# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:37:55 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2-chloro-2'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3
#
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
 CL9  CL9  2-chloro-2'-deoxyadenosine  ligand  31  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CL9
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
 CL9  C2    C   CR6   0   0.275  -2.9679  -0.6804   0.1124
 CL9  C4    C   CR56  0   0.505  -0.9694   0.1799   0.1536
 CL9  C5    C   CR56  0   0.004  -1.4446   1.4421  -0.1628
 CL9  C6    C   CR6   0   0.475  -2.8373   1.5553  -0.3382
 CL9  C8    C   CR15  0   0.100   0.6469   1.6361   0.0303
 CL9  CL    CL  CL    0  -0.112  -4.0225  -2.0504   0.2829
 CL9  N3    N   N     0  -0.434  -1.6970  -0.9300   0.3020
 CL9  N9    N   NR5   0  -0.529   0.3768   0.3182   0.2768
 CL9  N7    N   N     0  -0.448  -0.4157   2.3406  -0.2345
 CL9  N6    N   NH2   0  -0.811  -3.4410   2.6989  -0.6419
 CL9  N1    N   N     0  -0.453  -3.5780   0.4477  -0.1892
 CL9  C1'   C   CH1   0   0.179   1.3101  -0.7698   0.5732
 CL9  C2'   C   CH2   0  -0.539   1.7076  -1.5476  -0.6739
 CL9  C3'   C   CH1   0   0.012   2.9681  -0.8143  -1.1205
 CL9  O3'   O   OH1   0  -0.660   3.8696  -1.5710  -1.8767
 CL9  C4'   C   CH1   0   0.008   3.5905  -0.4582   0.2261
 CL9  O4'   O   O2    0  -0.495   2.4827  -0.2199   1.0960
 CL9  C5'   C   CH2   0  -0.157   4.4977   0.7454   0.1786
 CL9  O5'   O   OH1   0  -0.668   5.0817   0.9333   1.4433
 CL9  H8    H   HCR5  0   0.299   1.6507   2.0295   0.0698
 CL9  HN6   H   HNH2  0   0.418  -2.9168   3.5489  -0.7573
 CL9  HN6A  H   HNH2  0   0.410  -4.4405   2.7360  -0.7475
 CL9  H1'   H   HCH1  0   0.278   0.8153  -1.3994   1.3158
 CL9  H2'   H   HCH2  0   0.268   1.9641  -2.5718  -0.3934
 CL9  H2'A  H   HCH2  0   0.281   0.9178  -1.5850  -1.4234
 CL9  H3'   H   HCH1  0   0.221   2.6888   0.1086  -1.6497
 CL9  HO3'  H   HOH1  0   0.462   3.5202  -1.6587  -2.7687
 CL9  H4'   H   HCH1  0   0.241   4.1555  -1.3259   0.5937
 CL9  H5'   H   HCH2  0   0.213   5.2501   0.5564  -0.5979
 CL9  H5'A  H   HCH2  0   0.200   3.9222   1.6241  -0.1441
 CL9  HO5'  H   HOH1  0   0.459   5.6601   1.6999   1.3971

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
 CL9  C2   CL    single    1.737  0.020  1.737
 CL9  C2   N3    aromatic  1.309  0.020  1.309
 CL9  C2   N1    aromatic  1.318  0.020  1.318
 CL9  C4   C5    aromatic  1.385  0.020  1.385
 CL9  C4   N3    aromatic  1.335  0.020  1.335
 CL9  C4   N9    aromatic  1.359  0.020  1.359
 CL9  C5   C6    aromatic  1.408  0.020  1.408
 CL9  C5   N7    aromatic  1.368  0.020  1.368
