# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 17:36:14 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  32  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   CR16  0  -0.258  -1.3782   0.3685   0.8010
 P1Y  C02   C   CR6   0  -0.208  -2.4870  -0.0143   0.0696
 P1Y  C03   C   CR6   0   0.433  -2.7640  -1.3625  -0.1842
 P1Y  C04   C   CR16  0  -0.374  -1.8848  -2.3143   0.3258
 P1Y  C05   C   CR16  0  -0.287  -0.7727  -1.9250   1.0596
 P1Y  C06   C   CR6   0   0.098  -0.5035  -0.5877   1.3113
 P1Y  C07   C   CH2   0  -0.592   0.7299  -0.1743   2.0742
 P1Y  C08   C   CR6   0   0.345   1.8312   0.2091   1.1262
 P1Y  N09   N   N     0  -0.407   2.7453  -0.6786   0.8352
 P1Y  C10   C   CR6   0   0.004   3.7022  -0.3491  -0.0469
 P1Y  C11   C   CR6   0   0.262   3.7384   0.8940  -0.6497
 P1Y  C12   C   CR6   0   0.425   2.6963   1.7740  -0.2571
 P1Y  N13   N   N     0  -0.425   1.7769   1.4410   0.6013
 P1Y  O14   O   OH1   0  -0.588   4.6676   1.2649  -1.5273
 P1Y  O15   O   OH1   0  -0.605   2.7061   2.9763  -0.8127
 P1Y  C16   C   C     0   0.532   4.7302  -1.3874  -0.3469
 P1Y  O17   O   OH1   0  -0.581   4.5049  -2.5134   0.3081
 P1Y  O18   O   O     0  -0.421   5.6581  -1.2233  -1.0982
 P1Y  BR19  BR  BR    0  -0.038  -3.6592   1.3000  -0.6018
 P1Y  O20   O   O2    0  -0.454  -3.8615  -1.6430  -0.8975
 P1Y  C21   C   CH3   0  -0.439  -4.1802  -3.0009  -1.1446
 P1Y  H01   H   HCR6  0   0.272  -1.1867   1.4190   0.9813
 P1Y  H04   H   HCR6  0   0.290  -2.0574  -3.3688   0.1590
 P1Y  H05   H   HCR6  0   0.261  -0.1069  -2.6889   1.4421
 P1Y  H07   H   HCH2  0   0.280   0.5075   0.6683   2.7310
 P1Y  H07A  H   HCH2  0   0.276   1.0736  -1.0003   2.6952
 P1Y  HO17  H   HOH1  0   0.488   5.1908  -3.1589   0.0800
 P1Y  H21   H   HCH3  0   0.234  -3.4080  -3.4987  -1.7361
 P1Y  H21A  H   HCH3  0   0.234  -4.3318  -3.5564  -0.2162
 P1Y  H21B  H   HCH3  0   0.264  -5.1085  -2.9976  -1.7097
 P1Y  H10   H   HOH1  0   0.487   4.5039   2.1648  -1.8383
 P1Y  H11   H   HOH1  0   0.495   1.9692   3.5071  -0.4781

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  1.382  0.020  1.382
 P1Y  C01  H01   single    0.930  0.020  1.080
 P1Y  C02  BR19  single    1.885  0.020  1.885
 P1Y  C03  C02   aromatic  1.400  0.020  1.400
 P1Y  C03  O20   single    1.339  0.020  1.339
 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  1.393  0.020  1.393
 P1Y  C07  C06   single    1.508  0.020  1.508
 P1Y  C07  H07   single    0.970  0.020  1.090
 P1Y  C07  H07A  single    0.970  0.020  1.090
 P1Y  C08  C07   single    1.503  0.020  1.503
 P1Y  C08  N13   aromatic  1.340  0.020  1.340
 P1Y  N09  C08   aromatic  1.307  0.020  1.307
 P1Y  C10  N09   aromatic  1.343  0.020  1.343
