# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 08:27:50 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-[(phenylmethyl)amino]pyridine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(C(O)=O)c(NCc2ccccc2)cn1
#
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
 HRF  HRF  "5-(benzylamino)pyridine-2,4-dicarboxylic acid"  ligand  30  20  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HRF
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
 HRF  C10  C  CR16   0  -0.267   -0.4804  10.4326  -24.6476
 HRF  C13  C  C      0   0.375  -10.8317  12.4293  -23.3374
 HRF  C1   C  CR6    0   0.284   -6.6375  11.5022  -23.4846
 HRF  C2   C  CR16   0  -0.212   -7.5671  11.1886  -24.4965
 HRF  C3   C  CR6    0  -0.002   -9.3438  12.0972  -23.3733
 HRF  C4   C  CR16   0  -0.346   -8.5081  12.4187  -22.3083
 HRF  C5   C  CR6    0  -0.109   -7.1528  12.1294  -22.3249
 HRF  C6   C  CH2    0  -0.328   -4.7811  10.3955  -24.6694
 HRF  C7   C  CR6    0   0.088   -3.2757  10.4054  -24.6431
 HRF  C8   C  CR16   0  -0.311   -2.5561   9.2194  -24.5543
 HRF  C9   C  CR16   0  -0.238   -1.1658   9.2300  -24.5590
 HRF  C11  C  CR16   0  -0.239   -1.1919  11.6244  -24.7320
 HRF  C12  C  CR16   0  -0.286   -2.5785  11.6098  -24.7297
 HRF  C14  C  C      0   0.436   -6.3003  12.4668  -21.1069
 HRF  N1   N  N      0  -0.393   -8.8532  11.4778  -24.4458
 HRF  N2   N  NH1    0  -0.701   -5.3128  11.2303  -23.6241
 HRF  O1   O  OC    -1  -0.595  -11.2445  12.9723  -22.2906
 HRF  O2   O  O      0  -0.598  -11.5030  12.1363  -24.3436
 HRF  O3   O  O      0  -0.594   -5.1005  12.0962  -21.1292
 HRF  O4   O  OC    -1  -0.568   -6.8581  13.0710  -20.1774
 HRF  H08  H  HCR6   0   0.253    0.6020  10.4443  -24.6501
 HRF  H01  H  HCR6   0   0.247   -7.2353  10.6727  -25.3917
 HRF  H02  H  HCR6   0   0.234   -8.9257  12.9024  -21.4374
 HRF  H04  H  HCH2   0   0.240   -5.1119  10.7692  -25.6442
 HRF  H05  H  HCH2   0   0.233   -5.1428   9.3605  -24.6011
 HRF  H06  H  HCR6   0   0.250   -3.0860   8.2770  -24.4800
 HRF  H07  H  HCR6   0   0.253   -0.6206   8.2973  -24.4896
 HRF  H09  H  HCR6   0   0.253   -0.6637  12.5666  -24.8047
 HRF  H10  H  HCR6   0   0.249   -3.1263  12.5421  -24.8007
 HRF  H03  H  HNH1   0   0.392   -4.7987  11.3362  -22.7521

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
 HRF  C8   C9   aromatic  1.390  0.020  1.390
 HRF  C8   C7   aromatic  1.390  0.020  1.390
 HRF  C6   C7   single    1.506  0.020  1.506
 HRF  C6   N2   single    1.440  0.020  1.440
 HRF  C9   C10  aromatic  1.387  0.020  1.387
 HRF  C7   C12  aromatic  1.394  0.020  1.394
 HRF  C10  C11  aromatic  1.391  0.020  1.391
 HRF  C2   N1   aromatic  1.319  0.020  1.319
 HRF  C2   C1   aromatic  1.409  0.020  1.409
 HRF  C12  C11  aromatic  1.387  0.020  1.387
 HRF  N1   C3   aromatic  1.332  0.020  1.332
 HRF  O2   C13  deloc     1.245  0.020  1.245
 HRF  N2   C1   single    1.359  0.020  1.359
 HRF  C1   C5   aromatic  1.416  0.020  1.416
 HRF  C3   C13  single    1.525  0.020  1.525
 HRF  C3   C4   aromatic  1.391  0.020  1.391
 HRF  C13  O1   deloc     1.249  0.020  1.249
 HRF  C5   C4   aromatic  1.386  0.020  1.386
