# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:47:55 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(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)O[P](O)(=O)[C@H](Cl)[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
 FDJ  FDJ  5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine  ligand  44  30  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDJ
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
 FDJ  C2   C   CR6    0   0.742  -4.8793  -0.1511   0.7750
 FDJ  C4   C   CR6    0   0.558  -5.8418  -2.4323   0.8566
 FDJ  C5   C   CR6    0  -0.185  -5.6804  -2.5104  -0.5809
 FDJ  C6   C   CR16   0   0.059  -5.1548  -1.4464  -1.2120
 FDJ  C7   C   CH3    0  -0.707  -6.0980  -3.7570  -1.2892
 FDJ  O2   O   O      0  -0.471  -4.5409   0.8433   1.3811
 FDJ  N1   N   NR6    0  -0.567  -4.7714  -0.2867  -0.5895
 FDJ  N3   N   NR16   0  -0.734  -5.4162  -1.2401   1.4128
 FDJ  O4   O   O      0  -0.456  -6.3036  -3.3140   1.5583
 FDJ  PA   P   P      0   1.338   0.9003   1.5834   0.9745
 FDJ  PB   P   P      0   1.307   3.5426   0.5258   0.2492
 FDJ  PG   P   P      0   1.185   5.2973  -1.8726  -0.7792
 FDJ  C1'  C   CH1    0   0.221  -4.1807   0.7879  -1.3875
 FDJ  O1A  O   OP    -1  -0.802   0.3699   0.5937   1.9639
 FDJ  O2B  O   O      0  -0.803   3.7174   0.4692   1.7372
 FDJ  O1G  O   OP    -1  -0.894   6.0474  -1.5970   0.5225
 FDJ  C2'  C   CH2    0  -0.561  -4.8388   2.1645  -1.2553
 FDJ  O2A  O   O      0  -0.821   1.3902   2.9197   1.4497
 FDJ  O1B  O   OP    -1  -0.801   4.3769   1.4622  -0.5793
 FDJ  CL1  CL  CL     0  -0.239   2.5094  -2.2301   0.4269
 FDJ  O2G  O   OP    -1  -0.899   5.0359  -3.3550  -1.0486
 FDJ  C3'  C   CH1    0   0.023  -3.7806   3.0444  -0.5890
 FDJ  O3'  O   OH1    0  -0.670  -3.6847   4.3453  -1.1144
 FDJ  O3A  O   O2     0  -0.752   1.9436   0.9112  -0.0735
 FDJ  C3B  C   CH1    0  -0.769   3.5794  -1.1235  -0.5385
 FDJ  O3G  O   O      0  -0.896   5.8275  -1.1113  -1.9944
 FDJ  C4'  C   CH1    0   0.013  -2.4824   2.2934  -0.8864
 FDJ  O4'  O   O2     0  -0.488  -2.8333   0.9286  -1.0449
 FDJ  C5'  C   CH2    0  -0.148  -1.4549   2.4338   0.2096
 FDJ  O5'  O   O2     0  -0.627  -0.2500   1.8299  -0.1957
 FDJ  H1   H   HCR6   0   0.316  -5.0086  -1.4548  -2.2841
 FDJ  H2   H   HCH3   0   0.246  -7.1642  -3.9489  -1.1603
 FDJ  H3   H   HCH3   0   0.247  -5.8985  -3.6833  -2.3569
 FDJ  H4   H   HCH3   0   0.247  -5.5648  -4.6289  -0.9081
 FDJ  H5   H   HNR6   0   0.424  -5.5067  -1.1479   2.4174
 FDJ  H6   H   HCH1   0   0.252  -4.2718   0.4336  -2.4172
 FDJ  H9   H   HCH2   0   0.266  -5.0411   2.5489  -2.2565
 FDJ  H10  H   HCH2   0   0.274  -5.7852   2.1354  -0.7177
 FDJ  H13  H   HCH1   0   0.231  -3.9507   3.0788   0.4907
 FDJ  H14  H   HOH1   0   0.456  -4.3919   4.8750  -0.7354
 FDJ  H15  H   HCH1   0   0.251   3.0951  -1.0518  -1.5152
 FDJ  H16  H   HCH1   0   0.223  -2.0693   2.6788  -1.8307
 FDJ  H17  H   HCH2   0   0.204  -1.3150   3.5036   0.4102
 FDJ  H18  H   HCH2   0   0.206  -1.8518   1.9750   1.1231

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
