# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:09:34 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(C)cnc(Cn2cnc3c(Cl)nc(N)nc23)c1C
#
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
 94M  94M  6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine  ligand  37  22  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_94M
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
 94M  N1    N   N     0  -0.456   3.4820  -1.0540   0.6299
 94M  C2    C   CR6   0   0.553   2.4273  -1.6822   0.0653
 94M  N2    N   NH2   0  -0.822   2.3887  -3.0198   0.2000
 94M  N3    N   N     0  -0.473   1.4216  -1.0909  -0.5803
 94M  C4    C   CR56  0   0.528   1.5321   0.2218  -0.6214
 94M  C5    C   CR56  0   0.108   2.5618   0.9938  -0.0701
 94M  C6    C   CR6   0   0.111   3.5407   0.2483   0.5601
 94M  CL6   CL  CL    0  -0.082   4.8925   1.0351   1.2850
 94M  N7    N   N     0  -0.440   2.3447   2.3285  -0.2977
 94M  C8    C   CR15  0   0.118   1.2271   2.3558  -0.9578
 94M  N9    N   NR5   0  -0.490   0.6931   1.1179  -1.2003
 94M  CAA   C   CH3   0  -0.415  -5.2447  -1.8006  -0.3759
 94M  CAF   C   CR16  0  -0.129  -2.7848   1.6331   0.9279
 94M  CAH   C   CH2   0  -0.398  -0.5776   0.8193  -1.8230
 94M  NAI   N   N     0  -0.409  -1.8560   1.6948  -0.0119
 94M  CAN   C   CR6   0  -0.068  -3.5971   0.5278   1.1426
 94M  CAP   C   CR6   0  -0.029  -2.3819  -0.5524  -0.6632
 94M  CAR   C   CR6   0   0.192  -1.6591   0.6357  -0.7852
 94M  CAS   C   CR6   0   0.393  -3.3795  -0.5728   0.3162
 94M  HN2   H   HNH2  0   0.401   3.2120  -3.5047   0.5109
 94M  HN2A  H   HNH2  0   0.401   1.7213  -3.5431  -0.3396
 94M  H8    H   HCR5  0   0.295   0.7357   3.2485  -1.3142
 94M  HAA   H   HCH3  0   0.246  -5.7622  -2.7223  -0.1203
 94M  HAAA  H   HCH3  0   0.230  -5.9352  -0.9615  -0.2614
 94M  HAAB  H   HCH3  0   0.230  -4.9274  -1.8513  -1.4203
 94M  HAB   H   HCH3  0   0.248  -5.6477   0.4416   1.8024
 94M  HABA  H   HCH3  0   0.252  -4.5092  -0.3258   2.8957
 94M  HABB  H   HCH3  0   0.247  -4.5964   1.4314   2.8045
 94M  HAC   H   HCH3  0   0.265  -1.0206  -1.9702  -1.5211
 94M  HACA  H   HCH3  0   0.263  -2.5901  -2.6449  -1.1265
 94M  HACB  H   HCH3  0   0.256  -2.4118  -1.6181  -2.5418
 94M  HAF   H   HCR6  0   0.257  -2.9065   2.5158   1.5482
 94M  HAH   H   HCH2  0   0.300  -0.8314   1.6566  -2.4734
 94M  HAHA  H   HCH2  0   0.292  -0.4531  -0.0517  -2.4616
 94M  CAB   C   CH3   0  -0.717  -4.6408   0.5161   2.2162
 94M  CAC   C   CH3   0  -0.775  -2.0898  -1.7585  -1.5087
 94M  OAM   O   O2    0  -0.482  -4.1339  -1.6852   0.5071

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
 94M  N1   C2    aromatic  1.351  0.020  1.351
 94M  N1   C6    aromatic  1.305  0.020  1.305
 94M  C2   N2    single    1.345  0.020  1.345
 94M  C2   N3    aromatic  1.333  0.020  1.333
 94M  N3   C4    aromatic  1.318  0.020  1.318
 94M  C4   C5    aromatic  1.400  0.020  1.400
 94M  C4   N9    aromatic  1.357  0.020  1.357
 94M  C5   C6    aromatic  1.382  0.020  1.382
 94M  C5   N7    aromatic  1.371  0.020  1.371
 94M  C6   CL6   single    1.724  0.020  1.724
 94M  N7   C8    aromatic  1.298  0.020  1.298
 94M  C8   N9    aromatic  1.370  0.020  1.370
 94M  N9   CAH   single    1.446  0.020  1.446
 94M  CAA  OAM   single    1.424  0.020  1.424
 94M  CAB  CAN   single    1.497  0.020  1.497
 94M  CAC  CAP   single    1.502  0.020  1.502
 94M  CAF  NAI   aromatic  1.323  0.020  1.323
 94M  CAF  CAN   aromatic  1.388  0.020  1.388