 CL9  C6   N6    single    1.328  0.020  1.328
 CL9  C6   N1    aromatic  1.341  0.020  1.341
 CL9  C8   N9    aromatic  1.368  0.020  1.368
 CL9  C8   N7    aromatic  1.302  0.020  1.302
 CL9  N9   C1'   single    1.464  0.020  1.464
 CL9  C1'  C2'   single    1.523  0.020  1.523
 CL9  C1'  O4'   single    1.397  0.020  1.397
 CL9  C2'  C3'   single    1.525  0.020  1.525
 CL9  C3'  O3'   single    1.399  0.020  1.399
 CL9  C3'  C4'   single    1.526  0.020  1.526
 CL9  C4'  O4'   single    1.429  0.020  1.429
 CL9  C4'  C5'   single    1.508  0.020  1.508
 CL9  C5'  O5'   single    1.406  0.020  1.406
 CL9  C8   H8    single    0.930  0.020  1.080
 CL9  N6   HN6   single    0.860  0.020  1.020
 CL9  N6   HN6A  single    0.860  0.020  1.020
 CL9  C1'  H1'   single    0.970  0.020  1.090
 CL9  C2'  H2'   single    0.970  0.020  1.090
 CL9  C2'  H2'A  single    0.970  0.020  1.090
 CL9  C3'  H3'   single    0.970  0.020  1.090
 CL9  O3'  HO3'  single    0.850  0.020  0.980
 CL9  C4'  H4'   single    0.970  0.020  1.090
 CL9  C5'  H5'   single    0.970  0.020  1.090
 CL9  C5'  H5'A  single    0.970  0.020  1.090
 CL9  O5'  HO5'  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
 CL9  N1    C2   N3   130.24  3.000
 CL9  N1    C2   CL   114.62  3.000
 CL9  N3    C2   CL   115.14  3.000
 CL9  N9    C4   N3   127.91  3.000
 CL9  N9    C4   C5   105.53  3.000
 CL9  N3    C4   C5   126.56  3.000
 CL9  N7    C5   C6   133.20  3.000
 CL9  N7    C5   C4   110.63  3.000
 CL9  C6    C5   C4   116.16  3.000
 CL9  N1    C6   N6   119.05  3.000
 CL9  N1    C6   C5   117.78  3.000
 CL9  N6    C6   C5   123.17  3.000
 CL9  H8    C8   N7   124.71  3.000
 CL9  H8    C8   N9   121.91  3.000
 CL9  N7    C8   N9   113.38  3.000
 CL9  C4    N3   C2   110.76  3.000
 CL9  C1'   N9   C8   128.81  3.000
 CL9  C1'   N9   C4   125.05  3.000
 CL9  C8    N9   C4   106.11  3.000
 CL9  C8    N7   C5   104.35  3.000
 CL9  HN6A  N6   HN6  118.36  3.000
 CL9  HN6A  N6   C6   120.49  3.000
 CL9  HN6   N6   C6   121.14  3.000
 CL9  C6    N1   C2   118.49  3.000
 CL9  H1'   C1'  O4'  110.66  3.000
 CL9  H1'   C1'  C2'  112.38  3.000
 CL9  O4'   C1'  C2'  106.77  3.000
 CL9  H1'   C1'  N9   106.10  3.000
 CL9  O4'   C1'  N9   108.57  3.000
 CL9  C2'   C1'  N9   112.35  3.000
 CL9  H2'A  C2'  H2'  108.34  3.000
 CL9  H2'A  C2'  C3'  114.47  3.000
 CL9  H2'   C2'  C3'  109.38  3.000
 CL9  H2'A  C2'  C1'  113.07  3.000
 CL9  H2'   C2'  C1'  109.27  3.000
 CL9  C3'   C2'  C1'  102.12  3.000
 CL9  H3'   C3'  C4'  109.41  3.000
 CL9  H3'   C3'  O3'  110.94  3.000
 CL9  C4'   C3'  O3'  109.90  3.000
 CL9  H3'   C3'  C2'  109.54  3.000
 CL9  C4'   C3'  C2'  101.01  3.000
