# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:40:39 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=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
 94T  94T  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate'  ligand  46  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_94T
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
 94T  C2   C  CR6    0   0.736  -4.4203   1.6233   0.5847
 94T  C4   C  CR6    0   0.570  -3.5185   3.1964  -1.1074
 94T  C5   C  CR16   0  -0.511  -2.5029   2.2128  -1.3931
 94T  C6   C  CR16   0   0.099  -2.4968   1.0536  -0.7175
 94T  N1   N  NR6    0  -0.565  -3.4158   0.7390   0.2438
 94T  O2   O  O      0  -0.476  -5.2576   1.3900   1.4305
 94T  N3   N  NR16   0  -0.734  -4.4012   2.8018  -0.1138
 94T  O4   O  O      0  -0.462  -3.6381   4.2802  -1.6471
 94T  C1'  C  CH1    0   0.201  -3.3566  -0.5583   0.9093
 94T  O4'  O  O2     0  -0.489  -2.0373  -0.8244   1.2797
 94T  C2'  C  CH1    0  -0.044  -3.7865  -1.7227   0.0177
 94T  O2'  O  OH1    0  -0.653  -5.1749  -1.8616   0.0527
 94T  C3'  C  CH1    0  -0.029  -3.0021  -2.8790   0.6458
 94T  O3'  O  OH1    0  -0.667  -3.6130  -3.3151   1.8310
 94T  C4'  C  CH1    0  -0.043  -1.6920  -2.1848   0.9902
 94T  C5'  C  CH2    0  -0.164  -0.6904  -2.2631  -0.1469
 94T  O5'  O  O2     0  -0.616   0.3808  -1.3980   0.1370
 94T  PCS  P  P      0   1.344   1.8075  -1.6899  -0.6391
 94T  OCT  O  OP    -1  -0.790   2.5015  -2.8266   0.0422
 94T  OCU  O  O      0  -0.803   1.5795  -1.7189  -2.1176
 94T  OCV  O  O2     0  -0.734   2.4680  -0.2642  -0.1742
 94T  PCW  P  P      0   1.340   3.6839   0.4814  -0.9901
 94T  OCX  O  OP    -1  -0.802   4.6851  -0.5303  -1.4531
 94T  OCY  O  O      0  -0.797   3.1278   1.4863  -1.9492
 94T  OCZ  O  O2     0  -0.621   4.2423   1.2545   0.3486
 94T  CBF  C  CH2    0  -0.128   5.2332   2.2522   0.1704
 94T  CBG  C  CH2    0  -0.462   5.7057   2.7331   1.5280
 94T  CBH  C  CH3    0  -0.673   6.7647   3.8195   1.4024
 94T  H1   H  HCR6   0   0.294  -1.7510   2.4164  -2.1393
 94T  H2   H  HCR6   0   0.330  -1.7314   0.3137  -0.9003
 94T  H3   H  HNR6   0   0.427  -5.1322   3.4580   0.1325
 94T  H4   H  HCH1   0   0.273  -4.0089  -0.4928   1.7823
 94T  H5   H  HCH1   0   0.251  -3.4255  -1.5599  -1.0063
 94T  H6   H  HOH1   0   0.469  -5.4555  -2.3742  -0.7119
 94T  H7   H  HCH1   0   0.253  -2.8534  -3.7029  -0.0648
 94T  H8   H  HOH1   0   0.450  -4.5523  -3.4401   1.6518
 94T  H9   H  HCH1   0   0.263  -1.2424  -2.6142   1.8902
 94T  H10  H  HCH2   0   0.237  -0.3737  -3.3101  -0.2308
 94T  H11  H  HCH2   0   0.208  -1.1572  -1.9974  -1.1043
 94T  H14  H  HCH2   0   0.196   6.0878   1.8588  -0.3952
 94T  H15  H  HCH2   0   0.200   4.8324   3.0969  -0.4022
 94T  H16  H  HCH2   0   0.222   4.8510   3.1142   2.0939
 94T  H17  H  HCH2   0   0.222   6.1075   1.8878   2.0930
 94T  H18  H  HCH3   0   0.234   7.0959   4.1601   2.3831
 94T  H19  H  HCH3   0   0.221   7.6437   3.4597   0.8649
 94T  H20  H  HCH3   0   0.221   6.3832   4.6886   0.8638

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
 94T  OCU  PCS  deloc   1.496  0.020  1.496
 94T  CBH  CBG  single  1.522  0.020  1.522
