# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:56:20 2021
#   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  51  32  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   OH1   0  -0.590  11.3367   7.7335  15.2943
 5CI  C51  C   C     0   0.518  11.4092   9.0600  15.3632
 5CI  O31  O   O     0  -0.427  11.1130   9.6903  16.3454
 5CI  C41  C   CH2   0  -0.551  11.8676   9.6604  14.0609
 5CI  C31  C   CT    0   0.085  13.4097   9.7659  13.9198
 5CI  C21  C   CH2   0  -0.629  14.1020   8.3871  13.8965
 5CI  C11  C   C     0   0.581  14.2623   7.7275  15.2424
 5CI  O21  O   O     0  -0.457  14.2006   8.3010  16.3083
 5CI  O11  O   OH1   0  -0.574  14.5412   6.4449  15.1302
 5CI  O71  O   OH1   0  -0.662  13.9537  10.6071  14.8870
 5CI  C61  C   C     0   0.554  13.6745  10.4705  12.5688
 5CI  O51  O   O     0  -0.461  14.1495  11.5885  12.5191
 5CI  N5'  N   NH1   0  -0.638  13.3373   9.7690  11.4754
 5CI  C5'  C   CH2   0  -0.320  13.5402  10.2607  10.1322
 5CI  C4'  C   CH1   0   0.003  14.9729  10.1501   9.6579
 5CI  O4'  O   O2    0  -0.486  15.3727   8.7911   9.6856
 5CI  C3'  C   CH1   0   0.033  15.1754  10.5633   8.1960
 5CI  O3'  O   OH1   0  -0.655  15.3276  11.9383   8.0102
 5CI  C2'  C   CH1   0  -0.064  16.4377   9.7799   7.7913
 5CI  O2'  O   OH1   0  -0.653  17.5496  10.6253   7.8387
 5CI  C1'  C   CH1   0   0.187  16.5166   8.6813   8.8889
 5CI  N9   N   NR5   0  -0.566  16.6300   7.3199   8.4299
 5CI  C8   C   CR5   0   0.289  15.7462   6.5380   7.7286
 5CI  BR8  BR  BR    0   0.048  14.1044   7.1550   7.1364
 5CI  N7   N   N     0  -0.421  16.1532   5.3299   7.5224
 5CI  C5   C   CR56  0   0.001  17.3854   5.2831   8.1220
 5CI  C4   C   CR56  0   0.507  17.6986   6.5006   8.6960
 5CI  N3   N   N     0  -0.459  18.8091   6.8002   9.3590
 5CI  C2   C   CR16  0   0.052  19.6293   5.7646   9.4304
 5CI  N1   N   N     0  -0.470  19.4612   4.5438   8.9342
 5CI  C6   C   CR6   0   0.464  18.3401   4.2587   8.2622
 5CI  N6   N   NH2   0  -0.813  18.1719   3.0380   7.7561
 5CI  H1   H   HOH1  0   0.484  11.0587   7.3668  16.1474
 5CI  H2   H   HCH2  0   0.295  11.4582  10.6692  13.9941
 5CI  H3   H   HCH2  0   0.279  11.4534   9.0798  13.2366
 5CI  H4   H   HCH2  0   0.293  13.5968   7.6907  13.2262
 5CI  H5   H   HCH2  0   0.327  15.1174   8.5040  13.5006
 5CI  H6   H   HOH1  0   0.489  14.7062   6.0567  16.0032
 5CI  H7   H   HOH1  0   0.458  14.0092  10.1028  15.7124
 5CI  H8   H   HNH1  0   0.409  12.9863   8.8309  11.5651
 5CI  H9   H   HCH2  0   0.262  13.2264  11.3036  10.0671
 5CI  H10  H   HCH2  0   0.265  12.8879   9.6859   9.4739
 5CI  H11  H   HCH1  0   0.247  15.6312  10.7557  10.2966
 5CI  H12  H   HCH1  0   0.238  14.3352  10.1758   7.6080
 5CI  H13  H   HOH1  0   0.461  14.4689  12.3144   7.8016
 5CI  H14  H   HCH1  0   0.257  16.3246   9.3370   6.7957
 5CI  H15  H   HOH1  0   0.461  18.2866  10.1856   7.4048
 5CI  H16  H   HCH1  0   0.270  17.4253   8.8611   9.4761
