# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:07:58 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)C(F)(F)[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
 4BD  4BD  5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine  ligand  48  31  .  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_4BD
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
 4BD  PA    P  P     0   1.363   4.9655   5.8504  15.0196
 4BD  O1A   O  OH1   0  -0.726   3.5961   5.6929  15.8113
 4BD  O2A   O  O     0  -0.650   5.9083   6.8885  15.4733
 4BD  C3A   C  CT    0   0.250   5.7019   4.1415  15.0788
 4BD  F1A   F  F     0  -0.315   7.0057   4.2110  14.7243
 4BD  F2A   F  F     0  -0.331   5.6520   3.7278  16.3739
 4BD  O5'   O  O2    0  -0.607   4.5207   5.8520  13.4979
 4BD  PB    P  P     0   1.354   4.9050   2.8574  13.9864
 4BD  O1B   O  O     0  -0.630   5.4135   2.8833  12.6110
 4BD  O2B   O  OH1   0  -0.725   3.3437   3.0653  14.1191
 4BD  O3B   O  O2    0  -0.696   5.2995   1.5029  14.7733
 4BD  PG    P  P     0   1.482   4.6585   0.5405  15.9108
 4BD  O1G   O  OH1   0  -0.711   5.8153   0.4028  16.9786
 4BD  O2G   O  O     0  -0.661   4.2180  -0.7644  15.4094
 4BD  O3G   O  OH1   0  -0.758   3.5523   1.5360  16.4907
 4BD  C5'   C  CH2   0  -0.199   3.4021   6.5795  12.9656
 4BD  C4'   C  CH1   0   0.001   3.6144   6.8305  11.4973
 4BD  O4'   O  O2    0  -0.499   4.6846   7.7431  11.2907
 4BD  C1'   C  CH1   0   0.215   5.3378   7.4806  10.0825
 4BD  N1    N  NR6   0  -0.567   6.7692   7.2158  10.3582
 4BD  C6    C  CR16  0   0.047   7.2547   6.9935  11.6165
 4BD  C2    C  CR6   0   0.734   7.6058   7.2527   9.2705
 4BD  O2    O  O     0  -0.490   7.2080   7.4690   8.1415
 4BD  N3    N  NR16  0  -0.731   8.9247   7.0239   9.5532
 4BD  C4    C  CR6   0   0.559   9.4955   6.7796  10.7898
 4BD  O4    O  O     0  -0.458  10.6948   6.5900  10.8903
 4BD  C5    C  CR6   0  -0.177   8.5555   6.7796  11.8905
 4BD  C5M   C  CH3   0  -0.716   9.0699   6.5474  13.2735
 4BD  C2'   C  CH2   0  -0.550   4.6269   6.2897   9.4435
 4BD  C3'   C  CH1   0  -0.007   3.9596   5.6128  10.6356
 4BD  O3'   O  OH1   0  -0.654   2.8661   4.7937  10.3461
 4BD  HO1A  H  HOH1  0   0.513   3.5789   6.0917  16.6932
 4BD  HO2B  H  HOH1  0   0.506   2.9172   2.7949  14.9490
 4BD  HO1G  H  HOH1  0   0.504   6.1131   1.2060  17.4279
 4BD  HO3G  H  HOH1  0   0.523   2.8601   1.1203  17.0266
 4BD  H5'   H  HCH2  0   0.267   2.5004   5.9786  13.0886
 4BD  H5'A  H  HCH2  0   0.276   3.2636   7.5234  13.4962
 4BD  H4'   H  HCH1  0   0.257   2.6767   7.2756  11.1321
 4BD  H1'   H  HCH1  0   0.278   5.3070   8.3666   9.4471
 4BD  H6    H  HCR6  0   0.304   6.5204   7.0090  12.4053
 4BD  HN3   H  HNR6  0   0.425   9.5490   7.0390   8.7561
 4BD  H5M   H  HCH3  0   0.245   9.5074   5.5531  13.3738
 4BD  H5MA  H  HCH3  0   0.244   9.8466   7.2681  13.5317
 4BD  H5MB  H  HCH3  0   0.244   8.2730   6.6394  14.0084
 4BD  H2'   H  HCH2  0   0.265   3.8656   6.6599   8.7508
 4BD  H2'A  H  HCH2  0   0.286   5.2951   5.6358   8.8876
 4BD  H3'   H  HCH1  0   0.268   4.6791   4.9752  11.1551
 4BD  HO3'  H  HOH1  0   0.448   2.2373   5.2886   9.8089

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
 4BD  O5'  PA    single  1.585  0.020  1.585
 4BD  C3A  PA    single  1.862  0.020  1.862
 4BD  PA   O2A   double  1.474  0.020  1.474
