# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:13:21 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-(3-bromo-4-methoxybenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cc2nc(O)c(O)c(n2)C(O)=O)cc1Br
#
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
 P1Y  P1Y  '2-(3-bromo-4-methoxybenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid'  ligand  31  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1Y
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
 P1Y  C01   C   C1     0  -0.261  -1.3991  -0.0003   1.3054
 P1Y  C02   C   C      0  -0.212  -2.6708  -0.0907   0.7704
 P1Y  C03   C   C      0   0.428  -3.0861  -1.2258   0.0659
 P1Y  C04   C   C1     0  -0.375  -2.1750  -2.2688  -0.0798
 P1Y  C05   C   C1     0  -0.290  -0.8997  -2.1708   0.4603
 P1Y  C06   C   C      0   0.128  -0.4904  -1.0439   1.1577
 P1Y  C07   C   CH2    0  -0.601   0.8912  -0.9381   1.7311
 P1Y  C08   C   CR6    0   0.348   1.9055  -0.2872   0.8192
 P1Y  N09   N   N      0  -0.426   3.1525  -0.2829   1.2376
 P1Y  C10   C   CR6    0  -0.103   4.0672   0.3062   0.4609
 P1Y  C11   C   CR6    0   0.179   3.7261   0.8899  -0.7497
 P1Y  C12   C   CR6    0   0.424   2.3637   0.8240  -1.0988
 P1Y  N13   N   N      0  -0.420   1.4785   0.2476  -0.3253
 P1Y  O14   O   OH1    0  -0.657   4.5969   1.4857  -1.5602
 P1Y  O15   O   OH1    0  -0.597   1.9131   1.3483  -2.2369
 P1Y  C16   C   C      0   0.483   5.5141   0.3470   0.9101
 P1Y  O17   O   OC    -1  -0.534   5.8256  -0.1519   1.9864
 P1Y  O18   O   O      0  -0.625   6.2989   0.9258   0.0926
 P1Y  BR19  BR  BR     0  -0.043  -3.8814   1.3379   0.9942
 P1Y  O20   O   O2     0  -0.455  -4.3356  -1.2293  -0.4170
 P1Y  C21   C   CH3    0  -0.438  -4.7932  -2.3773  -1.1073
 P1Y  H01   H   H      0   0.270  -1.1052   0.8905   1.8473
 P1Y  H04   H   H      0   0.287  -2.4514  -3.1691  -0.6117
 P1Y  H05   H   H      0   0.259  -0.2145  -2.9996   0.3303
 P1Y  H07   H   HCH2   0   0.275   0.8640  -0.3687   2.6646
 P1Y  H07A  H   HCH2   0   0.273   1.2630  -1.9293   2.0005
 P1Y  H21   H   HCH3   0   0.233  -4.2034  -2.5766  -2.0052
 P1Y  H21A  H   HCH3   0   0.233  -4.7821  -3.2654  -0.4709
 P1Y  H21B  H   HCH3   0   0.263  -5.8182  -2.1679  -1.4015
 P1Y  H10   H   HOH1   0   0.469   5.4833   1.3730  -1.0365
 P1Y  H11   H   HOH1   0   0.484   2.6393   1.7446  -2.7368

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
 P1Y  C01  C02   aromatic  1.383  0.020  1.383
 P1Y  C01  H01   single    0.930  0.020  1.080
 P1Y  C02  BR19  single    1.886  0.020  1.886
 P1Y  C03  C02   aromatic  1.399  0.020  1.399
 P1Y  C03  O20   single    1.340  0.020  1.340
 P1Y  C04  C03   aromatic  1.393  0.020  1.393
 P1Y  C04  H04   single    0.930  0.020  1.080
 P1Y  C05  C04   aromatic  1.388  0.020  1.388
