# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:07:52 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: methyl 2-bromo-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cc(Nc2ncnc3[nH]ccc23)ccc1Br
#
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
 F8E  F8E  'methyl 2-bromo-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)benzoate'  ligand  32  21  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F8E
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
 F8E  BR    BR  BR    0  -0.030   4.2623  -1.1255   0.3957
 F8E  C1    C   CH3   0  -0.424   2.2643   3.7872   0.3467
 F8E  O2    O   O2    0  -0.446   1.7474   2.4675   0.5308
 F8E  C3    C   C     0   0.544   2.3856   1.4745  -0.0636
 F8E  O4    O   O     0  -0.430   3.3914   1.6121  -0.7111
 F8E  C5    C   CR6   0   0.044   1.6909   0.1710   0.1457
 F8E  C6    C   CR16  0  -0.336   0.2962   0.1687   0.1372
 F8E  C7    C   CR6   0   0.404  -0.4200  -1.0210   0.2535
 F8E  C8    C   CR16  0  -0.355   0.2945  -2.2132   0.4029
 F8E  C9    C   CR16  0  -0.208   1.6735  -2.2157   0.4325
 F8E  C10   C   CR6   0  -0.174   2.3820  -1.0294   0.2931
 F8E  N12   N   NH1   0  -0.780  -1.8035  -1.1186   0.2400
 F8E  C13   C   CR6   0   0.523  -2.7674  -0.1724   0.0746
 F8E  C14   C   CR56  0  -0.102  -4.1204  -0.5570   0.0779
 F8E  C15   C   CR15  0  -0.443  -4.8735  -1.7607   0.2183
 F8E  C16   C   CR15  0  -0.003  -6.1846  -1.3982   0.1138
 F8E  N17   N   NR15  0  -0.657  -6.2775  -0.0448  -0.0825
 F8E  C19   C   CR56  0   0.487  -5.0353   0.4887  -0.1072
 F8E  N20   N   N     0  -0.443  -4.7238   1.7756  -0.2756
 F8E  C21   C   CR16  0   0.054  -3.4282   1.9959  -0.2534
 F8E  N22   N   N     0  -0.495  -2.4473   1.1039  -0.0903
 F8E  HN17  H   HNR5  0   0.417  -7.1353   0.4713  -0.1969
 F8E  H1    H   HCH3  0   0.256   1.5857   4.4470   0.8782
 F8E  H1A   H   HCH3  0   0.243   3.2651   3.8807   0.7668
 F8E  H1B   H   HCH3  0   0.244   2.2871   4.0621  -0.7074
 F8E  H6    H   HCR6  0   0.307  -0.2414   1.0949   0.0193
 F8E  H8    H   HCR6  0   0.287  -0.2332  -3.1539   0.5044
 F8E  H9    H   HCR6  0   0.289   2.1921  -3.1553   0.5666
 F8E  HN12  H   HNH1  0   0.423  -2.1518  -2.0578   0.3575
 F8E  H15   H   HCR5  0   0.260  -4.5103  -2.7634   0.3774
 F8E  H16   H   HCR5  0   0.293  -7.0730  -2.0054   0.1650
 F8E  H21   H   HCR6  0   0.252  -3.1062   3.0232  -0.3824

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
 F8E  BR    C10   single    1.886  0.020  1.886
 F8E  O2    C1    single    1.429  0.020  1.429
 F8E  C1    H1    single    0.970  0.020  1.090
 F8E  C1    H1A   single    0.970  0.020  1.090
 F8E  C1    H1B   single    0.970  0.020  1.090
 F8E  C3    O2    single    1.322  0.020  1.322
 F8E  O4    C3    double    1.204  0.020  1.204
 F8E  C5    C3    single    1.492  0.020  1.492
 F8E  C10   C5    aromatic  1.393  0.020  1.393
 F8E  C5    C6    aromatic  1.395  0.020  1.395
 F8E  C7    C6    aromatic  1.393  0.020  1.393
 F8E  C6    H6    single    0.930  0.020  1.080
 F8E  C8    C7    aromatic  1.398  0.020  1.398
 F8E  C7    N12   single    1.387  0.020  1.387
