# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:15:19 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: 9-methyl-9H-purine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2c(N)nc(N)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
 W5M  W5M  9-methyl-9H-purine-2,6-diamine  ligand  20  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W5M
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
 W5M  C01   C  CH3   0  -0.527  -45.4539  -29.2518  2.0601
 W5M  C03   C  CR15  0   0.090  -47.7256  -28.8707  3.0755
 W5M  C05   C  CR56  0  -0.042  -47.3076  -29.0534  5.1336
 W5M  C06   C  CR6   0   0.453  -47.2648  -29.1266  6.5390
 W5M  C09   C  CR6   0   0.518  -44.9970  -29.5226  6.3739
 W5M  C12   C  CR56  0   0.493  -46.0959  -29.2334  4.4841
 W5M  N02   N  NR5   0  -0.496  -46.3803  -29.1091  3.1590
 W5M  N04   N  N     0  -0.451  -48.3178  -28.8260  4.2319
 W5M  N08   N  N     0  -0.522  -46.0951  -29.3615  7.1295
 W5M  N10   N  NH2   0  -0.825  -43.8540  -29.8098  7.0515
 W5M  N11   N  N     0  -0.513  -44.9147  -29.4711  5.0460
 W5M  H012  H  HCH3  0   0.263  -44.4672  -28.9239  2.3761
 W5M  H013  H  HCH3  0   0.258  -45.3913  -30.2875  1.7286
 W5M  H011  H  HCH3  0   0.264  -45.7784  -28.6330  1.2276
 W5M  H031  H  HCR5  0   0.283  -48.2072  -28.7297  2.1188
 W5M  H072  H  HNH2  0   0.398  -48.2824  -28.9814  8.2980
 W5M  H071  H  HNH2  0   0.407  -49.2422  -28.7448  6.8845
 W5M  H101  H  HNH2  0   0.385  -42.9847  -29.6663  6.5658
 W5M  H102  H  HNH2  0   0.385  -43.8385  -29.5912  8.0330
 W5M  N07   N  NH2   0  -0.822  -48.3556  -28.9766  7.2956

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
 W5M  C01  N02   single    1.444  0.020  1.444
 W5M  C03  N02   aromatic  1.369  0.020  1.369
 W5M  C03  N04   aromatic  1.300  0.020  1.300
 W5M  N02  C12   aromatic  1.361  0.020  1.361
 W5M  N04  C05   aromatic  1.373  0.020  1.373
 W5M  C12  C05   aromatic  1.386  0.020  1.386
 W5M  C12  N11   aromatic  1.330  0.020  1.330
 W5M  C05  C06   aromatic  1.408  0.020  1.408
 W5M  N11  C09   aromatic  1.331  0.020  1.331
 W5M  C09  N08   aromatic  1.343  0.020  1.343
 W5M  C09  N10   single    1.360  0.020  1.360
 W5M  C06  N08   aromatic  1.331  0.020  1.331
 W5M  C06  N07   single    1.336  0.020  1.336
 W5M  C01  H012  single    0.970  0.020  1.090
 W5M  C01  H013  single    0.970  0.020  1.090
 W5M  C01  H011  single    0.970  0.020  1.090
 W5M  C03  H031  single    0.930  0.020  1.080
 W5M  N07  H072  single    0.860  0.020  1.020
 W5M  N07  H071  single    0.860  0.020  1.020
 W5M  N10  H101  single    0.890  0.020  1.040
 W5M  N10  H102  single    0.890  0.020  1.040

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
 W5M  H011  C01  H013  108.99  3.000
 W5M  H011  C01  H012  108.78  3.000
 W5M  H013  C01  H012  108.85  3.000
 W5M  H011  C01  N02   109.58  3.000
 W5M  H013  C01  N02   111.25  3.000
 W5M  H012  C01  N02   109.35  3.000
 W5M  H031  C03  N04   125.47  3.000
 W5M  H031  C03  N02   120.99  3.000
 W5M  N04   C03  N02   113.54  3.000
 W5M  N04   C05  C12   110.91  3.000
