# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:16:50 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 3'-azido-3'-deoxythymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO)O2)C(=O)NC1=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
 AZZ  AZZ  3'-azido-3'-deoxythymidine  ligand  32  19  .  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_AZZ
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
 AZZ  O5'   O  OH1    0  -0.670   2.6482   3.2098   0.1807
 AZZ  C5'   C  CH2    0  -0.160   2.6667   1.9408  -0.4259
 AZZ  C4'   C  CH1    0   0.048   2.1955   0.9073   0.5665
 AZZ  O4'   O  O2     0  -0.487   0.8281   1.1081   0.8720
 AZZ  C3'   C  CH1    0  -0.161   2.2971  -0.5186   0.0246
 AZZ  N3'   N  N      0  -0.358   3.6139  -1.0580   0.3643
 AZZ  N4'   N  N      1   0.360   4.0718  -1.8900  -0.3966
 AZZ  N5'   N  N     -1  -0.218   4.5830  -2.6569  -1.0396
 AZZ  C2'   C  CH2    0  -0.517   1.1480  -1.2332   0.7313
 AZZ  C1'   C  CH1    0   0.214   0.1828  -0.1077   1.1241
 AZZ  N1    N  NR6    0  -0.568  -1.1132  -0.1112   0.4513
 AZZ  C2    C  CR6    0   0.744  -1.1729  -0.0707  -0.9225
 AZZ  O2    O  O      0  -0.472  -0.1930  -0.0753  -1.6379
 AZZ  N3    N  NR16   0  -0.734  -2.4430  -0.0311  -1.4354
 AZZ  C4    C  CR6    0   0.559  -3.6426  -0.0182  -0.7469
 AZZ  O4    O  O      0  -0.453  -4.7014   0.0202  -1.3461
 AZZ  C5    C  CR6    0  -0.184  -3.5021  -0.0505   0.6947
 AZZ  C5A   C  CH3    0  -0.706  -4.7305  -0.0356   1.5430
 AZZ  C6    C  CR16   0   0.059  -2.2594  -0.0885   1.2045
 AZZ  HO5'  H  HOH1   0   0.458   2.9291   3.8570  -0.4723
 AZZ  H5'   H  HCH2   0   0.205   2.0200   1.8980  -1.3117
 AZZ  H5'A  H  HCH2   0   0.204   3.6774   1.6545  -0.7462
 AZZ  H4'   H  HCH1   0   0.236   2.7984   0.9752   1.4837
 AZZ  H3'   H  HCH1   0   0.287   2.1494  -0.5269  -1.0568
 AZZ  H2'   H  HCH2   0   0.288   0.6846  -2.0066   0.1225
 AZZ  H2'A  H  HCH2   0   0.279   1.5190  -1.7058   1.6416
 AZZ  H1'   H  HCH1   0   0.260  -0.0605  -0.1918   2.1856
 AZZ  HN3   H  HNR6   0   0.426  -2.4978  -0.0056  -2.4464
 AZZ  H5A   H  HCH3   0   0.247  -5.3659  -0.8987   1.3397
 AZZ  H5AA  H  HCH3   0   0.247  -4.4722  -0.0542   2.6004
 AZZ  H5AB  H  HCH3   0   0.247  -5.3310   0.8566   1.3609
 AZZ  H6    H  HCR6   0   0.318  -2.1020  -0.1091   2.2744

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
 AZZ  O5'  C5'   single  1.407  0.020  1.407
 AZZ  C5'  C4'   single  1.508  0.020  1.508
 AZZ  C4'  O4'   single  1.415  0.020  1.415
 AZZ  C4'  C3'   single  1.529  0.020  1.529
 AZZ  O4'  C1'   single  1.399  0.020  1.399
 AZZ  C3'  N3'   single  1.463  0.020  1.463
 AZZ  C3'  C2'   single  1.527  0.020  1.527
 AZZ  N3'  N4'   double  1.217  0.020  1.217
 AZZ  N4'  N5'   double  1.124  0.020  1.124
 AZZ  C2'  C1'   single  1.534  0.020  1.534
 AZZ  C1'  N1    single  1.460  0.020  1.460
 AZZ  N1   C2    single  1.376  0.020  1.376
 AZZ  N1   C6    single  1.372  0.020  1.372
 AZZ  C2   O2    double  1.213  0.020  1.213
 AZZ  C2   N3    single  1.370  0.020  1.370
 AZZ  N3   C4    single  1.383  0.020  1.383
 AZZ  C4   O4    double  1.217  0.020  1.217
 AZZ  C4   C5    single  1.449  0.020  1.449
 AZZ  C5   C5A   single  1.493  0.020  1.493
 AZZ  C5   C6    double  1.344  0.020  1.344
 AZZ  O5'  HO5'  single  0.850  0.020  0.980
 AZZ  C5'  H5'   single  0.970  0.020  1.090
 AZZ  C5'  H5'A  single  0.970  0.020  1.090
 AZZ  C4'  H4'   single  0.970  0.020  1.090
 AZZ  C3'  H3'   single  0.970  0.020  1.090
 AZZ  C2'  H2'   single  0.970  0.020  1.090
 AZZ  C2'  H2'A  single  0.970  0.020  1.090
 AZZ  C1'  H1'   single  0.970  0.020  1.090
 AZZ  N3   HN3   single  0.860  0.020  1.020
 AZZ  C5A  H5A   single  0.970  0.020  1.090
