# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 01:46:20 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1nc(Cc2c([nH]c3ccccc23)c4ccccc4)nc(O)c1O
#
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
 P4Y  P4Y  '5,6-dihydroxy-2-[(2-phenyl-1H-indol-3-yl)methyl]pyrimidine-4-carboxylic acid'  ligand  42  27  .  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_P4Y
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
 P4Y  C01   C  CR16  0  -0.270   4.0791  -2.4898  -0.0563
 P4Y  C02   C  CR16  0  -0.284   4.7927  -1.7409  -1.0077
 P4Y  C03   C  CR16  0  -0.317   4.4213  -0.4494  -1.3280
 P4Y  C04   C  CR56  0   0.337   3.3116   0.0801  -0.6709
 P4Y  C05   C  CR56  0   0.057   2.5863  -0.6497   0.2946
 P4Y  C06   C  CR16  0  -0.354   2.9821  -1.9595   0.5936
 P4Y  N07   N  NR15  0  -0.738   2.7213   1.3030  -0.7820
 P4Y  C08   C  CR5   0   0.289   1.6661   1.3930   0.0921
 P4Y  C09   C  CR5   0  -0.027   1.5421   0.2051   0.7730
 P4Y  C10   C  CR6   0   0.066   0.8649   2.6180   0.1503
 P4Y  C11   C  CH2   0  -0.617   0.4537  -0.1919   1.7233
 P4Y  C12   C  CR6   0   0.331  -0.6071  -0.9811   1.0067
 P4Y  C13   C  CR16  0  -0.302   0.4476   3.2410  -1.0273
 P4Y  C14   C  CR16  0  -0.240  -0.2974   4.4097  -0.9821
 P4Y  C15   C  CR16  0  -0.261  -0.6390   4.9739   0.2398
 P4Y  C16   C  CR16  0  -0.242  -0.2227   4.3648   1.4166
 P4Y  C17   C  CR16  0  -0.314   0.5278   3.1996   1.3730
 P4Y  N18   N  N     0  -0.394  -1.6645  -0.3481   0.5701
 P4Y  C19   C  CR6   0  -0.033  -2.5724  -1.0534  -0.1205
 P4Y  C20   C  CR6   0   0.247  -2.4283  -2.4043  -0.3791
 P4Y  C21   C  CR6   0   0.451  -1.2501  -2.9866   0.1538
 P4Y  N22   N  N     0  -0.429  -0.3764  -2.2907   0.8237
 P4Y  C23   C  C     0   0.574  -3.7758  -0.3518  -0.6264
 P4Y  O24   O  OH1   0  -0.603  -3.2654  -3.1828  -1.0544
 P4Y  O25   O  OH1   0  -0.589  -1.0687  -4.2797  -0.0524
 P4Y  O26   O  O     0  -0.466  -4.6408  -0.9299  -1.2590
 P4Y  O27   O  OH1   0  -0.558  -3.8136   0.9239  -0.3329
 P4Y  H01   H  HCR6  0   0.245   4.3958  -3.5008   0.1657
 P4Y  H02   H  HCR6  0   0.249   5.6480  -2.1854  -1.5000
 P4Y  H03   H  HCR6  0   0.258   4.9690   0.1285  -2.0615
 P4Y  H06   H  HCR6  0   0.237   2.4327  -2.5499   1.3154
 P4Y  H11   H  HCH2  0   0.268   0.8641  -0.7906   2.5392
 P4Y  H11A  H  HCH2  0   0.270  -0.0141   0.6855   2.1649
 P4Y  H13   H  HCR6  0   0.255   0.6914   2.8016  -1.9868
 P4Y  H14   H  HCR6  0   0.258  -0.6146   4.8774  -1.9051
 P4Y  H15   H  HCR6  0   0.257  -1.2214   5.8853   0.2753
 P4Y  H16   H  HCR6  0   0.258  -0.4701   4.8054   2.3737
 P4Y  H17   H  HCR6  0   0.256   0.8738   2.7531   2.2964
 P4Y  HO27  H  HOH1  0   0.494  -4.6177   1.3256  -0.6967
 P4Y  HN07  H  HNR5  0   0.408   3.0731   2.0696  -1.3320
 P4Y  H141  H  HOH1  0   0.484  -4.0199  -2.6348  -1.3471
 P4Y  H151  H  HOH1  0   0.485  -0.2359  -4.5553   0.3568

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
 P4Y  C01  H01   single    0.930  0.020  1.080
 P4Y  C02  C01   aromatic  1.405  0.020  1.405
