# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:08:49 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-bromanyl-2-methyl-6-propyl-7~{H}-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1[nH]c2nc(C)ncc2c1Br
#
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
 J0F  J0F  5-bromanyl-2-methyl-6-propyl-7~{H}-pyrrolo[2,3-d]pyrimidine  ligand  26  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J0F
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
 J0F  C1   C   CR5   0   0.436  34.4363  37.7356  61.4110
 J0F  C2   C   CR5   0  -0.391  34.3729  37.2956  62.7041
 J0F  C4   C   CR56  0   0.492  33.1520  35.9034  61.4069
 J0F  C5   C   CR56  0   0.071  33.5627  36.1266  62.7344
 J0F  C6   C   CR16  0  -0.083  33.0995  35.2001  63.6555
 J0F  N3   N   NR15  0  -0.715  33.6830  36.8801  60.6366
 J0F  C8   C   CR6   0   0.338  32.0056  34.0786  61.9781
 J0F  C10  C   CH3   0  -0.728  31.1429  32.9140  61.6087
 J0F  C11  C   CH2   0  -0.508  35.1057  38.9184  60.8117
 J0F  C12  C   CH2   0  -0.420  34.1485  40.0940  60.5896
 J0F  C13  C   CH3   0  -0.665  34.8517  41.2780  59.9440
 J0F  N7   N   N     0  -0.428  32.3316  34.1928  63.2751
 J0F  N9   N   N     0  -0.435  32.3851  34.9015  61.0110
 J0F  BR1  BR  BR    0  -0.056  35.1838  38.0822  64.1852
 J0F  H1   H   HCR6  0   0.267  33.3483  35.2679  64.7100
 J0F  H2   H   HNR5  0   0.419  33.5671  36.9619  59.6372
 J0F  H3   H   HCH3  0   0.246  30.9133  32.9166  60.5461
 J0F  H4   H   HCH3  0   0.253  31.6417  31.9753  61.8543
 J0F  H5   H   HCH3  0   0.252  30.2080  32.9341  62.1698
 J0F  H6   H   HCH2  0   0.260  35.5556  38.6300  59.8572
 J0F  H7   H   HCH2  0   0.256  35.9272  39.2337  61.4575
 J0F  H8   H   HCH2  0   0.231  33.7188  40.3910  61.5492
 J0F  H9   H   HCH2  0   0.230  33.3134  39.7712  59.9628
 J0F  H10  H   HCH3  0   0.234  34.1622  42.1076  59.7879
 J0F  H11  H   HCH3  0   0.222  35.6703  41.6402  60.5681
 J0F  H12  H   HCH3  0   0.222  35.2707  41.0064  58.9738

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
 J0F  C13  C12  single    1.521  0.020  1.521
 J0F  C12  C11  single    1.532  0.020  1.532
 J0F  N3   C4   aromatic  1.353  0.020  1.353
 J0F  N3   C1   aromatic  1.378  0.020  1.378
 J0F  C11  C1   single    1.485  0.020  1.485
 J0F  N9   C4   aromatic  1.322  0.020  1.322
 J0F  N9   C8   aromatic  1.325  0.020  1.325
 J0F  C4   C5   aromatic  1.407  0.020  1.407
 J0F  C1   C2   aromatic  1.367  0.020  1.367
 J0F  C10  C8   single    1.496  0.020  1.496
 J0F  C8   N7   aromatic  1.342  0.020  1.342
 J0F  C2   C5   aromatic  1.423  0.020  1.423
 J0F  C2   BR1  single    1.863  0.020  1.863
 J0F  C5   C6   aromatic  1.386  0.020  1.386
 J0F  N7   C6   aromatic  1.323  0.020  1.323
 J0F  C6   H1   single    0.930  0.020  1.080
 J0F  N3   H2   single    0.860  0.020  1.020
 J0F  C10  H3   single    0.970  0.020  1.090
 J0F  C10  H4   single    0.970  0.020  1.090
 J0F  C10  H5   single    0.970  0.020  1.090
 J0F  C11  H6   single    0.970  0.020  1.090
 J0F  C11  H7   single    0.970  0.020  1.090
 J0F  C12  H8   single    0.970  0.020  1.090
 J0F  C12  H9   single    0.970  0.020  1.090
 J0F  C13  H10  single    0.970  0.020  1.090
 J0F  C13  H11  single    0.970  0.020  1.090
 J0F  C13  H12  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
 J0F  C11  C1   N3   120.93  3.000
 J0F  C11  C1   C2   131.20  3.000
 J0F  N3   C1   C2   107.84  3.000
 J0F  BR1  C2   C5   125.30  3.000
 J0F  BR1  C2   C1   126.58  3.000
