# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 04:34:26 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)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
 AZD  AZD  '3'-azido-3'-deoxythymidine 5'-(trihydrogen diphosphate)'  ligand  42  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AZD
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
 AZD  PA    P  P      0   1.512  49.1762   2.6366   9.2342
 AZD  O1A   O  O      0  -0.682  47.8595   2.1015   9.6067
 AZD  O2A   O  OH1    0  -0.715  49.5724   2.4816   7.7117
 AZD  O3A   O  O2     0  -0.699  49.3667   4.2280   9.4779
 AZD  PB    P  P      0   1.472  48.5140   5.1776  10.4831
 AZD  O1B   O  O      0  -0.677  47.1006   5.3565  10.1234
 AZD  O2B   O  OH1    0  -0.715  49.4248   6.4751  10.5139
 AZD  O3B   O  OH1    0  -0.735  48.8561   4.4568  11.8570
 AZD  O5'   O  O2     0  -0.591  50.4156   1.9995  10.0020
 AZD  C5'   C  CH2    0  -0.194  50.2744   1.2806  11.2348
 AZD  C4'   C  CH1    0   0.025  51.5903   1.3036  11.9772
 AZD  O4'   O  O2     0  -0.490  52.5821   0.5746  11.2729
 AZD  C3'   C  CH1    0  -0.205  52.1714   2.7169  12.1985
 AZD  N3'   N  N      0  -0.360  52.8568   2.8213  13.4945
 AZD  N4'   N  N      1   0.366  52.1400   2.8775  14.4786
 AZD  N5'   N  N     -1  -0.205  51.5643   2.9364  15.4413
 AZD  C2'   C  CH2    0  -0.514  53.2285   2.8174  11.1149
 AZD  C1'   C  CH1    0   0.206  53.7107   1.3763  11.0103
 AZD  N1    N  NR6    0  -0.569  54.2456   1.0096   9.7116
 AZD  C2    C  CR6    0   0.735  55.5457   0.5642   9.6135
 AZD  O2    O  O      0  -0.481  56.3052   0.4831  10.5571
 AZD  N3    N  NR16   0  -0.736  55.9270   0.2206   8.3433
 AZD  C4    C  CR6    0   0.564  55.1721   0.2538   7.1842
 AZD  O4    O  O      0  -0.450  55.6533  -0.0909   6.1213
 AZD  C5    C  CR6    0  -0.187  53.8112   0.7188   7.3700
 AZD  C5A   C  CH3    0  -0.707  52.8996   0.7839   6.1889
 AZD  C6    C  CR16   0   0.065  53.4282   1.0605   8.6101
 AZD  HOA2  H  HOH1   0   0.512  50.0294   3.2183   7.2839
 AZD  HOB2  H  HOH1   0   0.510  49.1311   7.1841   9.9250
 AZD  HOB3  H  HOH1   0   0.513  48.2622   4.6697  12.5909
 AZD  H5'1  H  HCH2   0   0.254  49.5070   1.7260  11.8698
 AZD  H5'2  H  HCH2   0   0.276  49.9829   0.2517  11.0184
 AZD  H4'   H  HCH1   0   0.275  51.3983   0.8114  12.9376
 AZD  H3'   H  HCH1   0   0.300  51.4093   3.4954  12.1111
 AZD  H2'1  H  HCH2   0   0.284  52.7799   3.1627  10.1840
 AZD  H2'2  H  HCH2   0   0.291  54.0337   3.5021  11.3746
 AZD  H1'   H  HCH1   0   0.279  54.4983   1.1824  11.7387
 AZD  HN3   H  HNR6   0   0.427  56.8825  -0.1035   8.2546
 AZD  H51   H  HCH3   0   0.239  51.9187   1.1582   6.4767
 AZD  H52   H  HCH3   0   0.249  53.2968   1.4426   5.4156
 AZD  H53   H  HCH3   0   0.249  52.7634  -0.1991   5.7363
 AZD  H6    H  HCR6   0   0.310  52.4182   1.3935   8.7981

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
 AZD  PA   O1A   double  1.469  0.020  1.469
 AZD  PA   O2A   single  1.581  0.020  1.581
 AZD  PA   O3A   single  1.621  0.020  1.621
 AZD  PA   O5'   single  1.591  0.020  1.591