 P4Y  C02  H02   single    0.930  0.020  1.080
 P4Y  C03  C02   aromatic  1.382  0.020  1.382
 P4Y  C03  H03   single    0.930  0.020  1.080
 P4Y  C04  C03   aromatic  1.394  0.020  1.394
 P4Y  C04  C05   aromatic  1.411  0.020  1.411
 P4Y  C05  C06   aromatic  1.401  0.020  1.401
 P4Y  C06  C01   aromatic  1.381  0.020  1.381
 P4Y  C06  H06   single    0.930  0.020  1.080
 P4Y  N07  C04   aromatic  1.362  0.020  1.362
 P4Y  N07  HN07  single    0.860  0.020  1.020
 P4Y  C08  N07   aromatic  1.373  0.020  1.373
 P4Y  C08  C09   aromatic  1.375  0.020  1.375
 P4Y  C09  C05   aromatic  1.432  0.020  1.432
 P4Y  C09  C11   single    1.498  0.020  1.498
 P4Y  C10  C08   single    1.465  0.020  1.465
 P4Y  C11  H11   single    0.970  0.020  1.090
 P4Y  C11  H11A  single    0.970  0.020  1.090
 P4Y  C12  C11   single    1.504  0.020  1.504
 P4Y  C12  N22   aromatic  1.342  0.020  1.342
 P4Y  C13  C10   aromatic  1.396  0.020  1.396
 P4Y  C13  H13   single    0.930  0.020  1.080
 P4Y  C14  C13   aromatic  1.387  0.020  1.387
 P4Y  C14  H14   single    0.930  0.020  1.080
 P4Y  C15  C14   aromatic  1.389  0.020  1.389
 P4Y  C15  C16   aromatic  1.389  0.020  1.389
 P4Y  C15  H15   single    0.930  0.020  1.080
 P4Y  C16  C17   aromatic  1.387  0.020  1.387
 P4Y  C16  H16   single    0.930  0.020  1.080
 P4Y  C17  C10   aromatic  1.395  0.020  1.395
 P4Y  C17  H17   single    0.930  0.020  1.080
 P4Y  N18  C12   aromatic  1.307  0.020  1.307
 P4Y  C19  N18   aromatic  1.341  0.020  1.341
 P4Y  C19  C20   aromatic  1.383  0.020  1.383
 P4Y  C20  C21   aromatic  1.418  0.020  1.418
 P4Y  C21  N22   aromatic  1.302  0.020  1.302
 P4Y  C21  O25   single    1.322  0.020  1.322
 P4Y  C23  C19   single    1.482  0.020  1.482
 P4Y  O24  C20   single    1.328  0.020  1.328
 P4Y  O26  C23   double    1.218  0.020  1.218
 P4Y  O27  C23   single    1.309  0.020  1.309
 P4Y  O27  HO27  single    0.850  0.020  0.980
 P4Y  O24  H141  single    0.850  0.020  0.980
 P4Y  O25  H151  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
 P4Y  H01   C01  C06  119.64  3.000
 P4Y  C06   C01  C02  121.15  3.000
 P4Y  H01   C01  C02  119.21  3.000
 P4Y  H02   C02  C03  119.40  3.000
 P4Y  C03   C02  C01  121.24  3.000
 P4Y  H02   C02  C01  119.36  3.000
 P4Y  H03   C03  C04  121.29  3.000
 P4Y  C04   C03  C02  117.38  3.000
 P4Y  H03   C03  C02  121.33  3.000
 P4Y  N07   C04  C05  107.30  3.000
 P4Y  N07   C04  C03  130.34  3.000
 P4Y  C05   C04  C03  122.36  3.000
 P4Y  C09   C05  C06  133.88  3.000
 P4Y  C09   C05  C04  107.14  3.000
 P4Y  C06   C05  C04  118.98  3.000
 P4Y  H06   C06  C05  120.60  3.000
 P4Y  H06   C06  C01  120.51  3.000
 P4Y  C05   C06  C01  118.89  3.000
 P4Y  HN07  N07  C08  124.49  3.000
 P4Y  C08   N07  C04  109.87  3.000
 P4Y  HN07  N07  C04  125.20  3.000
 P4Y  C10   C08  C09  130.81  3.000
 P4Y  C10   C08  N07  120.02  3.000
 P4Y  C09   C08  N07  109.15  3.000
 P4Y  C11   C09  C08  127.48  3.000
 P4Y  C11   C09  C05  125.70  3.000
