# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 04:13:08 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 8-bromo-5'-{[3-carboxy-2-(carboxymethyl)-2-hydroxypropanoyl]amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CNC(=O)C(O)(CC(O)=O)CC(O)=O)[C@@H](O)[C@H]3O)c(Br)nc12
#
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
 5CI  5CI  8-bromo-5'-{[3-carboxy-2-(carboxymethyl)-2-hydroxypropanoyl]amino}-5'-deoxyadenosine  ligand  49  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5CI
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
 5CI  O41  O   OC    -1  -0.745  -6.6312  -2.7309   0.0232
 5CI  C51  C   C      0   0.401  -5.4182  -2.5355  -0.1326
 5CI  O31  O   O      0  -0.385  -4.5193  -3.4065   0.0327
 5CI  C41  C   CH2    0  -0.630  -4.9558  -1.1518  -0.6048
 5CI  C31  C   CT     0   0.222  -3.6583  -0.6916   0.0712
 5CI  C21  C   CH2    0  -0.638  -3.8949  -0.4376   1.5630
 5CI  C11  C   C      0   0.391  -4.8420   0.7256   1.8929
 5CI  O21  O   O      0  -0.522  -4.8985   1.6576   1.0644
 5CI  O11  O   OC    -1  -0.687  -5.4477   0.6637   2.9803
 5CI  O71  O   OH1    0  -0.678  -2.6536  -1.6768  -0.1183
 5CI  C61  C   C      0   0.497  -3.0936   0.5460  -0.6405
 5CI  O51  O   O      0  -0.580  -3.5172   0.9403  -1.7171
 5CI  N5'  N   NH1    0  -0.524  -2.0028   1.0994  -0.0717
 5CI  C5'  C   CH2    0  -0.341  -1.1515   1.9876  -0.8205
 5CI  C4'  C   CH1    0  -0.009  -0.0668   2.5981   0.0485
 5CI  O4'  O   O2     0  -0.489   0.6469   1.5796   0.7747
 5CI  C3'  C   CH1    0  -0.030   0.9740   3.3111  -0.8120
 5CI  O3'  O   OH1    0  -0.581   1.5271   4.3749  -0.0842
 5CI  C2'  C   CH1    0  -0.023   1.9954   2.1851  -1.0105
 5CI  O2'  O   OH1    0  -0.566   3.2778   2.5963  -1.3668
 5CI  C1'  C   CH1    0   0.102   1.9903   1.5973   0.3957
 5CI  N9   N   NR5    0  -0.501   2.5943   0.2895   0.5145
 5CI  C8   C   CR5    0   0.267   2.1498  -0.9672   0.1754
 5CI  BR8  BR  BR     0   0.105   0.4290  -1.3304  -0.4020
 5CI  N7   N   N      0  -0.389   3.0212  -1.9028   0.3766
 5CI  C5   C   CR56   0   0.006   4.1205  -1.2476   0.8629
 5CI  C4   C   CR56   0   0.552   3.8803   0.1099   0.9572
 5CI  N3   N   N      0  -0.426   4.7285   1.0321   1.4005
 5CI  C2   C   CR16   0   0.029   5.8843   0.5020   1.7607
 5CI  N1   N   N      0  -0.393   6.2566  -0.7746   1.7221
 5CI  C6   C   CR6    0   0.364   5.3902  -1.6915   1.2789
 5CI  N6   N   NH2    0  -0.795   5.7483  -2.9748   1.2535
 5CI  H2   H   HCH2   0   0.121  -4.7924  -1.2088  -1.6860
 5CI  H3   H   HCH2   0   0.244  -5.7467  -0.4185  -0.4551
 5CI  H4   H   HCH2   0   0.264  -4.2526  -1.3579   2.0331
 5CI  H5   H   HCH2   0   0.218  -2.9355  -0.2369   2.0569
 5CI  H7   H   HOH1   0   0.433  -3.1632  -2.5385  -0.0141
 5CI  H8   H   HNH1   0   0.388  -1.5852   0.6013   0.6984
 5CI  H9   H   HCH2   0   0.264  -0.7021   1.4653  -1.6741
 5CI  H10  H   HCH2   0   0.255  -1.7406   2.8085  -1.2328
 5CI  H11  H   HCH1   0   0.230  -0.5179   3.2818   0.7737
 5CI  H12  H   HCH1   0   0.201   0.5467   3.6503  -1.7645