 HRF  C5   C14  single    1.525  0.020  1.525
 HRF  O3   C14  deloc     1.256  0.020  1.256
 HRF  C14  O4   deloc     1.241  0.020  1.241
 HRF  C10  H08  single    0.930  0.020  1.080
 HRF  C2   H01  single    0.930  0.020  1.080
 HRF  C4   H02  single    0.930  0.020  1.080
 HRF  C6   H04  single    0.970  0.020  1.090
 HRF  C6   H05  single    0.970  0.020  1.090
 HRF  C8   H06  single    0.930  0.020  1.080
 HRF  C9   H07  single    0.930  0.020  1.080
 HRF  C11  H09  single    0.930  0.020  1.080
 HRF  C12  H10  single    0.930  0.020  1.080
 HRF  N2   H03  single    0.890  0.020  1.040

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
 HRF  H08  C10  C11  120.15  3.000
 HRF  H08  C10  C9   120.24  3.000
 HRF  C11  C10  C9   119.61  3.000
 HRF  O2   C13  O1   126.98  3.000
 HRF  O1   C13  C3   115.89  3.000
 HRF  O2   C13  C3   117.13  3.000
 HRF  N2   C1   C5   121.83  3.000
 HRF  C5   C1   C2   116.52  3.000
 HRF  N2   C1   C2   121.64  3.000
 HRF  H01  C2   N1   115.72  3.000
 HRF  H01  C2   C1   119.75  3.000
 HRF  N1   C2   C1   124.52  3.000
 HRF  N1   C3   C4   120.16  3.000
 HRF  C4   C3   C13  121.18  3.000
 HRF  N1   C3   C13  118.66  3.000
 HRF  H02  C4   C5   118.76  3.000
 HRF  H02  C4   C3   119.23  3.000
 HRF  C5   C4   C3   122.00  3.000
 HRF  C14  C5   C4   119.41  3.000
 HRF  C14  C5   C1   123.30  3.000
 HRF  C4   C5   C1   117.28  3.000
 HRF  H05  C6   H04  106.11  3.000
 HRF  H05  C6   N2   112.31  3.000
 HRF  H04  C6   N2   109.69  3.000
 HRF  H05  C6   C7   109.53  3.000
 HRF  H04  C6   C7   108.38  3.000
 HRF  N2   C6   C7   110.66  3.000
 HRF  C12  C7   C8   118.82  3.000
 HRF  C12  C7   C6   120.30  3.000
 HRF  C8   C7   C6   120.87  3.000
 HRF  H06  C8   C9   119.73  3.000
 HRF  H06  C8   C7   119.55  3.000
 HRF  C9   C8   C7   120.73  3.000
 HRF  H07  C9   C8   119.78  3.000
 HRF  H07  C9   C10  120.15  3.000
 HRF  C8   C9   C10  120.06  3.000
 HRF  H09  C11  C12  119.82  3.000
 HRF  H09  C11  C10  120.02  3.000
 HRF  C12  C11  C10  120.17  3.000
 HRF  H10  C12  C11  119.76  3.000
 HRF  H10  C12  C7   119.63  3.000
 HRF  C11  C12  C7   120.61  3.000
 HRF  O4   C14  O3   125.90  3.000
 HRF  O4   C14  C5   117.05  3.000
 HRF  O3   C14  C5   117.05  3.000
 HRF  C3   N1   C2   119.47  3.000
 HRF  H03  N2   C6   119.73  3.000
 HRF  H03  N2   C1   112.55  3.000
 HRF  C6   N2   C1   123.39  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
 HRF  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 HRF  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 HRF  CONST_03  C3   N1   C2   C1      0.00   0.0  0
 HRF  CONST_04  C3   C4   C5   C1      0.00   0.0  0
 HRF  CONST_05  C4   C3   N1   C2      0.00   0.0  0
 HRF  CONST_06  C4   C5   C1   C2      0.00   0.0  0
 HRF  CONST_07  N1   C2   C1   C5      0.00   0.0  0
 HRF  CONST_08  N1   C3   C4   C5      0.00   0.0  0
 HRF  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 HRF  CONST_10  C11  C12  C7   C8      0.00   0.0  0
 HRF  CONST_11  C12  C7   C8   C9      0.00   0.0  0
 HRF  CONST_12  C12  C11  C10  C9      0.00   0.0  0
 HRF  CONST_13  C2   N1   C3   C13   180.00   0.0  0
 HRF  CONST_14  C5   C4   C3   C13   180.00   0.0  0