 4BD  PA   O1A   single  1.590  0.020  1.590
 4BD  O1A  HO1A  single  0.850  0.020  0.980
 4BD  F1A  C3A   single  1.353  0.020  1.353
 4BD  PB   C3A   single  1.865  0.020  1.865
 4BD  C3A  F2A   single  1.361  0.020  1.361
 4BD  C5'  O5'   single  1.437  0.020  1.437
 4BD  O1B  PB    double  1.467  0.020  1.467
 4BD  PB   O2B   single  1.581  0.020  1.581
 4BD  PB   O3B   single  1.615  0.020  1.615
 4BD  O2B  HO2B  single  0.850  0.020  0.980
 4BD  O3B  PG    single  1.622  0.020  1.622
 4BD  PG   O2G   double  1.466  0.020  1.466
 4BD  PG   O1G   single  1.580  0.020  1.580
 4BD  PG   O3G   single  1.597  0.020  1.597
 4BD  O1G  HO1G  single  0.850  0.020  0.980
 4BD  O3G  HO3G  single  0.850  0.020  0.980
 4BD  C4'  C5'   single  1.505  0.020  1.505
 4BD  C5'  H5'   single  0.970  0.020  1.090
 4BD  C5'  H5'A  single  0.970  0.020  1.090
 4BD  C3'  C4'   single  1.531  0.020  1.531
 4BD  O4'  C4'   single  1.422  0.020  1.422
 4BD  C4'  H4'   single  0.970  0.020  1.090
 4BD  C1'  O4'   single  1.398  0.020  1.398
 4BD  C2'  C1'   single  1.527  0.020  1.527
 4BD  C1'  N1    single  1.482  0.020  1.482
 4BD  C1'  H1'   single  0.970  0.020  1.090
 4BD  C2   N1    single  1.373  0.020  1.373
 4BD  N1   C6    single  1.367  0.020  1.367
 4BD  C6   C5    double  1.346  0.020  1.346
 4BD  C6   H6    single  0.930  0.020  1.080
 4BD  O2   C2    double  1.216  0.020  1.216
 4BD  C2   N3    single  1.368  0.020  1.368
 4BD  N3   C4    single  1.384  0.020  1.384
 4BD  N3   HN3   single  0.860  0.020  1.020
 4BD  C4   O4    double  1.218  0.020  1.218
 4BD  C4   C5    single  1.447  0.020  1.447
 4BD  C5   C5M   single  1.494  0.020  1.494
 4BD  C5M  H5M   single  0.970  0.020  1.090
 4BD  C5M  H5MA  single  0.970  0.020  1.090
 4BD  C5M  H5MB  single  0.970  0.020  1.090
 4BD  C2'  C3'   single  1.525  0.020  1.525
 4BD  C2'  H2'   single  0.970  0.020  1.090
 4BD  C2'  H2'A  single  0.970  0.020  1.090
 4BD  O3'  C3'   single  1.397  0.020  1.397
 4BD  C3'  H3'   single  0.970  0.020  1.090
 4BD  O3'  HO3'  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
 4BD  O5'   PA   C3A    98.19  3.000
 4BD  C3A   PA   O2A   112.56  3.000
 4BD  O5'   PA   O2A   118.31  3.000
 4BD  O2A   PA   O1A   117.88  3.000
 4BD  C3A   PA   O1A   103.53  3.000
 4BD  O5'   PA   O1A   103.68  3.000
 4BD  HO1A  O1A  PA    115.35  3.000
 4BD  PB    C3A  F2A   109.42  3.000
 4BD  F2A   C3A  F1A   107.49  3.000
 4BD  PB    C3A  F1A   107.08  3.000
 4BD  F2A   C3A  PA    107.15  3.000
 4BD  PB    C3A  PA    116.39  3.000
 4BD  F1A   C3A  PA    109.01  3.000
 4BD  C5'   O5'  PA    125.07  3.000
 4BD  O3B   PB   O2B   108.10  3.000
 4BD  O3B   PB   O1B   112.76  3.000
 4BD  O2B   PB   O1B   114.76  3.000
 4BD  O3B   PB   C3A   100.82  3.000
 4BD  O2B   PB   C3A   106.40  3.000
 4BD  O1B   PB   C3A   112.89  3.000
 4BD  HO2B  O2B  PB    117.95  3.000
 4BD  PG    O3B  PB    137.95  3.000
 4BD  O3G   PG   O2G   118.10  3.000
 4BD  O3G   PG   O1G   108.42  3.000
 4BD  O2G   PG   O1G   111.94  3.000
 4BD  O3G   PG   O3B    99.12  3.000
 4BD  O1G   PG   O3B   103.67  3.000
 4BD  O2G   PG   O3B   114.02  3.000
 4BD  HO1G  O1G  PG    117.83  3.000
 4BD  HO3G  O3G  PG    115.35  3.000
 4BD  H5'A  C5'  H5'   108.46  3.000
 4BD  H5'A  C5'  C4'   110.37  3.000
 4BD  H5'   C5'  C4'   108.59  3.000
 4BD  H5'A  C5'  O5'   110.89  3.000