 J0F  C5   C2   C1   108.12  3.000
 J0F  N9   C4   N3   127.18  3.000
 J0F  N9   C4   C5   124.88  3.000
 J0F  N3   C4   C5   107.94  3.000
 J0F  C6   C5   C4   115.04  3.000
 J0F  C6   C5   C2   138.92  3.000
 J0F  C4   C5   C2   106.05  3.000
 J0F  H1   C6   N7   117.39  3.000
 J0F  H1   C6   C5   121.81  3.000
 J0F  N7   C6   C5   120.80  3.000
 J0F  H2   N3   C4   125.26  3.000
 J0F  H2   N3   C1   124.67  3.000
 J0F  C4   N3   C1   110.05  3.000
 J0F  N9   C8   N7   125.64  3.000
 J0F  N7   C8   C10  116.43  3.000
 J0F  N9   C8   C10  117.93  3.000
 J0F  H5   C10  H4   106.98  3.000
 J0F  H5   C10  H3   108.77  3.000
 J0F  H4   C10  H3   108.59  3.000
 J0F  H5   C10  C8   110.67  3.000
 J0F  H4   C10  C8   110.53  3.000
 J0F  H3   C10  C8   111.18  3.000
 J0F  H7   C11  H6   106.43  3.000
 J0F  H7   C11  C12  109.53  3.000
 J0F  H6   C11  C12  109.43  3.000
 J0F  H7   C11  C1   109.30  3.000
 J0F  H6   C11  C1   109.11  3.000
 J0F  C12  C11  C1   112.83  3.000
 J0F  H9   C12  H8   106.46  3.000
 J0F  H9   C12  C13  109.87  3.000
 J0F  H8   C12  C13  110.06  3.000
 J0F  H9   C12  C11  109.51  3.000
 J0F  H8   C12  C11  109.08  3.000
 J0F  C13  C12  C11  111.72  3.000
 J0F  H12  C13  H11  107.64  3.000
 J0F  H12  C13  H10  107.76  3.000
 J0F  H11  C13  H10  107.70  3.000
 J0F  H12  C13  C12  111.17  3.000
 J0F  H11  C13  C12  111.25  3.000
 J0F  H10  C13  C12  111.15  3.000
 J0F  C8   N7   C6   118.93  3.000
 J0F  C8   N9   C4   114.71  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
 J0F  CONST_01  N9   C4   N3   C1    180.00   0.0  0
 J0F  CONST_02  C5   C4   N3   C1      0.00   0.0  0
 J0F  CONST_03  C4   C5   C2   C1      0.00   0.0  0
 J0F  CONST_04  C6   C5   C2   C1    180.00   0.0  0
 J0F  CONST_05  C4   N3   C1   C2      0.00   0.0  0
 J0F  CONST_06  N3   C4   C5   C2      0.00   0.0  0
 J0F  CONST_07  N9   C4   C5   C2    180.00   0.0  0
 J0F  CONST_08  N7   C6   C5   C2    180.00   0.0  0
 J0F  CONST_09  N7   C8   N9   C4      0.00   0.0  0
 J0F  CONST_10  N7   C6   C5   C4      0.00   0.0  0
 J0F  CONST_11  C8   N9   C4   C5      0.00   0.0  0
 J0F  CONST_12  N3   C1   C2   C5      0.00   0.0  0
 J0F  CONST_13  C8   N7   C6   C5      0.00   0.0  0
 J0F  CONST_14  N3   C4   C5   C6    180.00   0.0  0
 J0F  CONST_15  N9   C4   C5   C6      0.00   0.0  0
 J0F  CONST_16  N9   C8   N7   C6      0.00   0.0  0
 J0F  CONST_17  C8   N9   C4   N3    180.00   0.0  0
 J0F  CONST_18  C11  C1   N3   C4    180.00   0.0  0
 J0F  CONST_19  C10  C8   N9   C4    180.00   0.0  0
 J0F  CONST_20  BR1  C2   C5   C4    180.00   0.0  0
 J0F  CONST_21  C11  C1   C2   C5    180.00   0.0  0
 J0F  CONST_22  BR1  C2   C5   C6      0.00   0.0  0
 J0F  CONST_23  C10  C8   N7   C6    180.00   0.0  0
 J0F  CONST_24  BR1  C2   C1   N3    180.00   0.0  0
 J0F  CONST_25  H2   N3   C1   C2    180.00   0.0  0
 J0F  CONST_26  H1   C6   C5   C2      0.00   0.0  0
 J0F  Var_01    C12  C11  C1   C2    -98.25  30.0  1
 J0F  Var_02    H3   C10  C8   N7    178.71  30.0  2
 J0F  Var_03    C13  C12  C11  C1   -178.59  30.0  1
 J0F  Var_04    H10  C13  C12  C11   179.85  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
 J0F  plan-1  C1   0.020
 J0F  plan-1  C2   0.020
 J0F  plan-1  C4   0.020
 J0F  plan-1  C5   0.020
 J0F  plan-1  C6   0.020
 J0F  plan-1  N3   0.020
 J0F  plan-1  C8   0.020
 J0F  plan-1  C10  0.020
 J0F  plan-1  C11  0.020
 J0F  plan-1  N7   0.020
 J0F  plan-1  N9   0.020
 J0F  plan-1  BR1  0.020
 J0F  plan-1  H1   0.020
 J0F  plan-1  H2   0.020