 94M  CAH  CAR   single    1.510  0.020  1.510
 94M  NAI  CAR   aromatic  1.326  0.020  1.326
 94M  OAM  CAS   single    1.358  0.020  1.358
 94M  CAN  CAS   aromatic  1.393  0.020  1.393
 94M  CAP  CAR   aromatic  1.396  0.020  1.396
 94M  CAP  CAS   aromatic  1.398  0.020  1.398
 94M  N2   HN2   single    0.890  0.020  1.040
 94M  N2   HN2A  single    0.890  0.020  1.040
 94M  C8   H8    single    0.930  0.020  1.080
 94M  CAA  HAA   single    0.970  0.020  1.090
 94M  CAA  HAAA  single    0.970  0.020  1.090
 94M  CAA  HAAB  single    0.970  0.020  1.090
 94M  CAB  HAB   single    0.970  0.020  1.090
 94M  CAB  HABA  single    0.970  0.020  1.090
 94M  CAB  HABB  single    0.970  0.020  1.090
 94M  CAC  HAC   single    0.970  0.020  1.090
 94M  CAC  HACA  single    0.970  0.020  1.090
 94M  CAC  HACB  single    0.970  0.020  1.090
 94M  CAF  HAF   single    0.930  0.020  1.080
 94M  CAH  HAH   single    0.970  0.020  1.090
 94M  CAH  HAHA  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
 94M  C6    N1   C2    118.46  3.000
 94M  N3    C2   N2    117.90  3.000
 94M  N3    C2   N1    125.80  3.000
 94M  N2    C2   N1    116.29  3.000
 94M  HN2A  N2   HN2   117.32  3.000
 94M  HN2A  N2   C2    118.89  3.000
 94M  HN2   N2   C2    119.17  3.000
 94M  C4    N3   C2    113.18  3.000
 94M  N9    C4   C5    104.98  3.000
 94M  N9    C4   N3    128.25  3.000
 94M  C5    C4   N3    126.77  3.000
 94M  N7    C5   C6    135.46  3.000
 94M  N7    C5   C4    110.79  3.000
 94M  C6    C5   C4    113.76  3.000
 94M  CL6   C6   C5    120.05  3.000
 94M  CL6   C6   N1    117.91  3.000
 94M  C5    C6   N1    122.04  3.000
 94M  C8    N7   C5    103.96  3.000
 94M  H8    C8   N9    120.76  3.000
 94M  H8    C8   N7    125.25  3.000
 94M  N9    C8   N7    113.99  3.000
 94M  CAH   N9   C8    127.25  3.000
 94M  CAH   N9   C4    126.19  3.000
 94M  C8    N9   C4    106.27  3.000
 94M  HAAB  CAA  HAAA  108.62  3.000
 94M  HAAB  CAA  HAA   108.87  3.000
 94M  HAAA  CAA  HAA   109.00  3.000
 94M  HAAB  CAA  OAM   111.71  3.000
 94M  HAAA  CAA  OAM   111.46  3.000
 94M  HAA   CAA  OAM   107.11  3.000
 94M  HAF   CAF  CAN   119.56  3.000
 94M  HAF   CAF  NAI   116.53  3.000
 94M  CAN   CAF  NAI   123.91  3.000
 94M  HAHA  CAH  HAH   106.95  3.000
 94M  HAHA  CAH  CAR   112.85  3.000
 94M  HAH   CAH  CAR   109.67  3.000
 94M  HAHA  CAH  N9    108.52  3.000
 94M  HAH   CAH  N9    107.63  3.000
 94M  CAR   CAH  N9    111.01  3.000
 94M  CAR   NAI  CAF   118.77  3.000
 94M  CAS   CAN  CAF   116.47  3.000
 94M  CAS   CAN  CAB   121.87  3.000
 94M  CAF   CAN  CAB   121.66  3.000
 94M  CAS   CAP  CAR   116.29  3.000
 94M  CAS   CAP  CAC   121.43  3.000
 94M  CAR   CAP  CAC   122.26  3.000
 94M  CAP   CAR  NAI   123.50  3.000
 94M  CAP   CAR  CAH   122.30  3.000
 94M  NAI   CAR  CAH   114.21  3.000
 94M  CAP   CAS  CAN   121.02  3.000
 94M  CAP   CAS  OAM   120.45  3.000
 94M  CAN   CAS  OAM   118.50  3.000
 94M  HABB  CAB  HABA  107.91  3.000
 94M  HABB  CAB  HAB   107.45  3.000
 94M  HABA  CAB  HAB   107.16  3.000
 94M  HABB  CAB  CAN   110.64  3.000
 94M  HABA  CAB  CAN   111.65  3.000
 94M  HAB   CAB  CAN   111.83  3.000
 94M  HACB  CAC  HACA  107.58  3.000
 94M  HACB  CAC  HAC   107.67  3.000
 94M  HACA  CAC  HAC   107.28  3.000
 94M  HACB  CAC  CAP   111.86  3.000
 94M  HACA  CAC  CAP   111.56  3.000
 94M  HAC   CAC  CAP   110.68  3.000
 94M  CAS   OAM  CAA   114.38  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
