# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:23:30 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  42  25  .  2021-08-23  2021-08-23  
;
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   1.251  -4.9671  -1.3732   0.5226
 TBD  O1B   O  OP    -1  -0.853  -5.9151  -0.2201   0.7577
 TBD  O2B   O  OP    -1  -0.855  -4.8334  -2.3753   1.6456
 TBD  O3B   O  O      0  -0.859  -4.8939  -1.9147  -0.8866
 TBD  O3A   O  OC2    0  -0.730  -3.3471  -0.5539   0.6796
 TBD  PA    P  P      1   1.295  -2.6505   0.2119  -0.4812
 TBD  B1A   B  B     -1  -0.727  -3.5924   1.4737  -1.5404
 TBD  O2A   O  OP     0  -0.753  -1.9148  -0.8299  -1.4698
 TBD  O5'   O  OC2    0  -0.593  -1.4523   0.8986   0.3726
 TBD  C5'   C  CH2    0  -0.175  -0.5048   1.7471  -0.2661
 TBD  C4'   C  CH1    0   0.020   0.5975   2.0669   0.7114
 TBD  O4'   O  O2     0  -0.489   1.3232   0.8924   1.0221
 TBD  C1'   C  CH1    0   0.216   2.6850   1.1654   1.1901
 TBD  N1    N  NR6    0  -0.567   3.4705   0.1624   0.4731
 TBD  C6    C  CR16   0   0.060   4.2413  -0.7177   1.1879
 TBD  C2    C  CR6    0   0.744   3.3908   0.0777  -0.8973
 TBD  O2    O  O      0  -0.472   2.7141   0.8200  -1.5776
 TBD  N3    N  NR16   0  -0.734   4.1512  -0.9205  -1.4494
 TBD  C4    C  CR6    0   0.559   4.9662  -1.8311  -0.8014
 TBD  O4    O  O      0  -0.455   5.5905  -2.6637  -1.4334
 TBD  C5    C  CR6    0  -0.185   4.9871  -1.6925   0.6405
 TBD  C5A   C  CH3    0  -0.707   5.8266  -2.6284   1.4467
 TBD  C2'   C  CH2    0  -0.560   2.9193   2.6226   0.7808
 TBD  C3'   C  CH1    0   0.021   1.6024   3.0739   0.1476
 TBD  O3'   O  OH1    0  -0.668   1.1914   4.3700   0.5013
 TBD  H1B   H  H      0   0.013  -4.0422   2.2997  -0.7777
 TBD  H2B   H  H      0   0.010  -2.7772   1.9744  -2.2883
 TBD  H3B   H  H      0   0.026  -4.4611   0.8950  -2.1463
 TBD  H2AO  H  H      0   0.480  -1.5005  -1.5836  -1.0276
 TBD  H5'1  H  HCH2   0   0.232  -0.0801   1.2679  -1.1538
 TBD  H5'2  H  HCH2   0   0.240  -0.9782   2.6825  -0.5795
 TBD  H4'C  H  HCH1   0   0.236   0.1623   2.4874   1.6297
 TBD  H1'C  H  HCH1   0   0.256   2.9665   1.0270   2.2364
 TBD  HC6   H  HCR6   0   0.316   4.2196  -0.5733   2.2597
 TBD  HN3   H  HNR6   0   0.425   4.1017  -0.9908  -2.4586
 TBD  HCA1  H  HCH3   0   0.247   5.5522  -3.6678   1.2634
 TBD  HCA2  H  HCH3   0   0.247   6.8849  -2.5258   1.2019
 TBD  HCA3  H  HCH3   0   0.247   5.7102  -2.4348   2.5118
 TBD  H2'1  H  HCH2   0   0.269   3.1008   3.2095   1.6827
 TBD  H2'2  H  HCH2   0   0.276   3.7806   2.7484   0.1272
 TBD  H3'C  H  HCH1   0   0.237   1.6617   2.9720  -0.9394
 TBD  H3'O  H  HOH1   0   0.458   1.6491   4.9967  -0.0660

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   deloc   1.511  0.020  1.511
 TBD  PB   O2B   deloc   1.511  0.020  1.511
 TBD  PB   O3B   deloc   1.511  0.020  1.511
 TBD  PB   O3A   single  1.822  0.020  1.822
 TBD  O3A  PA    single  1.555  0.020  1.555
 TBD  PA   B1A   single  1.898  0.020  1.898
 TBD  PA   O2A   single  1.614  0.020  1.614
 TBD  PA   O5'   single  1.624  0.020  1.624
 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  1.423  0.020  1.423
 TBD  C5'  C4'   single  1.508  0.020  1.508
 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  1.415  0.020  1.415
 TBD  C4'  C3'   single  1.530  0.020  1.530
 TBD  C4'  H4'C  single  0.970  0.020  1.090
 TBD  O4'  C1'   single  1.399  0.020  1.399
 TBD  C1'  N1    single  1.462  0.020  1.462
