# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 21:22:29 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: trihydrido{5'-O-[(1R)-1,3,3-trihydroxy-3-oxidodiphosphoxanyl-kappaP~1~]thymidine}boron
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [BH3-][P@@+](O)(OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C)C(=O)NC2=O)O[P](O)(O)=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
 TBD  TBD  trihydrido{5'-O-[(1R)-1,3,3-trihydroxy-3-oxidodiphosphoxanyl-kappaP~1~]thymidine}boron  ligand  44  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TBD
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
 TBD  PB    P  P      0   1.482  -4.8710  -1.1789   0.4745
 TBD  O1B   O  OH1    0  -0.721  -5.9646  -0.0426   0.6457
 TBD  O2B   O  OH1    0  -0.717  -4.7258  -1.9540   1.8507
 TBD  O3B   O  O      0  -0.686  -5.0896  -1.9457  -0.7589
 TBD  O3A   O  OC2    0  -0.676  -3.4381  -0.4184   0.5536
 TBD  PA    P  P      1   1.298  -2.6078   0.2509  -0.6694
 TBD  B1A   B  B     -1  -0.694  -3.5630   1.4318  -1.7865
 TBD  O2A   O  OP     0  -0.717  -1.9730  -0.9490  -1.4981
 TBD  O5'   O  OC2    0  -0.571  -1.4622   0.8819   0.2425
 TBD  C5'   C  CH2    0  -0.193  -0.4917   1.7714  -0.3380
 TBD  C4'   C  CH1    0   0.020   0.5531   2.0792   0.7022
 TBD  O4'   O  O2     0  -0.487   1.2619   0.9023   1.0330
 TBD  C1'   C  CH1    0   0.213   2.6247   1.1604   1.2239
 TBD  N1    N  NR6    0  -0.566   3.4126   0.1672   0.4966
 TBD  C6    C  CR16   0   0.060   4.1707  -0.7313   1.2028
 TBD  C2    C  CR6    0   0.746   3.3478   0.1096  -0.8758
 TBD  O2    O  O      0  -0.474   2.6823   0.8695  -1.5483
 TBD  N3    N  NR16   0  -0.733   4.1075  -0.8822  -1.4393
 TBD  C4    C  CR6    0   0.559   4.9087  -1.8114  -0.8002
 TBD  O4    O  O      0  -0.454   5.5327  -2.6368  -1.4415
 TBD  C5    C  CR6    0  -0.185   4.9162  -1.6998   0.6444
 TBD  C5A   C  CH3    0  -0.707   5.7409  -2.6568   1.4411
 TBD  C2'   C  CH2    0  -0.559   2.8747   2.6238   0.8504
 TBD  C3'   C  CH1    0   0.019   1.5773   3.0989   0.1947
 TBD  O3'   O  OH1    0  -0.666   1.1598   4.3848   0.5741
 TBD  H1BO  H  HOH1   0   0.505  -5.9261   0.4768   1.4611
 TBD  H2BO  H  HOH1   0   0.512  -5.4430  -2.5762   2.0372
 TBD  H1B   H  H      0   0.045  -3.9926   2.2885  -1.0526
 TBD  H2B   H  H      0   0.042  -2.7540   1.8653  -2.5736
 TBD  H3B   H  H      0   0.045  -4.4322   0.7874  -2.3206
 TBD  H2AO  H  H      0   0.503  -1.4492  -1.6001  -1.0067
 TBD  H5'1  H  HCH2   0   0.253  -0.0238   1.3118  -1.2119
 TBD  H5'2  H  HCH2   0   0.263  -0.9789   2.6993  -0.6465
 TBD  H4'C  H  HCH1   0   0.246   0.0683   2.4863   1.6005
 TBD  H1'C  H  HCH1   0   0.259   2.8881   0.9965   2.2708
 TBD  HC6   H  HCR6   0   0.317   4.1382  -0.6076   2.2769
 TBD  HN3   H  HNR6   0   0.425   4.0690  -0.9325  -2.4502
 TBD  HCA1  H  HCH3   0   0.247   5.4566  -3.6903   1.2398
 TBD  HCA2  H  HCH3   0   0.248   6.8014  -2.5614   1.2037
 TBD  HCA3  H  HCH3   0   0.247   5.6199  -2.4787   2.5084
 TBD  H2'1  H  HCH2   0   0.271   3.0374   3.1910   1.7683
 TBD  H2'2  H  HCH2   0   0.279   3.7521   2.7577   0.2203
 TBD  H3'C  H  HCH1   0   0.241   1.6672   3.0290  -0.8925