 P4Y  C08   C09  C05  106.53  3.000
 P4Y  C17   C10  C13  118.74  3.000
 P4Y  C17   C10  C08  121.04  3.000
 P4Y  C13   C10  C08  120.21  3.000
 P4Y  H11A  C11  H11  107.49  3.000
 P4Y  H11A  C11  C12  108.26  3.000
 P4Y  H11   C11  C12  109.48  3.000
 P4Y  C12   C11  C09  110.43  3.000
 P4Y  H11A  C11  C09  110.86  3.000
 P4Y  H11   C11  C09  110.24  3.000
 P4Y  N22   C12  N18  124.46  3.000
 P4Y  N18   C12  C11  118.39  3.000
 P4Y  N22   C12  C11  117.11  3.000
 P4Y  H13   C13  C14  119.45  3.000
 P4Y  C14   C13  C10  120.61  3.000
 P4Y  H13   C13  C10  119.93  3.000
 P4Y  H14   C14  C15  120.18  3.000
 P4Y  C15   C14  C13  120.22  3.000
 P4Y  H14   C14  C13  119.60  3.000
 P4Y  H15   C15  C16  120.19  3.000
 P4Y  H15   C15  C14  120.23  3.000
 P4Y  C16   C15  C14  119.58  3.000
 P4Y  H16   C16  C17  119.58  3.000
 P4Y  H16   C16  C15  120.15  3.000
 P4Y  C17   C16  C15  120.27  3.000
 P4Y  H17   C17  C16  119.52  3.000
 P4Y  H17   C17  C10  119.89  3.000
 P4Y  C16   C17  C10  120.57  3.000
 P4Y  C19   N18  C12  117.70  3.000
 P4Y  C23   C19  C20  118.90  3.000
 P4Y  C23   C19  N18  118.45  3.000
 P4Y  C20   C19  N18  122.65  3.000
 P4Y  O24   C20  C21  118.31  3.000
 P4Y  O24   C20  C19  127.02  3.000
 P4Y  C21   C20  C19  114.67  3.000
 P4Y  O25   C21  N22  120.72  3.000
 P4Y  O25   C21  C20  117.20  3.000
 P4Y  N22   C21  C20  122.08  3.000
 P4Y  C21   N22  C12  118.44  3.000
 P4Y  O27   C23  O26  123.95  3.000
 P4Y  O27   C23  C19  114.09  3.000
 P4Y  O26   C23  C19  121.96  3.000
 P4Y  H141  O24  C20  108.08  3.000
 P4Y  H151  O25  C21  109.31  3.000
 P4Y  HO27  O27  C23  110.09  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
 P4Y  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 P4Y  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 P4Y  CONST_03  C09   C05  C06  C01   180.00   0.0  0
 P4Y  CONST_04  C05   C06  C01  C02     0.00   0.0  0
 P4Y  CONST_05  C05   C04  C03  C02     0.00   0.0  0
 P4Y  CONST_06  N07   C04  C03  C02   180.00   0.0  0
 P4Y  CONST_07  C06   C01  C02  C03     0.00   0.0  0
 P4Y  CONST_08  C06   C05  C04  C03     0.00   0.0  0
 P4Y  CONST_09  C09   C05  C04  C03   180.00   0.0  0
 P4Y  CONST_10  C08   N07  C04  C03   180.00   0.0  0
 P4Y  CONST_11  C08   C09  C05  C04     0.00   0.0  0
 P4Y  CONST_12  C09   C08  N07  C04     0.00   0.0  0
 P4Y  CONST_13  C10   C08  N07  C04   180.00   0.0  0
 P4Y  CONST_14  C08   N07  C04  C05     0.00   0.0  0
 P4Y  CONST_15  N07   C08  C09  C05     0.00   0.0  0
 P4Y  CONST_16  C10   C08  C09  C05   180.00   0.0  0
 P4Y  CONST_17  N07   C04  C05  C06   180.00   0.0  0
 P4Y  CONST_18  C08   C09  C05  C06   180.00   0.0  0
 P4Y  CONST_19  C09   C05  C04  N07     0.00   0.0  0
 P4Y  CONST_22  C14   C13  C10  C08   180.00   0.0  0
 P4Y  CONST_23  C16   C17  C10  C08   180.00   0.0  0
 P4Y  CONST_26  C15   C14  C13  C10     0.00   0.0  0
 P4Y  CONST_27  C15   C16  C17  C10     0.00   0.0  0
 P4Y  CONST_28  C20   C21  N22  C12     0.00   0.0  0
 P4Y  CONST_29  C20   C19  N18  C12     0.00   0.0  0