 P1Y  C05  C06   aromatic  1.387  0.020  1.387
 P1Y  C05  H05   single    0.930  0.020  1.080
 P1Y  C06  C01   aromatic  1.392  0.020  1.392
 P1Y  C07  C06   single    1.500  0.020  1.500
 P1Y  C07  H07   single    0.970  0.020  1.090
 P1Y  C07  H07A  single    0.970  0.020  1.090
 P1Y  C08  C07   single    1.511  0.020  1.511
 P1Y  C08  N13   aromatic  1.333  0.020  1.333
 P1Y  N09  C08   aromatic  1.315  0.020  1.315
 P1Y  C10  N09   aromatic  1.337  0.020  1.337
 P1Y  C10  C11   aromatic  1.387  0.020  1.387
 P1Y  C11  C12   aromatic  1.408  0.020  1.408
 P1Y  C12  O15   single    1.332  0.020  1.332
 P1Y  C12  N13   aromatic  1.309  0.020  1.309
 P1Y  O14  C11   single    1.330  0.020  1.330
 P1Y  C16  C10   single    1.516  0.020  1.516
 P1Y  C16  O17   deloc     1.227  0.020  1.227
 P1Y  O18  C16   deloc     1.273  0.020  1.273
 P1Y  C21  O20   single    1.416  0.020  1.416
 P1Y  C21  H21   single    0.970  0.020  1.090
 P1Y  C21  H21A  single    0.970  0.020  1.090
 P1Y  C21  H21B  single    0.970  0.020  1.090
 P1Y  O14  H10   single    0.850  0.020  0.980
 P1Y  O15  H11   single    0.850  0.020  0.980

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
 P1Y  H01   C01  C06   119.51  3.000
 P1Y  C06   C01  C02   120.69  3.000
 P1Y  H01   C01  C02   119.80  3.000
 P1Y  BR19  C02  C03   118.94  3.000
 P1Y  C03   C02  C01   121.40  3.000
 P1Y  BR19  C02  C01   119.66  3.000
 P1Y  O20   C03  C04   124.79  3.000
 P1Y  C04   C03  C02   117.79  3.000
 P1Y  O20   C03  C02   117.42  3.000
 P1Y  H04   C04  C05   119.00  3.000
 P1Y  C05   C04  C03   120.49  3.000
 P1Y  H04   C04  C03   120.52  3.000
 P1Y  H05   C05  C06   119.69  3.000
 P1Y  H05   C05  C04   118.71  3.000
 P1Y  C06   C05  C04   121.60  3.000
 P1Y  C07   C06  C05   121.43  3.000
 P1Y  C07   C06  C01   120.54  3.000
 P1Y  C05   C06  C01   118.03  3.000
 P1Y  H07A  C07  H07   105.68  3.000
 P1Y  H07A  C07  C08   108.14  3.000
 P1Y  H07   C07  C08   107.91  3.000
 P1Y  C08   C07  C06   114.71  3.000
 P1Y  H07A  C07  C06   110.11  3.000
 P1Y  H07   C07  C06   109.88  3.000
 P1Y  N13   C08  N09   125.12  3.000
 P1Y  N09   C08  C07   116.47  3.000
 P1Y  N13   C08  C07   118.41  3.000
 P1Y  C10   N09  C08   117.73  3.000
 P1Y  C16   C10  C11   118.84  3.000
 P1Y  C16   C10  N09   119.53  3.000
 P1Y  C11   C10  N09   121.63  3.000
 P1Y  O14   C11  C12   120.22  3.000
 P1Y  O14   C11  C10   124.01  3.000
 P1Y  C12   C11  C10   115.77  3.000
 P1Y  O15   C12  N13   116.71  3.000
 P1Y  N13   C12  C11   121.90  3.000
 P1Y  O15   C12  C11   121.39  3.000
 P1Y  C12   N13  C08   117.85  3.000
 P1Y  H10   O14  C11   101.74  3.000
 P1Y  H11   O15  C12   110.44  3.000
 P1Y  O18   C16  O17   126.31  3.000
 P1Y  O18   C16  C10   114.24  3.000
 P1Y  O17   C16  C10   119.45  3.000
