# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:17:59 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: [(1S,3S,4S)-3-(6-amino-9H-purin-9-yl)bicyclo[2.2.1]hept-1-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@]4(CO)CC[C@H]3C4
#
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
 M59  M59  '[(1S,3S,4S)-3-(6-amino-9H-purin-9-yl)bicyclo[2.2.1]hept-1-yl]methanol'  ligand  36  19  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M59
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
 M59  C2   C  CR56  0   0.479   1.6963   0.3147  -0.1392
 M59  N3   N  N     0  -0.459   2.0189   1.5954  -0.3177
 M59  C4   C  CR16  0   0.039   3.3216   1.7903  -0.2232
 M59  N5   N  N     0  -0.475   4.2775   0.8949   0.0159
 M59  C6   C  CR6   0   0.451   3.9389  -0.3866   0.1935
 M59  C7   C  CR56  0  -0.005   2.5751  -0.7254   0.1204
 M59  N8   N  NH2   0  -0.818   4.8930  -1.2860   0.4463
 M59  N14  N  N     0  -0.455   1.8976  -1.9074   0.2547
 M59  C15  C  CR15  0   0.100   0.6483  -1.5808   0.0787
 M59  N18  N  NR5   0  -0.513   0.4559  -0.2521  -0.1741
 M59  C1   C  CH1   0  -0.068  -0.7787   0.5022  -0.3481
 M59  C3   C  CH2   0  -0.452  -1.9310  -0.3053  -0.9912
 M59  C5   C  CT    0  -0.105  -3.0681  -0.1990   0.0418
 M59  C8   C  CH2   0  -0.421  -3.5814   1.2515   0.0201
 M59  C9   C  CH2   0  -0.445  -2.4166   2.0493   0.6603
 M59  C10  C  CH1   0  -0.261  -1.3832   0.9633   0.9904
 M59  C11  C  CH2   0  -0.433  -2.2843  -0.2149   1.3607
 M59  C12  C  CH2   0  -0.148  -4.1309  -1.2615  -0.0818
 M59  O13  O  OH1   0  -0.672  -4.7641  -1.1385  -1.3363
 M59  H1   H  HCR6  0   0.249   3.6636   2.8112  -0.3570
 M59  H2   H  HNH2  0   0.402   5.8609  -1.0157   0.4154
 M59  H3   H  HNH2  0   0.409   4.6771  -2.2661   0.4921
 M59  H4   H  HCR5  0   0.288  -0.1709  -2.2811   0.1185
 M59  H5   H  HCH1  0   0.273  -0.5010   1.3610  -0.9596
 M59  H6   H  HCH2  0   0.261  -2.2079   0.1044  -1.9618
 M59  H7   H  HCH2  0   0.253  -1.6569  -1.3488  -1.1609
 M59  H8   H  HCH2  0   0.234  -3.8233   1.5907  -0.9878
 M59  H9   H  HCH2  0   0.233  -4.4904   1.3391   0.6201
 M59  H10  H  HCH2  0   0.235  -2.0084   2.8163  -0.0012
 M59  H11  H  HCH2  0   0.244  -2.7385   2.5514   1.5736
 M59  H12  H  HCH1  0   0.244  -0.6330   1.2654   1.7214
 M59  H13  H  HCH2  0   0.248  -2.9126  -0.0116   2.2314
 M59  H14  H  HCH2  0   0.240  -1.7544  -1.1535   1.5434
 M59  H15  H  HCH2  0   0.196  -3.6666  -2.2508   0.0364
 M59  H16  H  HCH2  0   0.196  -4.8469  -1.1444   0.7435
 M59  H17  H  HOH1  0   0.454  -5.4093  -1.8463  -1.4184

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
 M59  N5   C4   aromatic  1.331  0.020  1.331
 M59  N5   C6   aromatic  1.337  0.020  1.337
 M59  C4   N3   aromatic  1.321  0.020  1.321
 M59  N8   C6   single    1.335  0.020  1.335
 M59  C6   C7   aromatic  1.407  0.020  1.407
 M59  N3   C2   aromatic  1.333  0.020  1.333
 M59  C7   C2   aromatic  1.386  0.020  1.386
 M59  C7   N14  aromatic  1.369  0.020  1.369
 M59  C2   N18  aromatic  1.364  0.020  1.364
