# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 04:55:24 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2
#
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
 3TT  3TT  '[[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid'  ligand  42  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3TT
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
 3TT  O3G  O  OH1   0  -0.726  -2.9749   3.4382  -1.0108
 3TT  PG   P  P     0   1.435  -3.6110   1.9793  -1.0976
 3TT  O1G  O  OH1   0  -0.740  -4.7958   1.8807  -0.0342
 3TT  O2G  O  O     0  -0.684  -4.0579   1.5388  -2.4307
 3TT  N3B  N  NH1   0  -0.958  -2.3829   1.0910  -0.3616
 3TT  PB   P  P     0   1.458  -2.6780  -0.2364   0.6093
 3TT  O2B  O  OH1   0  -0.718  -3.0053   0.3014   2.0651
 3TT  O1B  O  O     0  -0.677  -3.6869  -1.2110   0.1705
 3TT  O3A  O  O2    0  -0.694  -1.1579  -0.8061   0.6678
 3TT  PA   P  P     0   1.475  -0.7459  -2.3241   1.0777
 3TT  O1A  O  OH1   0  -0.730  -0.9163  -3.2109  -0.2203
 3TT  O2A  O  O     0  -0.671  -1.4938  -2.8595   2.2223
 3TT  O5'  O  O2    0  -0.573   0.8049  -2.0241   1.2614
 3TT  C5'  C  CH2   0  -0.205   1.8160  -3.0322   1.2032
 3TT  C4'  C  CR15  0  -0.079   2.7732  -2.7143   0.0766
 3TT  O4'  O  O     0  -0.467   3.3735  -1.4726   0.3092
 3TT  S3'  S  S2    0  -0.026   1.9442  -2.6313  -1.5694
 3TT  C2'  C  CH2   0  -0.588   2.0706  -0.8339  -1.5756
 3TT  C1'  C  CR15  0   0.196   3.3465  -0.5784  -0.7806
 3TT  N1   N  NR6   0  -0.559   3.4124   0.7628  -0.2491
 3TT  C2   C  CR6   0   0.604   4.3814   1.6632  -0.7360
 3TT  O2   O  O     0  -0.513   5.1503   1.2990  -1.6142
 3TT  N3   N  N     0  -0.540   4.4115   2.9011  -0.2070
 3TT  C4   C  CR6   0   0.521   3.5571   3.2685   0.7275
 3TT  N4   N  NH2   0  -0.804   3.6408   4.5054   1.2080
 3TT  C5   C  CR16  0  -0.470   2.5545   2.3819   1.2356
 3TT  C6   C  CR16  0   0.099   2.5325   1.1429   0.7153
 3TT  H1   H  HOH1  0   0.505  -3.3289   4.0565  -1.6653
 3TT  H2   H  HOH1  0   0.499  -4.6821   2.3704   0.7917
 3TT  H3   H  HNH1  0   0.447  -1.4749   1.1330  -0.8128
 3TT  H4   H  HOH1  0   0.503  -2.4232   0.9925   2.4108
 3TT  H5   H  HOH1  0   0.488  -0.2655  -3.0449  -0.9332
 3TT  H6   H  HCH2  0   0.290   2.3497  -3.0248   2.1545
 3TT  H7   H  HCH2  0   0.270   1.4039  -4.0336   1.0627
 3TT  H8   H  HCR5  0   0.304   3.5202  -3.5110   0.0184
 3TT  H9   H  HCH2  0   0.321   2.1746  -0.4797  -2.5992
 3TT  H10  H  HCH2  0   0.281   1.1943  -0.3665  -1.1268
 3TT  H11  H  HCR5  0   0.295   4.2149  -0.7194  -1.4238
 3TT  H12  H  HNH2  0   0.406   4.3392   5.1386   0.8568
 3TT  H13  H  HNH2  0   0.417   3.0154   4.8390   1.9202
 3TT  H14  H  HCR6  0   0.292   1.8561   2.6782   2.0034
 3TT  H15  H  HCR6  0   0.315   1.8234   0.4016   1.0563

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
 3TT  O2G  PG   double  1.473  0.020  1.473
 3TT  O1G  PG   single  1.595  0.020  1.595
