2  180.00  0.0  0
 5BT  CONST_09  HN4   N4  C4  N3    0.00  0.0  0
 5BT  CONST_10  HN4A  N4  C4  N3  180.00  0.0  0

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
 5BT  chir_01  C1'  N1   C2'  O4'  negativ
 5BT  chir_02  C3'  O3'  C4'  C2'  positiv
 5BT  chir_03  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
 5BT  plan-1  N1    0.020
 5BT  plan-1  C2    0.020
 5BT  plan-1  O2    0.020
 5BT  plan-1  N3    0.020
 5BT  plan-1  C4    0.020
 5BT  plan-1  N4    0.020
 5BT  plan-1  C5    0.020
 5BT  plan-1  BR5   0.020
 5BT  plan-1  C6    0.020
 5BT  plan-1  C1'   0.020
 5BT  plan-1  HN4   0.020
 5BT  plan-1  HN4A  0.020
 5BT  plan-1  H6    0.020