 TBD  H3'O  H  HOH1   0   0.459   1.6231   5.0261   0.0280

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
 TBD  PB   O1B   single  1.586  0.020  1.586
 TBD  PB   O2B   single  1.586  0.020  1.586
 TBD  PB   O3B   double  1.469  0.020  1.469
 TBD  PB   O3A   single  1.624  0.020  1.624
 TBD  O1B  H1BO  single  0.832  0.020  0.971
 TBD  O2B  H2BO  single  0.832  0.020  0.971
 TBD  O3A  PA    single  1.623  0.020  1.623
 TBD  PA   B1A   single  1.885  0.020  1.885
 TBD  PA   O2A   single  1.590  0.020  1.590
 TBD  PA   O5'   single  1.594  0.020  1.594
 TBD  B1A  H1B   single  1.040  0.020  1.214
 TBD  B1A  H2B   single  1.040  0.020  1.214
 TBD  B1A  H3B   single  1.040  0.020  1.214
 TBD  O2A  H2AO  single  0.850  0.020  0.980
 TBD  O5'  C5'   single  1.439  0.020  1.439
 TBD  C5'  C4'   single  1.506  0.020  1.506
 TBD  C5'  H5'1  single  0.970  0.020  1.090
 TBD  C5'  H5'2  single  0.970  0.020  1.090
 TBD  C4'  O4'   single  1.413  0.020  1.413
 TBD  C4'  C3'   single  1.532  0.020  1.532
 TBD  C4'  H4'C  single  0.970  0.020  1.090
 TBD  O4'  C1'   single  1.400  0.020  1.400
 TBD  C1'  N1    single  1.462  0.020  1.462
 TBD  C1'  C2'   single  1.531  0.020  1.531
 TBD  C1'  H1'C  single  0.970  0.020  1.090
 TBD  N1   C6    single  1.371  0.020  1.371
 TBD  N1   C2    single  1.375  0.020  1.375
 TBD  C6   C5    double  1.344  0.020  1.344
 TBD  C6   HC6   single  0.930  0.020  1.080
 TBD  C2   O2    double  1.214  0.020  1.214
 TBD  C2   N3    single  1.370  0.020  1.370
 TBD  N3   C4    single  1.383  0.020  1.383
 TBD  N3   HN3   single  0.860  0.020  1.020
 TBD  C4   O4    double  1.217  0.020  1.217
 TBD  C4   C5    single  1.449  0.020  1.449
 TBD  C5   C5A   single  1.494  0.020  1.494
 TBD  C5A  HCA1  single  0.970  0.020  1.090
 TBD  C5A  HCA2  single  0.970  0.020  1.090
 TBD  C5A  HCA3  single  0.970  0.020  1.090
 TBD  C2'  C3'   single  1.529  0.020  1.529
 TBD  C2'  H2'1  single  0.970  0.020  1.090
 TBD  C2'  H2'2  single  0.970  0.020  1.090
 TBD  C3'  O3'   single  1.404  0.020  1.404
 TBD  C3'  H3'C  single  0.970  0.020  1.090
 TBD  O3'  H3'O  single  0.850  0.020  0.980

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
 TBD  O3A   PB   O3B   114.62  3.000
 TBD  O3A   PB   O2B    96.07  3.000
 TBD  O3B   PB   O2B   119.15  3.000
 TBD  O3A   PB   O1B   105.52  3.000
 TBD  O3B   PB   O1B   111.22  3.000
 TBD  O2B   PB   O1B   108.64  3.000
 TBD  H1BO  O1B  PB    116.62  3.000
 TBD  H2BO  O2B  PB    114.43  3.000
 TBD  PA    O3A  PB    127.43  3.000
 TBD  O5'   PA   O2A   108.05  3.000
 TBD  O5'   PA   B1A   117.06  3.000
 TBD  O2A   PA   B1A   111.47  3.000
 TBD  O5'   PA   O3A    95.73  3.000
 TBD  O2A   PA   O3A   106.61  3.000
 TBD  B1A   PA   O3A   116.47  3.000
 TBD  H3B   B1A  H2B   112.66  3.000
 TBD  H3B   B1A  H1B   113.06  3.000
 TBD  H2B   B1A  H1B   112.30  3.000
 TBD  H3B   B1A  PA    107.02  3.000
 TBD  H2B   B1A  PA    105.74  3.000
 TBD  H1B   B1A  PA    105.34  3.000
 TBD  H2AO  O2A  PA    117.27  3.000
 TBD  C5'   O5'  PA    119.91  3.000
 TBD  H5'2  C5'  H5'1  108.81  3.000
 TBD  H5'2  C5'  C4'   109.32  3.000
 TBD  H5'1  C5'  C4'   109.95  3.000
 TBD  H5'2  C5'  O5'   109.77  3.000
