# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:04:16 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: 3'-(acetylamino)-3'-deoxythymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1C[C@@H](O[C@@H]1CO)N2C=C(C)C(=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
 ADT  ADT  3'-(acetylamino)-3'-deoxythymidine  ligand  37  20  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ADT
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
 ADT  N1    N  NR6   0  -0.568   0.2193  -0.5169  -1.4286
 ADT  C2    C  CR6   0   0.743   0.0822   0.8514  -1.4671
 ADT  O2    O  O     0  -0.471  -0.0227   1.5450  -0.4773
 ADT  N3    N  NR16  0  -0.734   0.0791   1.3868  -2.7290
 ADT  C4    C  CR6   0   0.559   0.1902   0.7252  -3.9383
 ADT  O4    O  O     0  -0.454   0.1714   1.3427  -4.9873
 ADT  C5    C  CR6   0  -0.185   0.3211  -0.7129  -3.8207
 ADT  C5M   C  CH3   0  -0.706   0.4473  -1.5311  -5.0633
 ADT  C6    C  CR16  0   0.059   0.3208  -1.2449  -2.5866
 ADT  C1'   C  CH1   0   0.218   0.1919  -1.2173  -0.1458
 ADT  O4'   O  O2    0  -0.489  -1.0713  -1.0684   0.4339
 ADT  C4'   C  CH1   0   0.051  -0.9709  -0.7637   1.8145
 ADT  C5'   C  CH2   0  -0.163  -2.0877   0.1652   2.2209
 ADT  O5'   O  OH1   0  -0.672  -3.3182  -0.5088   2.1051
 ADT  C3'   C  CH1   0  -0.117   0.4199  -0.1428   2.0131
 ADT  N3'   N  NH1   0  -0.635   0.9652  -0.4069   3.3183
 ADT  C8'   C  C     0   0.524   1.0819   0.5108   4.2974
 ADT  O8'   O  O     0  -0.504   0.7480   1.6801   4.1650
 ADT  C9'   C  CH3   0  -0.780   1.6582  -0.0071   5.5914
 ADT  C2'   C  CH2   0  -0.531   1.2341  -0.7711   0.8849
 ADT  HN3   H  HNR6  0   0.425  -0.0134   2.3945  -2.7678
 ADT  HM51  H  HCH3  0   0.247  -0.4157  -1.3994  -5.7170
 ADT  HM52  H  HCH3  0   0.247   1.3319  -1.2489  -5.6356
 ADT  HM53  H  HCH3  0   0.247   0.5277  -2.5904  -4.8251
 ADT  H6    H  HCR6  0   0.317   0.4092  -2.3140  -2.4462
 ADT  H1'   H  HCH1  0   0.257   0.3648  -2.2639  -0.4072
 ADT  H4'   H  HCH1  0   0.229  -1.0328  -1.6910   2.4035
 ADT  H5'1  H  HCH2  0   0.203  -1.8974   0.4906   3.2518
 ADT  H5'2  H  HCH2  0   0.205  -2.0466   1.0591   1.5856
 ADT  HO5'  H  HOH1  0   0.457  -4.0190   0.1098   2.3295
 ADT  H3'   H  HCH1  0   0.279   0.3666   0.9361   1.8873
 ADT  HN3'  H  HNH1  0   0.400   1.2382  -1.3557   3.5215
 ADT  H9'1  H  HCH3  0   0.266   2.5090   0.6085   5.8815
 ADT  H9'2  H  HCH3  0   0.268   0.9098   0.0829   6.3789
 ADT  H9'3  H  HCH3  0   0.249   1.9827  -1.0449   5.5431
 ADT  H2'1  H  HCH2  0   0.285   1.9859  -0.1006   0.4739
 ADT  H2'2  H  HCH2  0   0.272   1.7571  -1.6579   1.2484

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
 ADT  N1   C2    single  1.376  0.020  1.376
 ADT  N1   C6    single  1.372  0.020  1.372
 ADT  N1   C1'   single  1.462  0.020  1.462
