# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:50:46 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-[(2-methyl-1,3-thiazol-4-yl)methyl]-3H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1scc(Cn2cnc(N)c3ncnc23)n1
#
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
 W5A  W5A  3-[(2-methyl-1,3-thiazol-4-yl)methyl]-3H-purin-6-amine  ligand  27  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W5A
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
 W5A  C10   C  CR5   0   0.343  -44.5492  -28.6364   1.2379
 W5A  C13   C  CR5   0   0.056  -44.8227  -26.6915   0.2397
 W5A  C02   C  CR6   0   0.450  -47.6383  -28.9447   5.0251
 W5A  C03   C  CR56  0   0.033  -46.2575  -28.9979   5.2466
 W5A  C05   C  CR15  0   0.001  -44.2612  -28.9932   5.8688
 W5A  C07   C  CR56  0   0.434  -45.4196  -29.3444   4.1828
 W5A  C09   C  CH2   0  -0.426  -45.0807  -29.9080   1.8136
 W5A  C11   C  CR15  0  -0.533  -43.2471  -28.2601   1.2193
 W5A  C14   C  CH3   0  -0.725  -45.4943  -25.5296  -0.4025
 W5A  C16   C  CR16  0   0.159  -47.2766  -29.5554   2.8363
 W5A  N01   N  NH2   0  -0.804  -48.5188  -28.6193   5.9630
 W5A  N04   N  N     0  -0.471  -45.4786  -28.7726   6.3393
 W5A  N06   N  N     0  -0.479  -44.1510  -29.3444   4.5641
 W5A  N08   N  NR6   0  -0.475  -45.9455  -29.6341   2.9563
 W5A  N15   N  N     0  -0.384  -45.4265  -27.7448   0.6851
 W5A  N17   N  N     0  -0.475  -48.1066  -29.2397   3.7895
 W5A  S12   S  S2    0   0.219  -43.1046  -26.7272   0.4685
 W5A  H051  H  HCR5  0   0.237  -43.3818  -28.8981   6.4927
 W5A  H092  H  HCH2  0   0.302  -45.6696  -30.4500   1.0737
 W5A  H091  H  HCH2  0   0.300  -44.2717  -30.5578   2.1404
 W5A  H111  H  HCR5  0   0.307  -42.3916  -28.7933   1.6023
 W5A  H142  H  HCH3  0   0.264  -44.9851  -25.2298  -1.3175
 W5A  H141  H  HCH3  0   0.267  -46.5224  -25.7891  -0.6446
 W5A  H143  H  HCH3  0   0.269  -45.5065  -24.6677   0.2659
 W5A  H161  H  HCR6  0   0.301  -47.6771  -29.7875   1.8577
 W5A  H012  H  HNH2  0   0.410  -49.5033  -28.5998   5.7582
 W5A  H011  H  HNH2  0   0.417  -48.2200  -28.4053   6.8988

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
 W5A  C14  C13   single    1.488  0.020  1.488
 W5A  C13  S12   aromatic  1.734  0.020  1.734
 W5A  C13  N15   aromatic  1.293  0.020  1.293
 W5A  S12  C11   aromatic  1.713  0.020  1.713
 W5A  N15  C10   aromatic  1.368  0.020  1.368
 W5A  C10  C11   aromatic  1.356  0.020  1.356
 W5A  C10  C09   single    1.494  0.020  1.494
 W5A  C09  N08   single    1.459  0.020  1.459
 W5A  C16  N08   aromatic  1.339  0.020  1.339
 W5A  C16  N17   aromatic  1.303  0.020  1.303
 W5A  N08  C07   aromatic  1.366  0.020  1.366
 W5A  N17  C02   aromatic  1.354  0.020  1.354
