# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:09:33 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[(4-methoxyphenyl)methylamino]pyridine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNc2cnc(cc2C(O)=O)C(O)=O)cc1
#
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
 HR3  HR3  "5-((4-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid"  ligand  34  22  .  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_HR3
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
 HR3  C10  C  CR6    0   0.369   -0.4807  10.7284  -24.3881
 HR3  C13  C  CH3    0  -0.435    1.6439   9.7097  -24.1255
 HR3  C15  C  C      0   0.435   -6.4352  12.6404  -21.0414
 HR3  C1   C  C      0   0.284   -6.7001  11.6517  -23.4178
 HR3  C2   C  C1     0  -0.215   -7.6002  11.3082  -24.4473
 HR3  C3   C  C      0  -0.003   -9.4229  12.1773  -23.3672
 HR3  C4   C  C1     0  -0.346   -8.6185  12.5248  -22.2859
 HR3  C5   C  C      0  -0.109   -7.2560  12.2706  -22.2720
 HR3  C6   C  CH2    0  -0.331   -4.7882  10.6216  -24.5854
 HR3  C7   C  CR6    0   0.064   -3.2873  10.6541  -24.5042
 HR3  C8   C  CR16   0  -0.268   -2.5914  11.8485  -24.7010
 HR3  C9   C  CR16   0  -0.326   -1.2125  11.8919  -24.6460
 HR3  C11  C  CR16   0  -0.368   -1.1597   9.5323  -24.1819
 HR3  C12  C  CR16   0  -0.294   -2.5507   9.5107  -24.2400
 HR3  C14  C  C      0   0.374  -10.9178  12.4773  -23.3702
 HR3  N1   N  N      0  -0.393   -8.8940  11.5639  -24.4251
 HR3  N2   N  NH1    0  -0.696   -5.3686  11.4128  -23.5308
 HR3  O1   O  O2     0  -0.468    0.8596  10.8605  -24.3616
 HR3  O2   O  OC    -1  -0.595  -11.3683  13.0246  -22.3413
 HR3  O3   O  O      0  -0.599  -11.5584  12.1593  -24.3888
 HR3  O4   O  O      0  -0.594   -5.2222  12.3145  -21.0442
 HR3  O5   O  OC    -1  -0.568   -7.0283  13.2271  -20.1223
 HR3  H11  H  HCH3   0   0.257    2.6823  10.0309  -24.1545
 HR3  H12  H  HCH3   0   0.226    1.4403   9.2687  -23.1461
 HR3  H10  H  HCH3   0   0.227    1.4905   8.9460  -24.8928
 HR3  H01  H  H      0   0.247   -7.2358  10.7984  -25.3334
 HR3  H02  H  H      0   0.233   -9.0673  13.0032  -21.4275
 HR3  H04  H  HCH2   0   0.235   -5.0981  11.0204  -25.5572
 HR3  H05  H  HCH2   0   0.231   -5.1350   9.5796  -24.5582
 HR3  H06  H  HCR6   0   0.250   -3.1389  12.7604  -24.9095
 HR3  H07  H  HCR6   0   0.258   -0.6873  12.8253  -24.8081
 HR3  H08  H  HCR6   0   0.275   -0.6323   8.6107  -23.9763
 HR3  H09  H  HCR6   0   0.252   -3.0627   8.5696  -24.0772
 HR3  H03  H  HNH1   0   0.391   -4.8646  11.5505  -22.6584

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
 HR3  C6   C7   single    1.503  0.020  1.503
 HR3  C6   N2   single    1.441  0.020  1.441
 HR3  C12  C7   aromatic  1.386  0.020  1.386
 HR3  C12  C11  aromatic  1.392  0.020  1.392
 HR3  C7   C8   aromatic  1.396  0.020  1.396
 HR3  C11  C10  aromatic  1.391  0.020  1.391
 HR3  C2   N1   aromatic  1.319  0.020  1.319
 HR3  C2   C1   aromatic  1.410  0.020  1.410
 HR3  C8   C9   aromatic  1.381  0.020  1.381
 HR3  C10  C9   aromatic  1.398  0.020  1.398
 HR3  C10  O1   single    1.347  0.020  1.347
 HR3  N1   C3   aromatic  1.332  0.020  1.332
 HR3  N2   C1   single    1.357  0.020  1.357
 HR3  O3   C14  deloc     1.245  0.020  1.245
 HR3  O1   C13  single    1.413  0.020  1.413
 HR3  C1   C5   aromatic  1.416  0.020  1.416
 HR3  C3   C14  single    1.525  0.020  1.525
 HR3  C3   C4   aromatic  1.392  0.020  1.392
 HR3  C14  O2   deloc     1.249  0.020  1.249
