# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:50:53 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3'-deoxy-3'-(L-threonylamino)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23
#
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
 A3T  A3T  3'-deoxy-3'-(L-threonylamino)adenosine  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A3T
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
 A3T  C     C  C     0   0.545  -3.6523   0.2225  -0.7593
 A3T  N     N  NH2   0  -0.792  -5.9400   1.1859  -0.7361
 A3T  O     O  O     0  -0.485  -4.0682  -0.8349  -1.2076
 A3T  N1    N  N     0  -0.476   5.1827   1.4718  -0.5253
 A3T  C2    C  CR16  0   0.066   3.9969   2.0063  -0.7903
 A3T  N3    N  N     0  -0.514   2.7999   1.5167  -0.5080
 A3T  C4    C  CR56  0   0.521   2.8833   0.3395   0.1173
 A3T  C5    C  CR56  0   0.001   4.0411  -0.3428   0.4491
 A3T  C6    C  CR6   0   0.464   5.2502   0.2866   0.0963
 A3T  N6    N  NH2   0  -0.813   6.4434  -0.2479   0.3478
 A3T  N7    N  N     0  -0.454   3.7397  -1.5284   1.0660
 A3T  C8    C  CR15  0   0.111   2.4372  -1.5536   1.1075
 A3T  N8    N  NH1   0  -0.646  -2.3387   0.4890  -0.6426
 A3T  N9    N  NR5   0  -0.547   1.8620  -0.4484   0.5454
 A3T  CA    C  CH1   0  -0.249  -4.5837   1.3272  -0.2556
 A3T  CB    C  CH1   0   0.042  -4.5524   1.3522   1.2862
 A3T  OG    O  OH1   0  -0.666  -5.0398   0.1372   1.8142
 A3T  C1'   C  CH1   0   0.210   0.4544  -0.0733   0.4570
 A3T  C2'   C  CH1   0  -0.051   0.0543   0.2300  -1.0079
 A3T  O2'   O  OH1   0  -0.672   0.0300   1.5871  -1.3142
 A3T  C3'   C  CH1   0  -0.129  -1.3242  -0.4266  -1.1048
 A3T  C4'   C  CH1   0  -0.042  -1.1442  -1.6198  -0.1630
 A3T  O4'   O  O2    0  -0.480  -0.3423  -1.1136   0.9054
 A3T  C5'   C  CH2   0  -0.151  -0.4849  -2.8046  -0.8446
 A3T  O5'   O  OH1   0  -0.665  -0.2455  -3.7918   0.1261
 A3T  CG2   C  CH3   0  -0.688  -5.2933   2.5563   1.8425
 A3T  HN    H  HNH2  0   0.358  -6.0078   1.5333  -1.6833
 A3T  HNA   H  HNH2  0   0.345  -6.1828   0.2040  -0.7899
 A3T  HN6   H  HNH2  0   0.406   7.2831   0.2565   0.1210
 A3T  HN6A  H  HNH2  0   0.414   6.5290  -1.1145   0.8494
 A3T  H8    H  HCR5  0   0.294   1.8434  -2.3546   1.5184
 A3T  HN8   H  HNH1  0   0.404  -2.0541   1.4266  -0.4042
 A3T  HA    H  HCH1  0   0.264  -4.1912   2.2898  -0.5983
 A3T  HB    H  HCH1  0   0.231  -3.5079   1.4129   1.6058
 A3T  HOG   H  HOH1  0   0.443  -5.9910   0.1071   1.6626
 A3T  H1'   H  HCH1  0   0.277   0.3122   0.8090   1.0909
 A3T  H2'   H  HCH1  0   0.264   0.7302  -0.3154  -1.6797
 A3T  HO2'  H  HOH1  0   0.464   0.9380   1.9128  -1.1712
 A3T  H3'   H  HCH1  0   0.290  -1.5420  -0.7518  -2.1257
 A3T  H4'   H  HCH1  0   0.273  -2.0907  -1.9415   0.2745
 A3T  H5'   H  HCH2  0   0.219  -1.1629  -3.1556  -1.6341