 P4Y  CONST_30  C16   C17  C10  C13     0.00   0.0  0
 P4Y  CONST_31  C16   C15  C14  C13     0.00   0.0  0
 P4Y  CONST_32  C17   C10  C13  C14     0.00   0.0  0
 P4Y  CONST_33  C17   C16  C15  C14     0.00   0.0  0
 P4Y  CONST_34  C21   N22  C12  N18     0.00   0.0  0
 P4Y  CONST_35  C21   C20  C19  N18     0.00   0.0  0
 P4Y  CONST_36  N22   C12  N18  C19     0.00   0.0  0
 P4Y  CONST_37  N22   C21  C20  C19     0.00   0.0  0
 P4Y  CONST_38  C11   C09  C05  C04   180.00   0.0  0
 P4Y  CONST_39  C11   C09  C05  C06     0.00   0.0  0
 P4Y  CONST_40  C11   C09  C08  N07   180.00   0.0  0
 P4Y  CONST_41  C11   C09  C08  C10     0.00   0.0  0
 P4Y  CONST_42  C21   N22  C12  C11   180.00   0.0  0
 P4Y  CONST_43  C19   N18  C12  C11   180.00   0.0  0
 P4Y  CONST_44  O25   C21  N22  C12   180.00   0.0  0
 P4Y  CONST_45  C23   C19  N18  C12   180.00   0.0  0
 P4Y  CONST_46  O24   C20  C19  N18   180.00   0.0  0
 P4Y  CONST_47  O25   C21  C20  C19   180.00   0.0  0
 P4Y  CONST_48  C23   C19  C20  C21   180.00   0.0  0
 P4Y  CONST_49  O24   C20  C21  N22   180.00   0.0  0
 P4Y  CONST_50  H03   C03  C02  C01   180.00   0.0  0
 P4Y  CONST_51  H06   C06  C01  C02   180.00   0.0  0
 P4Y  CONST_52  H01   C01  C02  C03   180.00   0.0  0
 P4Y  CONST_53  HN07  N07  C04  C03     0.00   0.0  0
 P4Y  CONST_54  H02   C02  C03  C04   180.00   0.0  0
 P4Y  CONST_55  H13   C13  C10  C08     0.00   0.0  0
 P4Y  CONST_56  H17   C17  C10  C08     0.00   0.0  0
 P4Y  CONST_57  H14   C14  C13  C10   180.00   0.0  0
 P4Y  CONST_58  H16   C16  C17  C10   180.00   0.0  0
 P4Y  CONST_59  H15   C15  C14  C13   180.00   0.0  0
 P4Y  CONST_60  HO27  O27  C23  C19   180.00   0.0  0
 P4Y  Var_01    C12   C11  C09  C05   -77.72  30.0  2
 P4Y  Var_02    N22   C12  C11  C09    82.29  30.0  1
 P4Y  Var_03    O26   C23  C19  N18  -179.91  30.0  2

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
 P4Y  plan-1  C11   0.020
 P4Y  plan-1  C12   0.020
 P4Y  plan-1  N18   0.020
 P4Y  plan-1  C19   0.020
 P4Y  plan-1  C20   0.020
 P4Y  plan-1  C21   0.020
 P4Y  plan-1  N22   0.020
 P4Y  plan-1  C23   0.020
 P4Y  plan-1  O24   0.020
 P4Y  plan-1  O25   0.020
 P4Y  plan-2  C08   0.020
 P4Y  plan-2  C10   0.020
 P4Y  plan-2  C13   0.020
 P4Y  plan-2  C14   0.020
 P4Y  plan-2  C15   0.020
 P4Y  plan-2  C16   0.020
 P4Y  plan-2  C17   0.020
 P4Y  plan-2  H13   0.020
 P4Y  plan-2  H14   0.020
 P4Y  plan-2  H15   0.020
 P4Y  plan-2  H16   0.020
 P4Y  plan-2  H17   0.020
 P4Y  plan-3  C01   0.020
 P4Y  plan-3  C02   0.020
 P4Y  plan-3  C03   0.020
 P4Y  plan-3  C04   0.020
 P4Y  plan-3  C05   0.020
 P4Y  plan-3  C06   0.020
 P4Y  plan-3  N07   0.020
 P4Y  plan-3  C08   0.020
 P4Y  plan-3  C09   0.020
 P4Y  plan-3  C10   0.020
 P4Y  plan-3  C11   0.020
 P4Y  plan-3  H01   0.020
 P4Y  plan-3  H02   0.020
 P4Y  plan-3  H03   0.020
 P4Y  plan-3  H06   0.020
 P4Y  plan-3  HN07  0.020
 P4Y  plan-4  C19   0.020
 P4Y  plan-4  C23   0.020
 P4Y  plan-4  O26   0.020
 P4Y  plan-4  O27   0.020
 P4Y  plan-4  HO27  0.020