 P1Y  C21   O20  C03   118.65  3.000
 P1Y  H21B  C21  H21A  108.90  3.000
 P1Y  H21B  C21  H21   108.78  3.000
 P1Y  H21A  C21  H21   108.96  3.000
 P1Y  H21B  C21  O20   106.30  3.000
 P1Y  H21A  C21  O20   111.83  3.000
 P1Y  H21   C21  O20   111.97  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
 P1Y  CONST_01  C04   C03  C02  C01    0.00   0.0  0
 P1Y  CONST_02  C04   C05  C06  C01    0.00   0.0  0
 P1Y  CONST_03  C05   C06  C01  C02    0.00   0.0  0
 P1Y  CONST_04  C05   C04  C03  C02    0.00   0.0  0
 P1Y  CONST_05  C06   C01  C02  C03    0.00   0.0  0
 P1Y  CONST_06  C06   C05  C04  C03    0.00   0.0  0
 P1Y  CONST_07  C11   C12  N13  C08    0.00   0.0  0
 P1Y  CONST_08  C11   C10  N09  C08    0.00   0.0  0
 P1Y  CONST_09  C12   N13  C08  N09    0.00   0.0  0
 P1Y  CONST_10  C12   C11  C10  N09    0.00   0.0  0
 P1Y  CONST_11  N13   C08  N09  C10    0.00   0.0  0
 P1Y  CONST_12  N13   C12  C11  C10    0.00   0.0  0
 P1Y  CONST_13  O20   C03  C02  C01  180.00   0.0  0
 P1Y  CONST_14  C07   C06  C01  C02  180.00   0.0  0
 P1Y  CONST_15  BR19  C02  C03  C04  180.00   0.0  0
 P1Y  CONST_16  C07   C06  C05  C04  180.00   0.0  0
 P1Y  CONST_17  O20   C03  C04  C05  180.00   0.0  0
 P1Y  CONST_18  BR19  C02  C01  C06  180.00   0.0  0
 P1Y  CONST_19  C12   N13  C08  C07  180.00   0.0  0
 P1Y  CONST_20  C10   N09  C08  C07  180.00   0.0  0
 P1Y  CONST_21  O15   C12  N13  C08  180.00   0.0  0
 P1Y  CONST_22  C16   C10  N09  C08  180.00   0.0  0
 P1Y  CONST_23  O14   C11  C10  N09  180.00   0.0  0
 P1Y  CONST_24  O15   C12  C11  C10  180.00   0.0  0
 P1Y  CONST_25  C16   C10  C11  C12  180.00   0.0  0
 P1Y  CONST_26  O14   C11  C12  N13  180.00   0.0  0
 P1Y  CONST_27  H05   C05  C06  C01  180.00   0.0  0
 P1Y  CONST_28  H04   C04  C03  C02  180.00   0.0  0
 P1Y  CONST_29  H01   C01  C02  C03  180.00   0.0  0
 P1Y  Var_01    C08   C07  C06  C01  -87.58  30.0  2
 P1Y  Var_02    N13   C08  C07  C06    6.63  30.0  2
 P1Y  Var_03    O17   C16  C10  N09   -0.58  30.0  2
 P1Y  Var_04    H21   C21  O20  C03  -61.67  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
 P1Y  plan-1  C01   0.020
 P1Y  plan-1  C02   0.020
 P1Y  plan-1  C03   0.020
 P1Y  plan-1  C04   0.020
 P1Y  plan-1  C05   0.020
 P1Y  plan-1  C06   0.020
 P1Y  plan-1  C07   0.020
 P1Y  plan-1  BR19  0.020
 P1Y  plan-1  O20   0.020
 P1Y  plan-1  H01   0.020
 P1Y  plan-1  H04   0.020
 P1Y  plan-1  H05   0.020
 P1Y  plan-2  C07   0.020
 P1Y  plan-2  C08   0.020
 P1Y  plan-2  N09   0.020
 P1Y  plan-2  C10   0.020
 P1Y  plan-2  C11   0.020
 P1Y  plan-2  C12   0.020
 P1Y  plan-2  N13   0.020
 P1Y  plan-2  O14   0.020
 P1Y  plan-2  O15   0.020
 P1Y  plan-2  C16   0.020
 P1Y  plan-3  C10   0.020
 P1Y  plan-3  C16   0.020
 P1Y  plan-3  O17   0.020
 P1Y  plan-3  O18   0.020