 5CI  H17  H   HCR6  0   0.257  20.5612   5.9300   9.9594
 5CI  H18  H   HNH2  0   0.407  18.8481   2.3172   7.9412
 5CI  H19  H   HNH2  0   0.414  17.3180   2.7805   7.2935

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    1.332  0.020  1.332
 5CI  BR8  C8   single    1.851  0.020  1.851
 5CI  N7   C8   aromatic  1.291  0.020  1.291
 5CI  N7   C5   aromatic  1.371  0.020  1.371
 5CI  C8   N9   aromatic  1.373  0.020  1.373
 5CI  C6   C5   aromatic  1.407  0.020  1.407
 5CI  C6   N1   aromatic  1.338  0.020  1.338
 5CI  C5   C4   aromatic  1.382  0.020  1.382
 5CI  C2'  O2'  single    1.398  0.020  1.398
 5CI  C2'  C3'  single    1.540  0.020  1.540
 5CI  C2'  C1'  single    1.555  0.020  1.555
 5CI  N1   C2   aromatic  1.328  0.020  1.328
 5CI  N9   C4   aromatic  1.373  0.020  1.373
 5CI  N9   C1'  single    1.441  0.020  1.441
 5CI  C4   N3   aromatic  1.328  0.020  1.328
 5CI  O3'  C3'  single    1.396  0.020  1.396
 5CI  C3'  C4'  single    1.533  0.020  1.533
 5CI  C2   N3   aromatic  1.323  0.020  1.323
 5CI  C1'  O4'  single    1.398  0.020  1.398
 5CI  O4'  C4'  single    1.417  0.020  1.417
 5CI  C4'  C5'  single    1.513  0.020  1.513
 5CI  C5'  N5'  single    1.445  0.020  1.445
 5CI  N5'  C61  single    1.342  0.020  1.342
 5CI  O51  C61  double    1.216  0.020  1.216
 5CI  C61  C31  single    1.547  0.020  1.547
 5CI  C31  C21  single    1.543  0.020  1.543
 5CI  C31  C41  single    1.552  0.020  1.552
 5CI  C31  O71  single    1.393  0.020  1.393
 5CI  C21  C11  single    1.507  0.020  1.507
 5CI  C41  C51  single    1.506  0.020  1.506
 5CI  C11  O21  double    1.212  0.020  1.212
 5CI  C11  O11  single    1.317  0.020  1.317
 5CI  O31  C51  double    1.204  0.020  1.204
 5CI  C51  O41  single    1.330  0.020  1.330
 5CI  O41  H1   single    0.850  0.020  0.980
 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  O11  H6   single    0.850  0.020  0.980
 5CI  O71  H7   single    0.850  0.020  0.980
 5CI  N5'  H8   single    0.860  0.020  1.020
 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  H1   O41  C51  110.32  3.000
 5CI  C41  C51  O31  124.87  3.000
 5CI  O31  C51  O41  123.43  3.000
 5CI  C41  C51  O41  111.68  3.000
 5CI  H3   C41  H2   107.68  3.000
 5CI  H3   C41  C31  110.19  3.000
 5CI  H2   C41  C31  107.73  3.000
 5CI  H3   C41  C51  109.02  3.000
 5CI  H2   C41  C51  107.91  3.000
 5CI  C31  C41  C51  114.09  3.000
 5CI  C61  C31  O71  105.34  3.000
 5CI  O71  C31  C21  112.02  3.000
 5CI  C61  C31  C21  108.48  3.000
 5CI  O71  C31  C41  111.48  3.000
 5CI  C21  C31  C41  112.74  3.000
 5CI  C61  C31  C41  106.29  3.000
 5CI  H5   C21  H4   105.97  3.000
 5CI  H5   C21  C11  105.70  3.000
 5CI  H4   C21  C11  108.58  3.000
 5CI  H5   C21  C31  109.02  3.000
 5CI  H4   C21  C31  111.84  3.000
 5CI  C11  C21  C31  115.17  3.000
 5CI  O11  C11  O21  123.12  3.000
 5CI  O11  C11  C21  111.87  3.000
 5CI  O21  C11  C21  124.94  3.000
 5CI  H6   O11  C11  110.44  3.000
 5CI  H7   O71  C31  107.44  3.000
