# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:37:08 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 5'-chloro-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CCl)[C@@H](O)[C@H]3O
#
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
 5CD  5CD  5'-chloro-5'-deoxyadenosine  ligand  31  19  .  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_5CD
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
 5CD  N9    N   NR5   0  -0.536   0.5232   0.1509  -0.3472
 5CD  C8    C   CR15  0   0.101   0.4394   1.4014   0.2017
 5CD  N7    N   N     0  -0.450   1.5928   1.8833   0.5636
 5CD  C5    C   CR56  0  -0.001   2.4910   0.9032   0.2351
 5CD  C4    C   CR56  0   0.487   1.8458  -0.1822  -0.3357
 5CD  N3    N   N     0  -0.458   2.4125  -1.3045  -0.7750
 5CD  C2    C   CR16  0   0.039   3.7234  -1.2840  -0.6075
 5CD  N1    N   N     0  -0.474   4.4746  -0.3216  -0.0785
 5CD  C6    C   CR6   0   0.458   3.8892   0.7988   0.3595
 5CD  N6    N   NH2   0  -0.816   4.6396   1.7595   0.9007
 5CD  O2'   O   OH1   0  -0.662  -1.4008  -2.8879  -0.6858
 5CD  C2'   C   CR15  0  -0.045  -0.8672  -1.8457   0.0817
 5CD  C3'   C   CR15  0  -0.034  -1.9468  -1.2000   0.9579
 5CD  O3'   O   OH1   0  -0.654  -2.8146  -2.1124   1.5632
 5CD  C4'   C   CR15  0   0.052  -2.6997  -0.3556  -0.0719
 5CD  C5'   C   CH2   0  -0.480  -3.3845   0.8365   0.5417
 5CD  CL    CL  CL    0  -0.156  -4.2135   1.8191  -0.7104
 5CD  O4'   O   O     0  -0.489  -1.7069   0.0620  -1.0019
 5CD  C1'   C   CR15  0   0.173  -0.5424  -0.6967  -0.8702
 5CD  H8    H   HCR5  0   0.297  -0.4992   1.9230   0.3009
 5CD  H2    H   HCR6  0   0.253   4.2621  -2.1638  -0.9432
 5CD  H6N1  H   HNH2  0   0.404   5.6409   1.6703   0.9175
 5CD  H6N2  H   HNH2  0   0.411   4.2357   2.6351   1.1825
 5CD  H2'   H   HOH1  0   0.454  -1.9814  -3.4085  -0.1172
 5CD  HA    H   HCR5  0   0.265   0.0091  -2.1667   0.6570
 5CD  H3'   H   HCR5  0   0.250  -1.4656  -0.5472   1.6986
 5CD  HB    H   HOH1  0   0.471  -2.4245  -2.4115   2.3910
 5CD  H4'   H   HCR5  0   0.261  -3.4439  -0.9759  -0.5840
 5CD  H5'1  H   HCH2  0   0.304  -4.1415   0.5038   1.2493
 5CD  H5'2  H   HCH2  0   0.286  -2.6845   1.4904   1.0586
 5CD  H1'   H   HCR5  0   0.288  -0.2133  -1.0661  -1.8451

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
 5CD  N9   C8    aromatic  1.368  0.020  1.368
 5CD  N9   C4    aromatic  1.364  0.020  1.364
 5CD  N9   C1'   single    1.459  0.020  1.459
 5CD  C8   N7    aromatic  1.301  0.020  1.301
 5CD  C8   H8    single    0.930  0.020  1.080
 5CD  N7   C5    aromatic  1.369  0.020  1.369
 5CD  C5   C4    aromatic  1.386  0.020  1.386
 5CD  C5   C6    aromatic  1.408  0.020  1.408
