# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 02:24:51 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine
#   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)C[P](O)(=O)N[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
 N6T  N6T  2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine  ligand  49  29  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N6T
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
 N6T  O4   O  O     0  -0.459  10.8636   7.3418  10.8242
 N6T  C4   C  CR6   0   0.559   9.6498   7.3617  10.7198
 N6T  C5   C  CR6   0  -0.184   8.7147   7.1055  11.7939
 N6T  C7   C  CH3   0  -0.721   9.2440   6.7865  13.1541
 N6T  C6   C  CR16  0   0.039   7.3980   7.1706  11.5200
 N6T  N3   N  NR16  0  -0.731   9.0545   7.6470   9.5032
 N6T  C2   C  CR6   0   0.731   7.7174   7.6900   9.2130
 N6T  O2   O  O     0  -0.490   7.3010   7.9152   8.0923
 N6T  N1   N  NR6   0  -0.562   6.8905   7.4556  10.2831
 N6T  C1'  C  CH1   0   0.198   5.4364   7.4575  10.0041
 N6T  C2'  C  CH2   0  -0.534   4.9501   6.1255   9.4371
 N6T  C3'  C  CH1   0   0.015   4.4455   5.4020  10.6754
 N6T  O3'  O  OH1   0  -0.692   3.5161   4.4076  10.3734
 N6T  O4'  O  O2    0  -0.498   4.7416   7.6675  11.1991
 N6T  C4'  C  CH1   0  -0.002   3.8574   6.5801  11.4590
 N6T  C5'  C  CH2   0  -0.206   3.6706   6.3912  12.9423
 N6T  O5'  O  O2    0  -0.598   4.9091   5.9835  13.5239
 N6T  PA   P  P     0   1.425   5.1377   5.4858  15.0291
 N6T  O1A  O  OH1   0  -0.736   3.8106   5.8536  15.8408
 N6T  O2A  O  O     0  -0.677   6.4176   5.9998  15.5647
 N6T  C3A  C  CH2   0  -1.056   5.0904   3.6775  15.0024
 N6T  PB   P  P     0   1.400   3.7537   2.8016  14.1690
 N6T  O1B  O  O     0  -0.694   3.6658   3.0170  12.6990
 N6T  O2B  O  OH1   0  -0.726   2.4853   3.2652  15.0183
 N6T  N3B  N  NH1   0  -0.948   3.9919   1.1637  14.4553
 N6T  PG   P  P     0   1.444   4.2563   0.3302  15.8823
 N6T  O2G  O  O     0  -0.688   3.7443  -1.0534  15.8577
 N6T  O1G  O  OH1   0  -0.734   5.8282   0.5043  16.0934
 N6T  O3G  O  OH1   0  -0.743   3.6848   1.3013  17.0150
 N6T  H1   H  HCH3  0   0.251   8.4315   6.6095  13.8573
 N6T  H2   H  HCH3  0   0.243   9.8710   5.8936  13.1369
 N6T  H3   H  HCH3  0   0.243   9.8560   7.6002  13.5462
 N6T  H4   H  HCR6  0   0.320   6.6677   7.0064  12.2964
 N6T  H5   H  HNR6  0   0.424   9.6739   7.8235   8.7216
 N6T  H6   H  HCH1  0   0.276   5.2589   8.2874   9.3204
 N6T  H7   H  HCH2  0   0.264   4.1193   6.3053   8.7500
 N6T  H8   H  HCH2  0   0.279   5.7236   5.5848   8.8941
 N6T  H9   H  HCH1  0   0.224   5.2986   4.9868  11.2277
 N6T  H10  H  HOH1  0   0.459   3.4500   3.8396  11.1612
 N6T  H11  H  HCH1  0   0.249   2.8625   6.8073  11.0508
 N6T  H12  H  HCH2  0   0.267   3.3320   7.3222  13.4021
 N6T  H13  H  HCH2  0   0.244   2.8902   5.6419  13.0913
 N6T  H14  H  HOH1  0   0.501   3.8020   6.7487  16.2093
 N6T  H15  H  HCH2  0   0.335   5.1551   3.3566  16.0447
 N6T  H16  H  HCH2  0   0.343   6.0145   3.3493  14.5187
 N6T  H17  H  HOH1  0   0.500   1.6439   2.9070  14.6989
 N6T  H18  H  HNH1  0   0.445   4.0608   0.6056  13.6108
 N6T  H19  H  HOH1  0   0.500   6.1944  -0.0186  16.8202
 N6T  H20  H  HOH1  0   0.500   2.7289   1.2473  17.1507

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
 N6T  O2   C2   double  1.217  0.020  1.217
 N6T  C2   N3   single  1.369  0.020  1.369