 5CI  H13  H   HOH1   0   0.458   2.3433   4.6436  -0.5217
 5CI  H14  H   HCH1   0   0.163   1.5835   1.4526  -1.7156
 5CI  H15  H   HOH1   0   0.473   3.3423   2.6161  -2.3264
 5CI  H16  H   HCH1   0   0.275   2.5822   2.2413   1.0557
 5CI  H17  H   HCR6   0   0.203   6.6322   1.1945   2.1316
 5CI  H18  H   HNH2   0   0.405   5.1121  -3.6867   0.9406
 5CI  H19  H   HNH2   0   0.400   6.6608  -3.2530   1.5705

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
 5CI  N6   C6   single    1.333  0.020  1.333
 5CI  BR8  C8   single    1.851  0.020  1.851
 5CI  N7   C8   aromatic  1.294  0.020  1.294
 5CI  N7   C5   aromatic  1.369  0.020  1.369
 5CI  C8   N9   aromatic  1.375  0.020  1.375
 5CI  C6   C5   aromatic  1.408  0.020  1.408
 5CI  C6   N1   aromatic  1.337  0.020  1.337
 5CI  C5   C4   aromatic  1.382  0.020  1.382
 5CI  C2'  O2'  single    1.393  0.020  1.393
 5CI  C2'  C3'  single    1.533  0.020  1.533
 5CI  C2'  C1'  single    1.524  0.020  1.524
 5CI  N1   C2   aromatic  1.330  0.020  1.330
 5CI  N9   C4   aromatic  1.372  0.020  1.372
 5CI  N9   C1'  single    1.445  0.020  1.445
 5CI  C4   N3   aromatic  1.329  0.020  1.329
 5CI  O3'  C3'  single    1.403  0.020  1.403
 5CI  C3'  C4'  single    1.527  0.020  1.527
 5CI  C2   N3   aromatic  1.322  0.020  1.322
 5CI  C1'  O4'  single    1.396  0.020  1.396
 5CI  O4'  C4'  single    1.440  0.020  1.440
 5CI  C4'  C5'  single    1.518  0.020  1.518
 5CI  C5'  N5'  single    1.440  0.020  1.440
 5CI  N5'  C61  single    1.349  0.020  1.349
 5CI  O51  C61  double    1.222  0.020  1.222
 5CI  C61  C31  single    1.535  0.020  1.535
 5CI  C31  C21  single    1.532  0.020  1.532
 5CI  C31  C41  single    1.534  0.020  1.534
 5CI  C31  O71  single    1.420  0.020  1.420
 5CI  C21  C11  single    1.536  0.020  1.536
 5CI  C41  C51  single    1.533  0.020  1.533
 5CI  C11  O21  deloc     1.248  0.020  1.248
 5CI  C11  O11  deloc     1.246  0.020  1.246
 5CI  O31  C51  deloc     1.262  0.020  1.262
 5CI  C51  O41  deloc     1.238  0.020  1.238
 5CI  C41  H2   single    0.970  0.020  1.090
 5CI  C41  H3   single    0.970  0.020  1.090
 5CI  C21  H4   single    0.970  0.020  1.090
 5CI  C21  H5   single    0.970  0.020  1.090
 5CI  O71  H7   single    0.850  0.020  0.980
 5CI  N5'  H8   single    0.890  0.020  1.040
 5CI  C5'  H9   single    0.970  0.020  1.090
 5CI  C5'  H10  single    0.970  0.020  1.090
 5CI  C4'  H11  single    0.970  0.020  1.090
 5CI  C3'  H12  single    0.970  0.020  1.090
 5CI  O3'  H13  single    0.850  0.020  0.980
 5CI  C2'  H14  single    0.970  0.020  1.090
 5CI  O2'  H15  single    0.850  0.020  0.980
 5CI  C1'  H16  single    0.970  0.020  1.090
 5CI  C2   H17  single    0.930  0.020  1.080
 5CI  N6   H18  single    0.860  0.020  1.020
 5CI  N6   H19  single    0.860  0.020  1.020

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
 5CI  C41  C51  O31  116.62  3.000
 5CI  O31  C51  O41  124.89  3.000
 5CI  C41  C51  O41  118.45  3.000
 5CI  H3   C41  H2   106.21  3.000