 94T  O5'  PCS  single  1.650  0.020  1.650
 94T  O5'  C5'  single  1.406  0.020  1.406
 94T  PCS  OCT  deloc   1.496  0.020  1.496
 94T  PCS  OCV  single  1.639  0.020  1.639
 94T  CBG  CBF  single  1.516  0.020  1.516
 94T  C4'  O4'  single  1.433  0.020  1.433
 94T  C4'  C5'  single  1.517  0.020  1.517
 94T  C4'  C3'  single  1.522  0.020  1.522
 94T  O4'  C1'  single  1.396  0.020  1.396
 94T  O2   C2   double  1.213  0.020  1.213
 94T  O3'  C3'  single  1.403  0.020  1.403
 94T  C1'  N1   single  1.459  0.020  1.459
 94T  C1'  C2'  single  1.528  0.020  1.528
 94T  C2   N1   single  1.381  0.020  1.381
 94T  C2   N3   single  1.370  0.020  1.370
 94T  C3'  C2'  single  1.532  0.020  1.532
 94T  OCV  PCW  single  1.643  0.020  1.643
 94T  CBF  OCZ  single  1.417  0.020  1.417
 94T  N1   C6   single  1.367  0.020  1.367
 94T  N3   C4   single  1.386  0.020  1.386
 94T  OCY  PCW  deloc   1.496  0.020  1.496
 94T  OCZ  PCW  single  1.644  0.020  1.644
 94T  C2'  O2'  single  1.396  0.020  1.396
 94T  C6   C5   double  1.342  0.020  1.342
 94T  C4   C5   single  1.442  0.020  1.442
 94T  C4   O4   double  1.217  0.020  1.217
 94T  PCW  OCX  deloc   1.497  0.020  1.497
 94T  C5   H1   single  0.930  0.020  1.080
 94T  C6   H2   single  0.930  0.020  1.080
 94T  N3   H3   single  0.860  0.020  1.020
 94T  C1'  H4   single  0.970  0.020  1.090
 94T  C2'  H5   single  0.970  0.020  1.090
 94T  O2'  H6   single  0.850  0.020  0.980
 94T  C3'  H7   single  0.970  0.020  1.090
 94T  O3'  H8   single  0.850  0.020  0.980
 94T  C4'  H9   single  0.970  0.020  1.090
 94T  C5'  H10  single  0.970  0.020  1.090
 94T  C5'  H11  single  0.970  0.020  1.090
 94T  CBF  H14  single  0.970  0.020  1.090
 94T  CBF  H15  single  0.970  0.020  1.090
 94T  CBG  H16  single  0.970  0.020  1.090
 94T  CBG  H17  single  0.970  0.020  1.090
 94T  CBH  H18  single  0.970  0.020  1.090
 94T  CBH  H19  single  0.970  0.020  1.090
 94T  CBH  H20  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
 94T  N3   C2   O2   122.05  3.000
 94T  N3   C2   N1   114.50  3.000
 94T  O2   C2   N1   123.45  3.000
 94T  O4   C4   N3   120.59  3.000
 94T  O4   C4   C5   126.07  3.000
 94T  N3   C4   C5   113.34  3.000
 94T  H1   C5   C6   120.54  3.000
 94T  H1   C5   C4   119.94  3.000
 94T  C6   C5   C4   119.51  3.000
 94T  H2   C6   N1   115.97  3.000
 94T  H2   C6   C5   120.65  3.000
 94T  N1   C6   C5   123.37  3.000
 94T  C1'  N1   C6   119.88  3.000
 94T  C6   N1   C2   121.02  3.000
 94T  C1'  N1   C2   119.08  3.000
 94T  H3   N3   C4   116.71  3.000
 94T  H3   N3   C2   115.04  3.000
 94T  C4   N3   C2   128.25  3.000
 94T  H4   C1'  C2'  110.13  3.000
 94T  H4   C1'  O4'  111.35  3.000
 94T  C2'  C1'  O4'  105.98  3.000
 94T  H4   C1'  N1   106.69  3.000
 94T  C2'  C1'  N1   113.57  3.000
 94T  O4'  C1'  N1   109.19  3.000
 94T  C4'  O4'  C1'  110.80  3.000
 94T  H5   C2'  C3'  109.03  3.000
 94T  H5   C2'  O2'  111.42  3.000
 94T  C3'  C2'  O2'  115.09  3.000
 94T  H5   C2'  C1'  109.79  3.000
 94T  O2'  C2'  C1'  109.93  3.000
 94T  C3'  C2'  C1'  101.07  3.000
 94T  H6   O2'  C2'  108.85  3.000
 94T  H7   C3'  C4'  111.84  3.000
 94T  H7   C3'  O3'  111.86  3.000
