# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:04:47 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: [(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid
#   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
 EJH  EJH  '[(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid'  ligand  44  30  .  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_EJH
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
 EJH  C2   C   CR6    0   0.699  -5.0818  -0.2150   0.7832
 EJH  C4   C   CR6    0   0.567  -6.2253  -2.4181   0.7654
 EJH  C5   C   CR6    0  -0.147  -6.0177  -2.4721  -0.6677
 EJH  C6   C   CR16   0   0.067  -5.3876  -1.4372  -1.2485
 EJH  C7   C   CH3    0  -0.722  -6.5042  -3.6651  -1.4228
 EJH  O2   O   O      0  -0.443  -4.6990   0.7382   1.4269
 EJH  N1   N   NR6    0  -0.580  -4.9313  -0.3309  -0.5795
 EJH  N3   N   NR16   0  -0.669  -5.7229  -1.2808   1.3703
 EJH  O4   O   O      0  -0.494  -6.7884  -3.2738   1.4237
 EJH  PA   P   P      0   1.339   1.1392   1.8168   0.7333
 EJH  PB   P   P      0   1.280   3.6095   0.4540  -0.0295
 EJH  PG   P   P      0   1.168   5.5052  -2.0829   0.0061
 EJH  C1'  C   CH1    0   0.241  -4.2342   0.7185  -1.3206
 EJH  O1A  O   OP    -1  -0.960   0.9472   1.6345   2.2094
 EJH  O2B  O   O      0  -0.813   4.1910   1.1684   1.1581
 EJH  O1G  O   OP    -1  -0.988   6.3481  -1.2337   0.9573
 EJH  C2'  C   CH2    0  -0.561  -4.8021   2.1353  -1.1810
 EJH  O2A  O   O      0  -0.668   1.6347   3.1300   0.2067
 EJH  O1B  O   OP    -1  -0.829   3.9946   0.8589  -1.4214
 EJH  CL1  CL  CL     0  -0.213   2.6355  -2.2260  -0.8973
 EJH  O2G  O   OP    -1  -0.979   5.3360  -3.5373   0.4525
 EJH  C3'  C   CH1    0   0.054  -3.6980   2.9339  -0.4867
 EJH  O3'  O   OH1    0  -0.690  -3.4958   4.2274  -0.9984
 EJH  O3A  O   O2     0  -0.786   1.9416   0.5667   0.0793
 EJH  C3B  C   CH1    0  -0.748   3.7779  -1.3504   0.2163
 EJH  O3G  O   O      0  -0.708   5.8559  -1.9251  -1.4694
 EJH  C4'  C   CH1    0  -0.022  -2.4520   2.0922  -0.7619
 EJH  O4'  O   O2     0  -0.435  -2.9000   0.7553  -0.9016
 EJH  C5'  C   CH2    0  -0.147  -1.4243   2.1714   0.3388
 EJH  O5'  O   O2     0  -0.553  -0.2808   1.4373  -0.0305
 EJH  H1   H   HCR6   0   0.289  -5.1995  -1.4246  -2.3140
 EJH  H2   H   HCH3   0   0.245  -6.0427  -4.5825  -1.0550
 EJH  H3   H   HCH3   0   0.283  -7.5839  -3.7850  -1.3242
 EJH  H4   H   HCH3   0   0.209  -6.2723  -3.5761  -2.4827
 EJH  H5   H   HNR6   0   0.446  -5.8429  -1.2090   2.3735
 EJH  H6   H   HCH1   0   0.231  -4.2948   0.3977  -2.3638
 EJH  H9   H   HCH2   0   0.250  -4.9627   2.5460  -2.1794
 EJH  H10  H   HCH2   0   0.230  -5.7569   2.1636  -0.6589
 EJH  H13  H   HCH1   0   0.233  -3.8883   2.9724   0.5899
 EJH  H14  H   HOH1   0   0.453  -4.1737   4.8041  -0.6349
 EJH  H15  H   HCH1   0   0.302   3.4199  -1.5807   1.2232
 EJH  H16  H   HCH1   0   0.215  -2.0037   2.4339  -1.7069
 EJH  H17  H   HCH2   0   0.211  -1.1960   3.2328   0.4996
 EJH  H18  H   HCH2   0   0.143  -1.8613   1.7846   1.2670

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