 5CI  H3   C41  C31  110.60  3.000
 5CI  H2   C41  C31  108.94  3.000
 5CI  H3   C41  C51  110.26  3.000
 5CI  H2   C41  C51  107.59  3.000
 5CI  C31  C41  C51  112.96  3.000
 5CI  C61  C31  O71  103.72  3.000
 5CI  O71  C31  C21  110.75  3.000
 5CI  C61  C31  C21  112.00  3.000
 5CI  O71  C31  C41  109.37  3.000
 5CI  C21  C31  C41  110.39  3.000
 5CI  C61  C31  C41  110.41  3.000
 5CI  H5   C21  H4   104.26  3.000
 5CI  H5   C21  C11  107.69  3.000
 5CI  H4   C21  C11  110.08  3.000
 5CI  H5   C21  C31  109.49  3.000
 5CI  H4   C21  C31  109.24  3.000
 5CI  C11  C21  C31  115.47  3.000
 5CI  O11  C11  O21  126.46  3.000
 5CI  O11  C11  C21  116.71  3.000
 5CI  O21  C11  C21  116.80  3.000
 5CI  H7   O71  C31  102.83  3.000
 5CI  N5'  C61  O51  121.29  3.000
 5CI  O51  C61  C31  122.75  3.000
 5CI  N5'  C61  C31  115.64  3.000
 5CI  H8   N5'  C5'  117.21  3.000
 5CI  H8   N5'  C61  117.03  3.000
 5CI  C5'  N5'  C61  120.78  3.000
 5CI  H10  C5'  H9   106.57  3.000
 5CI  H10  C5'  C4'  107.43  3.000
 5CI  H9   C5'  C4'  110.13  3.000
 5CI  H10  C5'  N5'  109.95  3.000
 5CI  H9   C5'  N5'  110.68  3.000
 5CI  C4'  C5'  N5'  111.89  3.000
 5CI  H11  C4'  C3'  111.27  3.000
 5CI  H11  C4'  O4'  108.18  3.000
 5CI  C3'  C4'  O4'  106.06  3.000
 5CI  H11  C4'  C5'  109.64  3.000
 5CI  O4'  C4'  C5'  111.00  3.000
 5CI  C3'  C4'  C5'  110.62  3.000
 5CI  C1'  O4'  C4'  109.33  3.000
 5CI  H12  C3'  C2'  111.96  3.000
 5CI  H12  C3'  O3'  111.68  3.000
 5CI  C2'  C3'  O3'  111.19  3.000
 5CI  H12  C3'  C4'  111.58  3.000
 5CI  O3'  C3'  C4'  109.30  3.000
 5CI  C2'  C3'  C4'  100.61  3.000
 5CI  H13  O3'  C3'  108.04  3.000
 5CI  H14  C2'  C1'  109.53  3.000
 5CI  H14  C2'  O2'  112.23  3.000
 5CI  C1'  C2'  O2'  110.67  3.000
 5CI  H14  C2'  C3'  108.88  3.000
 5CI  C1'  C2'  C3'   99.30  3.000
 5CI  O2'  C2'  C3'  115.44  3.000
 5CI  H15  O2'  C2'  108.85  3.000
 5CI  H16  C1'  N9   104.87  3.000
 5CI  H16  C1'  C2'  109.10  3.000
 5CI  N9   C1'  C2'  115.05  3.000
 5CI  H16  C1'  O4'  111.33  3.000
 5CI  N9   C1'  O4'  111.61  3.000
 5CI  C2'  C1'  O4'  104.99  3.000
 5CI  C4   N9   C8   105.24  3.000
 5CI  C4   N9   C1'  122.46  3.000
 5CI  C8   N9   C1'  132.17  3.000
 5CI  N7   C8   BR8  122.17  3.000
 5CI  N7   C8   N9   113.86  3.000
 5CI  BR8  C8   N9   123.82  3.000
 5CI  C5   N7   C8   104.47  3.000
 5CI  C6   C5   C4   116.51  3.000
 5CI  C4   C5   N7   110.78  3.000
 5CI  C6   C5   N7   132.70  3.000
 5CI  N3   C4   C5   126.41  3.000
 5CI  N3   C4   N9   127.95  3.000
 5CI  C5   C4   N9   105.64  3.000
 5CI  C2   N3   C4   111.76  3.000
 5CI  H17  C2   N1   115.44  3.000
 5CI  H17  C2   N3   116.11  3.000
 5CI  N1   C2   N3   128.45  3.000
 5CI  C6   N1   C2   119.10  3.000
 5CI  N6   C6   N1   119.51  3.000
 5CI  N1   C6   C5   117.78  3.000
 5CI  N6   C6   C5   122.71  3.000
 5CI  H19  N6   H18  118.48  3.000
 5CI  H19  N6   C6   120.29  3.000
 5CI  H18  N6   C6   121.21  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