 W5A  C07  N06   aromatic  1.325  0.020  1.325
 W5A  C07  C03   aromatic  1.398  0.020  1.398
 W5A  N06  C05   aromatic  1.356  0.020  1.356
 W5A  C02  C03   aromatic  1.400  0.020  1.400
 W5A  C02  N01   single    1.327  0.020  1.327
 W5A  C03  N04   aromatic  1.361  0.020  1.361
 W5A  C05  N04   aromatic  1.324  0.020  1.324
 W5A  C05  H051  single    0.930  0.020  1.080
 W5A  C09  H092  single    0.970  0.020  1.090
 W5A  C09  H091  single    0.970  0.020  1.090
 W5A  C11  H111  single    0.930  0.020  1.080
 W5A  C14  H142  single    0.970  0.020  1.090
 W5A  C14  H141  single    0.970  0.020  1.090
 W5A  C14  H143  single    0.970  0.020  1.090
 W5A  C16  H161  single    0.930  0.020  1.080
 W5A  N01  H012  single    0.860  0.020  1.020
 W5A  N01  H011  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
 W5A  N15   C10  C11   115.45  3.000
 W5A  C11   C10  C09   125.69  3.000
 W5A  N15   C10  C09   118.86  3.000
 W5A  S12   C13  N15   113.61  3.000
 W5A  N15   C13  C14   125.03  3.000
 W5A  S12   C13  C14   121.36  3.000
 W5A  N17   C02  N01   117.97  3.000
 W5A  N01   C02  C03   123.52  3.000
 W5A  N17   C02  C03   118.51  3.000
 W5A  N04   C03  C07   108.01  3.000
 W5A  N04   C03  C02   133.28  3.000
 W5A  C07   C03  C02   118.71  3.000
 W5A  H051  C05  N06   120.76  3.000
 W5A  H051  C05  N04   121.86  3.000
 W5A  N06   C05  N04   117.39  3.000
 W5A  N08   C07  N06   128.85  3.000
 W5A  N06   C07  C03   110.79  3.000
 W5A  N08   C07  C03   120.35  3.000
 W5A  H091  C09  H092  107.98  3.000
 W5A  H091  C09  N08   108.52  3.000
 W5A  H092  C09  N08   107.74  3.000
 W5A  H091  C09  C10   111.08  3.000
 W5A  H092  C09  C10   110.73  3.000
 W5A  N08   C09  C10   110.67  3.000
 W5A  H111  C11  S12   122.16  3.000
 W5A  H111  C11  C10   128.31  3.000
 W5A  S12   C11  C10   109.53  3.000
 W5A  H143  C14  H141  108.32  3.000
 W5A  H143  C14  H142  107.61  3.000
 W5A  H141  C14  H142  108.70  3.000
 W5A  H143  C14  C13   110.95  3.000
 W5A  H141  C14  C13   109.66  3.000
 W5A  H142  C14  C13   111.50  3.000
 W5A  H161  C16  N17   118.53  3.000
 W5A  H161  C16  N08   115.86  3.000
 W5A  N17   C16  N08   125.60  3.000
 W5A  H011  N01  H012  118.44  3.000
 W5A  H011  N01  C02   120.86  3.000
 W5A  H012  N01  C02   120.69  3.000
 W5A  C05   N04  C03   102.32  3.000
 W5A  C07   N06  C05   101.49  3.000
 W5A  C16   N08  C09   122.02  3.000
 W5A  C16   N08  C07   116.80  3.000
 W5A  C09   N08  C07   121.00  3.000
 W5A  C13   N15  C10   111.76  3.000
 W5A  C16   N17  C02   120.01  3.000
 W5A  C11   S12  C13    89.65  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
 W5A  CONST_01  S12   C13  N15  C10     0.00   0.0  0
 W5A  CONST_02  C13   S12  C11  C10     0.00   0.0  0