 AZD  O2A  HOA2  single  0.850  0.020  0.980
 AZD  O3A  PB    single  1.625  0.020  1.625
 AZD  PB   O1B   double  1.469  0.020  1.469
 AZD  PB   O2B   single  1.586  0.020  1.586
 AZD  PB   O3B   single  1.589  0.020  1.589
 AZD  O2B  HOB2  single  0.850  0.020  0.980
 AZD  O3B  HOB3  single  0.850  0.020  0.980
 AZD  O5'  C5'   single  1.434  0.020  1.434
 AZD  C5'  C4'   single  1.511  0.020  1.511
 AZD  C5'  H5'1  single  0.970  0.020  1.090
 AZD  C5'  H5'2  single  0.970  0.020  1.090
 AZD  C4'  O4'   single  1.418  0.020  1.418
 AZD  C4'  C3'   single  1.544  0.020  1.544
 AZD  C4'  H4'   single  0.970  0.020  1.090
 AZD  O4'  C1'   single  1.409  0.020  1.409
 AZD  C3'  N3'   single  1.470  0.020  1.470
 AZD  C3'  C2'   single  1.517  0.020  1.517
 AZD  C3'  H3'   single  0.970  0.020  1.090
 AZD  N3'  N4'   double  1.219  0.020  1.219
 AZD  N4'  N5'   double  1.123  0.020  1.123
 AZD  C2'  C1'   single  1.523  0.020  1.523
 AZD  C2'  H2'1  single  0.970  0.020  1.090
 AZD  C2'  H2'2  single  0.970  0.020  1.090
 AZD  C1'  N1    single  1.452  0.020  1.452
 AZD  C1'  H1'   single  0.970  0.020  1.090
 AZD  N1   C2    single  1.378  0.020  1.378
 AZD  N1   C6    single  1.373  0.020  1.373
 AZD  C2   O2    double  1.214  0.020  1.214
 AZD  C2   N3    single  1.370  0.020  1.370
 AZD  N3   C4    single  1.384  0.020  1.384
 AZD  N3   HN3   single  0.860  0.020  1.020
 AZD  C4   O4    double  1.217  0.020  1.217
 AZD  C4   C5    single  1.450  0.020  1.450
 AZD  C5   C5A   single  1.493  0.020  1.493
 AZD  C5   C6    double  1.342  0.020  1.342
 AZD  C5A  H51   single  0.970  0.020  1.090
 AZD  C5A  H52   single  0.970  0.020  1.090
 AZD  C5A  H53   single  0.970  0.020  1.090
 AZD  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
 AZD  O5'   PA   O3A   103.24  3.000
 AZD  O5'   PA   O2A   103.31  3.000
 AZD  O3A   PA   O2A   102.22  3.000
 AZD  O5'   PA   O1A   115.46  3.000
 AZD  O3A   PA   O1A   115.13  3.000
 AZD  O2A   PA   O1A   115.66  3.000
 AZD  HOA2  O2A  PA    118.02  3.000
 AZD  PB    O3A  PA    127.24  3.000
 AZD  O3B   PB   O2B   103.35  3.000
 AZD  O3B   PB   O1B   118.30  3.000
 AZD  O2B   PB   O1B   117.24  3.000
 AZD  O3B   PB   O3A    99.02  3.000
 AZD  O2B   PB   O3A   100.89  3.000
 AZD  O1B   PB   O3A   115.12  3.000
 AZD  HOB2  O2B  PB    114.43  3.000
 AZD  HOB3  O3B  PB    115.07  3.000
 AZD  C5'   O5'  PA    122.61  3.000
 AZD  H5'2  C5'  H5'1  108.21  3.000
 AZD  H5'2  C5'  C4'   110.15  3.000
 AZD  H5'1  C5'  C4'   108.68  3.000
 AZD  H5'2  C5'  O5'   109.18  3.000
 AZD  H5'1  C5'  O5'   111.40  3.000
 AZD  C4'   C5'  O5'   109.21  3.000
 AZD  H4'   C4'  C3'   110.56  3.000
 AZD  H4'   C4'  O4'   109.07  3.000
 AZD  C3'   C4'  O4'   106.17  3.000
 AZD  H4'   C4'  C5'   105.73  3.000
 AZD  C3'   C4'  C5'   114.34  3.000
 AZD  O4'   C4'  C5'   110.93  3.000
 AZD  C1'   O4'  C4'   111.11  3.000
 AZD  H3'   C3'  C2'   112.43  3.000
 AZD  H3'   C3'  N3'   110.19  3.000
 AZD  C2'   C3'  N3'   107.47  3.000
 AZD  H3'   C3'  C4'   112.22  3.000