 EJH  O2   C2   double  1.212  0.020  1.212
 EJH  C2   N3   single  1.375  0.020  1.375
 EJH  C2   N1   single  1.376  0.020  1.376
 EJH  N3   C4   single  1.383  0.020  1.383
 EJH  C2'  C1'  single  1.533  0.020  1.533
 EJH  C2'  C3'  single  1.529  0.020  1.529
 EJH  C1'  N1   single  1.462  0.020  1.462
 EJH  C1'  O4'  single  1.399  0.020  1.399
 EJH  N1   C6   single  1.371  0.020  1.371
 EJH  C4   O4   double  1.218  0.020  1.218
 EJH  C4   C5   single  1.449  0.020  1.449
 EJH  O3'  C3'  single  1.406  0.020  1.406
 EJH  C3'  C4'  single  1.529  0.020  1.529
 EJH  O4'  C4'  single  1.417  0.020  1.417
 EJH  C6   C5   double  1.344  0.020  1.344
 EJH  C5   C7   single  1.493  0.020  1.493
 EJH  C4'  C5'  single  1.508  0.020  1.508
 EJH  O2B  PB   deloc   1.503  0.020  1.503
 EJH  C5'  O5'  single  1.408  0.020  1.408
 EJH  O5'  PA   single  1.656  0.020  1.656
 EJH  O3A  PB   single  1.675  0.020  1.675
 EJH  O3A  PA   single  1.623  0.020  1.623
 EJH  PB   O1B  deloc   1.500  0.020  1.500
 EJH  PB   C3B  single  1.829  0.020  1.829
 EJH  PA   O2A  deloc   1.499  0.020  1.499
 EJH  PA   O1A  deloc   1.500  0.020  1.500
 EJH  CL1  C3B  single  1.820  0.020  1.820
 EJH  C3B  PG   single  1.888  0.020  1.888
 EJH  PG   O3G  deloc   1.525  0.020  1.525
 EJH  PG   O1G  deloc   1.529  0.020  1.529
 EJH  PG   O2G  deloc   1.531  0.020  1.531
 EJH  C6   H1   single  0.930  0.020  1.080
 EJH  C7   H2   single  0.970  0.020  1.090
 EJH  C7   H3   single  0.970  0.020  1.090
 EJH  C7   H4   single  0.970  0.020  1.090
 EJH  N3   H5   single  0.860  0.020  1.020
 EJH  C1'  H6   single  0.970  0.020  1.090
 EJH  C2'  H9   single  0.970  0.020  1.090
 EJH  C2'  H10  single  0.970  0.020  1.090
 EJH  C3'  H13  single  0.970  0.020  1.090
 EJH  O3'  H14  single  0.850  0.020  0.980
 EJH  C3B  H15  single  0.970  0.020  1.090
 EJH  C4'  H16  single  0.970  0.020  1.090
 EJH  C5'  H17  single  0.970  0.020  1.090
 EJH  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
 EJH  N3   C2   N1   114.11  3.000
 EJH  N1   C2   O2   123.89  3.000
 EJH  N3   C2   O2   121.99  3.000
 EJH  O4   C4   N3   120.63  3.000
 EJH  O4   C4   C5   125.08  3.000
 EJH  N3   C4   C5   114.29  3.000
 EJH  C7   C5   C6   123.33  3.000
 EJH  C7   C5   C4   118.90  3.000
 EJH  C6   C5   C4   117.77  3.000
 EJH  H1   C6   N1   114.41  3.000
 EJH  H1   C6   C5   121.07  3.000
 EJH  N1   C6   C5   124.51  3.000
 EJH  H4   C7   H3   107.93  3.000
 EJH  H4   C7   H2   107.87  3.000
 EJH  H3   C7   H2   107.21  3.000
 EJH  H4   C7   C5   110.96  3.000
 EJH  H3   C7   C5   111.38  3.000
 EJH  H2   C7   C5   111.32  3.000
 EJH  C1'  N1   C6   119.38  3.000
 EJH  C6   N1   C2   120.99  3.000
 EJH  C1'  N1   C2   119.60  3.000
 EJH  H5   N3   C4   116.65  3.000
 EJH  H5   N3   C2   115.03  3.000
 EJH  C4   N3   C2   128.31  3.000
 EJH  O5'  PA   O3A   93.53  3.000
 EJH  O3A  PA   O2A  111.70  3.000
 EJH  O5'  PA   O2A  108.79  3.000
 EJH  O2A  PA   O1A  119.64  3.000
 EJH  O3A  PA   O1A  111.48  3.000
 EJH  O5'  PA   O1A  108.44  3.000