 M59  N14  C15  aromatic  1.303  0.020  1.303
 M59  N18  C1   single    1.457  0.020  1.457
 M59  N18  C15  aromatic  1.366  0.020  1.366
 M59  C1   C3   single    1.547  0.020  1.547
 M59  C1   C10  single    1.539  0.020  1.539
 M59  C3   C5   single    1.540  0.020  1.540
 M59  C10  C9   single    1.535  0.020  1.535
 M59  C10  C11  single    1.529  0.020  1.529
 M59  C9   C8   single    1.550  0.020  1.550
 M59  C5   C11  single    1.534  0.020  1.534
 M59  C5   C8   single    1.539  0.020  1.539
 M59  C5   C12  single    1.508  0.020  1.508
 M59  C12  O13  single    1.411  0.020  1.411
 M59  C4   H1   single    0.930  0.020  1.080
 M59  N8   H2   single    0.860  0.020  1.020
 M59  N8   H3   single    0.860  0.020  1.020
 M59  C15  H4   single    0.930  0.020  1.080
 M59  C1   H5   single    0.970  0.020  1.090
 M59  C3   H6   single    0.970  0.020  1.090
 M59  C3   H7   single    0.970  0.020  1.090
 M59  C8   H8   single    0.970  0.020  1.090
 M59  C8   H9   single    0.970  0.020  1.090
 M59  C9   H10  single    0.970  0.020  1.090
 M59  C9   H11  single    0.970  0.020  1.090
 M59  C10  H12  single    0.970  0.020  1.090
 M59  C11  H13  single    0.970  0.020  1.090
 M59  C11  H14  single    0.970  0.020  1.090
 M59  C12  H15  single    0.970  0.020  1.090
 M59  C12  H16  single    0.970  0.020  1.090
 M59  O13  H17  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
 M59  N18  C2   C7   105.63  3.000
 M59  N18  C2   N3   128.02  3.000
 M59  C7   C2   N3   126.35  3.000
 M59  C4   N3   C2   111.78  3.000
 M59  H1   C4   N5   115.38  3.000
 M59  H1   C4   N3   116.17  3.000
 M59  N5   C4   N3   128.45  3.000
 M59  C6   N5   C4   119.11  3.000
 M59  N8   C6   C7   122.70  3.000
 M59  C7   C6   N5   117.99  3.000
 M59  N8   C6   N5   119.31  3.000
 M59  N14  C7   C6   133.03  3.000
 M59  N14  C7   C2   110.64  3.000
 M59  C6   C7   C2   116.33  3.000
 M59  H3   N8   H2   118.07  3.000
 M59  H3   N8   C6   120.80  3.000
 M59  H2   N8   C6   120.07  3.000
 M59  C15  N14  C7   104.17  3.000
 M59  H4   C15  N18  122.10  3.000
 M59  H4   C15  N14  124.09  3.000
 M59  N18  C15  N14  113.81  3.000
 M59  C1   N18  C15  130.15  3.000
 M59  C15  N18  C2   105.74  3.000
 M59  C1   N18  C2   123.94  3.000
 M59  H5   C1   C10  110.59  3.000
 M59  H5   C1   C3   111.58  3.000
 M59  C10  C1   C3   103.02  3.000
 M59  H5   C1   N18  105.00  3.000
 M59  C10  C1   N18  112.58  3.000
 M59  C3   C1   N18  114.24  3.000
 M59  H7   C3   H6   106.54  3.000
 M59  H7   C3   C5   110.83  3.000
 M59  H6   C3   C5   112.59  3.000
 M59  H7   C3   C1   112.10  3.000
 M59  H6   C3   C1   111.31  3.000
 M59  C5   C3   C1   103.60  3.000
 M59  C12  C5   C11  115.04  3.000
 M59  C12  C5   C8   115.33  3.000
 M59  C11  C5   C8   101.09  3.000
 M59  C12  C5   C3   114.64  3.000
 M59  C8   C5   C3   107.57  3.000
 M59  C11  C5   C3   101.46  3.000
 M59  H9   C8   H8   107.34  3.000
 M59  H9   C8   C9   110.91  3.000
 M59  H8   C8   C9   112.85  3.000
 M59  H9   C8   C5   110.20  3.000
 M59  H8   C8   C5   112.35  3.000