 TBD  H5'1  C5'  O5'   110.58  3.000
 TBD  C4'   C5'  O5'   108.40  3.000
 TBD  H4'C  C4'  C3'   108.62  3.000
 TBD  H4'C  C4'  O4'   109.78  3.000
 TBD  C3'   C4'  O4'   107.25  3.000
 TBD  H4'C  C4'  C5'   109.53  3.000
 TBD  C3'   C4'  C5'   111.78  3.000
 TBD  O4'   C4'  C5'   109.84  3.000
 TBD  C1'   O4'  C4'   111.51  3.000
 TBD  H1'C  C1'  C2'   109.76  3.000
 TBD  H1'C  C1'  N1    104.19  3.000
 TBD  C2'   C1'  N1    116.11  3.000
 TBD  H1'C  C1'  O4'   109.75  3.000
 TBD  C2'   C1'  O4'   107.57  3.000
 TBD  N1    C1'  O4'   109.36  3.000
 TBD  C2    N1   C6    120.83  3.000
 TBD  C2    N1   C1'   119.98  3.000
 TBD  C6    N1   C1'   119.14  3.000
 TBD  HC6   C6   C5    120.78  3.000
 TBD  HC6   C6   N1    114.82  3.000
 TBD  C5    C6   N1    124.40  3.000
 TBD  N3    C2   O2    121.96  3.000
 TBD  N3    C2   N1    114.49  3.000
 TBD  O2    C2   N1    123.55  3.000
 TBD  HN3   N3   C4    116.72  3.000
 TBD  HN3   N3   C2    115.17  3.000
 TBD  C4    N3   C2    128.11  3.000
 TBD  C5    C4   O4    125.09  3.000
 TBD  C5    C4   N3    114.32  3.000
 TBD  O4    C4   N3    120.59  3.000
 TBD  C5A   C5   C4    119.04  3.000
 TBD  C5A   C5   C6    123.13  3.000
 TBD  C4    C5   C6    117.84  3.000
 TBD  HCA3  C5A  HCA2  107.88  3.000
 TBD  HCA3  C5A  HCA1  107.88  3.000
 TBD  HCA2  C5A  HCA1  107.22  3.000
 TBD  HCA3  C5A  C5    110.90  3.000
 TBD  HCA2  C5A  C5    111.39  3.000
 TBD  HCA1  C5A  C5    111.40  3.000
 TBD  H2'2  C2'  H2'1  107.63  3.000
 TBD  H2'2  C2'  C3'   113.42  3.000
 TBD  H2'1  C2'  C3'   109.01  3.000
 TBD  H2'2  C2'  C1'   112.98  3.000
 TBD  H2'1  C2'  C1'   108.42  3.000
 TBD  C3'   C2'  C1'   105.25  3.000
 TBD  H3'C  C3'  O3'   110.59  3.000
 TBD  H3'C  C3'  C2'   109.68  3.000
 TBD  O3'   C3'  C2'   114.89  3.000
 TBD  H3'C  C3'  C4'   110.00  3.000
 TBD  O3'   C3'  C4'   108.74  3.000
 TBD  C2'   C3'  C4'   102.62  3.000
 TBD  H3'O  O3'  C3'   108.30  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
 TBD  CONST_01  N3    C2   N1   C1'   180.00   0.0  0
 TBD  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 TBD  CONST_03  N3    C2   N1   C6      0.00   0.0  0
 TBD  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 TBD  CONST_05  O2    C2   N1   C1'     0.00   0.0  0
 TBD  CONST_06  O2    C2   N1   C6    180.00   0.0  0
 TBD  CONST_07  O4    C4   N3   C2    180.00   0.0  0
 TBD  CONST_08  C4    N3   C2   O2    180.00   0.0  0
 TBD  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 TBD  Var_01    HCA1  C5A  C5   C6    122.22  30.0  3
 TBD  Var_02    C4'   C5'  O5'  PA   -173.33  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
 TBD  chir_01  PA   B1A  O2A  O5'  negativ
 TBD  chir_02  C4'  O4'  C3'  C5'  negativ
 TBD  chir_03  C1'  O4'  N1   C2'  negativ
 TBD  chir_04  C3'  O3'  C4'  C2'  positiv

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
 TBD  plan-1  C1'  0.020
 TBD  plan-1  N1   0.020
 TBD  plan-1  C6   0.020
 TBD  plan-1  C2   0.020
 TBD  plan-1  O2   0.020
 TBD  plan-1  N3   0.020
 TBD  plan-1  C4   0.020
 TBD  plan-1  O4   0.020
 TBD  plan-1  C5   0.020
 TBD  plan-1  C5A  0.020
 TBD  plan-1  HC6  0.020
 TBD  plan-1  HN3  0.020