 N6T  C2   N1   single  1.373  0.020  1.373
 N6T  N3   C4   single  1.384  0.020  1.384
 N6T  C2'  C1'  single  1.527  0.020  1.527
 N6T  C2'  C3'  single  1.520  0.020  1.520
 N6T  C1'  N1   single  1.481  0.020  1.481
 N6T  C1'  O4'  single  1.398  0.020  1.398
 N6T  N1   C6   single  1.367  0.020  1.367
 N6T  O3'  C3'  single  1.394  0.020  1.394
 N6T  C4   O4   double  1.218  0.020  1.218
 N6T  C4   C5   single  1.447  0.020  1.447
 N6T  C3'  C4'  single  1.532  0.020  1.532
 N6T  O4'  C4'  single  1.425  0.020  1.425
 N6T  C4'  C5'  single  1.507  0.020  1.507
 N6T  C6   C5   double  1.346  0.020  1.346
 N6T  C5   C7   single  1.494  0.020  1.494
 N6T  O1B  PB   double  1.488  0.020  1.488
 N6T  C5'  O5'  single  1.428  0.020  1.428
 N6T  O5'  PA   single  1.602  0.020  1.602
 N6T  PB   O2B  single  1.595  0.020  1.595
 N6T  PB   C3A  single  1.802  0.020  1.802
 N6T  PB   N3B  single  1.680  0.020  1.680
 N6T  C3A  PA   single  1.809  0.020  1.809
 N6T  N3B  PG   single  1.674  0.020  1.674
 N6T  PA   O2A  double  1.480  0.020  1.480
 N6T  PA   O1A  single  1.599  0.020  1.599
 N6T  PG   O2G  double  1.475  0.020  1.475
 N6T  PG   O3G  single  1.598  0.020  1.598
 N6T  PG   O1G  single  1.596  0.020  1.596
 N6T  C7   H1   single  0.970  0.020  1.090
 N6T  C7   H2   single  0.970  0.020  1.090
 N6T  C7   H3   single  0.970  0.020  1.090
 N6T  C6   H4   single  0.930  0.020  1.080
 N6T  N3   H5   single  0.860  0.020  1.020
 N6T  C1'  H6   single  0.970  0.020  1.090
 N6T  C2'  H7   single  0.970  0.020  1.090
 N6T  C2'  H8   single  0.970  0.020  1.090
 N6T  C3'  H9   single  0.970  0.020  1.090
 N6T  O3'  H10  single  0.850  0.020  0.980
 N6T  C4'  H11  single  0.970  0.020  1.090
 N6T  C5'  H12  single  0.970  0.020  1.090
 N6T  C5'  H13  single  0.970  0.020  1.090
 N6T  O1A  H14  single  0.850  0.020  0.980
 N6T  C3A  H15  single  0.970  0.020  1.090
 N6T  C3A  H16  single  0.970  0.020  1.090
 N6T  O2B  H17  single  0.850  0.020  0.980
 N6T  N3B  H18  single  0.860  0.020  1.020
 N6T  O1G  H19  single  0.850  0.020  0.980
 N6T  O3G  H20  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
 N6T  N3   C4   C5   114.27  3.000
 N6T  C5   C4   O4   125.26  3.000
 N6T  N3   C4   O4   120.47  3.000
 N6T  C6   C5   C7   122.82  3.000
 N6T  C7   C5   C4   118.99  3.000
 N6T  C6   C5   C4   118.19  3.000
 N6T  H3   C7   H2   107.08  3.000
 N6T  H3   C7   H1   107.91  3.000
 N6T  H2   C7   H1   107.81  3.000
 N6T  H3   C7   C5   111.51  3.000
 N6T  H2   C7   C5   111.34  3.000
 N6T  H1   C7   C5   110.99  3.000
 N6T  H4   C6   N1   115.58  3.000
 N6T  H4   C6   C5   120.55  3.000
 N6T  N1   C6   C5   123.87  3.000
 N6T  H5   N3   C2   115.36  3.000
 N6T  H5   N3   C4   116.82  3.000
 N6T  C2   N3   C4   127.80  3.000
 N6T  N1   C2   O2   122.93  3.000
 N6T  N1   C2   N3   114.70  3.000
 N6T  O2   C2   N3   122.37  3.000
 N6T  C1'  N1   C2   116.40  3.000
 N6T  C1'  N1   C6   122.37  3.000
 N6T  C2   N1   C6   121.16  3.000
 N6T  H6   C1'  O4'  109.93  3.000
 N6T  H6   C1'  C2'  112.30  3.000
 N6T  O4'  C1'  C2'  106.87  3.000
 N6T  H6   C1'  N1   106.20  3.000
 N6T  O4'  C1'  N1   109.10  3.000
 N6T  C2'  C1'  N1   112.44  3.000
 N6T  H8   C2'  H7   107.95  3.000
 N6T  H8   C2'  C3'  113.93  3.000
 N6T  H7   C2'  C3'  109.76  3.000
 N6T  H8   C2'  C1'  113.08  3.000
 N6T  H7   C2'  C1'  109.39  3.000
 N6T  C3'  C2'  C1'  102.61  3.000