 ADT  C2   O2    double  1.213  0.020  1.213
 ADT  C2   N3    single  1.371  0.020  1.371
 ADT  N3   C4    single  1.383  0.020  1.383
 ADT  N3   HN3   single  0.860  0.020  1.020
 ADT  C4   O4    double  1.217  0.020  1.217
 ADT  C4   C5    single  1.449  0.020  1.449
 ADT  C5   C5M   single  1.493  0.020  1.493
 ADT  C5   C6    double  1.344  0.020  1.344
 ADT  C5M  HM51  single  0.970  0.020  1.090
 ADT  C5M  HM52  single  0.970  0.020  1.090
 ADT  C5M  HM53  single  0.970  0.020  1.090
 ADT  C6   H6    single  0.930  0.020  1.080
 ADT  C1'  O4'   single  1.398  0.020  1.398
 ADT  C1'  C2'   single  1.532  0.020  1.532
 ADT  C1'  H1'   single  0.970  0.020  1.090
 ADT  O4'  C4'   single  1.417  0.020  1.417
 ADT  C4'  C5'   single  1.508  0.020  1.508
 ADT  C4'  C3'   single  1.536  0.020  1.536
 ADT  C4'  H4'   single  0.970  0.020  1.090
 ADT  C5'  O5'   single  1.408  0.020  1.408
 ADT  C5'  H5'1  single  0.970  0.020  1.090
 ADT  C5'  H5'2  single  0.970  0.020  1.090
 ADT  O5'  HO5'  single  0.850  0.020  0.980
 ADT  C3'  N3'   single  1.439  0.020  1.439
 ADT  C3'  C2'   single  1.527  0.020  1.527
 ADT  C3'  H3'   single  0.970  0.020  1.090
 ADT  N3'  C8'   single  1.347  0.020  1.347
 ADT  N3'  HN3'  single  0.860  0.020  1.020
 ADT  C8'  O8'   double  1.223  0.020  1.223
 ADT  C8'  C9'   single  1.508  0.020  1.508
 ADT  C9'  H9'1  single  0.970  0.020  1.090
 ADT  C9'  H9'2  single  0.970  0.020  1.090
 ADT  C9'  H9'3  single  0.970  0.020  1.090
 ADT  C2'  H2'1  single  0.970  0.020  1.090
 ADT  C2'  H2'2  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
 ADT  C1'   N1   C6    119.21  3.000
 ADT  C1'   N1   C2    119.95  3.000
 ADT  C6    N1   C2    120.78  3.000
 ADT  N3    C2   O2    121.84  3.000
 ADT  N3    C2   N1    114.48  3.000
 ADT  O2    C2   N1    123.67  3.000
 ADT  HN3   N3   C4    116.73  3.000
 ADT  HN3   N3   C2    115.10  3.000
 ADT  C4    N3   C2    128.17  3.000
 ADT  C5    C4   O4    125.09  3.000
 ADT  C5    C4   N3    114.27  3.000
 ADT  O4    C4   N3    120.64  3.000
 ADT  C6    C5   C5M   123.18  3.000
 ADT  C6    C5   C4    117.87  3.000
 ADT  C5M   C5   C4    118.95  3.000
 ADT  HM53  C5M  HM52  107.86  3.000
 ADT  HM53  C5M  HM51  107.88  3.000
 ADT  HM52  C5M  HM51  107.22  3.000
 ADT  HM53  C5M  C5    110.94  3.000
 ADT  HM52  C5M  C5    111.31  3.000
 ADT  HM51  C5M  C5    111.46  3.000
 ADT  H6    C6   C5    120.69  3.000
 ADT  H6    C6   N1    114.90  3.000
 ADT  C5    C6   N1    124.41  3.000
 ADT  H1'   C1'  C2'   109.41  3.000
 ADT  H1'   C1'  O4'   110.14  3.000
 ADT  C2'   C1'  O4'   107.74  3.000
 ADT  H1'   C1'  N1    104.24  3.000
 ADT  C2'   C1'  N1    115.98  3.000
 ADT  O4'   C1'  N1    109.26  3.000
 ADT  C4'   O4'  C1'   111.27  3.000
 ADT  H4'   C4'  C3'   108.82  3.000
 ADT  H4'   C4'  C5'   109.46  3.000