 W5M  C12   C05  C06   115.74  3.000
 W5M  N04   C05  C06   133.35  3.000
 W5M  N08   C06  N07   119.08  3.000
 W5M  N07   C06  C05   122.32  3.000
 W5M  N08   C06  C05   118.60  3.000
 W5M  N11   C09  N10   116.96  3.000
 W5M  N10   C09  N08   115.62  3.000
 W5M  N11   C09  N08   127.39  3.000
 W5M  N11   C12  N02   127.84  3.000
 W5M  N11   C12  C05   126.99  3.000
 W5M  N02   C12  C05   105.17  3.000
 W5M  C12   N02  C03   106.30  3.000
 W5M  C12   N02  C01   126.71  3.000
 W5M  C03   N02  C01   126.95  3.000
 W5M  C05   N04  C03   104.08  3.000
 W5M  C09   N08  C06   119.35  3.000
 W5M  H102  N10  H101  115.27  3.000
 W5M  H102  N10  C09   116.97  3.000
 W5M  H101  N10  C09   117.11  3.000
 W5M  C12   N11  C09   111.93  3.000
 W5M  H071  N07  H072  118.27  3.000
 W5M  H071  N07  C06   120.99  3.000
 W5M  H072  N07  C06   120.32  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
 W5M  CONST_01  C05   C12  N02  C03    0.00   0.0  0
 W5M  CONST_02  N11   C12  N02  C03  180.00   0.0  0
 W5M  CONST_03  C12   C05  N04  C03    0.00   0.0  0
 W5M  CONST_04  C06   C05  N04  C03  180.00   0.0  0
 W5M  CONST_05  N02   C03  N04  C05    0.00   0.0  0
 W5M  CONST_06  C09   N11  C12  C05    0.00   0.0  0
 W5M  CONST_07  C09   N08  C06  C05    0.00   0.0  0
 W5M  CONST_08  N02   C12  C05  C06  180.00   0.0  0
 W5M  CONST_09  N11   C12  C05  C06    0.00   0.0  0
 W5M  CONST_10  N11   C09  N08  C06    0.00   0.0  0
 W5M  CONST_11  N02   C12  N11  C09  180.00   0.0  0
 W5M  CONST_12  N04   C03  N02  C12    0.00   0.0  0
 W5M  CONST_13  N08   C06  C05  C12    0.00   0.0  0
 W5M  CONST_14  N08   C09  N11  C12    0.00   0.0  0
 W5M  CONST_15  N04   C05  C12  N02    0.00   0.0  0
 W5M  CONST_16  N11   C12  C05  N04  180.00   0.0  0
 W5M  CONST_17  N08   C06  C05  N04  180.00   0.0  0
 W5M  CONST_18  N04   C03  N02  C01  180.00   0.0  0
 W5M  CONST_19  C05   C12  N02  C01  180.00   0.0  0
 W5M  CONST_20  N11   C12  N02  C01    0.00   0.0  0
 W5M  CONST_21  N10   C09  N08  C06  180.00   0.0  0
 W5M  CONST_22  N07   C06  N08  C09  180.00   0.0  0
 W5M  CONST_23  N07   C06  C05  C12  180.00   0.0  0
 W5M  CONST_24  N10   C09  N11  C12  180.00   0.0  0
 W5M  CONST_25  N07   C06  C05  N04    0.00   0.0  0
 W5M  CONST_26  H031  C03  N04  C05  180.00   0.0  0
 W5M  CONST_27  H072  N07  C06  C05  180.00   0.0  0
 W5M  CONST_28  H071  N07  C06  C05    0.00   0.0  0
 W5M  Var_01    H012  C01  N02  C03  150.84  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
 W5M  plan-1  C01   0.020
 W5M  plan-1  C03   0.020
 W5M  plan-1  C05   0.020
 W5M  plan-1  C06   0.020
 W5M  plan-1  C09   0.020
 W5M  plan-1  C12   0.020
 W5M  plan-1  N02   0.020
 W5M  plan-1  N04   0.020
 W5M  plan-1  N08   0.020
 W5M  plan-1  N10   0.020
 W5M  plan-1  N11   0.020
 W5M  plan-1  H031  0.020
 W5M  plan-1  N07   0.020
 W5M  plan-2  C09   0.020
 W5M  plan-2  N10   0.020
 W5M  plan-2  H101  0.020
 W5M  plan-2  H102  0.020
 W5M  plan-3  C06   0.020
 W5M  plan-3  H072  0.020
 W5M  plan-3  H071  0.020
 W5M  plan-3  N07   0.020