 TBD  C1'  C2'   single  1.532  0.020  1.532
 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  1.213  0.020  1.213
 TBD  C2   N3    single  1.371  0.020  1.371
 TBD  N3   C4    single  1.383  0.020  1.383
 TBD  N3   HN3   single  0.860  0.020  1.020
 TBD  C4   O4    double  1.218  0.020  1.218
 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  1.405  0.020  1.405
 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   101.44  3.000
 TBD  O3A   PB   O2B    98.95  3.000
 TBD  O3B   PB   O2B   116.81  3.000
 TBD  O3A   PB   O1B   101.61  3.000
 TBD  O3B   PB   O1B   116.66  3.000
 TBD  O2B   PB   O1B   116.48  3.000
 TBD  PA    O3A  PB    123.73  3.000
 TBD  O5'   PA   O2A   105.00  3.000
 TBD  O5'   PA   B1A   112.24  3.000
 TBD  O2A   PA   B1A   108.28  3.000
 TBD  O5'   PA   O3A    98.41  3.000
 TBD  O2A   PA   O3A   110.09  3.000
 TBD  B1A   PA   O3A   121.44  3.000
 TBD  H3B   B1A  H2B   111.82  3.000
 TBD  H3B   B1A  H1B   112.08  3.000
 TBD  H2B   B1A  H1B   110.86  3.000
 TBD  H3B   B1A  PA    108.58  3.000
 TBD  H2B   B1A  PA    106.54  3.000
 TBD  H1B   B1A  PA    106.64  3.000
 TBD  H2AO  O2A  PA    114.73  3.000
 TBD  C5'   O5'  PA    120.49  3.000
 TBD  H5'2  C5'  H5'1  108.05  3.000
 TBD  H5'2  C5'  C4'   108.70  3.000
 TBD  H5'1  C5'  C4'   109.57  3.000
 TBD  H5'2  C5'  O5'   110.49  3.000
 TBD  H5'1  C5'  O5'   111.18  3.000
 TBD  C4'   C5'  O5'   108.80  3.000
 TBD  H4'C  C4'  C3'   108.42  3.000
 TBD  H4'C  C4'  O4'   109.69  3.000
 TBD  C3'   C4'  O4'   106.88  3.000
 TBD  H4'C  C4'  C5'   109.46  3.000
 TBD  C3'   C4'  C5'   112.39  3.000
 TBD  O4'   C4'  C5'   109.95  3.000
 TBD  C1'   O4'  C4'   111.32  3.000
 TBD  H1'C  C1'  C2'   109.70  3.000
 TBD  H1'C  C1'  N1    104.15  3.000
 TBD  C2'   C1'  N1    116.08  3.000
 TBD  H1'C  C1'  O4'   109.94  3.000
 TBD  C2'   C1'  O4'   107.60  3.000
 TBD  N1    C1'  O4'   109.28  3.000
 TBD  C2    N1   C6    120.83  3.000
 TBD  C2    N1   C1'   119.99  3.000
 TBD  C6    N1   C1'   119.13  3.000
 TBD  HC6   C6   C5    120.77  3.000
 TBD  HC6   C6   N1    114.81  3.000
 TBD  C5    C6   N1    124.42  3.000
 TBD  N3    C2   O2    121.94  3.000
 TBD  N3    C2   N1    114.46  3.000
 TBD  O2    C2   N1    123.60  3.000
 TBD  HN3   N3   C4    116.74  3.000
 TBD  HN3   N3   C2    115.13  3.000
 TBD  C4    N3   C2    128.13  3.000
 TBD  C5    C4   O4    125.08  3.000
 TBD  C5    C4   N3    114.32  3.000
 TBD  O4    C4   N3    120.60  3.000
 TBD  C5A   C5   C4    119.04  3.000
 TBD  C5A   C5   C6    123.13  3.000
 TBD  C4    C5   C6    117.83  3.000
 TBD  HCA3  C5A  HCA2  107.85  3.000
 TBD  HCA3  C5A  HCA1  107.87  3.000
 TBD  HCA2  C5A  HCA1  107.22  3.000
 TBD  HCA3  C5A  C5    110.89  3.000
 TBD  HCA2  C5A  C5    111.42  3.000
 TBD  HCA1  C5A  C5    111.41  3.000
 TBD  H2'2  C2'  H2'1  107.61  3.000
 TBD  H2'2  C2'  C3'   113.49  3.000
 TBD  H2'1  C2'  C3'   109.07  3.000
 TBD  H2'2  C2'  C1'   113.05  3.000
 TBD  H2'1  C2'  C1'   108.44  3.000
 TBD  C3'   C2'  C1'   105.05  3.000
 TBD  H3'C  C3'  O3'   110.62  3.000
 TBD  H3'C  C3'  C2'   109.72  3.000
 TBD  O3'   C3'  C2'   114.82  3.000
 TBD  H3'C  C3'  C4'   109.91  3.000
 TBD  O3'   C3'  C4'   108.80  3.000
 TBD  C2'   C3'  C4'   102.63  3.000
 TBD  H3'O  O3'  C3'   108.28  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    122.65  30.0  3
 TBD  Var_02    C4'   C5'  O5'  PA   -171.49  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

