# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 09:55:58 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[(2-methoxyphenyl)methylamino]pyridine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CNc2cnc(cc2C(O)=O)C(O)=O
#
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
 HRL  HRL  "5-((2-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_HRL
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
 HRL  C15   C  C      0   0.375  -11.0304  12.6389  -23.7609
 HRL  C20   C  C      0   0.436   -6.3344  13.3940  -22.0562
 HRL  C1    C  CH3    0  -0.433   -3.4977   6.4475  -25.7074
 HRL  C3    C  CR6    0   0.366   -3.0749   8.6885  -25.0312
 HRL  C4    C  CR16   0  -0.380   -1.6967   8.5144  -25.0918
 HRL  C5    C  CR16   0  -0.252   -0.8505   9.5761  -24.7888
 HRL  C6    C  CR16   0  -0.267   -1.3727  10.8055  -24.4321
 HRL  C7    C  CR16   0  -0.307   -2.7536  10.9713  -24.3732
 HRL  C8    C  CR6    0  -0.032   -3.6222   9.9283  -24.6575
 HRL  C9    C  CH2    0  -0.284   -5.1220  10.0715  -24.6144
 HRL  C11   C  CR6    0   0.284   -6.8510  11.6502  -23.8952
 HRL  C12   C  CR16   0  -0.205   -7.8478  11.0362  -24.6766
 HRL  C14   C  CR6    0   0.001   -9.5420  12.3077  -23.8071
 HRL  C18   C  CR16   0  -0.344   -8.6296  12.9706  -22.9921
 HRL  C19   C  CR6    0  -0.111   -7.2781  12.6633  -23.0054
 HRL  N13   N  N      0  -0.394   -9.1285  11.3526  -24.6380
 HRL  O16   O  O      0  -0.598  -11.7719  12.0274  -24.5515
 HRL  O17   O  OC    -1  -0.594  -11.3750  13.4987  -22.9229
 HRL  O21   O  OC    -1  -0.565   -6.7961  14.3632  -21.4354
 HRL  O22   O  O      0  -0.593   -5.1626  12.9494  -21.9622
 HRL  H11   H  HCH3   0   0.258   -4.3780   5.8331  -25.8802
 HRL  H13   H  HCH3   0   0.227   -2.9126   6.4896  -26.6300
 HRL  H12   H  HCH3   0   0.227   -2.8907   5.9809  -24.9272
 HRL  H41   H  HCR6   0   0.276   -1.2659   7.5634  -25.3751
 HRL  H51   H  HCR6   0   0.253    0.2205   9.4287  -24.8391
 HRL  H61   H  HCR6   0   0.248   -0.7189  11.6362  -24.2020
 HRL  H71   H  HCR6   0   0.242   -3.1510  11.9409  -24.1024
 HRL  H92   H  HCH2   0   0.244   -5.4936  10.0301  -25.6440
 HRL  H91   H  HCH2   0   0.231   -5.5597   9.1996  -24.1090
 HRL  H121  H  HCR6   0   0.246   -7.5808  10.2428  -25.3672
 HRL  H181  H  HCR6   0   0.234   -8.9838  13.7395  -22.3218
 HRL  H101  H  HNH1   0   0.397   -5.0093  11.6547  -23.1980
 HRL  N10   N  NH1    0  -0.720   -5.5357  11.3011  -23.9963
 HRL  O2    O  O2     0  -0.467   -3.9680   7.7216  -25.3213

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
 HRL  O2   C3    single    1.348  0.020  1.348
 HRL  O2   C1    single    1.412  0.020  1.412
 HRL  C9   C8    single    1.507  0.020  1.507
 HRL  C9   N10   single    1.437  0.020  1.437
 HRL  C3   C8    aromatic  1.406  0.020  1.406
 HRL  C3   C4    aromatic  1.390  0.020  1.390
 HRL  C8   C7    aromatic  1.387  0.020  1.387
 HRL  C4   C5    aromatic  1.391  0.020  1.391
 HRL  C12  N13   aromatic  1.320  0.020  1.320
 HRL  C12  C11   aromatic  1.408  0.020  1.408
 HRL  C7   C6    aromatic  1.392  0.020  1.392
 HRL  C5   C6    aromatic  1.383  0.020  1.383
 HRL  N13  C14   aromatic  1.332  0.020  1.332
 HRL  O16  C15   deloc     1.244  0.020  1.244
 HRL  N10  C11   single    1.365  0.020  1.365
 HRL  C11  C19   aromatic  1.414  0.020  1.414
 HRL  C14  C15   single    1.526  0.020  1.526
 HRL  C14  C18   aromatic  1.391  0.020  1.391