 94T  C4'  C3'  O3'  108.99  3.000
 94T  H7   C3'  C2'  111.74  3.000
 94T  O3'  C3'  C2'  110.98  3.000
 94T  C4'  C3'  C2'  100.91  3.000
 94T  H8   O3'  C3'  107.91  3.000
 94T  H9   C4'  C5'  108.97  3.000
 94T  H9   C4'  C3'  111.15  3.000
 94T  C5'  C4'  C3'  112.03  3.000
 94T  H9   C4'  O4'  107.79  3.000
 94T  C3'  C4'  O4'  105.74  3.000
 94T  C5'  C4'  O4'  111.06  3.000
 94T  H11  C5'  H10  106.68  3.000
 94T  H11  C5'  O5'  110.56  3.000
 94T  H10  C5'  O5'  112.50  3.000
 94T  H11  C5'  C4'  111.13  3.000
 94T  H10  C5'  C4'  107.28  3.000
 94T  O5'  C5'  C4'  108.65  3.000
 94T  PCS  O5'  C5'  117.06  3.000
 94T  OCV  PCS  OCU  111.02  3.000
 94T  OCV  PCS  OCT  110.18  3.000
 94T  OCU  PCS  OCT  120.40  3.000
 94T  OCV  PCS  O5'   93.50  3.000
 94T  OCT  PCS  O5'  108.74  3.000
 94T  OCU  PCS  O5'  109.66  3.000
 94T  PCW  OCV  PCS  123.51  3.000
 94T  OCZ  PCW  OCY  109.41  3.000
 94T  OCZ  PCW  OCX  110.03  3.000
 94T  OCY  PCW  OCX  120.28  3.000
 94T  OCX  PCW  OCV  109.99  3.000
 94T  OCZ  PCW  OCV   93.46  3.000
 94T  OCY  PCW  OCV  110.36  3.000
 94T  CBF  OCZ  PCW  117.79  3.000
 94T  H15  CBF  H14  106.95  3.000
 94T  H15  CBF  CBG  109.71  3.000
 94T  H14  CBF  CBG  109.42  3.000
 94T  H15  CBF  OCZ  110.63  3.000
 94T  H14  CBF  OCZ  110.90  3.000
 94T  CBG  CBF  OCZ  109.19  3.000
 94T  H17  CBG  H16  106.81  3.000
 94T  H17  CBG  CBH  109.80  3.000
 94T  H16  CBG  CBH  109.74  3.000
 94T  H17  CBG  CBF  109.40  3.000
 94T  H16  CBG  CBF  109.29  3.000
 94T  CBH  CBG  CBF  111.68  3.000
 94T  H20  CBH  H19  107.52  3.000
 94T  H20  CBH  H18  107.55  3.000
 94T  H19  CBH  H18  107.54  3.000
 94T  H20  CBH  CBG  111.46  3.000
 94T  H19  CBH  CBG  111.45  3.000
 94T  H18  CBH  CBG  111.12  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
 94T  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 94T  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 94T  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 94T  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 94T  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 94T  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 94T  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 94T  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 94T  CONST_09  H3   N3   C4   C5    180.00   0.0  0
 94T  Var_01    OCU  PCS  O5'  C5'    55.03  30.0  3
 94T  Var_02    OCY  PCW  OCV  PCS    94.44  30.0  3
 94T  Var_03    CBG  CBF  OCZ  PCW  -174.28  30.0  1
 94T  Var_04    CBH  CBG  CBF  OCZ  -179.43  30.0  1
 94T  Var_05    H10  C5'  O5'  PCS    40.19  30.0  3
 94T  Var_06    H18  CBH  CBG  CBF   179.86  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
 94T  chir_01  C1'  O4'  N1   C2'  negativ
 94T  chir_02  C2'  O2'  C1'  C3'  negativ
 94T  chir_03  C3'  O3'  C4'  C2'  positiv
 94T  chir_04  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
 94T  plan-1  C2   0.020
 94T  plan-1  C4   0.020
 94T  plan-1  C5   0.020
 94T  plan-1  C6   0.020
 94T  plan-1  N1   0.020
 94T  plan-1  O2   0.020
 94T  plan-1  N3   0.020
 94T  plan-1  O4   0.020
 94T  plan-1  C1'  0.020
 94T  plan-1  H1   0.020
 94T  plan-1  H2   0.020
 94T  plan-1  H3   0.020