 W5A  CONST_03  C11   C10  N15  C13     0.00   0.0  0
 W5A  CONST_04  N08   C16  N17  C02     0.00   0.0  0
 W5A  CONST_05  N08   C07  C03  C02     0.00   0.0  0
 W5A  CONST_06  N06   C07  C03  C02   180.00   0.0  0
 W5A  CONST_07  C05   N04  C03  C02   180.00   0.0  0
 W5A  CONST_08  C16   N08  C07  C03     0.00   0.0  0
 W5A  CONST_09  C05   N06  C07  C03     0.00   0.0  0
 W5A  CONST_10  C16   N17  C02  C03     0.00   0.0  0
 W5A  CONST_11  N06   C05  N04  C03     0.00   0.0  0
 W5A  CONST_12  N08   C07  N06  C05   180.00   0.0  0
 W5A  CONST_13  C07   C03  N04  C05     0.00   0.0  0
 W5A  CONST_14  N17   C16  N08  C07     0.00   0.0  0
 W5A  CONST_15  N04   C05  N06  C07     0.00   0.0  0
 W5A  CONST_16  N17   C02  C03  C07     0.00   0.0  0
 W5A  CONST_17  N15   C13  S12  C11     0.00   0.0  0
 W5A  CONST_18  N06   C07  N08  C16   180.00   0.0  0
 W5A  CONST_19  N08   C07  C03  N04   180.00   0.0  0
 W5A  CONST_20  N06   C07  C03  N04     0.00   0.0  0
 W5A  CONST_21  N17   C02  C03  N04   180.00   0.0  0
 W5A  CONST_22  S12   C11  C10  N15     0.00   0.0  0
 W5A  CONST_23  C14   C13  N15  C10   180.00   0.0  0
 W5A  CONST_24  C09   C10  N15  C13   180.00   0.0  0
 W5A  CONST_25  C09   N08  C07  C03   180.00   0.0  0
 W5A  CONST_26  N01   C02  C03  C07   180.00   0.0  0
 W5A  CONST_27  S12   C11  C10  C09   180.00   0.0  0
 W5A  CONST_28  N17   C16  N08  C09   180.00   0.0  0
 W5A  CONST_29  N06   C07  N08  C09     0.00   0.0  0
 W5A  CONST_30  C14   C13  S12  C11   180.00   0.0  0
 W5A  CONST_31  N01   C02  N17  C16   180.00   0.0  0
 W5A  CONST_32  N04   C03  C02  N01     0.00   0.0  0
 W5A  CONST_33  H111  C11  S12  C13   180.00   0.0  0
 W5A  CONST_34  H161  C16  N17  C02   180.00   0.0  0
 W5A  CONST_35  H051  C05  N04  C03   180.00   0.0  0
 W5A  CONST_36  H012  N01  C02  C03   180.00   0.0  0
 W5A  CONST_37  H011  N01  C02  C03     0.00   0.0  0
 W5A  Var_01    C16   N08  C09  C10    95.94  30.0  2
 W5A  Var_02    N08   C09  C10  C11   115.08  30.0  2
 W5A  Var_03    H142  C14  C13  N15  -133.18  30.0  2

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
 W5A  plan-1  C10   0.020
 W5A  plan-1  C13   0.020
 W5A  plan-1  C09   0.020
 W5A  plan-1  C11   0.020
 W5A  plan-1  C14   0.020
 W5A  plan-1  N15   0.020
 W5A  plan-1  S12   0.020
 W5A  plan-1  H111  0.020
 W5A  plan-2  C02   0.020
 W5A  plan-2  C03   0.020
 W5A  plan-2  C05   0.020
 W5A  plan-2  C07   0.020
 W5A  plan-2  C09   0.020
 W5A  plan-2  C16   0.020
 W5A  plan-2  N01   0.020
 W5A  plan-2  N04   0.020
 W5A  plan-2  N06   0.020
 W5A  plan-2  N08   0.020
 W5A  plan-2  N17   0.020
 W5A  plan-2  H051  0.020
 W5A  plan-2  H161  0.020
 W5A  plan-3  C02   0.020
 W5A  plan-3  N01   0.020
 W5A  plan-3  H012  0.020
 W5A  plan-3  H011  0.020