 HRL  C15  O17   deloc     1.249  0.020  1.249
 HRL  C19  C18   aromatic  1.386  0.020  1.386
 HRL  C19  C20   single    1.525  0.020  1.525
 HRL  O22  C20   deloc     1.257  0.020  1.257
 HRL  C20  O21   deloc     1.240  0.020  1.240
 HRL  C1   H11   single    0.970  0.020  1.090
 HRL  C1   H13   single    0.970  0.020  1.090
 HRL  C1   H12   single    0.970  0.020  1.090
 HRL  C4   H41   single    0.930  0.020  1.080
 HRL  C5   H51   single    0.930  0.020  1.080
 HRL  C6   H61   single    0.930  0.020  1.080
 HRL  C7   H71   single    0.930  0.020  1.080
 HRL  C9   H92   single    0.970  0.020  1.090
 HRL  C9   H91   single    0.970  0.020  1.090
 HRL  C12  H121  single    0.930  0.020  1.080
 HRL  C18  H181  single    0.930  0.020  1.080
 HRL  N10  H101  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
 HRL  O17   C15  O16  126.87  3.000
 HRL  O17   C15  C14  116.03  3.000
 HRL  O16   C15  C14  117.09  3.000
 HRL  O22   C20  O21  125.88  3.000
 HRL  O21   C20  C19  117.11  3.000
 HRL  O22   C20  C19  117.00  3.000
 HRL  H12   C1   H13  108.76  3.000
 HRL  H12   C1   H11  108.77  3.000
 HRL  H13   C1   H11  108.72  3.000
 HRL  H12   C1   O2   112.02  3.000
 HRL  H13   C1   O2   111.98  3.000
 HRL  H11   C1   O2   106.48  3.000
 HRL  O2    C3   C8   115.59  3.000
 HRL  C8    C3   C4   120.53  3.000
 HRL  O2    C3   C4   123.88  3.000
 HRL  H41   C4   C5   119.06  3.000
 HRL  H41   C4   C3   121.08  3.000
 HRL  C5    C4   C3   119.86  3.000
 HRL  H51   C5   C6   120.46  3.000
 HRL  H51   C5   C4   119.20  3.000
 HRL  C6    C5   C4   120.34  3.000
 HRL  H61   C6   C7   119.94  3.000
 HRL  H61   C6   C5   120.63  3.000
 HRL  C7    C6   C5   119.44  3.000
 HRL  H71   C7   C8   119.68  3.000
 HRL  H71   C7   C6   118.78  3.000
 HRL  C8    C7   C6   121.54  3.000
 HRL  C9    C8   C7   123.09  3.000
 HRL  C7    C8   C3   118.29  3.000
 HRL  C9    C8   C3   118.60  3.000
 HRL  H91   C9   H92  105.50  3.000
 HRL  H91   C9   N10  111.50  3.000
 HRL  H92   C9   N10  109.81  3.000
 HRL  H91   C9   C8   109.53  3.000
 HRL  H92   C9   C8   107.88  3.000
 HRL  N10   C9   C8   112.34  3.000
 HRL  N10   C11  C19  121.40  3.000
 HRL  C19   C11  C12  116.61  3.000
 HRL  N10   C11  C12  121.99  3.000
 HRL  H121  C12  N13  115.64  3.000
 HRL  H121  C12  C11  119.87  3.000
 HRL  N13   C12  C11  124.49  3.000
 HRL  N13   C14  C18  120.23  3.000
 HRL  C18   C14  C15  121.24  3.000
 HRL  N13   C14  C15  118.52  3.000
 HRL  H181  C18  C19  118.93  3.000
 HRL  H181  C18  C14  119.19  3.000
 HRL  C19   C18  C14  121.88  3.000
 HRL  C18   C19  C11  117.34  3.000
 HRL  C18   C19  C20  119.42  3.000
 HRL  C11   C19  C20  123.22  3.000
 HRL  C14   N13  C12  119.44  3.000
 HRL  H101  N10  C11  110.54  3.000
 HRL  H101  N10  C9   119.01  3.000
 HRL  C11   N10  C9   121.89  3.000
 HRL  C3    O2   C1   119.05  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
 HRL  CONST_01  C6    C7   C8   C3      0.00   0.0  0
 HRL  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 HRL  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 HRL  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 HRL  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 HRL  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 HRL  CONST_07  C14   N13  C12  C11     0.00   0.0  0
 HRL  CONST_08  C14   C18  C19  C11     0.00   0.0  0
