# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:16:15 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 9-cyclopropyl-~{N}-methyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2n(cnc12)C3CC3
#
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
 OYT  OYT  9-cyclopropyl-~{N}-methyl-purin-6-amine  ligand  25  14  .  2022-08-10  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OYT
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
 OYT  C10  C  CR15  0   0.110  1.7805   2.8619  3.1779
 OYT  N12  N  N     0  -0.450  3.4965   1.8593  6.0460
 OYT  C13  C  CR16  0   0.037  3.5414   0.5873  6.3968
 OYT  C01  C  CH3   0  -0.513  1.8475  -2.6727  4.5165
 OYT  C03  C  CR6   0   0.493  2.2844  -0.2683  4.6699
 OYT  C04  C  CR56  0  -0.001  2.1631   1.0503  4.1861
 OYT  C05  C  CR56  0   0.476  2.7894   2.0378  4.9299
 OYT  C07  C  CH1   0  -0.107  2.9961   4.5069  4.6172
 OYT  C08  C  CH2   0  -0.482  2.5069   5.1327  5.8826
 OYT  C09  C  CH2   0  -0.501  2.0365   5.6516  4.5607
 OYT  N02  N  NH1   0  -0.643  1.7268  -1.3123  4.0534
 OYT  N06  N  NR5   0  -0.504  2.5266   3.2034  4.2698
 OYT  N11  N  N     0  -0.452  1.5356   1.5866  3.0922
 OYT  N14  N  N     0  -0.487  2.9895  -0.4616  5.7890
 OYT  H1   H  HCR5  0   0.291  1.4431   3.6129  2.4789
 OYT  H2   H  HCR6  0   0.245  4.1006   0.3599  7.2986
 OYT  H3   H  HCH3  0   0.251  1.2949  -3.3135  3.8355
 OYT  H4   H  HCH3  0   0.237  2.8862  -3.0054  4.5342
 OYT  H5   H  HCH3  0   0.237  1.4343  -2.7976  5.5180
 OYT  H6   H  HCH1  0   0.288  4.0228   4.6934  4.3244
 OYT  H7   H  HCH2  0   0.267  3.2170   5.7176  6.4512
 OYT  H8   H  HCH2  0   0.266  1.8027   4.5690  6.4801
 OYT  H9   H  HCH2  0   0.270  2.4208   6.5971  4.2034
 OYT  H10  H  HCH2  0   0.268  1.0128   5.4465  4.2748
 OYT  H11  H  HNH1  0   0.406  1.2071  -1.1353  3.2106

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
 OYT  N11  C10  aromatic  1.301  0.020  1.301
 OYT  N11  C04  aromatic  1.370  0.020  1.370
 OYT  C10  N06  aromatic  1.366  0.020  1.366
 OYT  N02  C01  single    1.442  0.020  1.442
 OYT  N02  C03  single    1.334  0.020  1.334
 OYT  C04  C03  aromatic  1.410  0.020  1.410
 OYT  C04  C05  aromatic  1.386  0.020  1.386
 OYT  N06  C07  single    1.428  0.020  1.428
 OYT  N06  C05  aromatic  1.365  0.020  1.365
 OYT  C09  C07  single    1.495  0.020  1.495
 OYT  C09  C08  single    1.496  0.020  1.496
 OYT  C07  C08  single    1.494  0.020  1.494
 OYT  C03  N14  aromatic  1.337  0.020  1.337
 OYT  C05  N12  aromatic  1.333  0.020  1.333
 OYT  N14  C13  aromatic  1.332  0.020  1.332
 OYT  N12  C13  aromatic  1.320  0.020  1.320
 OYT  C10  H1   single    0.930  0.020  1.080
 OYT  C13  H2   single    0.930  0.020  1.080
 OYT  C01  H3   single    0.970  0.020  1.090
 OYT  C01  H4   single    0.970  0.020  1.090
 OYT  C01  H5   single    0.970  0.020  1.090
 OYT  C07  H6   single    0.970  0.020  1.090
 OYT  C08  H7   single    0.970  0.020  1.090
 OYT  C08  H8   single    0.970  0.020  1.090
 OYT  C09  H9   single    0.970  0.020  1.090
 OYT  C09  H10  single    0.970  0.020  1.090
 OYT  N02  H11  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
 OYT  H1   C10  N11  125.46  3.000
 OYT  H1   C10  N06  120.94  3.000
 OYT  N11  C10  N06  113.61  3.000
 OYT  C05  N12  C13  111.69  3.000
 OYT  H2   C13  N14  115.32  3.000
 OYT  H2   C13  N12  116.12  3.000
 OYT  N14  C13  N12  128.56  3.000
 OYT  H5   C01  H4   108.11  3.000
 OYT  H5   C01  H3   108.39  3.000
 OYT  H4   C01  H3   108.35  3.000
 OYT  H5   C01  N02  111.79  3.000
 OYT  H4   C01  N02  111.87  3.000