 P1Y  C10  C11   aromatic  1.382  0.020  1.382
 P1Y  C11  C12   aromatic  1.419  0.020  1.419
 P1Y  C12  O15   single    1.325  0.020  1.325
 P1Y  C12  N13   aromatic  1.301  0.020  1.301
 P1Y  O14  C11   single    1.331  0.020  1.331
 P1Y  C16  C10   single    1.492  0.020  1.492
 P1Y  C16  O17   single    1.322  0.020  1.322
 P1Y  O17  HO17  single    0.850  0.020  0.980
 P1Y  O18  C16   double    1.205  0.020  1.205
 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   119.60  3.000
 P1Y  C06   C01  C02   120.49  3.000
 P1Y  H01   C01  C02   119.91  3.000
 P1Y  BR19  C02  C03   118.95  3.000
 P1Y  C03   C02  C01   121.43  3.000
 P1Y  BR19  C02  C01   119.62  3.000
 P1Y  O20   C03  C04   124.72  3.000
 P1Y  C04   C03  C02   117.84  3.000
 P1Y  O20   C03  C02   117.44  3.000
 P1Y  H04   C04  C05   118.88  3.000
 P1Y  C05   C04  C03   120.51  3.000
 P1Y  H04   C04  C03   120.61  3.000
 P1Y  H05   C05  C06   119.77  3.000
 P1Y  H05   C05  C04   118.77  3.000
 P1Y  C06   C05  C04   121.46  3.000
 P1Y  C07   C06  C05   120.99  3.000
 P1Y  C07   C06  C01   120.72  3.000
 P1Y  C05   C06  C01   118.26  3.000
 P1Y  H07A  C07  H07   107.86  3.000
 P1Y  H07A  C07  C08   108.78  3.000
 P1Y  H07   C07  C08   109.39  3.000
 P1Y  C08   C07  C06   110.50  3.000
 P1Y  H07A  C07  C06   109.80  3.000
 P1Y  H07   C07  C06   110.46  3.000
 P1Y  N13   C08  N09   124.43  3.000
 P1Y  N09   C08  C07   118.67  3.000
 P1Y  N13   C08  C07   116.86  3.000
 P1Y  C10   N09  C08   118.56  3.000
 P1Y  C16   C10  C11   121.35  3.000
 P1Y  C16   C10  N09   116.91  3.000
 P1Y  C11   C10  N09   121.74  3.000
 P1Y  O14   C11  C12   121.48  3.000
 P1Y  O14   C11  C10   123.82  3.000
 P1Y  C12   C11  C10   114.70  3.000
 P1Y  O15   C12  N13   120.95  3.000
 P1Y  N13   C12  C11   122.86  3.000
 P1Y  O15   C12  C11   116.19  3.000
 P1Y  C12   N13  C08   117.71  3.000
 P1Y  H10   O14  C11   110.71  3.000
 P1Y  H11   O15  C12   110.32  3.000
 P1Y  O18   C16  O17   123.78  3.000
 P1Y  O18   C16  C10   124.15  3.000
 P1Y  O17   C16  C10   112.07  3.000
 P1Y  HO17  O17  C16   109.27  3.000
 P1Y  C21   O20  C03   118.58  3.000
 P1Y  H21B  C21  H21A  108.95  3.000
 P1Y  H21B  C21  H21   108.88  3.000
 P1Y  H21A  C21  H21   109.05  3.000
 P1Y  H21B  C21  O20   106.26  3.000
 P1Y  H21A  C21  O20   111.74  3.000
 P1Y  H21   C21  O20   111.85  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  CONST_30  HO17  O17  C16  C10  180.00   0.0  0
 P1Y  Var_01    C08   C07  C06  C01  -81.08  30.0  2
 P1Y  Var_02    N13   C08  C07  C06   80.53  30.0  3
 P1Y  Var_03    O17   C16  C10  N09    1.41  30.0  3
 P1Y  Var_04    H21   C21  O20  C03  -62.73  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
 P1Y  plan-3  HO17  0.020