 3TT  PG   N3B  single  1.685  0.020  1.685
 3TT  PG   O3G  single  1.594  0.020  1.594
 3TT  N3B  PB   single  1.671  0.020  1.671
 3TT  O2A  PA   double  1.468  0.020  1.468
 3TT  PB   O1B  double  1.470  0.020  1.470
 3TT  PB   O2B  single  1.586  0.020  1.586
 3TT  PB   O3A  single  1.624  0.020  1.624
 3TT  O1A  PA   single  1.581  0.020  1.581
 3TT  PA   O3A  single  1.625  0.020  1.625
 3TT  PA   O5'  single  1.590  0.020  1.590
 3TT  O5'  C5'  single  1.429  0.020  1.429
 3TT  N4   C4   single  1.330  0.020  1.330
 3TT  C5   C4   single  1.432  0.020  1.432
 3TT  C5   C6   double  1.344  0.020  1.344
 3TT  C5'  C4'  single  1.512  0.020  1.512
 3TT  C4   N3   double  1.318  0.020  1.318
 3TT  C6   N1   single  1.360  0.020  1.360
 3TT  O4'  C4'  single  1.399  0.020  1.399
 3TT  O4'  C1'  single  1.410  0.020  1.410
 3TT  C4'  S3'  single  1.845  0.020  1.845
 3TT  N3   C2   single  1.346  0.020  1.346
 3TT  N1   C2   single  1.410  0.020  1.410
 3TT  N1   C1'  single  1.444  0.020  1.444
 3TT  C2   O2   double  1.223  0.020  1.223
 3TT  C1'  C2'  single  1.525  0.020  1.525
 3TT  S3'  C2'  single  1.802  0.020  1.802
 3TT  O3G  H1   single  0.850  0.020  0.980
 3TT  O1G  H2   single  0.850  0.020  0.980
 3TT  N3B  H3   single  0.890  0.020  1.040
 3TT  O2B  H4   single  0.850  0.020  0.980
 3TT  O1A  H5   single  0.850  0.020  0.980
 3TT  C5'  H6   single  0.970  0.020  1.090
 3TT  C5'  H7   single  0.970  0.020  1.090
 3TT  C4'  H8   single  0.970  0.020  1.090
 3TT  C2'  H9   single  0.970  0.020  1.090
 3TT  C2'  H10  single  0.970  0.020  1.090
 3TT  C1'  H11  single  0.970  0.020  1.090
 3TT  N4   H12  single  0.860  0.020  1.020
 3TT  N4   H13  single  0.860  0.020  1.020
 3TT  C5   H14  single  0.930  0.020  1.080
 3TT  C6   H15  single  0.930  0.020  1.080

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
 3TT  H1   O3G  PG   113.71  3.000
 3TT  N3B  PG   O2G  117.30  3.000
 3TT  N3B  PG   O1G  102.57  3.000
 3TT  O2G  PG   O1G  111.06  3.000
 3TT  N3B  PG   O3G   99.67  3.000
 3TT  O1G  PG   O3G  108.46  3.000
 3TT  O2G  PG   O3G  116.36  3.000
 3TT  H2   O1G  PG   116.79  3.000
 3TT  H3   N3B  PB   116.70  3.000
 3TT  H3   N3B  PG   115.85  3.000
 3TT  PB   N3B  PG   122.95  3.000
 3TT  O3A  PB   O1B  114.87  3.000
 3TT  O3A  PB   O2B  106.20  3.000
 3TT  O1B  PB   O2B  110.93  3.000
 3TT  O3A  PB   N3B   97.72  3.000
 3TT  O2B  PB   N3B  107.49  3.000
 3TT  O1B  PB   N3B  118.33  3.000
 3TT  H4   O2B  PB   116.49  3.000
 3TT  PA   O3A  PB   125.02  3.000
 3TT  O5'  PA   O2A  118.39  3.000
 3TT  O5'  PA   O1A  107.80  3.000
 3TT  O2A  PA   O1A  112.36  3.000
 3TT  O5'  PA   O3A   95.75  3.000
 3TT  O1A  PA   O3A  106.82  3.000
 3TT  O2A  PA   O3A  114.08  3.000
 3TT  H5   O1A  PA   115.52  3.000
 3TT  C5'  O5'  PA   123.52  3.000
 3TT  H7   C5'  H6   107.64  3.000
 3TT  H7   C5'  C4'  109.62  3.000
 3TT  H6   C5'  C4'  109.79  3.000