 FDJ  O2   C2   double  1.213  0.020  1.213
 FDJ  C2   N3   single  1.371  0.020  1.371
 FDJ  C2   N1   single  1.375  0.020  1.375
 FDJ  N3   C4   single  1.383  0.020  1.383
 FDJ  C2'  C1'  single  1.531  0.020  1.531
 FDJ  C2'  C3'  single  1.529  0.020  1.529
 FDJ  C1'  N1   single  1.463  0.020  1.463
 FDJ  C1'  O4'  single  1.397  0.020  1.397
 FDJ  N1   C6   single  1.371  0.020  1.371
 FDJ  C4   O4   double  1.218  0.020  1.218
 FDJ  C4   C5   single  1.449  0.020  1.449
 FDJ  O3'  C3'  single  1.406  0.020  1.406
 FDJ  C3'  C4'  single  1.529  0.020  1.529
 FDJ  O4'  C4'  single  1.418  0.020  1.418
 FDJ  C6   C5   double  1.344  0.020  1.344
 FDJ  C4'  C5'  single  1.509  0.020  1.509
 FDJ  C5   C7   single  1.493  0.020  1.493
 FDJ  O2B  PB   deloc   1.499  0.020  1.499
 FDJ  C5'  O5'  single  1.407  0.020  1.407
 FDJ  O5'  PA   single  1.659  0.020  1.659
 FDJ  O3A  PB   single  1.676  0.020  1.676
 FDJ  O3A  PA   single  1.624  0.020  1.624
 FDJ  PB   O1B  deloc   1.503  0.020  1.503
 FDJ  PB   C3B  single  1.828  0.020  1.828
 FDJ  CL1  C3B  single  1.817  0.020  1.817
 FDJ  PA   O2A  deloc   1.501  0.020  1.501
 FDJ  PA   O1A  deloc   1.497  0.020  1.497
 FDJ  C3B  PG   single  1.890  0.020  1.890
 FDJ  O3G  PG   deloc   1.529  0.020  1.529
 FDJ  PG   O1G  deloc   1.527  0.020  1.527
 FDJ  PG   O2G  deloc   1.529  0.020  1.529
 FDJ  C6   H1   single  0.930  0.020  1.080
 FDJ  C7   H2   single  0.970  0.020  1.090
 FDJ  C7   H3   single  0.970  0.020  1.090
 FDJ  C7   H4   single  0.970  0.020  1.090
 FDJ  N3   H5   single  0.860  0.020  1.020
 FDJ  C1'  H6   single  0.970  0.020  1.090
 FDJ  C2'  H9   single  0.970  0.020  1.090
 FDJ  C2'  H10  single  0.970  0.020  1.090
 FDJ  C3'  H13  single  0.970  0.020  1.090
 FDJ  O3'  H14  single  0.850  0.020  0.980
 FDJ  C3B  H15  single  0.970  0.020  1.090
 FDJ  C4'  H16  single  0.970  0.020  1.090
 FDJ  C5'  H17  single  0.970  0.020  1.090
 FDJ  C5'  H18  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
 FDJ  N3   C2   N1   114.45  3.000
 FDJ  N1   C2   O2   123.69  3.000
 FDJ  N3   C2   O2   121.86  3.000
 FDJ  O4   C4   N3   120.61  3.000
 FDJ  O4   C4   C5   125.10  3.000
 FDJ  N3   C4   C5   114.29  3.000
 FDJ  C7   C5   C6   123.19  3.000
 FDJ  C7   C5   C4   118.98  3.000
 FDJ  C6   C5   C4   117.83  3.000
 FDJ  H1   C6   N1   114.75  3.000
 FDJ  H1   C6   C5   120.79  3.000
 FDJ  N1   C6   C5   124.46  3.000
 FDJ  H4   C7   H3   107.89  3.000
 FDJ  H4   C7   H2   107.21  3.000
 FDJ  H3   C7   H2   107.87  3.000
 FDJ  H4   C7   C5   111.40  3.000
 FDJ  H3   C7   C5   110.94  3.000
 FDJ  H2   C7   C5   111.35  3.000
 FDJ  C1'  N1   C6   119.12  3.000
 FDJ  C6   N1   C2   120.79  3.000
 FDJ  C1'  N1   C2   120.03  3.000
 FDJ  H5   N3   C4   116.74  3.000
 FDJ  H5   N3   C2   115.09  3.000
 FDJ  C4   N3   C2   128.17  3.000
 FDJ  O5'  PA   O3A   92.97  3.000
 FDJ  O3A  PA   O2A  111.30  3.000
 FDJ  O5'  PA   O2A  108.50  3.000
 FDJ  O2A  PA   O1A  119.69  3.000
 FDJ  O3A  PA   O1A  112.37  3.000
 FDJ  O5'  PA   O1A  108.59  3.000
 FDJ  C3B  PB   O3A   98.26  3.000