 A3T  H5'A  H  HCH2  0   0.203   0.4437  -2.4946  -1.3414
 A3T  HO5'  H  HOH1  0   0.460   0.2633  -4.4975  -0.2826
 A3T  HG2   H  HCH3  0   0.228  -6.3473   2.5359   1.5628
 A3T  HG2A  H  HCH3  0   0.236  -5.2248   2.5776   2.9306
 A3T  HG2B  H  HCH3  0   0.227  -4.8650   3.4844   1.4622
 A3T  H2    H  HCR6  0   0.260   4.0139   2.9620  -1.3021

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
 A3T  C    O     double    1.222  0.020  1.222
 A3T  C    N8    single    1.345  0.020  1.345
 A3T  C    CA    single    1.530  0.020  1.530
 A3T  N    CA    single    1.446  0.020  1.446
 A3T  N1   C2    aromatic  1.327  0.020  1.327
 A3T  N1   C6    aromatic  1.340  0.020  1.340
 A3T  C2   N3    aromatic  1.324  0.020  1.324
 A3T  N3   C4    aromatic  1.336  0.020  1.336
 A3T  C4   C5    aromatic  1.384  0.020  1.384
 A3T  C4   N9    aromatic  1.359  0.020  1.359
 A3T  C5   C6    aromatic  1.408  0.020  1.408
 A3T  C5   N7    aromatic  1.370  0.020  1.370
 A3T  C6   N6    single    1.331  0.020  1.331
 A3T  N7   C8    aromatic  1.303  0.020  1.303
 A3T  C8   N9    aromatic  1.367  0.020  1.367
 A3T  N8   C3'   single    1.443  0.020  1.443
 A3T  N9   C1'   single    1.459  0.020  1.459
 A3T  CA   CB    single    1.542  0.020  1.542
 A3T  CB   OG    single    1.412  0.020  1.412
 A3T  CB   CG2   single    1.519  0.020  1.519
 A3T  C1'  C2'   single    1.548  0.020  1.548
 A3T  C1'  O4'   single    1.385  0.020  1.385
 A3T  C2'  O2'   single    1.391  0.020  1.391
 A3T  C2'  C3'   single    1.530  0.020  1.530
 A3T  C3'  C4'   single    1.531  0.020  1.531
 A3T  C4'  O4'   single    1.429  0.020  1.429
 A3T  C4'  C5'   single    1.517  0.020  1.517
 A3T  C5'  O5'   single    1.405  0.020  1.405
 A3T  N    HN    single    0.890  0.020  1.040
 A3T  N    HNA   single    0.890  0.020  1.040
 A3T  C2   H2    single    0.930  0.020  1.080
 A3T  N6   HN6   single    0.860  0.020  1.020
 A3T  N6   HN6A  single    0.860  0.020  1.020
 A3T  C8   H8    single    0.930  0.020  1.080
 A3T  N8   HN8   single    0.860  0.020  1.020
 A3T  CA   HA    single    0.970  0.020  1.090
 A3T  CB   HB    single    0.970  0.020  1.090
 A3T  OG   HOG   single    0.850  0.020  0.980
 A3T  C1'  H1'   single    0.970  0.020  1.090
 A3T  C2'  H2'   single    0.970  0.020  1.090
 A3T  O2'  HO2'  single    0.850  0.020  0.980
 A3T  C3'  H3'   single    0.970  0.020  1.090
 A3T  C4'  H4'   single    0.970  0.020  1.090
 A3T  C5'  H5'   single    0.970  0.020  1.090
 A3T  C5'  H5'A  single    0.970  0.020  1.090
 A3T  O5'  HO5'  single    0.850  0.020  0.980
 A3T  CG2  HG2   single    0.970  0.020  1.090
 A3T  CG2  HG2A  single    0.970  0.020  1.090
 A3T  CG2  HG2B  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
 A3T  CA    C    N8    115.01  3.000
 A3T  CA    C    O     122.58  3.000
 A3T  N8    C    O     122.39  3.000
