# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:53:58 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@H](Cl)[P](O)(O)=O)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
 DJJ  DJJ  5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine  ligand  42  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJJ
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
 DJJ  C4   C   CR6    0   0.533  -6.0915  -2.7909   0.2758
 DJJ  N4   N   NH2    0  -0.750  -6.6016  -3.8914   0.8242
 DJJ  C5   C   CR16   0  -0.437  -6.0471  -2.6632  -1.1448
 DJJ  C6   C   CR16   0   0.140  -5.5193  -1.5189  -1.6213
 DJJ  N3   N   N      0  -0.553  -5.6317  -1.8489   1.0758
 DJJ  C2   C   CR6    0   0.548  -5.1005  -0.7173   0.5914
 DJJ  O2   O   O      0  -0.578  -4.6469   0.1594   1.3141
 DJJ  N1   N   NR6    0  -0.567  -5.0598  -0.5439  -0.8008
 DJJ  C1'  C   CR15   0   0.225  -4.5009   0.6665  -1.3918
 DJJ  C2'  C   CH2    0  -0.561  -5.1292   1.9830  -0.9272
 DJJ  C3'  C   CR15   0   0.038  -4.0173   2.7055  -0.1703
 DJJ  O3'  O   OH1    0  -0.673  -3.9381   4.0886  -0.4143
 DJJ  O4'  O   O      0  -0.397  -3.1292   0.7343  -1.1159
 DJJ  C4'  C   CR15   0  -0.010  -2.7520   2.0395  -0.7106
 DJJ  C5'  C   CH2    0  -0.172  -1.6517   1.9659   0.3212
 DJJ  O5'  O   O2     0  -0.641  -0.5034   1.3697  -0.2382
 DJJ  PA   P   P      0   1.355   0.9346   1.7111   0.5133
 DJJ  O1A  O   OP    -1  -0.836   0.7548   1.4604   1.9806
 DJJ  O2A  O   O      0  -0.641   1.4233   3.0479   0.0396
 DJJ  O3A  O   O2     0  -0.700   1.7354   0.5045  -0.2326
 DJJ  PB   P   P      0   1.231   3.4161   0.4123  -0.2155
 DJJ  O2B  O   O      0  -0.847   3.8976   1.1545   0.9965
 DJJ  O1B  O   OP    -1  -0.948   3.8875   0.8036  -1.5842
 DJJ  C3B  C   CH1    0  -0.749   3.5740  -1.3849   0.0626
 DJJ  CL1  CL  CL     0  -0.207   2.9790  -2.2466  -1.4331
 DJJ  PG   P   P      0   1.147   5.3056  -1.9692   0.5297
 DJJ  O1G  O   OP    -1  -0.885   5.4289  -1.5603   1.9960
 DJJ  O2G  O   OP    -1  -0.949   5.2661  -3.4848   0.3168
 DJJ  O3G  O   O      0  -0.835   6.2437  -1.2234  -0.4158
 DJJ  H1   H   HNH2   0   0.421  -6.9736  -4.6360   0.2614
 DJJ  H2   H   HNH2   0   0.428  -6.6321  -3.9920   1.8241
 DJJ  H3   H   HCR6   0   0.263  -6.4055  -3.4348  -1.8087
 DJJ  H4   H   HCR6   0   0.344  -5.4358  -1.3339  -2.6832
 DJJ  H5   H   HCR5   0   0.280  -4.6571   0.5436  -2.4661
 DJJ  H6   H   HCH2   0   0.249  -5.4065   2.5695  -1.8049
 DJJ  H7   H   HCH2   0   0.260  -6.0308   1.8379  -0.3343
 DJJ  H8   H   HCR5   0   0.229  -4.1127   2.5074   0.9020
 DJJ  H9   H   HOH1   0   0.452  -4.6230   4.5252   0.0999
 DJJ  H10  H   HCR5   0   0.096  -2.4012   2.6166  -1.5806
 DJJ  H11  H   HCH2   0   0.240  -1.4596   2.9923   0.6595
 DJJ  H12  H   HCH2   0   0.190  -2.0048   1.3986   1.1906
 DJJ  H15  H   HCH1   0   0.267   2.8826  -1.6900   0.8524

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
 DJJ  O2   C2   double  1.223  0.020  1.223
 DJJ  C2   N3   single  1.341  0.020  1.341