 5CD  C4   N3    aromatic  1.332  0.020  1.332
 5CD  N3   C2    aromatic  1.322  0.020  1.322
 5CD  C2   N1    aromatic  1.331  0.020  1.331
 5CD  C2   H2    single    0.930  0.020  1.080
 5CD  N1   C6    aromatic  1.338  0.020  1.338
 5CD  C6   N6    single    1.334  0.020  1.334
 5CD  N6   H6N1  single    0.860  0.020  1.020
 5CD  N6   H6N2  single    0.860  0.020  1.020
 5CD  O2'  C2'   single    1.400  0.020  1.400
 5CD  O2'  H2'   single    0.850  0.020  0.980
 5CD  C2'  C3'   single    1.533  0.020  1.533
 5CD  C2'  C1'   single    1.527  0.020  1.527
 5CD  C2'  HA    single    0.970  0.020  1.090
 5CD  C3'  O3'   single    1.397  0.020  1.397
 5CD  C3'  C4'   single    1.530  0.020  1.530
 5CD  C3'  H3'   single    0.970  0.020  1.090
 5CD  O3'  HB    single    0.850  0.020  0.980
 5CD  C4'  C5'   single    1.506  0.020  1.506
 5CD  C4'  O4'   single    1.423  0.020  1.423
 5CD  C4'  H4'   single    0.970  0.020  1.090
 5CD  C5'  CL    single    1.795  0.020  1.795
 5CD  C5'  H5'1  single    0.970  0.020  1.090
 5CD  C5'  H5'2  single    0.970  0.020  1.090
 5CD  O4'  C1'   single    1.396  0.020  1.396
 5CD  C1'  H1'   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
 5CD  C1'   N9   C4    124.72  3.000
 5CD  C1'   N9   C8    129.07  3.000
 5CD  C4    N9   C8    106.21  3.000
 5CD  H8    C8   N7    124.52  3.000
 5CD  H8    C8   N9    122.16  3.000
 5CD  N7    C8   N9    113.31  3.000
 5CD  C5    N7   C8    104.45  3.000
 5CD  C6    C5   C4    116.16  3.000
 5CD  C6    C5   N7    133.10  3.000
 5CD  C4    C5   N7    110.73  3.000
 5CD  N3    C4   C5    126.71  3.000
 5CD  N3    C4   N9    128.00  3.000
 5CD  C5    C4   N9    105.29  3.000
 5CD  C2    N3   C4    111.54  3.000
 5CD  H2    C2   N1    115.43  3.000
 5CD  H2    C2   N3    116.15  3.000
 5CD  N1    C2   N3    128.43  3.000
 5CD  C6    N1   C2    119.27  3.000
 5CD  N6    C6   N1    119.33  3.000
 5CD  N6    C6   C5    122.77  3.000
 5CD  N1    C6   C5    117.89  3.000
 5CD  H6N2  N6   H6N1  118.23  3.000
 5CD  H6N2  N6   C6    121.03  3.000
 5CD  H6N1  N6   C6    120.21  3.000
 5CD  H2'   O2'  C2'   107.93  3.000
 5CD  HA    C2'  C1'   112.17  3.000
 5CD  HA    C2'  C3'   112.73  3.000
 5CD  C1'   C2'  C3'   100.91  3.000
 5CD  HA    C2'  O2'   111.99  3.000
 5CD  C1'   C2'  O2'   107.42  3.000
 5CD  C3'   C2'  O2'   111.01  3.000
 5CD  H3'   C3'  C4'   109.97  3.000
 5CD  H3'   C3'  O3'   111.60  3.000
 5CD  C4'   C3'  O3'   110.27  3.000
 5CD  H3'   C3'  C2'   109.11  3.000
 5CD  C4'   C3'  C2'   101.20  3.000
 5CD  O3'   C3'  C2'   114.21  3.000
 5CD  HB    O3'  C3'   108.89  3.000
 5CD  H4'   C4'  O4'   109.55  3.000
 5CD  H4'   C4'  C5'   109.26  3.000
 5CD  O4'   C4'  C5'   110.57  3.000