 OYT  H3   C01  N02  108.22  3.000
 OYT  N14  C03  N02  119.61  3.000
 OYT  N14  C03  C04  117.90  3.000
 OYT  N02  C03  C04  122.49  3.000
 OYT  N11  C04  C05  110.88  3.000
 OYT  C05  C04  C03  116.32  3.000
 OYT  N11  C04  C03  132.79  3.000
 OYT  N06  C05  C04  105.19  3.000
 OYT  N06  C05  N12  128.41  3.000
 OYT  C04  C05  N12  126.41  3.000
 OYT  H6   C07  N06  113.75  3.000
 OYT  H6   C07  C09  117.79  3.000
 OYT  N06  C07  C09  118.60  3.000
 OYT  H6   C07  C08  117.84  3.000
 OYT  C09  C07  C08   60.07  3.000
 OYT  N06  C07  C08  118.72  3.000
 OYT  H8   C08  H7   114.76  3.000
 OYT  H8   C08  C09  117.65  3.000
 OYT  H7   C08  C09  118.91  3.000
 OYT  H8   C08  C07  117.55  3.000
 OYT  H7   C08  C07  117.18  3.000
 OYT  C09  C08  C07   59.99  3.000
 OYT  H10  C09  H9   114.48  3.000
 OYT  H10  C09  C08  117.71  3.000
 OYT  H9   C09  C08  118.92  3.000
 OYT  H10  C09  C07  118.17  3.000
 OYT  H9   C09  C07  116.99  3.000
 OYT  C08  C09  C07   59.94  3.000
 OYT  H11  N02  C03  117.73  3.000
 OYT  H11  N02  C01  118.57  3.000
 OYT  C03  N02  C01  123.69  3.000
 OYT  C07  N06  C05  126.76  3.000
 OYT  C05  N06  C10  106.15  3.000
 OYT  C07  N06  C10  127.02  3.000
 OYT  C04  N11  C10  104.17  3.000
 OYT  C03  N14  C13  119.12  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
 OYT  CONST_01  C03  C04  N11  C10  180.00   0.0  0
 OYT  CONST_02  C05  C04  N11  C10    0.00   0.0  0
 OYT  CONST_03  C04  C05  N06  C10    0.00   0.0  0
 OYT  CONST_04  N12  C05  N06  C10  180.00   0.0  0
 OYT  CONST_05  N11  C04  C05  N12  180.00   0.0  0
 OYT  CONST_06  C03  C04  C05  N12    0.00   0.0  0
 OYT  CONST_07  C03  N14  C13  N12    0.00   0.0  0
 OYT  CONST_08  C04  C03  N14  C13    0.00   0.0  0
 OYT  CONST_09  C04  C05  N12  C13    0.00   0.0  0
 OYT  CONST_10  N06  C05  N12  C13  180.00   0.0  0
 OYT  CONST_11  N06  C05  C04  C03  180.00   0.0  0
 OYT  CONST_12  N06  C10  N11  C04    0.00   0.0  0
 OYT  CONST_13  N14  C03  C04  C05    0.00   0.0  0
 OYT  CONST_14  N11  C10  N06  C05    0.00   0.0  0
 OYT  CONST_15  N14  C13  N12  C05    0.00   0.0  0
 OYT  CONST_16  N11  C04  C05  N06    0.00   0.0  0
 OYT  CONST_17  N14  C03  C04  N11  180.00   0.0  0
 OYT  CONST_18  C07  N06  C05  N12    0.00   0.0  0
 OYT  CONST_19  C07  N06  C05  C04  180.00   0.0  0
 OYT  CONST_20  N11  C10  N06  C07  180.00   0.0  0
 OYT  CONST_21  N02  C03  N14  C13  180.00   0.0  0
 OYT  CONST_22  N02  C03  C04  C05  180.00   0.0  0
 OYT  CONST_23  N11  C04  C03  N02    0.00   0.0  0
 OYT  CONST_24  H2   C13  N14  C03  180.00   0.0  0
 OYT  CONST_25  H1   C10  N11  C04  180.00   0.0  0
 OYT  CONST_26  C04  C03  N02  C01  180.00   0.0  0
 OYT  CONST_27  N14  C03  N02  C01    0.00   0.0  0
 OYT  CONST_28  H11  N02  C03  C04    0.00   0.0  0
 OYT  Var_01    C09  C07  N06  C10   47.05  30.0  2
 OYT  Var_02    N06  C07  C09  C08  108.52  30.0  1
 OYT  Var_03    H7   C08  C09  C07  106.48  30.0  1
 OYT  Var_04    H3   C01  N02  C03  179.63  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
 OYT  chir_01  C07  N06  C09  C08  both

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
 OYT  plan-1  C10  0.020
 OYT  plan-1  N12  0.020
 OYT  plan-1  C13  0.020
 OYT  plan-1  C03  0.020
 OYT  plan-1  C04  0.020
 OYT  plan-1  C05  0.020
 OYT  plan-1  C07  0.020
 OYT  plan-1  N02  0.020
 OYT  plan-1  N06  0.020
 OYT  plan-1  N11  0.020
 OYT  plan-1  N14  0.020
 OYT  plan-1  H1   0.020
 OYT  plan-1  H2   0.020
 OYT  plan-2  C01  0.020
 OYT  plan-2  C03  0.020
 OYT  plan-2  N02  0.020
 OYT  plan-2  H11  0.020