 5CI  N5'  C61  O51  123.06  3.000
 5CI  O51  C61  C31  121.44  3.000
 5CI  N5'  C61  C31  115.50  3.000
 5CI  H8   N5'  C5'  116.71  3.000
 5CI  H8   N5'  C61  120.17  3.000
 5CI  C5'  N5'  C61  122.97  3.000
 5CI  H10  C5'  H9   107.20  3.000
 5CI  H10  C5'  C4'  109.79  3.000
 5CI  H9   C5'  C4'  108.87  3.000
 5CI  H10  C5'  N5'  107.33  3.000
 5CI  H9   C5'  N5'  109.91  3.000
 5CI  C4'  C5'  N5'  113.55  3.000
 5CI  H11  C4'  C3'  109.06  3.000
 5CI  H11  C4'  O4'  110.37  3.000
 5CI  C3'  C4'  O4'  103.88  3.000
 5CI  H11  C4'  C5'  110.16  3.000
 5CI  O4'  C4'  C5'  109.34  3.000
 5CI  C3'  C4'  C5'  113.85  3.000
 5CI  C1'  O4'  C4'  107.16  3.000
 5CI  H12  C3'  C2'  107.91  3.000
 5CI  H12  C3'  O3'  111.12  3.000
 5CI  C2'  C3'  O3'  112.14  3.000
 5CI  H12  C3'  C4'  108.36  3.000
 5CI  O3'  C3'  C4'  114.01  3.000
 5CI  C2'  C3'  C4'  102.82  3.000
 5CI  H13  O3'  C3'  108.49  3.000
 5CI  H14  C2'  C1'  111.17  3.000
 5CI  H14  C2'  O2'  110.94  3.000
 5CI  C1'  C2'  O2'  111.29  3.000
 5CI  H14  C2'  C3'  111.09  3.000
 5CI  C1'  C2'  C3'  102.45  3.000
 5CI  O2'  C2'  C3'  109.60  3.000
 5CI  H15  O2'  C2'  108.53  3.000
 5CI  H16  C1'  N9   105.08  3.000
 5CI  H16  C1'  C2'  107.71  3.000
 5CI  N9   C1'  C2'  116.53  3.000
 5CI  H16  C1'  O4'  111.09  3.000
 5CI  N9   C1'  O4'  108.66  3.000
 5CI  C2'  C1'  O4'  107.77  3.000
 5CI  C4   N9   C8   105.09  3.000
 5CI  C4   N9   C1'  124.29  3.000
 5CI  C8   N9   C1'  130.55  3.000
 5CI  N7   C8   BR8  122.70  3.000
 5CI  N7   C8   N9   114.30  3.000
 5CI  BR8  C8   N9   123.00  3.000
 5CI  C5   N7   C8   104.20  3.000
 5CI  C6   C5   C4   116.50  3.000
 5CI  C4   C5   N7   110.81  3.000
 5CI  C6   C5   N7   132.69  3.000
 5CI  N3   C4   C5   126.57  3.000
 5CI  N3   C4   N9   127.83  3.000
 5CI  C5   C4   N9   105.60  3.000
 5CI  C2   N3   C4   111.65  3.000
 5CI  H17  C2   N1   115.54  3.000
 5CI  H17  C2   N3   116.09  3.000
 5CI  N1   C2   N3   128.37  3.000
 5CI  C6   N1   C2   119.31  3.000
 5CI  N6   C6   N1   119.47  3.000
 5CI  N1   C6   C5   117.60  3.000
 5CI  N6   C6   C5   122.93  3.000
 5CI  H19  N6   H18  118.20  3.000
 5CI  H19  N6   C6   121.14  3.000
 5CI  H18  N6   C6   120.14  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    180.00   0.0  0
 5CI  CONST_29  H19  N6   C6   C5      0.00   0.0  0
 5CI  CONST_30  C5'  N5'  C61  C31   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  CONST_33  H1   O41  C51  O31     0.00   0.0  0
 5CI  CONST_34  H6   O11  C11  C21   180.00   0.0  0
 5CI  Var_01    C4'  C5'  N5'  C61    77.86  30.0  1
 5CI  Var_02    C31  C41  C51  O41   -87.73  30.0  2
 5CI  Var_03    C61  C31  C41  C51  -176.92  30.0  1
 5CI  Var_04    N5'  C61  C31  C41   -67.48  30.0  3
 5CI  Var_05    C11  C21  C31  C41   -78.28  30.0  3
 5CI  Var_06    O21  C11  C21  C31   -18.75  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-4  H1   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
 5CI  plan-5  H6   0.020