 AZD  C2'   C3'  C4'   102.74  3.000
 AZD  N3'   C3'  C4'   111.53  3.000
 AZD  N4'   N3'  C3'   116.16  3.000
 AZD  N5'   N4'  N3'   174.80  3.000
 AZD  H2'2  C2'  H2'1  108.00  3.000
 AZD  H2'2  C2'  C1'   112.17  3.000
 AZD  H2'1  C2'  C1'   111.81  3.000
 AZD  H2'2  C2'  C3'   112.75  3.000
 AZD  H2'1  C2'  C3'   110.14  3.000
 AZD  C1'   C2'  C3'   101.94  3.000
 AZD  H1'   C1'  N1    106.65  3.000
 AZD  H1'   C1'  C2'   110.55  3.000
 AZD  N1    C1'  C2'   114.65  3.000
 AZD  H1'   C1'  O4'   110.67  3.000
 AZD  N1    C1'  O4'   108.55  3.000
 AZD  C2'   C1'  O4'   105.78  3.000
 AZD  C6    N1   C2    121.12  3.000
 AZD  C6    N1   C1'   119.28  3.000
 AZD  C2    N1   C1'   119.54  3.000
 AZD  N3    C2   O2    121.99  3.000
 AZD  N3    C2   N1    114.18  3.000
 AZD  O2    C2   N1    123.82  3.000
 AZD  HN3   N3   C4    116.68  3.000
 AZD  HN3   N3   C2    115.09  3.000
 AZD  C4    N3   C2    128.24  3.000
 AZD  C5    C4   O4    125.03  3.000
 AZD  C5    C4   N3    114.35  3.000
 AZD  O4    C4   N3    120.62  3.000
 AZD  C6    C5   C5A   123.05  3.000
 AZD  C6    C5   C4    117.89  3.000
 AZD  C5A   C5   C4    119.05  3.000
 AZD  H53   C5A  H52   107.19  3.000
 AZD  H53   C5A  H51   107.88  3.000
 AZD  H52   C5A  H51   107.93  3.000
 AZD  H53   C5A  C5    111.41  3.000
 AZD  H52   C5A  C5    111.40  3.000
 AZD  H51   C5A  C5    110.85  3.000
 AZD  H6    C6   C5    120.41  3.000
 AZD  H6    C6   N1    115.39  3.000
 AZD  C5    C6   N1    124.20  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
 AZD  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 AZD  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 AZD  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 AZD  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 AZD  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 AZD  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 AZD  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 AZD  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 AZD  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 AZD  CONST_10  N5'  N4'  N3'  C3'   180.00   0.0  0
 AZD  Var_01    H51  C5A  C5   C4   -179.47  30.0  3
 AZD  Var_02    C4'  C5'  O5'  PA   -156.97  30.0  3
 AZD  Var_03    O1B  PB   O3A  PA    -66.52  30.0  3
 AZD  Var_04    O5'  PA   O3A  PB   -105.40  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
 AZD  chir_02  C4'  C5'  O4'  C3'  negativ
 AZD  chir_03  C3'  N3'  C2'  C4'  negativ
 AZD  chir_04  C1'  O4'  N1   C2'  negativ
 AZD  chir_05  PA   O2A  O3A  O5'  both

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
 AZD  plan-1  C1'  0.020
 AZD  plan-1  N1   0.020
 AZD  plan-1  C2   0.020
 AZD  plan-1  O2   0.020
 AZD  plan-1  N3   0.020
 AZD  plan-1  C4   0.020
 AZD  plan-1  O4   0.020
 AZD  plan-1  C5   0.020
 AZD  plan-1  C5A  0.020
 AZD  plan-1  C6   0.020
 AZD  plan-1  HN3  0.020
 AZD  plan-1  H6   0.020
 AZD  plan-2  C4'  0.020
 AZD  plan-2  C3'  0.020
 AZD  plan-2  N3'  0.020
 AZD  plan-2  N4'  0.020
 AZD  plan-2  N5'  0.020
 AZD  plan-2  C2'  0.020
 AZD  plan-2  H3'  0.020