 DJJ  C2   N1   single  1.404  0.020  1.404
 DJJ  N3   C4   double  1.319  0.020  1.319
 DJJ  C2'  C1'  single  1.531  0.020  1.531
 DJJ  C2'  C3'  single  1.527  0.020  1.527
 DJJ  C1'  N1   single  1.458  0.020  1.458
 DJJ  C1'  O4'  single  1.401  0.020  1.401
 DJJ  N1   C6   single  1.355  0.020  1.355
 DJJ  O3'  C3'  single  1.407  0.020  1.407
 DJJ  C4   N4   single  1.331  0.020  1.331
 DJJ  C4   C5   single  1.427  0.020  1.427
 DJJ  C3'  C4'  single  1.528  0.020  1.528
 DJJ  O4'  C4'  single  1.418  0.020  1.418
 DJJ  C6   C5   double  1.347  0.020  1.347
 DJJ  C4'  C5'  single  1.510  0.020  1.510
 DJJ  O2B  PB   deloc   1.500  0.020  1.500
 DJJ  C5'  O5'  single  1.410  0.020  1.410
 DJJ  O5'  PA   single  1.658  0.020  1.658
 DJJ  PB   O3A  single  1.683  0.020  1.683
 DJJ  PB   O1B  deloc   1.500  0.020  1.500
 DJJ  PB   C3B  single  1.825  0.020  1.825
 DJJ  O3A  PA   single  1.629  0.020  1.629
 DJJ  C3B  CL1  single  1.826  0.020  1.826
 DJJ  C3B  PG   single  1.886  0.020  1.886
 DJJ  PA   O2A  deloc   1.500  0.020  1.500
 DJJ  PA   O1A  deloc   1.499  0.020  1.499
 DJJ  O3G  PG   deloc   1.527  0.020  1.527
 DJJ  PG   O1G  deloc   1.527  0.020  1.527
 DJJ  PG   O2G  deloc   1.531  0.020  1.531
 DJJ  N4   H1   single  0.860  0.020  1.020
 DJJ  N4   H2   single  0.860  0.020  1.020
 DJJ  C5   H3   single  0.930  0.020  1.080
 DJJ  C6   H4   single  0.930  0.020  1.080
 DJJ  C1'  H5   single  0.970  0.020  1.090
 DJJ  C2'  H6   single  0.970  0.020  1.090
 DJJ  C2'  H7   single  0.970  0.020  1.090
 DJJ  C3'  H8   single  0.970  0.020  1.090
 DJJ  O3'  H9   single  0.850  0.020  0.980
 DJJ  C4'  H10  single  0.970  0.020  1.090
 DJJ  C5'  H11  single  0.970  0.020  1.090
 DJJ  C5'  H12  single  0.970  0.020  1.090
 DJJ  C3B  H15  single  0.970  0.020  1.090

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
 DJJ  N3   C4   C5   121.95  3.000
 DJJ  C5   C4   N4   119.74  3.000
 DJJ  N3   C4   N4   118.31  3.000
 DJJ  H2   N4   H1   118.14  3.000
 DJJ  H2   N4   C4   120.27  3.000
 DJJ  H1   N4   C4   121.58  3.000
 DJJ  H3   C5   C6   121.32  3.000
 DJJ  H3   C5   C4   122.56  3.000
 DJJ  C6   C5   C4   116.12  3.000
 DJJ  H4   C6   N1   116.46  3.000
 DJJ  H4   C6   C5   121.53  3.000
 DJJ  N1   C6   C5   122.01  3.000
 DJJ  C2   N3   C4   121.46  3.000
 DJJ  N1   C2   O2   119.12  3.000
 DJJ  N1   C2   N3   118.31  3.000
 DJJ  O2   C2   N3   122.57  3.000
 DJJ  C1'  N1   C2   121.04  3.000
 DJJ  C1'  N1   C6   118.81  3.000
 DJJ  C2   N1   C6   120.13  3.000
 DJJ  H5   C1'  O4'  109.83  3.000
 DJJ  H5   C1'  C2'  109.66  3.000
 DJJ  O4'  C1'  C2'  107.49  3.000
 DJJ  H5   C1'  N1   104.49  3.000
 DJJ  O4'  C1'  N1   109.61  3.000
 DJJ  C2'  C1'  N1   115.68  3.000
 DJJ  H7   C2'  H6   107.41  3.000
 DJJ  H7   C2'  C3'  113.34  3.000
 DJJ  H6   C2'  C3'  109.23  3.000
 DJJ  H7   C2'  C1'  112.99  3.000
 DJJ  H6   C2'  C1'  108.80  3.000
 DJJ  C3'  C2'  C1'  104.98  3.000