 HR3  C5   C4   aromatic  1.386  0.020  1.386
 HR3  C5   C15  single    1.525  0.020  1.525
 HR3  O4   C15  deloc     1.256  0.020  1.256
 HR3  C15  O5   deloc     1.241  0.020  1.241
 HR3  C13  H11  single    0.970  0.020  1.090
 HR3  C13  H12  single    0.970  0.020  1.090
 HR3  C13  H10  single    0.970  0.020  1.090
 HR3  C2   H01  single    0.930  0.020  1.080
 HR3  C4   H02  single    0.930  0.020  1.080
 HR3  C6   H04  single    0.970  0.020  1.090
 HR3  C6   H05  single    0.970  0.020  1.090
 HR3  C8   H06  single    0.930  0.020  1.080
 HR3  C9   H07  single    0.930  0.020  1.080
 HR3  C11  H08  single    0.930  0.020  1.080
 HR3  C12  H09  single    0.930  0.020  1.080
 HR3  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
 HR3  O1   C10  C11  124.55  3.000
 HR3  O1   C10  C9   116.27  3.000
 HR3  C11  C10  C9   119.18  3.000
 HR3  H10  C13  H12  108.71  3.000
 HR3  H10  C13  H11  108.76  3.000
 HR3  H12  C13  H11  108.72  3.000
 HR3  H10  C13  O1   111.96  3.000
 HR3  H12  C13  O1   112.02  3.000
 HR3  H11  C13  O1   106.57  3.000
 HR3  O5   C15  O4   125.85  3.000
 HR3  O5   C15  C5   117.07  3.000
 HR3  O4   C15  C5   117.07  3.000
 HR3  N2   C1   C5   121.96  3.000
 HR3  C5   C1   C2   116.53  3.000
 HR3  N2   C1   C2   121.50  3.000
 HR3  H01  C2   N1   115.73  3.000
 HR3  H01  C2   C1   119.74  3.000
 HR3  N1   C2   C1   124.52  3.000
 HR3  N1   C3   C14  118.57  3.000
 HR3  C14  C3   C4   121.27  3.000
 HR3  N1   C3   C4   120.16  3.000
 HR3  H02  C4   C5   118.79  3.000
 HR3  H02  C4   C3   119.20  3.000
 HR3  C5   C4   C3   122.01  3.000
 HR3  C4   C5   C1   117.26  3.000
 HR3  C4   C5   C15  119.52  3.000
 HR3  C1   C5   C15  123.21  3.000
 HR3  H05  C6   H04  106.14  3.000
 HR3  H05  C6   N2   112.06  3.000
 HR3  H04  C6   N2   109.61  3.000
 HR3  H05  C6   C7   109.53  3.000
 HR3  H04  C6   C7   108.82  3.000
 HR3  N2   C6   C7   110.54  3.000
 HR3  C12  C7   C8   117.90  3.000
 HR3  C8   C7   C6   120.56  3.000
 HR3  C12  C7   C6   121.54  3.000
 HR3  H06  C8   C9   119.06  3.000
 HR3  H06  C8   C7   119.67  3.000
 HR3  C9   C8   C7   121.27  3.000
 HR3  H07  C9   C8   120.35  3.000
 HR3  H07  C9   C10  119.40  3.000
 HR3  C8   C9   C10  120.25  3.000
 HR3  H08  C11  C12  118.81  3.000
 HR3  H08  C11  C10  121.54  3.000
 HR3  C12  C11  C10  119.66  3.000
 HR3  H09  C12  C11  118.63  3.000
 HR3  H09  C12  C7   119.62  3.000
 HR3  C11  C12  C7   121.75  3.000
 HR3  O3   C14  O2   126.89  3.000
 HR3  O2   C14  C3   115.99  3.000
 HR3  O3   C14  C3   117.12  3.000
 HR3  C3   N1   C2   119.47  3.000
 HR3  H03  N2   C6   120.18  3.000
 HR3  H03  N2   C1   113.01  3.000
 HR3  C6   N2   C1   123.56  3.000
 HR3  C13  O1   C10  118.41  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
 HR3  CONST_01  C7   C12  C11  C10     0.00   0.0  0
 HR3  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 HR3  CONST_03  C3   N1   C2   C1      0.00   0.0  0
 HR3  CONST_04  C3   C4   C5   C1      0.00   0.0  0
 HR3  CONST_05  C4   C3   N1   C2      0.00   0.0  0
 HR3  CONST_06  C4   C5   C1   C2      0.00   0.0  0
 HR3  CONST_07  N1   C2   C1   C5      0.00   0.0  0
 HR3  CONST_08  N1   C3   C4   C5      0.00   0.0  0
 HR3  CONST_09  C11  C12  C7   C8      0.00   0.0  0
 HR3  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 HR3  CONST_11  C12  C7   C8   C9      0.00   0.0  0
 HR3  CONST_12  C12  C11  C10  C9      0.00   0.0  0
 HR3  CONST_13  C2   C1   C5   C15   180.00   0.0  0
