# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:36:10 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  48  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 PERFECT
;

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   0.725  -1.1733   1.9601   0.9623
 94T  C4   C  CR6   0   0.569  -0.4301   2.9667  -1.1803
 94T  C5   C  CR16  0  -0.340  -0.6588   1.6830  -1.7947
 94T  C6   C  CR16  0  -0.004  -1.1166   0.6685  -1.0493
 94T  N1   N  NR6   0  -0.499  -1.3881   0.7723   0.2872
 94T  O2   O  O     0  -0.562  -1.3716   2.1002   2.1499
 94T  N3   N  NR16  0  -0.666  -0.7301   2.9889   0.1741
 94T  O4   O  O     0  -0.596  -0.0124   3.9648  -1.7354
 94T  C1'  C  CR15  0   0.145  -1.7421  -0.4163   1.0369
 94T  O4'  O  O     0  -0.492  -0.7067  -1.3556   0.9023
 94T  C2'  C  CR15  0   0.062  -2.9985  -1.1387   0.5588
 94T  O2'  O  OH1   0  -0.660  -4.1343  -0.5159   1.0755
 94T  C3'  C  CR15  0  -0.077  -2.7380  -2.5527   1.0997
 94T  O3'  O  OH1   0  -0.666  -3.0247  -2.6294   2.4694
 94T  C4'  C  CR15  0   0.015  -1.2275  -2.6828   0.9104
 94T  C5'  C  CH2   0  -0.200  -0.8913  -3.3786  -0.3945
 94T  O5'  O  O2    0  -0.601   0.5140  -3.3011  -0.6707
 94T  PCS  P  P     0   1.476   1.1066  -2.2492  -1.7020
 94T  OCT  O  OH1   0  -0.724   2.3448  -2.9876  -2.3576
 94T  OCU  O  O     0  -0.712   0.1804  -1.7073  -2.7073
 94T  OCV  O  O2    0  -0.610   1.7566  -1.1499  -0.7052
 94T  PCW  P  P     0   1.482   2.7051   0.1057  -1.0696
 94T  OCX  O  OH1   0  -0.625   4.1725  -0.3636  -0.6725
 94T  OCY  O  O     0  -0.823   2.6654   0.5496  -2.4697
 94T  OCZ  O  O2    0  -0.515   2.1961   1.0971   0.0575
 94T  CBF  C  CH2   0  -0.155   2.8900   2.3454   0.2764
 94T  CBG  C  CH2   0  -0.461   2.6387   2.8065   1.6939
 94T  CBH  C  CH3   0  -0.658   3.4001   4.0934   1.9800
 94T  H1   H  HCR6  0   0.326  -0.4545   1.5446  -2.8444
 94T  H2   H  HCR6  0   0.339  -1.2899  -0.2965  -1.4977
 94T  H3   H  HNR6  0   0.462  -0.6057   3.8727   0.6526
 94T  H4   H  HCR5  0   0.272  -1.8692  -0.1057   2.0759
 94T  H5   H  HCR5  0   0.259  -3.0258  -1.1730  -0.5379
 94T  H6   H  HOH1  0   0.460  -4.8953  -0.7597   0.5391
 94T  H7   H  HCR5  0   0.283  -3.2870  -3.3111   0.5262
 94T  H8   H  HOH1  0   0.425  -3.9148  -2.2857   2.6089
 94T  H9   H  HCR5  0   0.250  -0.7813  -3.2379   1.7409
 94T  H10  H  HCH2  0   0.237  -1.1332  -4.4378  -0.3144
 94T  H11  H  HCH2  0   0.239  -1.4650  -2.9722  -1.2315
 94T  H12  H  HOH1  0   0.509   2.9692  -3.4329  -1.7683
 94T  H13  H  HOH1  0   0.541   4.2926  -0.7051   0.2242
 94T  H14  H  HCH2  0   0.193   3.9642   2.2145   0.1168
 94T  H15  H  HCH2  0   0.243   2.5317   3.0805  -0.4475