 M59  C9   C8   C5   103.22  3.000
 M59  H11  C9   H10  107.11  3.000
 M59  H11  C9   C10  110.14  3.000
 M59  H10  C9   C10  112.06  3.000
 M59  H11  C9   C8   111.15  3.000
 M59  H10  C9   C8   113.09  3.000
 M59  C10  C9   C8   103.33  3.000
 M59  H12  C10  C11  117.18  3.000
 M59  H12  C10  C9   114.29  3.000
 M59  C11  C10  C9   101.56  3.000
 M59  H12  C10  C1   113.32  3.000
 M59  C11  C10  C1   102.20  3.000
 M59  C9   C10  C1   106.82  3.000
 M59  H14  C11  H13  107.77  3.000
 M59  H14  C11  C10  114.61  3.000
 M59  H13  C11  C10  112.87  3.000
 M59  H14  C11  C5   113.58  3.000
 M59  H13  C11  C5   112.91  3.000
 M59  C10  C11  C5    94.87  3.000
 M59  H16  C12  H15  106.88  3.000
 M59  H16  C12  O13  111.48  3.000
 M59  H15  C12  O13  111.33  3.000
 M59  H16  C12  C5   108.82  3.000
 M59  H15  C12  C5   109.12  3.000
 M59  O13  C12  C5   109.14  3.000
 M59  H17  O13  C12  108.24  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
 M59  CONST_01  N5   C4   N3   C2     0.00   0.0  0
 M59  CONST_02  N5   C6   C7   C2     0.00   0.0  0
 M59  CONST_03  C15  N14  C7   C2     0.00   0.0  0
 M59  CONST_04  N14  C15  N18  C2     0.00   0.0  0
 M59  CONST_05  C6   N5   C4   N3     0.00   0.0  0
 M59  CONST_06  C6   C7   C2   N3     0.00   0.0  0
 M59  CONST_07  N14  C7   C2   N3   180.00   0.0  0
 M59  CONST_08  C15  N18  C2   N3   180.00   0.0  0
 M59  CONST_09  C7   C6   N5   C4     0.00   0.0  0
 M59  CONST_10  C7   C2   N3   C4     0.00   0.0  0
 M59  CONST_11  N18  C2   N3   C4   180.00   0.0  0
 M59  CONST_12  N14  C7   C6   N5   180.00   0.0  0
 M59  CONST_13  N18  C2   C7   C6   180.00   0.0  0
 M59  CONST_14  C15  N14  C7   C6   180.00   0.0  0
 M59  CONST_15  C15  N18  C2   C7     0.00   0.0  0
 M59  CONST_16  N18  C15  N14  C7     0.00   0.0  0
 M59  CONST_17  N18  C2   C7   N14    0.00   0.0  0
 M59  CONST_18  C1   N18  C2   N3     0.00   0.0  0
 M59  CONST_19  C1   N18  C2   C7   180.00   0.0  0
 M59  CONST_20  C1   N18  C15  N14  180.00   0.0  0
 M59  CONST_21  N8   C6   C7   C2   180.00   0.0  0
 M59  CONST_22  N8   C6   N5   C4   180.00   0.0  0
 M59  CONST_23  N14  C7   C6   N8     0.00   0.0  0
 M59  CONST_24  H1   C4   N3   C2   180.00   0.0  0
 M59  CONST_25  H4   C15  N18  C2   180.00   0.0  0
 M59  CONST_26  H2   N8   C6   N5     0.00   0.0  0
 M59  CONST_27  H3   N8   C6   N5   180.00   0.0  0
 M59  Var_01    C10  C9   C8   C5    -0.74  30.0  1

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
 M59  chir_01  C1   N18  C3  C10  negativ
 M59  chir_02  C5   C3   C8  C12  negativ
 M59  chir_03  C10  C1   C9  C11  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
 M59  plan-1  C2   0.020
 M59  plan-1  N3   0.020
 M59  plan-1  C4   0.020
 M59  plan-1  N5   0.020
 M59  plan-1  C6   0.020
 M59  plan-1  C7   0.020
 M59  plan-1  N8   0.020
 M59  plan-1  N14  0.020
 M59  plan-1  C15  0.020
 M59  plan-1  N18  0.020
 M59  plan-1  C1   0.020
 M59  plan-1  H1   0.020
 M59  plan-1  H4   0.020
 M59  plan-2  C6   0.020
 M59  plan-2  N8   0.020
 M59  plan-2  H2   0.020
 M59  plan-2  H3   0.020