 CL9  O3'   C3'  C2'  115.52  3.000
 CL9  HO3'  O3'  C3'  108.45  3.000
 CL9  H4'   C4'  C5'  109.36  3.000
 CL9  H4'   C4'  O4'  109.07  3.000
 CL9  C5'   C4'  O4'  110.64  3.000
 CL9  H4'   C4'  C3'  108.71  3.000
 CL9  C5'   C4'  C3'  113.83  3.000
 CL9  O4'   C4'  C3'  105.07  3.000
 CL9  C4'   O4'  C1'  110.95  3.000
 CL9  H5'A  C5'  H5'  106.79  3.000
 CL9  H5'A  C5'  O5'  112.02  3.000
 CL9  H5'   C5'  O5'  112.00  3.000
 CL9  H5'A  C5'  C4'  109.42  3.000
 CL9  H5'   C5'  C4'  107.29  3.000
 CL9  O5'   C5'  C4'  109.17  3.000
 CL9  HO5'  O5'  C5'  108.26  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
 CL9  CONST_01  C5    C4  N3  C2    0.00  0.0  0
 CL9  CONST_02  N9    C4  N3  C2  180.00  0.0  0
 CL9  CONST_03  C5    C6  N1  C2    0.00  0.0  0
 CL9  CONST_04  N1    C6  C5  C4    0.00  0.0  0
 CL9  CONST_05  C8    N7  C5  C4    0.00  0.0  0
 CL9  CONST_06  N1    C2  N3  C4    0.00  0.0  0
 CL9  CONST_07  N7    C8  N9  C4    0.00  0.0  0
 CL9  CONST_08  C8    N9  C4  C5    0.00  0.0  0
 CL9  CONST_09  N9    C8  N7  C5    0.00  0.0  0
 CL9  CONST_10  N3    C4  C5  C6    0.00  0.0  0
 CL9  CONST_11  N9    C4  C5  C6  180.00  0.0  0
 CL9  CONST_12  C8    N7  C5  C6  180.00  0.0  0
 CL9  CONST_13  N3    C2  N1  C6    0.00  0.0  0
 CL9  CONST_14  N3    C4  N9  C8  180.00  0.0  0
 CL9  CONST_15  N7    C5  C4  N3  180.00  0.0  0
 CL9  CONST_16  N7    C5  C4  N9    0.00  0.0  0
 CL9  CONST_17  N1    C6  C5  N7  180.00  0.0  0
 CL9  CONST_18  C1'   N9  C4  C5  180.00  0.0  0
 CL9  CONST_19  C1'   N9  C4  N3    0.00  0.0  0
 CL9  CONST_20  C1'   N9  C8  N7  180.00  0.0  0
 CL9  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 CL9  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 CL9  CONST_23  CL    C2  N3  C4  180.00  0.0  0
 CL9  CONST_24  CL    C2  N1  C6  180.00  0.0  0
 CL9  CONST_25  N6    C6  C5  N7    0.00  0.0  0
 CL9  CONST_26  H8    C8  N9  C4  180.00  0.0  0
 CL9  CONST_27  HN6   N6  C6  C5    0.00  0.0  0
 CL9  CONST_28  HN6A  N6  C6  C5  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
 CL9  chir_01  C1'  N9   C2'  O4'  negativ
 CL9  chir_02  C3'  O3'  C4'  C2'  positiv
 CL9  chir_03  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
 CL9  plan-1  C2    0.020
 CL9  plan-1  C4    0.020
 CL9  plan-1  C5    0.020
 CL9  plan-1  C6    0.020
 CL9  plan-1  C8    0.020
 CL9  plan-1  CL    0.020
 CL9  plan-1  N3    0.020
 CL9  plan-1  N9    0.020
 CL9  plan-1  N7    0.020
 CL9  plan-1  N6    0.020
 CL9  plan-1  N1    0.020
 CL9  plan-1  C1'   0.020
 CL9  plan-1  H8    0.020
 CL9  plan-2  C6    0.020
 CL9  plan-2  N6    0.020
 CL9  plan-2  HN6   0.020
 CL9  plan-2  HN6A  0.020