 94T  H16  H  HCH2  0   0.247   1.5697   2.9631   1.8509
 94T  H17  H  HCH2  0   0.233   2.9522   2.0234   2.3878
 94T  H18  H  HCH3  0   0.209   3.1956   4.4474   2.9896
 94T  H19  H  HCH3  0   0.239   4.4773   3.9440   1.8932
 94T  H20  H  HCH3  0   0.202   3.1196   4.8888   1.2875

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  double  1.470  0.020  1.470
 94T  CBH  CBG  single  1.522  0.020  1.522
 94T  O5'  PCS  single  1.588  0.020  1.588
 94T  O5'  C5'  single  1.434  0.020  1.434
 94T  PCS  OCT  single  1.584  0.020  1.584
 94T  PCS  OCV  single  1.620  0.020  1.620
 94T  CBG  CBF  single  1.512  0.020  1.512
 94T  C4'  O4'  single  1.426  0.020  1.426
 94T  C4'  C5'  single  1.517  0.020  1.517
 94T  C4'  C3'  single  1.528  0.020  1.528
 94T  O4'  C1'  single  1.404  0.020  1.404
 94T  O2   C2   double  1.212  0.020  1.212
 94T  O3'  C3'  single  1.401  0.020  1.401
 94T  C1'  N1   single  1.449  0.020  1.449
 94T  C1'  C2'  single  1.526  0.020  1.526
 94T  C2   N1   single  1.383  0.020  1.383
 94T  C2   N3   single  1.370  0.020  1.370
 94T  C3'  C2'  single  1.536  0.020  1.536
 94T  OCV  PCW  single  1.615  0.020  1.615
 94T  CBF  OCZ  single  1.445  0.020  1.445
 94T  N1   C6   single  1.368  0.020  1.368
 94T  N3   C4   single  1.387  0.020  1.387
 94T  OCY  PCW  double  1.469  0.020  1.469
 94T  OCZ  PCW  single  1.585  0.020  1.585
 94T  C2'  O2'  single  1.395  0.020  1.395
 94T  C6   C5   double  1.340  0.020  1.340
 94T  C4   C5   single  1.441  0.020  1.441
 94T  C4   O4   double  1.216  0.020  1.216
 94T  PCW  OCX  single  1.591  0.020  1.591
 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  OCT  H12  single  0.850  0.020  0.980
 94T  OCX  H13  single  0.850  0.020  0.980
 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   122.00  3.000
 94T  N3   C2   N1   114.48  3.000
 94T  O2   C2   N1   123.51  3.000
 94T  O4   C4   N3   120.44  3.000
 94T  O4   C4   C5   126.22  3.000
 94T  N3   C4   C5   113.33  3.000
 94T  H1   C5   C6   120.61  3.000
 94T  H1   C5   C4   119.95  3.000
 94T  C6   C5   C4   119.44  3.000
 94T  H2   C6   N1   116.26  3.000
 94T  H2   C6   C5   120.10  3.000
 94T  N1   C6   C5   123.65  3.000
 94T  C1'  N1   C6   119.46  3.000
 94T  C6   N1   C2   120.75  3.000
 94T  C1'  N1   C2   119.33  3.000
 94T  H3   N3   C4   116.66  3.000
 94T  H3   N3   C2   115.04  3.000
 94T  C4   N3   C2   128.30  3.000
 94T  H4   C1'  C2'  109.69  3.000
 94T  H4   C1'  O4'  111.55  3.000
 94T  C2'  C1'  O4'  105.09  3.000
 94T  H4   C1'  N1   106.70  3.000
 94T  C2'  C1'  N1   115.29  3.000
 94T  O4'  C1'  N1   108.59  3.000
 94T  C4'  O4'  C1'  110.65  3.000
 94T  H5   C2'  C3'  109.11  3.000