 N6T  H9   C3'  C4'  109.38  3.000
 N6T  H9   C3'  O3'  110.93  3.000
 N6T  C4'  C3'  O3'  113.79  3.000
 N6T  H9   C3'  C2'  109.38  3.000
 N6T  C4'  C3'  C2'  100.26  3.000
 N6T  O3'  C3'  C2'  112.60  3.000
 N6T  H10  O3'  C3'  106.63  3.000
 N6T  C4'  O4'  C1'  110.45  3.000
 N6T  H11  C4'  C5'  106.22  3.000
 N6T  H11  C4'  O4'  109.64  3.000
 N6T  C5'  C4'  O4'  110.61  3.000
 N6T  H11  C4'  C3'  108.45  3.000
 N6T  C5'  C4'  C3'  117.04  3.000
 N6T  O4'  C4'  C3'  104.79  3.000
 N6T  H13  C5'  H12  107.81  3.000
 N6T  H13  C5'  O5'  111.61  3.000
 N6T  H12  C5'  O5'  109.93  3.000
 N6T  H13  C5'  C4'  107.99  3.000
 N6T  H12  C5'  C4'  110.24  3.000
 N6T  O5'  C5'  C4'  109.23  3.000
 N6T  PA   O5'  C5'  126.54  3.000
 N6T  C3A  PA   O2A  112.04  3.000
 N6T  O2A  PA   O1A  117.03  3.000
 N6T  C3A  PA   O1A  102.46  3.000
 N6T  O1A  PA   O5'  106.69  3.000
 N6T  O2A  PA   O5'  110.83  3.000
 N6T  C3A  PA   O5'  107.04  3.000
 N6T  H14  O1A  PA   114.42  3.000
 N6T  H16  C3A  H15  106.49  3.000
 N6T  H16  C3A  PB   106.04  3.000
 N6T  H15  C3A  PB   110.02  3.000
 N6T  H16  C3A  PA   106.53  3.000
 N6T  H15  C3A  PA   106.14  3.000
 N6T  PB   C3A  PA   120.80  3.000
 N6T  N3B  PB   O2B  107.78  3.000
 N6T  N3B  PB   O1B  108.53  3.000
 N6T  O2B  PB   O1B  115.90  3.000
 N6T  N3B  PB   C3A  106.85  3.000
 N6T  O2B  PB   C3A  101.67  3.000
 N6T  O1B  PB   C3A  115.48  3.000
 N6T  H17  O2B  PB   114.05  3.000
 N6T  H18  N3B  PG   115.15  3.000
 N6T  H18  N3B  PB   113.84  3.000
 N6T  PG   N3B  PB   130.80  3.000
 N6T  O3G  PG   O1G  101.08  3.000
 N6T  O1G  PG   O2G  116.51  3.000
 N6T  O3G  PG   O2G  117.24  3.000
 N6T  O1G  PG   N3B  102.36  3.000
 N6T  O3G  PG   N3B  104.20  3.000
 N6T  O2G  PG   N3B  113.45  3.000
 N6T  H19  O1G  PG   114.42  3.000
 N6T  H20  O3G  PG   114.78  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
 N6T  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 N6T  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 N6T  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 N6T  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 N6T  CONST_05  C2   N3   C4   O4    180.00   0.0  0
 N6T  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 N6T  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 N6T  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 N6T  CONST_09  H5   N3   C4   C5    180.00   0.0  0
 N6T  Var_01    H1   C7   C5   C4   -179.53  30.0  3
 N6T  Var_02    C3A  PA   O5'  C5'    96.15  30.0  3
 N6T  Var_03    PB   C3A  PA   O5'   -48.95  30.0  1
 N6T  Var_04    O1B  PB   C3A  PA     63.27  30.0  1
 N6T  Var_05    PG   N3B  PB   C3A    50.71  30.0  3
 N6T  Var_06    O2G  PG   N3B  PB    150.13  30.0  3
 N6T  Var_07    H12  C5'  O5'  PA     67.46  30.0  2

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
 N6T  chir_01  C1'  C2'  N1   O4'  positiv
 N6T  chir_02  C3'  O3'  C4'  C2'  positiv
 N6T  chir_03  C4'  O4'  C3'  C5'  negativ
 N6T  chir_04  PA   C3A  O2A  O1A  both
 N6T  chir_05  PB   O1B  N3B  C3A  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
 N6T  plan-1  O4   0.020
 N6T  plan-1  C4   0.020
 N6T  plan-1  C5   0.020
 N6T  plan-1  C7   0.020
 N6T  plan-1  C6   0.020
 N6T  plan-1  N3   0.020
 N6T  plan-1  C2   0.020
 N6T  plan-1  O2   0.020
 N6T  plan-1  N1   0.020
 N6T  plan-1  C1'  0.020
 N6T  plan-1  H4   0.020
 N6T  plan-1  H5   0.020