 A3T  HNA   N    HN    105.50  3.000
 A3T  HNA   N    CA    109.71  3.000
 A3T  HN    N    CA    109.91  3.000
 A3T  C6    N1   C2    119.59  3.000
 A3T  H2    C2   N3    116.16  3.000
 A3T  H2    C2   N1    115.80  3.000
 A3T  N3    C2   N1    128.04  3.000
 A3T  C4    N3   C2    111.68  3.000
 A3T  N9    C4   C5    105.50  3.000
 A3T  N9    C4   N3    127.70  3.000
 A3T  C5    C4   N3    126.79  3.000
 A3T  N7    C5   C6    133.51  3.000
 A3T  N7    C5   C4    110.52  3.000
 A3T  C6    C5   C4    115.97  3.000
 A3T  N6    C6   C5    122.87  3.000
 A3T  N6    C6   N1    119.20  3.000
 A3T  C5    C6   N1    117.92  3.000
 A3T  HN6A  N6   HN6   118.30  3.000
 A3T  HN6A  N6   C6    121.12  3.000
 A3T  HN6   N6   C6    120.29  3.000
 A3T  C8    N7   C5    104.53  3.000
 A3T  H8    C8   N9    121.70  3.000
 A3T  H8    C8   N7    125.22  3.000
 A3T  N9    C8   N7    113.07  3.000
 A3T  HN8   N8   C3'   117.86  3.000
 A3T  HN8   N8   C     118.70  3.000
 A3T  C3'   N8   C     122.21  3.000
 A3T  C1'   N9   C8    129.69  3.000
 A3T  C1'   N9   C4    123.83  3.000
 A3T  C8    N9   C4    106.38  3.000
 A3T  HA    CA   CB    106.94  3.000
 A3T  HA    CA   N     108.56  3.000
 A3T  CB    CA   N     110.66  3.000
 A3T  HA    CA   C     108.28  3.000
 A3T  CB    CA   C     109.17  3.000
 A3T  N     CA   C     113.02  3.000
 A3T  HB    CB   CG2   108.34  3.000
 A3T  HB    CB   OG    105.56  3.000
 A3T  CG2   CB   OG    112.14  3.000
 A3T  HB    CB   CA    108.20  3.000
 A3T  CG2   CB   CA    111.65  3.000
 A3T  OG    CB   CA    110.67  3.000
 A3T  HOG   OG   CB    107.99  3.000
 A3T  H1'   C1'  O4'   110.06  3.000
 A3T  H1'   C1'  C2'   110.86  3.000
 A3T  O4'   C1'  C2'   107.75  3.000
 A3T  H1'   C1'  N9    107.28  3.000
 A3T  O4'   C1'  N9    110.01  3.000
 A3T  C2'   C1'  N9    110.91  3.000
 A3T  H2'   C2'  C3'   107.62  3.000
 A3T  H2'   C2'  O2'   111.13  3.000
 A3T  C3'   C2'  O2'   112.88  3.000
 A3T  H2'   C2'  C1'   108.82  3.000
 A3T  C3'   C2'  C1'   102.04  3.000
 A3T  O2'   C2'  C1'   113.82  3.000
 A3T  HO2'  O2'  C2'   106.09  3.000
 A3T  H3'   C3'  C4'   111.48  3.000
 A3T  H3'   C3'  C2'   111.48  3.000
 A3T  C4'   C3'  C2'   100.93  3.000
 A3T  H3'   C3'  N8    110.35  3.000
 A3T  C4'   C3'  N8    112.36  3.000
 A3T  C2'   C3'  N8    109.93  3.000
 A3T  H4'   C4'  C5'   109.07  3.000
 A3T  H4'   C4'  O4'   106.95  3.000
 A3T  C5'   C4'  O4'   111.63  3.000
 A3T  H4'   C4'  C3'   111.99  3.000
 A3T  C5'   C4'  C3'   112.54  3.000
 A3T  O4'   C4'  C3'   104.48  3.000
 A3T  C4'   O4'  C1'   110.30  3.000
 A3T  H5'A  C5'  H5'   106.68  3.000
 A3T  H5'A  C5'  O5'   111.53  3.000
 A3T  H5'   C5'  O5'   112.17  3.000
 A3T  H5'A  C5'  C4'   110.50  3.000
 A3T  H5'   C5'  C4'   107.71  3.000
 A3T  O5'   C5'  C4'   108.20  3.000
 A3T  HO5'  O5'  C5'   108.20  3.000