 94T  H5   C2'  O2'  111.34  3.000
 94T  C3'  C2'  O2'  114.76  3.000
 94T  H5   C2'  C1'  110.38  3.000
 94T  O2'  C2'  C1'  110.06  3.000
 94T  C3'  C2'  C1'  100.70  3.000
 94T  H6   O2'  C2'  108.92  3.000
 94T  H7   C3'  C4'  111.77  3.000
 94T  H7   C3'  O3'  111.74  3.000
 94T  C4'  C3'  O3'  108.58  3.000
 94T  H7   C3'  C2'  111.53  3.000
 94T  O3'  C3'  C2'  111.09  3.000
 94T  C4'  C3'  C2'  101.68  3.000
 94T  H8   O3'  C3'  108.10  3.000
 94T  H9   C4'  C5'  109.26  3.000
 94T  H9   C4'  C3'  110.63  3.000
 94T  C5'  C4'  C3'  111.40  3.000
 94T  H9   C4'  O4'  109.13  3.000
 94T  C3'  C4'  O4'  106.41  3.000
 94T  C5'  C4'  O4'  109.95  3.000
 94T  H11  C5'  H10  107.53  3.000
 94T  H11  C5'  O5'  110.29  3.000
 94T  H10  C5'  O5'  106.51  3.000
 94T  H11  C5'  C4'  111.84  3.000
 94T  H10  C5'  C4'  109.49  3.000
 94T  O5'  C5'  C4'  110.98  3.000
 94T  PCS  O5'  C5'  121.77  3.000
 94T  OCV  PCS  OCU  115.05  3.000
 94T  OCV  PCS  OCT  104.91  3.000
 94T  OCU  PCS  OCT  112.41  3.000
 94T  OCV  PCS  O5'  101.52  3.000
 94T  OCT  PCS  O5'  104.58  3.000
 94T  OCU  PCS  O5'  116.94  3.000
 94T  H12  OCT  PCS  117.85  3.000
 94T  PCW  OCV  PCS  128.63  3.000
 94T  OCZ  PCW  OCY  118.69  3.000
 94T  OCZ  PCW  OCX  107.65  3.000
 94T  OCY  PCW  OCX  110.60  3.000
 94T  OCX  PCW  OCV  104.83  3.000
 94T  OCZ  PCW  OCV   97.89  3.000
 94T  OCY  PCW  OCV  115.72  3.000
 94T  H13  OCX  PCW  116.75  3.000
 94T  CBF  OCZ  PCW  119.60  3.000
 94T  H15  CBF  H14  107.82  3.000
 94T  H15  CBF  CBG  111.20  3.000
 94T  H14  CBF  CBG  109.67  3.000
 94T  H15  CBF  OCZ  108.88  3.000
 94T  H14  CBF  OCZ  110.25  3.000
 94T  CBG  CBF  OCZ  109.01  3.000
 94T  H17  CBG  H16  107.01  3.000
 94T  H17  CBG  CBH  110.07  3.000
 94T  H16  CBG  CBH  109.96  3.000
 94T  H17  CBG  CBF  109.23  3.000
 94T  H16  CBG  CBF  109.96  3.000
 94T  CBH  CBG  CBF  110.54  3.000
 94T  H20  CBH  H19  107.64  3.000
 94T  H20  CBH  H18  107.64  3.000
 94T  H19  CBH  H18  107.68  3.000
 94T  H20  CBH  CBG  111.61  3.000
 94T  H19  CBH  CBG  111.29  3.000
 94T  H18  CBH  CBG  110.79  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'   -21.70  30.0  3
 94T  Var_02    OCY  PCW  OCV  PCS    19.59  30.0  3
 94T  Var_03    CBG  CBF  OCZ  PCW  -155.84  30.0  2
 94T  Var_04    CBH  CBG  CBF  OCZ   177.76  30.0  2
 94T  Var_05    H10  C5'  O5'  PCS   140.07  30.0  3
 94T  Var_06    H18  CBH  CBG  CBF   178.10  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
 94T  chir_05  PCS  O5'  OCT  OCV  both
 94T  chir_06  PCW  OCY  OCZ  OCX  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
 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