 HRF  CONST_15  C14  C5   C1   C2    180.00   0.0  0
 HRF  CONST_16  C14  C5   C4   C3    180.00   0.0  0
 HRF  CONST_17  N2   C1   C5   C4    180.00   0.0  0
 HRF  CONST_18  C9   C8   C7   C6    180.00   0.0  0
 HRF  CONST_19  C11  C12  C7   C6    180.00   0.0  0
 HRF  CONST_20  N2   C1   C2   N1    180.00   0.0  0
 HRF  CONST_21  H06  C8   C9   C10   180.00   0.0  0
 HRF  CONST_22  H10  C12  C11  C10   180.00   0.0  0
 HRF  CONST_23  H02  C4   C5   C1    180.00   0.0  0
 HRF  CONST_24  H01  C2   N1   C3    180.00   0.0  0
 HRF  CONST_25  H01  C2   C1   C5    180.00   0.0  0
 HRF  CONST_26  H07  C9   C8   C7    180.00   0.0  0
 HRF  CONST_27  H09  C11  C12  C7    180.00   0.0  0
 HRF  CONST_28  H08  C10  C9   C8    180.00   0.0  0
 HRF  CONST_29  H10  C12  C7   C8    180.00   0.0  0
 HRF  CONST_30  H09  C11  C10  C9    180.00   0.0  0
 HRF  CONST_31  H07  C9   C10  C11   180.00   0.0  0
 HRF  CONST_32  H06  C8   C7   C12   180.00   0.0  0
 HRF  CONST_33  H08  C10  C11  C12   180.00   0.0  0
 HRF  CONST_34  H02  C4   C3   N1    180.00   0.0  0
 HRF  CONST_35  C6   N2   C1   C2      0.00   0.0  0
 HRF  CONST_36  C6   N2   C1   C5    180.00   0.0  0
 HRF  CONST_37  H03  N2   C1   C2    180.00   0.0  0
 HRF  CONST_38  H03  N2   C1   C5      0.00   0.0  0
 HRF  Var_01    C7   C6   N2   C1    174.01  30.0  2
 HRF  Var_02    O3   C14  C5   C1     -3.87  30.0  2
 HRF  Var_03    O4   C14  C5   C1    176.83  30.0  2
 HRF  Var_04    O2   C13  C3   C4    178.35  30.0  2
 HRF  Var_05    O1   C13  C3   C4     -1.57  30.0  2
 HRF  Var_06    O3   C14  C5   C4    174.84  30.0  2
 HRF  Var_07    O4   C14  C5   C4     -4.46  30.0  2
 HRF  Var_08    N2   C6   C7   C8    124.82  30.0  2
 HRF  Var_09    N2   C6   C7   C12   -56.23  30.0  2
 HRF  Var_10    O2   C13  C3   N1     -2.22  30.0  2
 HRF  Var_11    O1   C13  C3   N1    177.85  30.0  2
 HRF  Var_12    H04  C6   C7   C8   -114.87  30.0  2
 HRF  Var_13    H05  C6   C7   C8      0.48  30.0  2
 HRF  Var_14    H04  C6   C7   C12    64.08  30.0  2
 HRF  Var_15    H05  C6   C7   C12   179.43  30.0  2
 HRF  Var_16    H04  C6   N2   C1     54.48  30.0  2
 HRF  Var_17    H05  C6   N2   C1    -63.25  30.0  2
 HRF  Var_18    H03  N2   C6   C7    -31.11  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
 HRF  plan-1  C13  0.020
 HRF  plan-1  C1   0.020
 HRF  plan-1  C2   0.020
 HRF  plan-1  C3   0.020
 HRF  plan-1  C4   0.020
 HRF  plan-1  C5   0.020
 HRF  plan-1  C14  0.020
 HRF  plan-1  N1   0.020
 HRF  plan-1  N2   0.020
 HRF  plan-1  H01  0.020
 HRF  plan-1  H02  0.020
 HRF  plan-2  C10  0.020
 HRF  plan-2  C6   0.020
 HRF  plan-2  C7   0.020
 HRF  plan-2  C8   0.020
 HRF  plan-2  C9   0.020
 HRF  plan-2  C11  0.020
 HRF  plan-2  C12  0.020
 HRF  plan-2  H08  0.020
 HRF  plan-2  H06  0.020
 HRF  plan-2  H07  0.020
 HRF  plan-2  H09  0.020
 HRF  plan-2  H10  0.020
 HRF  plan-3  C1   0.020
 HRF  plan-3  C6   0.020
 HRF  plan-3  N2   0.020
 HRF  plan-3  H03  0.020
 HRF  plan-4  C13  0.020
 HRF  plan-4  C3   0.020
 HRF  plan-4  O1   0.020
 HRF  plan-4  O2   0.020
 HRF  plan-5  C5   0.020
 HRF  plan-5  C14  0.020
 HRF  plan-5  O3   0.020
 HRF  plan-5  O4   0.020