 F8E  C9    C8    aromatic  1.379  0.020  1.379
 F8E  C8    H8    single    0.930  0.020  1.080
 F8E  C9    C10   aromatic  1.389  0.020  1.389
 F8E  C9    H9    single    0.930  0.020  1.080
 F8E  C13   N12   single    1.361  0.020  1.361
 F8E  N12   HN12  single    0.860  0.020  1.020
 F8E  N22   C13   aromatic  1.326  0.020  1.326
 F8E  C13   C14   aromatic  1.407  0.020  1.407
 F8E  C19   C14   aromatic  1.402  0.020  1.402
 F8E  C14   C15   aromatic  1.427  0.020  1.427
 F8E  C16   C15   aromatic  1.364  0.020  1.364
 F8E  C15   H15   single    0.930  0.020  1.080
 F8E  N17   C16   aromatic  1.371  0.020  1.371
 F8E  C16   H16   single    0.930  0.020  1.080
 F8E  C19   N17   aromatic  1.352  0.020  1.352
 F8E  HN17  N17   single    0.860  0.020  1.020
 F8E  N20   C19   aromatic  1.335  0.020  1.335
 F8E  C21   N20   aromatic  1.314  0.020  1.314
 F8E  C21   N22   aromatic  1.336  0.020  1.336
 F8E  C21   H21   single    0.930  0.020  1.080

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
 F8E  H1B   C1   H1A  109.40  3.000
 F8E  H1B   C1   H1   109.48  3.000
 F8E  H1A   C1   H1   109.46  3.000
 F8E  H1B   C1   O2   111.42  3.000
 F8E  H1A   C1   O2   111.21  3.000
 F8E  H1    C1   O2   105.79  3.000
 F8E  C3    O2   C1   117.47  3.000
 F8E  C5    C3   O4   124.35  3.000
 F8E  C5    C3   O2   111.62  3.000
 F8E  O4    C3   O2   124.01  3.000
 F8E  C10   C5   C6   119.69  3.000
 F8E  C6    C5   C3   117.80  3.000
 F8E  C10   C5   C3   122.46  3.000
 F8E  H6    C6   C7   119.12  3.000
 F8E  H6    C6   C5   119.88  3.000
 F8E  C7    C6   C5   120.99  3.000
 F8E  N12   C7   C8   116.80  3.000
 F8E  N12   C7   C6   124.88  3.000
 F8E  C8    C7   C6   118.32  3.000
 F8E  H8    C8   C9   118.90  3.000
 F8E  H8    C8   C7   120.11  3.000
 F8E  C9    C8   C7   120.99  3.000
 F8E  H9    C9   C10  120.66  3.000
 F8E  H9    C9   C8   118.92  3.000
 F8E  C10   C9   C8   120.42  3.000
 F8E  C9    C10  C5   119.58  3.000
 F8E  C9    C10  BR   117.37  3.000
 F8E  C5    C10  BR   122.99  3.000
 F8E  HN12  N12  C13  114.65  3.000
 F8E  HN12  N12  C7   114.13  3.000
 F8E  C13   N12  C7   131.21  3.000
 F8E  N22   C13  C14  119.71  3.000
 F8E  C14   C13  N12  119.40  3.000
 F8E  N22   C13  N12  120.89  3.000
 F8E  C19   C14  C15  107.33  3.000
 F8E  C15   C14  C13  137.62  3.000
 F8E  C19   C14  C13  115.05  3.000
 F8E  H15   C15  C16  125.60  3.000
 F8E  H15   C15  C14  128.41  3.000
 F8E  C16   C15  C14  106.00  3.000
 F8E  H16   C16  N17  120.49  3.000
 F8E  H16   C16  C15  129.73  3.000
 F8E  N17   C16  C15  109.78  3.000
 F8E  HN17  N17  C19  125.31  3.000
 F8E  HN17  N17  C16  125.43  3.000
 F8E  C19   N17  C16  109.26  3.000
 F8E  N20   C19  N17  126.66  3.000
 F8E  N20   C19  C14  125.71  3.000
 F8E  N17   C19  C14  107.63  3.000
 F8E  C21   N20  C19  112.92  3.000
 F8E  H21   C21  N22  115.42  3.000
 F8E  H21   C21  N20  116.71  3.000
 F8E  N22   C21  N20  127.88  3.000
 F8E  C21   N22  C13  118.72  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
 F8E  CONST_01  C8    C9   C10  C5      0.00   0.0  0
 F8E  CONST_02  C8    C7   C6   C5      0.00   0.0  0