 FDJ  C3B  PB   O1B  108.26  3.000
 FDJ  O3A  PB   O1B  106.27  3.000
 FDJ  C3B  PB   O2B  113.03  3.000
 FDJ  O1B  PB   O2B  120.39  3.000
 FDJ  O3A  PB   O2B  108.12  3.000
 FDJ  O3G  PG   C3B  102.66  3.000
 FDJ  O3G  PG   O2G  113.70  3.000
 FDJ  C3B  PG   O2G  104.56  3.000
 FDJ  O2G  PG   O1G  114.15  3.000
 FDJ  O3G  PG   O1G  114.66  3.000
 FDJ  C3B  PG   O1G  105.45  3.000
 FDJ  H6   C1'  O4'  110.12  3.000
 FDJ  H6   C1'  C2'  109.69  3.000
 FDJ  O4'  C1'  C2'  107.62  3.000
 FDJ  H6   C1'  N1   104.01  3.000
 FDJ  O4'  C1'  N1   109.24  3.000
 FDJ  C2'  C1'  N1   116.08  3.000
 FDJ  H10  C2'  H9   107.54  3.000
 FDJ  H10  C2'  C3'  113.68  3.000
 FDJ  H9   C2'  C3'  108.98  3.000
 FDJ  H10  C2'  C1'  113.09  3.000
 FDJ  H9   C2'  C1'  108.48  3.000
 FDJ  C3'  C2'  C1'  104.92  3.000
 FDJ  H13  C3'  C4'  109.85  3.000
 FDJ  H13  C3'  O3'  110.51  3.000
 FDJ  C4'  C3'  O3'  108.89  3.000
 FDJ  H13  C3'  C2'  109.92  3.000
 FDJ  C4'  C3'  C2'  102.72  3.000
 FDJ  O3'  C3'  C2'  114.63  3.000
 FDJ  H14  O3'  C3'  108.19  3.000
 FDJ  PB   O3A  PA   125.71  3.000
 FDJ  H15  C3B  CL1  104.71  3.000
 FDJ  H15  C3B  PG   108.37  3.000
 FDJ  CL1  C3B  PG   111.20  3.000
 FDJ  H15  C3B  PB   108.49  3.000
 FDJ  PG   C3B  PB   115.52  3.000
 FDJ  CL1  C3B  PB   107.98  3.000
 FDJ  H16  C4'  C5'  109.58  3.000
 FDJ  H16  C4'  O4'  109.51  3.000
 FDJ  C5'  C4'  O4'  109.83  3.000
 FDJ  H16  C4'  C3'  108.28  3.000
 FDJ  C5'  C4'  C3'  113.03  3.000
 FDJ  O4'  C4'  C3'  106.52  3.000
 FDJ  C4'  O4'  C1'  111.28  3.000
 FDJ  H18  C5'  H17  107.56  3.000
 FDJ  H18  C5'  O5'  111.73  3.000
 FDJ  H17  C5'  O5'  111.21  3.000
 FDJ  H18  C5'  C4'  108.65  3.000
 FDJ  H17  C5'  C4'  108.08  3.000
 FDJ  O5'  C5'  C4'  109.51  3.000
 FDJ  C5'  O5'  PA   117.02  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
 FDJ  CONST_01  C5   C4   N3   C2     0.00   0.0  0
 FDJ  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 FDJ  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 FDJ  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 FDJ  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 FDJ  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 FDJ  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 FDJ  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 FDJ  CONST_09  H5   N3   C4   C5   180.00   0.0  0
 FDJ  Var_01    H2   C7   C5   C4    61.15  30.0  3
 FDJ  Var_02    C4'  C5'  O5'  PA  -167.18  30.0  2
 FDJ  Var_03    O2B  PB   O3A  PA    18.63  30.0  3
 FDJ  Var_04    O5'  PA   O3A  PB   171.07  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
 FDJ  chir_03  C1'  C2'  N1   O4'  positiv
 FDJ  chir_04  C3'  O3'  C4'  C2'  positiv
 FDJ  chir_05  C3B  PB   CL1  PG   positiv
 FDJ  chir_06  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
 FDJ  plan-1  C2   0.020
 FDJ  plan-1  C4   0.020
 FDJ  plan-1  C5   0.020
 FDJ  plan-1  C6   0.020
 FDJ  plan-1  C7   0.020
 FDJ  plan-1  O2   0.020
 FDJ  plan-1  N1   0.020
 FDJ  plan-1  N3   0.020
 FDJ  plan-1  O4   0.020
 FDJ  plan-1  C1'  0.020
 FDJ  plan-1  H1   0.020
 FDJ  plan-1  H5   0.020