 DJJ  H8   C3'  C4'  109.85  3.000
 DJJ  H8   C3'  O3'  110.66  3.000
 DJJ  C4'  C3'  O3'  108.69  3.000
 DJJ  H8   C3'  C2'  109.67  3.000
 DJJ  C4'  C3'  C2'  102.79  3.000
 DJJ  O3'  C3'  C2'  114.85  3.000
 DJJ  H9   O3'  C3'  108.28  3.000
 DJJ  C4'  O4'  C1'  111.18  3.000
 DJJ  H10  C4'  C5'  109.46  3.000
 DJJ  H10  C4'  O4'  109.96  3.000
 DJJ  C5'  C4'  O4'  110.14  3.000
 DJJ  H10  C4'  C3'  108.34  3.000
 DJJ  C5'  C4'  C3'  112.51  3.000
 DJJ  O4'  C4'  C3'  106.38  3.000
 DJJ  H12  C5'  H11  107.20  3.000
 DJJ  H12  C5'  O5'  110.99  3.000
 DJJ  H11  C5'  O5'  112.04  3.000
 DJJ  H12  C5'  C4'  109.40  3.000
 DJJ  H11  C5'  C4'  107.01  3.000
 DJJ  O5'  C5'  C4'  110.06  3.000
 DJJ  PA   O5'  C5'  116.07  3.000
 DJJ  O3A  PA   O2A  110.81  3.000
 DJJ  O2A  PA   O1A  119.81  3.000
 DJJ  O3A  PA   O1A  112.53  3.000
 DJJ  O1A  PA   O5'  107.77  3.000
 DJJ  O2A  PA   O5'  108.84  3.000
 DJJ  O3A  PA   O5'   93.80  3.000
 DJJ  PB   O3A  PA   121.79  3.000
 DJJ  C3B  PB   O1B  111.64  3.000
 DJJ  C3B  PB   O2B  109.65  3.000
 DJJ  O1B  PB   O2B  120.48  3.000
 DJJ  C3B  PB   O3A   98.15  3.000
 DJJ  O1B  PB   O3A  106.88  3.000
 DJJ  O2B  PB   O3A  107.55  3.000
 DJJ  H15  C3B  PG   108.38  3.000
 DJJ  H15  C3B  CL1  104.72  3.000
 DJJ  PG   C3B  CL1  110.84  3.000
 DJJ  H15  C3B  PB   109.28  3.000
 DJJ  PG   C3B  PB   114.97  3.000
 DJJ  CL1  C3B  PB   108.16  3.000
 DJJ  O3G  PG   O2G  114.42  3.000
 DJJ  O2G  PG   O1G  113.62  3.000
 DJJ  O3G  PG   O1G  114.47  3.000
 DJJ  O2G  PG   C3B  104.39  3.000
 DJJ  O1G  PG   C3B  103.24  3.000
 DJJ  O3G  PG   C3B  105.04  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
 DJJ  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 DJJ  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 DJJ  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 DJJ  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 DJJ  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 DJJ  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 DJJ  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 DJJ  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 DJJ  CONST_09  H1   N4   C4   C5     0.00   0.0  0
 DJJ  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 DJJ  Var_01    O3A  PA   O5'  C5'  165.16  30.0  3
 DJJ  Var_02    O2B  PB   O3A  PA    24.54  30.0  1
 DJJ  Var_03    H11  C5'  O5'  PA    38.79  30.0  2

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
 DJJ  chir_01  C1'  C2'  N1   O4'  positiv
 DJJ  chir_02  C3'  O3'  C4'  C2'  positiv
 DJJ  chir_03  C4'  O4'  C3'  C5'  negativ
 DJJ  chir_06  C3B  PB   CL1  PG   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
 DJJ  plan-1  C4   0.020
 DJJ  plan-1  N4   0.020
 DJJ  plan-1  C5   0.020
 DJJ  plan-1  C6   0.020
 DJJ  plan-1  N3   0.020
 DJJ  plan-1  C2   0.020
 DJJ  plan-1  O2   0.020
 DJJ  plan-1  N1   0.020
 DJJ  plan-1  C1'  0.020
 DJJ  plan-1  H1   0.020
 DJJ  plan-1  H2   0.020
 DJJ  plan-1  H3   0.020
 DJJ  plan-1  H4   0.020