 EJH  C3B  PB   O3A   98.58  3.000
 EJH  C3B  PB   O1B  111.56  3.000
 EJH  O3A  PB   O1B  107.32  3.000
 EJH  C3B  PB   O2B  109.10  3.000
 EJH  O1B  PB   O2B  120.37  3.000
 EJH  O3A  PB   O2B  107.57  3.000
 EJH  O3G  PG   C3B  106.14  3.000
 EJH  O3G  PG   O2G  113.95  3.000
 EJH  C3B  PG   O2G  103.59  3.000
 EJH  O2G  PG   O1G  114.04  3.000
 EJH  O3G  PG   O1G  114.70  3.000
 EJH  C3B  PG   O1G  102.69  3.000
 EJH  H6   C1'  O4'  110.27  3.000
 EJH  H6   C1'  C2'  109.73  3.000
 EJH  O4'  C1'  C2'  107.57  3.000
 EJH  H6   C1'  N1   104.28  3.000
 EJH  O4'  C1'  N1   108.78  3.000
 EJH  C2'  C1'  N1   116.15  3.000
 EJH  H10  C2'  H9   107.46  3.000
 EJH  H10  C2'  C3'  113.70  3.000
 EJH  H9   C2'  C3'  108.97  3.000
 EJH  H10  C2'  C1'  113.12  3.000
 EJH  H9   C2'  C1'  108.60  3.000
 EJH  C3'  C2'  C1'  104.86  3.000
 EJH  H13  C3'  C4'  109.77  3.000
 EJH  H13  C3'  O3'  110.54  3.000
 EJH  C4'  C3'  O3'  108.90  3.000
 EJH  H13  C3'  C2'  109.85  3.000
 EJH  C4'  C3'  C2'  102.66  3.000
 EJH  O3'  C3'  C2'  114.78  3.000
 EJH  H14  O3'  C3'  108.24  3.000
 EJH  PB   O3A  PA   124.76  3.000
 EJH  H15  C3B  CL1  104.88  3.000
 EJH  H15  C3B  PG   108.69  3.000
 EJH  CL1  C3B  PG   108.63  3.000
 EJH  H15  C3B  PB   107.55  3.000
 EJH  PG   C3B  PB   116.87  3.000
 EJH  CL1  C3B  PB   109.55  3.000
 EJH  H16  C4'  C5'  109.44  3.000
 EJH  H16  C4'  O4'  109.70  3.000
 EJH  C5'  C4'  O4'  109.70  3.000
 EJH  H16  C4'  C3'  108.40  3.000
 EJH  C5'  C4'  C3'  113.28  3.000
 EJH  O4'  C4'  C3'  106.24  3.000
 EJH  C4'  O4'  C1'  110.85  3.000
 EJH  H18  C5'  H17  107.46  3.000
 EJH  H18  C5'  O5'  111.21  3.000
 EJH  H17  C5'  O5'  111.94  3.000
 EJH  H18  C5'  C4'  109.13  3.000
 EJH  H17  C5'  C4'  107.43  3.000
 EJH  O5'  C5'  C4'  109.55  3.000
 EJH  C5'  O5'  PA   117.12  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
 EJH  CONST_01  C5   C4   N3   C2    0.00   0.0  0
 EJH  CONST_02  N1   C2   N3   C4    0.00   0.0  0
 EJH  CONST_03  N3   C2   N1   C6    0.00   0.0  0
 EJH  CONST_04  C1'  N1   C2   N3  180.00   0.0  0
 EJH  CONST_05  O4   C4   N3   C2  180.00   0.0  0
 EJH  CONST_06  O2   C2   N3   C4  180.00   0.0  0
 EJH  CONST_07  O2   C2   N1   C6  180.00   0.0  0
 EJH  CONST_08  C1'  N1   C2   O2    0.00   0.0  0
 EJH  CONST_09  H5   N3   C4   C5  180.00   0.0  0
 EJH  Var_01    H2   C7   C5   C4  -59.24  30.0  3
 EJH  Var_02    C4'  C5'  O5'  PA  158.48  30.0  2
 EJH  Var_03    O2B  PB   O3A  PA   31.83  30.0  3
 EJH  Var_04    O5'  PA   O3A  PB  160.53  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
 EJH  chir_03  C1'  C2'  N1   O4'  positiv
 EJH  chir_04  C3'  O3'  C4'  C2'  positiv
 EJH  chir_05  C3B  PB   CL1  PG   negativ
 EJH  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
 EJH  plan-1  C2   0.020
 EJH  plan-1  C4   0.020
 EJH  plan-1  C5   0.020
 EJH  plan-1  C6   0.020
 EJH  plan-1  C7   0.020
 EJH  plan-1  O2   0.020
 EJH  plan-1  N1   0.020
 EJH  plan-1  N3   0.020
 EJH  plan-1  O4   0.020
 EJH  plan-1  C1'  0.020
 EJH  plan-1  H1   0.020
 EJH  plan-1  H5   0.020