 94M  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 94M  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 94M  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 94M  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 94M  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 94M  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 94M  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 94M  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 94M  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 94M  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 94M  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 94M  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 94M  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 94M  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 94M  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 94M  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 94M  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 94M  CONST_18  CAP   CAR  NAI  CAF     0.00   0.0  0
 94M  CONST_19  CAP   CAS  CAN  CAF     0.00   0.0  0
 94M  CONST_20  CAS   CAN  CAF  NAI     0.00   0.0  0
 94M  CONST_21  CAS   CAP  CAR  NAI     0.00   0.0  0
 94M  CONST_22  CAR   NAI  CAF  CAN     0.00   0.0  0
 94M  CONST_23  CAR   CAP  CAS  CAN     0.00   0.0  0
 94M  CONST_24  CL6   C6   N1   C2    180.00   0.0  0
 94M  CONST_25  C6    N1   C2   N2    180.00   0.0  0
 94M  CONST_26  C4    N3   C2   N2    180.00   0.0  0
 94M  CONST_27  CAH   N9   C4   N3      0.00   0.0  0
 94M  CONST_28  CL6   C6   C5   C4    180.00   0.0  0
 94M  CONST_29  CAH   N9   C4   C5    180.00   0.0  0
 94M  CONST_30  N7    C5   C6   CL6     0.00   0.0  0
 94M  CONST_31  CAH   N9   C8   N7    180.00   0.0  0
 94M  CONST_32  NAI   CAF  CAN  CAB   180.00   0.0  0
 94M  CONST_33  CAP   CAS  CAN  CAB   180.00   0.0  0
 94M  CONST_34  NAI   CAR  CAP  CAC   180.00   0.0  0
 94M  CONST_35  CAN   CAS  CAP  CAC   180.00   0.0  0
 94M  CONST_36  CAH   CAR  NAI  CAF   180.00   0.0  0
 94M  CONST_37  OAM   CAS  CAN  CAF   180.00   0.0  0
 94M  CONST_38  CAS   CAP  CAR  CAH   180.00   0.0  0
 94M  CONST_39  CAR   CAP  CAS  OAM   180.00   0.0  0
 94M  CONST_40  H8    C8   N9   C4    180.00   0.0  0
 94M  CONST_41  HAF   CAF  NAI  CAR   180.00   0.0  0
 94M  CONST_42  HN2   N2   C2   N1      0.00   0.0  0
 94M  CONST_43  HN2A  N2   C2   N1    180.00   0.0  0
 94M  Var_01    CAR   CAH  N9   C4     79.11  30.0  2
 94M  Var_02    NAI   CAR  CAH  N9     59.47  30.0  2
 94M  Var_03    CAN   CAS  OAM  CAA    98.12  30.0  2
 94M  Var_04    HAB   CAB  CAN  CAF   115.52  30.0  2
 94M  Var_05    HAC   CAC  CAP  CAR    47.74  30.0  2
 94M  Var_06    HAA   CAA  OAM  CAS  -179.87  30.0  3

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
 94M  plan-1  CAF   0.020
 94M  plan-1  CAH   0.020
 94M  plan-1  NAI   0.020
 94M  plan-1  CAN   0.020
 94M  plan-1  CAP   0.020
 94M  plan-1  CAR   0.020
 94M  plan-1  CAS   0.020
 94M  plan-1  HAF   0.020
 94M  plan-1  CAB   0.020
 94M  plan-1  CAC   0.020
 94M  plan-1  OAM   0.020
 94M  plan-2  N1    0.020
 94M  plan-2  C2    0.020
 94M  plan-2  N2    0.020
 94M  plan-2  N3    0.020
 94M  plan-2  C4    0.020
 94M  plan-2  C5    0.020
 94M  plan-2  C6    0.020
 94M  plan-2  CL6   0.020
 94M  plan-2  N7    0.020
 94M  plan-2  C8    0.020
 94M  plan-2  N9    0.020
 94M  plan-2  CAH   0.020
 94M  plan-2  H8    0.020
 94M  plan-3  C2    0.020
 94M  plan-3  N2    0.020
 94M  plan-3  HN2   0.020
 94M  plan-3  HN2A  0.020