 5CD  H4'   C4'  C3'   109.66  3.000
 5CD  O4'   C4'  C3'   104.98  3.000
 5CD  C5'   C4'  C3'   112.74  3.000
 5CD  H5'2  C5'  H5'1  108.80  3.000
 5CD  H5'2  C5'  CL    107.43  3.000
 5CD  H5'1  C5'  CL    107.44  3.000
 5CD  H5'2  C5'  C4'   112.13  3.000
 5CD  H5'1  C5'  C4'   109.83  3.000
 5CD  CL    C5'  C4'   111.05  3.000
 5CD  C1'   O4'  C4'   111.15  3.000
 5CD  H1'   C1'  O4'   110.52  3.000
 5CD  H1'   C1'  C2'   111.45  3.000
 5CD  O4'   C1'  C2'   106.88  3.000
 5CD  H1'   C1'  N9    107.23  3.000
 5CD  O4'   C1'  N9    109.11  3.000
 5CD  C2'   C1'  N9    111.66  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
 5CD  CONST_01  C5    N7  C8  N9    0.00  0.0  0
 5CD  CONST_02  N7    C5  C4  N9    0.00  0.0  0
 5CD  CONST_03  C6    C5  C4  N9  180.00  0.0  0
 5CD  CONST_04  C2    N3  C4  N9  180.00  0.0  0
 5CD  CONST_05  C5    C4  N9  C8    0.00  0.0  0
 5CD  CONST_06  N3    C4  N9  C8  180.00  0.0  0
 5CD  CONST_07  C4    C5  N7  C8    0.00  0.0  0
 5CD  CONST_08  C6    C5  N7  C8  180.00  0.0  0
 5CD  CONST_09  C4    N9  C8  N7    0.00  0.0  0
 5CD  CONST_10  N3    C4  C5  N7  180.00  0.0  0
 5CD  CONST_11  N1    C6  C5  N7  180.00  0.0  0
 5CD  CONST_12  C2    N3  C4  C5    0.00  0.0  0
 5CD  CONST_13  C2    N1  C6  C5    0.00  0.0  0
 5CD  CONST_14  N1    C6  C5  C4    0.00  0.0  0
 5CD  CONST_15  N1    C2  N3  C4    0.00  0.0  0
 5CD  CONST_16  C6    C5  C4  N3    0.00  0.0  0
 5CD  CONST_17  C6    N1  C2  N3    0.00  0.0  0
 5CD  CONST_18  C1'   N9  C8  N7  180.00  0.0  0
 5CD  CONST_19  C1'   N9  C4  C5  180.00  0.0  0
 5CD  CONST_20  C1'   N9  C4  N3    0.00  0.0  0
 5CD  CONST_21  N6    C6  C5  N7    0.00  0.0  0
 5CD  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 5CD  CONST_23  N6    C6  N1  C2  180.00  0.0  0
 5CD  CONST_24  H8    C8  N7  C5  180.00  0.0  0
 5CD  CONST_25  H2    C2  N3  C4  180.00  0.0  0
 5CD  CONST_26  H6N1  N6  C6  C5  180.00  0.0  0
 5CD  CONST_27  H6N2  N6  C6  C5    0.00  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
 5CD  chir_01  C2'  O2'  C3'  C1'  positiv
 5CD  chir_02  C3'  O3'  C4'  C2'  positiv
 5CD  chir_03  C4'  O4'  C3'  C5'  negativ
 5CD  chir_04  C1'  O4'  N9   C2'  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
 5CD  plan-1  N9    0.020
 5CD  plan-1  C8    0.020
 5CD  plan-1  N7    0.020
 5CD  plan-1  C5    0.020
 5CD  plan-1  C4    0.020
 5CD  plan-1  N3    0.020
 5CD  plan-1  C2    0.020
 5CD  plan-1  N1    0.020
 5CD  plan-1  C6    0.020
 5CD  plan-1  N6    0.020
 5CD  plan-1  C1'   0.020
 5CD  plan-1  H8    0.020
 5CD  plan-1  H2    0.020
 5CD  plan-2  C6    0.020
 5CD  plan-2  N6    0.020
 5CD  plan-2  H6N1  0.020
 5CD  plan-2  H6N2  0.020