 5CI  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 5CI  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 5CI  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 5CI  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 5CI  CONST_05  C6   C5   N7   C8   180.00   0.0  0
 5CI  CONST_06  C4   C5   N7   C8     0.00   0.0  0
 5CI  CONST_07  C5   C4   N9   C8     0.00   0.0  0
 5CI  CONST_08  N3   C4   N9   C8   180.00   0.0  0
 5CI  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 5CI  CONST_10  N1   C6   C5   N7   180.00   0.0  0
 5CI  CONST_11  N3   C4   C5   N7   180.00   0.0  0
 5CI  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 5CI  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 5CI  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 5CI  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 5CI  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 5CI  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 5CI  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 5CI  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 5CI  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 5CI  CONST_21  BR8  C8   N9   C1'    0.00   0.0  0
 5CI  CONST_22  C5   N7   C8   BR8  180.00   0.0  0
 5CI  CONST_23  C4   N9   C8   BR8  180.00   0.0  0
 5CI  CONST_24  N6   C6   C5   N7     0.00   0.0  0
 5CI  CONST_25  N6   C6   C5   C4   180.00   0.0  0
 5CI  CONST_26  N6   C6   N1   C2   180.00   0.0  0
 5CI  CONST_27  H17  C2   N3   C4   180.00   0.0  0
 5CI  CONST_28  H18  N6   C6   C5     0.00   0.0  0
 5CI  CONST_29  H19  N6   C6   C5   180.00   0.0  0
 5CI  CONST_31  C5'  N5'  C61  O51    0.00   0.0  0
 5CI  CONST_32  H8   N5'  C61  C31    0.00   0.0  0
 5CI  Var_01    C4'  C5'  N5'  C61  174.40  30.0  1
 5CI  Var_02    C31  C41  C51  O41  141.62  30.0  3
 5CI  Var_03    C61  C31  C41  C51  168.30  30.0  2
 5CI  Var_04    N5'  C61  C31  C41  175.34  30.0  1
 5CI  Var_05    C11  C21  C31  C41  -65.60  30.0  3
 5CI  Var_06    O21  C11  C21  C31  -28.31  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
 5CI  chir_01  C4'  C3'  O4'  C5'  positiv
 5CI  chir_02  C3'  O3'  C2'  C4'  negativ
 5CI  chir_03  C2'  O2'  C1'  C3'  negativ
 5CI  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
 5CI  plan-1  C1'  0.020
 5CI  plan-1  N9   0.020
 5CI  plan-1  C8   0.020
 5CI  plan-1  BR8  0.020
 5CI  plan-1  N7   0.020
 5CI  plan-1  C5   0.020
 5CI  plan-1  C4   0.020
 5CI  plan-1  N3   0.020
 5CI  plan-1  C2   0.020
 5CI  plan-1  N1   0.020
 5CI  plan-1  C6   0.020
 5CI  plan-1  N6   0.020
 5CI  plan-1  H17  0.020
 5CI  plan-2  C6   0.020
 5CI  plan-2  N6   0.020
 5CI  plan-2  H18  0.020
 5CI  plan-2  H19  0.020
 5CI  plan-3  C31  0.020
 5CI  plan-3  C61  0.020
 5CI  plan-3  O51  0.020
 5CI  plan-3  N5'  0.020
 5CI  plan-3  C5'  0.020
 5CI  plan-3  H8   0.020
 5CI  plan-4  O41  0.020
 5CI  plan-4  C51  0.020
 5CI  plan-4  O31  0.020
 5CI  plan-4  C41  0.020
 5CI  plan-5  C21  0.020
 5CI  plan-5  C11  0.020
 5CI  plan-5  O21  0.020
 5CI  plan-5  O11  0.020