 A3T  HG2B  CG2  HG2A  107.86  3.000
 A3T  HG2B  CG2  HG2   107.82  3.000
 A3T  HG2A  CG2  HG2   108.48  3.000
 A3T  HG2B  CG2  CB    110.80  3.000
 A3T  HG2A  CG2  CB    110.50  3.000
 A3T  HG2   CG2  CB    111.26  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
 A3T  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 A3T  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 A3T  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 A3T  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 A3T  CONST_05  C5    C4  N3  C2    0.00  0.0  0
 A3T  CONST_06  N9    C4  N3  C2  180.00  0.0  0
 A3T  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 A3T  CONST_08  C6    C5  C4  N3    0.00  0.0  0
 A3T  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 A3T  CONST_10  C8    N9  C4  N3  180.00  0.0  0
 A3T  CONST_11  C8    N7  C5  C4    0.00  0.0  0
 A3T  CONST_12  N7    C8  N9  C4    0.00  0.0  0
 A3T  CONST_13  C8    N9  C4  C5    0.00  0.0  0
 A3T  CONST_14  N9    C8  N7  C5    0.00  0.0  0
 A3T  CONST_15  N9    C4  C5  C6  180.00  0.0  0
 A3T  CONST_16  C8    N7  C5  C6  180.00  0.0  0
 A3T  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 A3T  CONST_18  C1'   N9  C4  N3    0.00  0.0  0
 A3T  CONST_19  C1'   N9  C4  C5  180.00  0.0  0
 A3T  CONST_20  C1'   N9  C8  N7  180.00  0.0  0
 A3T  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 A3T  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 A3T  CONST_23  N7    C5  C6  N6    0.00  0.0  0
 A3T  CONST_24  H2    C2  N3  C4  180.00  0.0  0
 A3T  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 A3T  CONST_26  HN6   N6  C6  N1    0.00  0.0  0
 A3T  CONST_27  HN6A  N6  C6  N1  180.00  0.0  0
 A3T  CONST_28  C3'   N8  C   O     0.00  0.0  0
 A3T  CONST_29  C3'   N8  C   CA  180.00  0.0  0
 A3T  CONST_30  HN8   N8  C   O   180.00  0.0  0

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
 A3T  chir_01  CA   C    N    CB   negativ
 A3T  chir_02  CB   OG   CA   CG2  negativ
 A3T  chir_03  C1'  O4'  N9   C2'  negativ
 A3T  chir_04  C2'  O2'  C1'  C3'  negativ
 A3T  chir_05  C3'  N8   C4'  C2'  positiv
 A3T  chir_06  C4'  O4'  C3'  C5'  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
 A3T  plan-1  N1    0.020
 A3T  plan-1  C2    0.020
 A3T  plan-1  N3    0.020
 A3T  plan-1  C4    0.020
 A3T  plan-1  C5    0.020
 A3T  plan-1  C6    0.020
 A3T  plan-1  N6    0.020
 A3T  plan-1  N7    0.020
 A3T  plan-1  C8    0.020
 A3T  plan-1  N9    0.020
 A3T  plan-1  C1'   0.020
 A3T  plan-1  H8    0.020
 A3T  plan-1  H2    0.020
 A3T  plan-2  C6    0.020
 A3T  plan-2  N6    0.020
 A3T  plan-2  HN6   0.020
 A3T  plan-2  HN6A  0.020
 A3T  plan-3  C     0.020
 A3T  plan-3  O     0.020
 A3T  plan-3  N8    0.020
 A3T  plan-3  CA    0.020
 A3T  plan-3  C3'   0.020
 A3T  plan-3  HN8   0.020