 HR3  CONST_14  C3   C4   C5   C15   180.00   0.0  0
 HR3  CONST_15  C14  C3   N1   C2    180.00   0.0  0
 HR3  CONST_16  N2   C1   C5   C4    180.00   0.0  0
 HR3  CONST_17  C14  C3   C4   C5    180.00   0.0  0
 HR3  CONST_18  C11  C12  C7   C6    180.00   0.0  0
 HR3  CONST_19  C9   C8   C7   C6    180.00   0.0  0
 HR3  CONST_20  O1   C10  C9   C8    180.00   0.0  0
 HR3  CONST_21  O1   C10  C11  C12   180.00   0.0  0
 HR3  CONST_22  N2   C1   C2   N1    180.00   0.0  0
 HR3  CONST_23  H09  C12  C11  C10   180.00   0.0  0
 HR3  CONST_24  H06  C8   C9   C10   180.00   0.0  0
 HR3  CONST_25  H02  C4   C5   C1    180.00   0.0  0
 HR3  CONST_26  H01  C2   N1   C3    180.00   0.0  0
 HR3  CONST_27  H01  C2   C1   C5    180.00   0.0  0
 HR3  CONST_28  H08  C11  C12  C7    180.00   0.0  0
 HR3  CONST_29  H07  C9   C8   C7    180.00   0.0  0
 HR3  CONST_30  H09  C12  C7   C8    180.00   0.0  0
 HR3  CONST_31  H08  C11  C10  C9    180.00   0.0  0
 HR3  CONST_32  H07  C9   C10  C11   180.00   0.0  0
 HR3  CONST_33  H06  C8   C7   C12   180.00   0.0  0
 HR3  CONST_34  H02  C4   C3   N1    180.00   0.0  0
 HR3  CONST_35  C6   N2   C1   C2      0.00   0.0  0
 HR3  CONST_36  C6   N2   C1   C5    180.00   0.0  0
 HR3  CONST_37  H03  N2   C1   C2    180.00   0.0  0
 HR3  CONST_38  H03  N2   C1   C5      0.00   0.0  0
 HR3  Var_01    C11  C10  O1   C13     0.82  30.0  2
 HR3  Var_02    C9   C10  O1   C13  -179.03  30.0  2
 HR3  Var_03    C7   C6   N2   C1    174.67  30.0  1
 HR3  Var_04    O4   C15  C5   C1     -3.34  30.0  2
 HR3  Var_05    O5   C15  C5   C1    177.22  30.0  2
 HR3  Var_06    O3   C14  C3   C4    178.48  30.0  2
 HR3  Var_07    O2   C14  C3   C4     -1.30  30.0  2
 HR3  Var_08    O4   C15  C5   C4    175.67  30.0  2
 HR3  Var_09    O5   C15  C5   C4     -3.77  30.0  2
 HR3  Var_10    N2   C6   C7   C8    -64.73  30.0  2
 HR3  Var_11    N2   C6   C7   C12   115.56  30.0  2
 HR3  Var_12    O3   C14  C3   N1     -1.87  30.0  2
 HR3  Var_13    O2   C14  C3   N1    178.35  30.0  2
 HR3  Var_14    H04  C6   C7   C8     55.68  30.0  2
 HR3  Var_15    H05  C6   C7   C8    171.31  30.0  2
 HR3  Var_16    H04  C6   C7   C12  -124.02  30.0  2
 HR3  Var_17    H05  C6   C7   C12    -8.39  30.0  2
 HR3  Var_18    H11  C13  O1   C10   179.45  30.0  3
 HR3  Var_19    H12  C13  O1   C10   -61.77  30.0  3
 HR3  Var_20    H10  C13  O1   C10    60.66  30.0  3
 HR3  Var_21    H04  C6   N2   C1     54.73  30.0  1
 HR3  Var_22    H05  C6   N2   C1    -62.84  30.0  1
 HR3  Var_23    H03  N2   C6   C7    -27.13  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
 HR3  plan-1  C15  0.020
 HR3  plan-1  C1   0.020
 HR3  plan-1  C2   0.020
 HR3  plan-1  C3   0.020
 HR3  plan-1  C4   0.020
 HR3  plan-1  C5   0.020
 HR3  plan-1  C14  0.020
 HR3  plan-1  N1   0.020
 HR3  plan-1  N2   0.020
 HR3  plan-1  H01  0.020
 HR3  plan-1  H02  0.020
 HR3  plan-2  C10  0.020
 HR3  plan-2  C6   0.020
 HR3  plan-2  C7   0.020
 HR3  plan-2  C8   0.020
 HR3  plan-2  C9   0.020
 HR3  plan-2  C11  0.020
 HR3  plan-2  C12  0.020
 HR3  plan-2  O1   0.020
 HR3  plan-2  H06  0.020
 HR3  plan-2  H07  0.020
 HR3  plan-2  H08  0.020
 HR3  plan-2  H09  0.020
 HR3  plan-3  C1   0.020
 HR3  plan-3  C6   0.020
 HR3  plan-3  N2   0.020
 HR3  plan-3  H03  0.020
 HR3  plan-4  C15  0.020
 HR3  plan-4  C5   0.020
 HR3  plan-4  O4   0.020
 HR3  plan-4  O5   0.020
 HR3  plan-5  C3   0.020
 HR3  plan-5  C14  0.020
 HR3  plan-5  O2   0.020
 HR3  plan-5  O3   0.020