 4BD  H5'   C5'  O5'   108.84  3.000
 4BD  C4'   C5'  O5'   109.65  3.000
 4BD  H4'   C4'  C3'   109.08  3.000
 4BD  H4'   C4'  O4'   109.49  3.000
 4BD  C3'   C4'  O4'   105.01  3.000
 4BD  H4'   C4'  C5'   105.73  3.000
 4BD  O4'   C4'  C5'   110.80  3.000
 4BD  C3'   C4'  C5'   116.64  3.000
 4BD  C1'   O4'  C4'   110.90  3.000
 4BD  H1'   C1'  C2'   112.12  3.000
 4BD  H1'   C1'  N1    106.31  3.000
 4BD  C2'   C1'  N1    112.84  3.000
 4BD  H1'   C1'  O4'   109.74  3.000
 4BD  N1    C1'  O4'   108.91  3.000
 4BD  C2'   C1'  O4'   106.89  3.000
 4BD  C2    N1   C6    121.16  3.000
 4BD  C6    N1   C1'   122.92  3.000
 4BD  C2    N1   C1'   115.89  3.000
 4BD  H6    C6   C5    120.77  3.000
 4BD  H6    C6   N1    115.43  3.000
 4BD  C5    C6   N1    123.79  3.000
 4BD  N3    C2   O2    122.46  3.000
 4BD  N3    C2   N1    114.79  3.000
 4BD  O2    C2   N1    122.75  3.000
 4BD  HN3   N3   C4    116.87  3.000
 4BD  HN3   N3   C2    115.41  3.000
 4BD  C4    N3   C2    127.72  3.000
 4BD  C5    C4   O4    125.21  3.000
 4BD  C5    C4   N3    114.31  3.000
 4BD  O4    C4   N3    120.48  3.000
 4BD  C5M   C5   C4    118.71  3.000
 4BD  C5M   C5   C6    123.08  3.000
 4BD  C4    C5   C6    118.21  3.000
 4BD  H5MB  C5M  H5MA  107.80  3.000
 4BD  H5MB  C5M  H5M   107.98  3.000
 4BD  H5MA  C5M  H5M   107.15  3.000
 4BD  H5MB  C5M  C5    111.11  3.000
 4BD  H5MA  C5M  C5    111.21  3.000
 4BD  H5M   C5M  C5    111.40  3.000
 4BD  H2'A  C2'  H2'   107.90  3.000
 4BD  H2'A  C2'  C3'   113.68  3.000
 4BD  H2'   C2'  C3'   109.93  3.000
 4BD  H2'A  C2'  C1'   113.37  3.000
 4BD  H2'   C2'  C1'   108.97  3.000
 4BD  C3'   C2'  C1'   102.88  3.000
 4BD  H3'   C3'  O3'   105.77  3.000
 4BD  H3'   C3'  C2'   110.04  3.000
 4BD  O3'   C3'  C2'   116.17  3.000
 4BD  H3'   C3'  C4'   110.18  3.000
 4BD  O3'   C3'  C4'   113.99  3.000
 4BD  C2'   C3'  C4'   100.70  3.000
 4BD  HO3'  O3'  C3'   108.97  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
 4BD  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 4BD  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 4BD  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 4BD  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 4BD  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 4BD  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 4BD  CONST_07  O4   C4   N3   C2    180.00   0.0  0
 4BD  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 4BD  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 4BD  Var_01    H5M  C5M  C5   C6    116.81  30.0  3
 4BD  Var_02    C4'  C5'  O5'  PA    155.98  30.0  2
 4BD  Var_03    O1B  PB   C3A  PA     84.31  30.0  1
 4BD  Var_04    F1A  C3A  PA   O1A  -165.41  30.0  1
 4BD  Var_05    O2G  PG   O3B  PB    109.50  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
 4BD  chir_03  C4'  C5'  C3'  O4'  positiv
 4BD  chir_04  C1'  O4'  N1   C2'  negativ
 4BD  chir_05  C3'  O3'  C4'  C2'  positiv
 4BD  chir_06  PA   C3A  O2A  O1A  both
 4BD  chir_07  PB   O2B  O1B  C3A  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
 4BD  plan-1  C1'  0.020
 4BD  plan-1  N1   0.020
 4BD  plan-1  C6   0.020
 4BD  plan-1  C2   0.020
 4BD  plan-1  O2   0.020
 4BD  plan-1  N3   0.020
 4BD  plan-1  C4   0.020
 4BD  plan-1  O4   0.020
 4BD  plan-1  C5   0.020
 4BD  plan-1  C5M  0.020
 4BD  plan-1  H6   0.020
 4BD  plan-1  HN3  0.020