 3TT  H7   C5'  O5'  112.66  3.000
 3TT  H6   C5'  O5'  107.81  3.000
 3TT  C4'  C5'  O5'  109.27  3.000
 3TT  H8   C4'  S3'  106.99  3.000
 3TT  H8   C4'  O4'  111.25  3.000
 3TT  S3'  C4'  O4'  107.53  3.000
 3TT  H8   C4'  C5'  108.59  3.000
 3TT  S3'  C4'  C5'  112.94  3.000
 3TT  O4'  C4'  C5'  109.54  3.000
 3TT  C1'  O4'  C4'  115.23  3.000
 3TT  C2'  S3'  C4'   90.95  3.000
 3TT  H10  C2'  H9   108.94  3.000
 3TT  H10  C2'  C1'  112.72  3.000
 3TT  H9   C2'  C1'  110.85  3.000
 3TT  H10  C2'  S3'  111.71  3.000
 3TT  H9   C2'  S3'  109.56  3.000
 3TT  C1'  C2'  S3'  102.94  3.000
 3TT  H11  C1'  N1   107.51  3.000
 3TT  H11  C1'  C2'  109.72  3.000
 3TT  N1   C1'  C2'  112.68  3.000
 3TT  H11  C1'  O4'  111.03  3.000
 3TT  C2'  C1'  O4'  108.23  3.000
 3TT  N1   C1'  O4'  107.68  3.000
 3TT  C6   N1   C2   120.75  3.000
 3TT  C2   N1   C1'  119.84  3.000
 3TT  C6   N1   C1'  119.41  3.000
 3TT  N3   C2   O2   122.82  3.000
 3TT  O2   C2   N1   119.35  3.000
 3TT  N3   C2   N1   117.84  3.000
 3TT  C4   N3   C2   121.34  3.000
 3TT  C5   C4   N4   119.47  3.000
 3TT  C5   C4   N3   122.20  3.000
 3TT  N4   C4   N3   118.33  3.000
 3TT  H13  N4   H12  118.08  3.000
 3TT  H13  N4   C4   121.72  3.000
 3TT  H12  N4   C4   120.20  3.000
 3TT  H14  C5   C6   121.19  3.000
 3TT  H14  C5   C4   122.38  3.000
 3TT  C6   C5   C4   116.42  3.000
 3TT  H15  C6   C5   121.38  3.000
 3TT  H15  C6   N1   117.16  3.000
 3TT  C5   C6   N1   121.45  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
 3TT  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 3TT  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 3TT  CONST_03  C5   C4   N3   C2     0.00   0.0  0
 3TT  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 3TT  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 3TT  CONST_06  N4   C4   N3   C2   180.00   0.0  0
 3TT  CONST_07  C4   N3   C2   O2   180.00   0.0  0
 3TT  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 3TT  CONST_09  H12  N4   C4   N3     0.00   0.0  0
 3TT  CONST_10  H13  N4   C4   N3   180.00   0.0  0
 3TT  Var_01    C1'  C2'  S3'  C4'   30.76  30.0  1
 3TT  Var_02    C4'  C5'  O5'  PA   119.60  30.0  3
 3TT  Var_03    PB   N3B  PG   O3G  144.65  30.0  3
 3TT  Var_04    O1B  PB   N3B  PG    43.11  30.0  3
 3TT  Var_05    O2A  PA   O3A  PB   -42.10  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
 3TT  chir_03  C4'  C5'  O4'  S3'  positiv
 3TT  chir_04  C1'  O4'  N1   C2'  positiv
 3TT  chir_05  PB   O1B  O2B  O3A  both
 3TT  chir_06  PA   O1A  O3A  O5'  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
 3TT  plan-1  C1'  0.020
 3TT  plan-1  N1   0.020
 3TT  plan-1  C2   0.020
 3TT  plan-1  O2   0.020
 3TT  plan-1  N3   0.020
 3TT  plan-1  C4   0.020
 3TT  plan-1  N4   0.020
 3TT  plan-1  C5   0.020
 3TT  plan-1  C6   0.020
 3TT  plan-1  H12  0.020
 3TT  plan-1  H13  0.020
 3TT  plan-1  H14  0.020
 3TT  plan-1  H15  0.020