 AZZ  C5A  H5AA  single  0.970  0.020  1.090
 AZZ  C5A  H5AB  single  0.970  0.020  1.090
 AZZ  C6   H6    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
 AZZ  HO5'  O5'  C5'   108.09  3.000
 AZZ  H5'A  C5'  H5'   107.26  3.000
 AZZ  H5'A  C5'  C4'   107.50  3.000
 AZZ  H5'   C5'  C4'   108.67  3.000
 AZZ  H5'A  C5'  O5'   111.91  3.000
 AZZ  H5'   C5'  O5'   112.05  3.000
 AZZ  C4'   C5'  O5'   109.29  3.000
 AZZ  H4'   C4'  C3'   108.47  3.000
 AZZ  H4'   C4'  O4'   109.93  3.000
 AZZ  C3'   C4'  O4'   105.84  3.000
 AZZ  H4'   C4'  C5'   109.58  3.000
 AZZ  C3'   C4'  C5'   112.65  3.000
 AZZ  O4'   C4'  C5'   110.28  3.000
 AZZ  C1'   O4'  C4'   111.17  3.000
 AZZ  H3'   C3'  C2'   110.69  3.000
 AZZ  H3'   C3'  N3'   110.43  3.000
 AZZ  C2'   C3'  N3'   113.42  3.000
 AZZ  H3'   C3'  C4'   110.44  3.000
 AZZ  C2'   C3'  C4'   102.86  3.000
 AZZ  N3'   C3'  C4'   108.75  3.000
 AZZ  N4'   N3'  C3'   116.46  3.000
 AZZ  N5'   N4'  N3'   174.56  3.000
 AZZ  H2'A  C2'  H2'   107.70  3.000
 AZZ  H2'A  C2'  C1'   108.56  3.000
 AZZ  H2'   C2'  C1'   113.38  3.000
 AZZ  H2'A  C2'  C3'   109.46  3.000
 AZZ  H2'   C2'  C3'   113.22  3.000
 AZZ  C1'   C2'  C3'   104.40  3.000
 AZZ  H1'   C1'  N1    104.48  3.000
 AZZ  H1'   C1'  C2'   109.41  3.000
 AZZ  N1    C1'  C2'   116.02  3.000
 AZZ  H1'   C1'  O4'   110.16  3.000
 AZZ  N1    C1'  O4'   109.17  3.000
 AZZ  C2'   C1'  O4'   107.53  3.000
 AZZ  C6    N1   C2    120.77  3.000
 AZZ  C6    N1   C1'   119.25  3.000
 AZZ  C2    N1   C1'   119.90  3.000
 AZZ  N3    C2   O2    121.87  3.000
 AZZ  N3    C2   N1    114.51  3.000
 AZZ  O2    C2   N1    123.62  3.000
 AZZ  HN3   N3   C4    116.72  3.000
 AZZ  HN3   N3   C2    115.12  3.000
 AZZ  C4    N3   C2    128.16  3.000
 AZZ  C5    C4   O4    125.09  3.000
 AZZ  C5    C4   N3    114.27  3.000
 AZZ  O4    C4   N3    120.65  3.000
 AZZ  C6    C5   C5A   123.07  3.000
 AZZ  C6    C5   C4    117.89  3.000
 AZZ  C5A   C5   C4    119.04  3.000
 AZZ  H5AB  C5A  H5AA  107.86  3.000
 AZZ  H5AB  C5A  H5A   107.18  3.000
 AZZ  H5AA  C5A  H5A   107.80  3.000
 AZZ  H5AB  C5A  C5    111.49  3.000
 AZZ  H5AA  C5A  C5    110.89  3.000
 AZZ  H5A   C5A  C5    111.44  3.000
 AZZ  H6    C6   C5    120.69  3.000
 AZZ  H6    C6   N1    114.91  3.000
 AZZ  C5    C6   N1    124.39  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
 AZZ  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 AZZ  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 AZZ  CONST_03  C5   C4   N3   C2     0.00   0.0  0
 AZZ  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 AZZ  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 AZZ  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 AZZ  CONST_07  C6   N1   C2   O2   180.00   0.0  0
 AZZ  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 AZZ  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 AZZ  CONST_10  N5'  N4'  N3'  C3'  180.00   0.0  0
 AZZ  Var_01    H5A  C5A  C5   C4    60.43  30.0  3

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
 AZZ  chir_01  C4'  C5'  O4'  C3'  negativ
 AZZ  chir_02  C3'  N3'  C2'  C4'  negativ
 AZZ  chir_03  C1'  O4'  N1   C2'  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
 AZZ  plan-1  C1'  0.020
 AZZ  plan-1  N1   0.020
 AZZ  plan-1  C2   0.020
 AZZ  plan-1  O2   0.020
 AZZ  plan-1  N3   0.020
 AZZ  plan-1  C4   0.020
 AZZ  plan-1  O4   0.020
 AZZ  plan-1  C5   0.020
 AZZ  plan-1  C5A  0.020
 AZZ  plan-1  C6   0.020
 AZZ  plan-1  HN3  0.020
 AZZ  plan-1  H6   0.020
 AZZ  plan-2  C4'  0.020
 AZZ  plan-2  C3'  0.020
 AZZ  plan-2  N3'  0.020
 AZZ  plan-2  N4'  0.020
 AZZ  plan-2  N5'  0.020
 AZZ  plan-2  C2'  0.020
 AZZ  plan-2  H3'  0.020