 ADT  C3'   C4'  C5'   112.74  3.000
 ADT  H4'   C4'  O4'   109.65  3.000
 ADT  C3'   C4'  O4'   106.08  3.000
 ADT  C5'   C4'  O4'   110.02  3.000
 ADT  H5'2  C5'  H5'1  107.20  3.000
 ADT  H5'2  C5'  O5'   112.03  3.000
 ADT  H5'1  C5'  O5'   111.76  3.000
 ADT  H5'2  C5'  C4'   108.54  3.000
 ADT  H5'1  C5'  C4'   107.89  3.000
 ADT  O5'   C5'  C4'   109.28  3.000
 ADT  HO5'  O5'  C5'   108.06  3.000
 ADT  H3'   C3'  C2'   110.43  3.000
 ADT  H3'   C3'  N3'   107.79  3.000
 ADT  C2'   C3'  N3'   113.12  3.000
 ADT  H3'   C3'  C4'   109.98  3.000
 ADT  C2'   C3'  C4'   102.77  3.000
 ADT  N3'   C3'  C4'   112.72  3.000
 ADT  HN3'  N3'  C8'   118.11  3.000
 ADT  HN3'  N3'  C3'   117.28  3.000
 ADT  C8'   N3'  C3'   124.55  3.000
 ADT  C9'   C8'  O8'   121.70  3.000
 ADT  C9'   C8'  N3'   115.01  3.000
 ADT  O8'   C8'  N3'   123.29  3.000
 ADT  H9'3  C9'  H9'2  108.39  3.000
 ADT  H9'3  C9'  H9'1  108.53  3.000
 ADT  H9'2  C9'  H9'1  107.28  3.000
 ADT  H9'3  C9'  C8'   113.78  3.000
 ADT  H9'2  C9'  C8'   109.21  3.000
 ADT  H9'1  C9'  C8'   109.44  3.000
 ADT  H2'2  C2'  H2'1  107.18  3.000
 ADT  H2'2  C2'  C3'   110.10  3.000
 ADT  H2'1  C2'  C3'   113.21  3.000
 ADT  H2'2  C2'  C1'   108.25  3.000
 ADT  H2'1  C2'  C1'   113.29  3.000
 ADT  C3'   C2'  C1'   104.73  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
 ADT  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 ADT  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 ADT  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 ADT  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 ADT  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 ADT  CONST_06  C6    N1   C2   O2   180.00   0.0  0
 ADT  CONST_07  C1'   N1   C2   O2     0.00   0.0  0
 ADT  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 ADT  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 ADT  CONST_10  O8'   C8'  N3'  C3'    0.00   0.0  0
 ADT  CONST_11  C9'   C8'  N3'  C3'  180.00   0.0  0
 ADT  CONST_12  HN3'  N3'  C8'  O8'  180.00   0.0  0
 ADT  Var_01    HM51  C5M  C5   C4   -59.19  30.0  3
 ADT  Var_02    H9'1  C9'  C8'  N3'  126.26  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
 ADT  chir_01  C1'  N1   O4'  C2'  positiv
 ADT  chir_02  C4'  O4'  C5'  C3'  positiv
 ADT  chir_03  C3'  N3'  C2'  C4'  negativ

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
 ADT  plan-1  N1    0.020
 ADT  plan-1  C2    0.020
 ADT  plan-1  O2    0.020
 ADT  plan-1  N3    0.020
 ADT  plan-1  C4    0.020
 ADT  plan-1  O4    0.020
 ADT  plan-1  C5    0.020
 ADT  plan-1  C5M   0.020
 ADT  plan-1  C6    0.020
 ADT  plan-1  C1'   0.020
 ADT  plan-1  HN3   0.020
 ADT  plan-1  H6    0.020
 ADT  plan-2  C3'   0.020
 ADT  plan-2  N3'   0.020
 ADT  plan-2  C8'   0.020
 ADT  plan-2  O8'   0.020
 ADT  plan-2  C9'   0.020
 ADT  plan-2  HN3'  0.020