 F8E  CONST_03  C9    C10  C5   C6      0.00   0.0  0
 F8E  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 F8E  CONST_05  C10   C5   C6   C7      0.00   0.0  0
 F8E  CONST_06  C10   C9   C8   C7      0.00   0.0  0
 F8E  CONST_07  N20   C21  N22  C13     0.00   0.0  0
 F8E  CONST_08  N17   C19  C14  C13   180.00   0.0  0
 F8E  CONST_09  N20   C19  C14  C13     0.00   0.0  0
 F8E  CONST_10  C16   C15  C14  C13   180.00   0.0  0
 F8E  CONST_11  C21   N22  C13  C14     0.00   0.0  0
 F8E  CONST_12  C16   N17  C19  C14     0.00   0.0  0
 F8E  CONST_13  C21   N20  C19  C14     0.00   0.0  0
 F8E  CONST_14  N17   C16  C15  C14     0.00   0.0  0
 F8E  CONST_15  N22   C13  C14  C15   180.00   0.0  0
 F8E  CONST_16  N17   C19  C14  C15     0.00   0.0  0
 F8E  CONST_17  N20   C19  C14  C15   180.00   0.0  0
 F8E  CONST_18  C19   N17  C16  C15     0.00   0.0  0
 F8E  CONST_19  C19   C14  C15  C16     0.00   0.0  0
 F8E  CONST_20  N20   C19  N17  C16   180.00   0.0  0
 F8E  CONST_21  C21   N20  C19  N17   180.00   0.0  0
 F8E  CONST_22  N22   C13  C14  C19     0.00   0.0  0
 F8E  CONST_23  N22   C21  N20  C19     0.00   0.0  0
 F8E  CONST_24  C6    C5   C10  BR    180.00   0.0  0
 F8E  CONST_25  C8    C9   C10  BR    180.00   0.0  0
 F8E  CONST_26  C9    C10  C5   C3    180.00   0.0  0
 F8E  CONST_27  C7    C6   C5   C3    180.00   0.0  0
 F8E  CONST_28  N12   C7   C6   C5    180.00   0.0  0
 F8E  CONST_29  N12   C7   C8   C9    180.00   0.0  0
 F8E  CONST_30  C21   N22  C13  N12   180.00   0.0  0
 F8E  CONST_31  C19   C14  C13  N12   180.00   0.0  0
 F8E  CONST_32  C15   C14  C13  N12     0.00   0.0  0
 F8E  CONST_33  H9    C9   C10  C5    180.00   0.0  0
 F8E  CONST_34  H8    C8   C7   C6    180.00   0.0  0
 F8E  CONST_35  H6    C6   C7   C8    180.00   0.0  0
 F8E  CONST_36  H21   C21  N22  C13   180.00   0.0  0
 F8E  CONST_37  H15   C15  C14  C13     0.00   0.0  0
 F8E  CONST_38  HN17  N17  C19  C14   180.00   0.0  0
 F8E  CONST_39  H16   C16  C15  C14   180.00   0.0  0
 F8E  Var_01    C13   N12  C7   C6      2.57  30.0  2
 F8E  Var_02    N22   C13  N12  C7     -1.24  30.0  1
 F8E  Var_03    C10   C5   C3   O2   -144.89  30.0  2
 F8E  Var_04    C5    C3   O2   C1   -176.52  30.0  1
 F8E  Var_05    H1    C1   O2   C3    178.00  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
 F8E  plan-1  BR    0.020
 F8E  plan-1  C3    0.020
 F8E  plan-1  C5    0.020
 F8E  plan-1  C6    0.020
 F8E  plan-1  C7    0.020
 F8E  plan-1  C8    0.020
 F8E  plan-1  C9    0.020
 F8E  plan-1  C10   0.020
 F8E  plan-1  N12   0.020
 F8E  plan-1  H6    0.020
 F8E  plan-1  H8    0.020
 F8E  plan-1  H9    0.020
 F8E  plan-2  N12   0.020
 F8E  plan-2  C13   0.020
 F8E  plan-2  C14   0.020
 F8E  plan-2  C15   0.020
 F8E  plan-2  C16   0.020
 F8E  plan-2  N17   0.020
 F8E  plan-2  C19   0.020
 F8E  plan-2  N20   0.020
 F8E  plan-2  C21   0.020
 F8E  plan-2  N22   0.020
 F8E  plan-2  HN17  0.020
 F8E  plan-2  H15   0.020
 F8E  plan-2  H16   0.020
 F8E  plan-2  H21   0.020
 F8E  plan-3  O2    0.020
 F8E  plan-3  C3    0.020
 F8E  plan-3  O4    0.020
 F8E  plan-3  C5    0.020