 HRL  CONST_09  C18   C14  N13  C12     0.00   0.0  0
 HRL  CONST_10  C18   C19  C11  C12     0.00   0.0  0
 HRL  CONST_11  N13   C12  C11  C19     0.00   0.0  0
 HRL  CONST_12  N13   C14  C18  C19     0.00   0.0  0
 HRL  CONST_13  C12   N13  C14  C15   180.00   0.0  0
 HRL  CONST_14  C19   C18  C14  C15   180.00   0.0  0
 HRL  CONST_15  C12   C11  C19  C20   180.00   0.0  0
 HRL  CONST_16  C14   C18  C19  C20   180.00   0.0  0
 HRL  CONST_17  C9    C8   C3   C4    180.00   0.0  0
 HRL  CONST_18  O2    C3   C4   C5    180.00   0.0  0
 HRL  CONST_19  C9    C8   C7   C6    180.00   0.0  0
 HRL  CONST_20  O2    C3   C8   C7    180.00   0.0  0
 HRL  CONST_21  N10   C11  C19  C18   180.00   0.0  0
 HRL  CONST_22  N13   C12  C11  N10   180.00   0.0  0
 HRL  CONST_23  H71   C7   C8   C3    180.00   0.0  0
 HRL  CONST_24  H51   C5   C4   C3    180.00   0.0  0
 HRL  CONST_25  H61   C6   C5   C4    180.00   0.0  0
 HRL  CONST_26  H71   C7   C6   C5    180.00   0.0  0
 HRL  CONST_27  H41   C4   C5   C6    180.00   0.0  0
 HRL  CONST_28  H51   C5   C6   C7    180.00   0.0  0
 HRL  CONST_29  H41   C4   C3   C8    180.00   0.0  0
 HRL  CONST_30  H61   C6   C7   C8    180.00   0.0  0
 HRL  CONST_31  H181  C18  C19  C11   180.00   0.0  0
 HRL  CONST_32  H121  C12  N13  C14   180.00   0.0  0
 HRL  CONST_33  H121  C12  C11  C19   180.00   0.0  0
 HRL  CONST_34  H181  C18  C14  N13   180.00   0.0  0
 HRL  Var_01    C8    C3   O2   C1    179.90  30.0  2
 HRL  Var_02    C4    C3   O2   C1      0.23  30.0  2
 HRL  Var_03    N10   C9   C8   C3    169.73  30.0  2
 HRL  Var_04    N10   C9   C8   C7    -11.69  30.0  2
 HRL  Var_05    C11   N10  C9   C8    177.77  30.0  3
 HRL  Var_06    O22   C20  C19  C11    -8.77  30.0  2
 HRL  Var_07    O21   C20  C19  C11   172.04  30.0  2
 HRL  Var_08    O16   C15  C14  C18   177.89  30.0  2
 HRL  Var_09    O17   C15  C14  C18    -2.34  30.0  2
 HRL  Var_10    O22   C20  C19  C18   169.78  30.0  2
 HRL  Var_11    O21   C20  C19  C18    -9.41  30.0  2
 HRL  Var_12    O16   C15  C14  N13    -2.90  30.0  2
 HRL  Var_13    O17   C15  C14  N13   176.87  30.0  2
 HRL  Var_14    H92   C9   C8   C3    -69.09  30.0  2
 HRL  Var_15    H91   C9   C8   C3     45.26  30.0  2
 HRL  Var_16    H92   C9   C8   C7    109.48  30.0  2
 HRL  Var_17    H91   C9   C8   C7   -136.16  30.0  2
 HRL  Var_18    H11   C1   O2   C3    179.43  30.0  3
 HRL  Var_19    H13   C1   O2   C3    -61.86  30.0  3
 HRL  Var_20    H12   C1   O2   C3     60.64  30.0  3
 HRL  Var_21    H101  N10  C9   C8    -37.39  30.0  3
 HRL  Var_22    H92   C9   N10  C11    57.71  30.0  2
 HRL  Var_23    H91   C9   N10  C11   -58.85  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
 HRL  plan-1  C3    0.020
 HRL  plan-1  C4    0.020
 HRL  plan-1  C5    0.020
 HRL  plan-1  C6    0.020
 HRL  plan-1  C7    0.020
 HRL  plan-1  C8    0.020
 HRL  plan-1  C9    0.020
 HRL  plan-1  H41   0.020
 HRL  plan-1  H51   0.020
 HRL  plan-1  H61   0.020
 HRL  plan-1  H71   0.020
 HRL  plan-1  O2    0.020
 HRL  plan-2  C15   0.020
 HRL  plan-2  C20   0.020
 HRL  plan-2  C11   0.020
 HRL  plan-2  C12   0.020
 HRL  plan-2  C14   0.020
 HRL  plan-2  C18   0.020
 HRL  plan-2  C19   0.020
 HRL  plan-2  N13   0.020
 HRL  plan-2  H121  0.020
 HRL  plan-2  H181  0.020
 HRL  plan-2  N10   0.020
 HRL  plan-3  C9    0.020
 HRL  plan-3  C11   0.020
 HRL  plan-3  H101  0.020
 HRL  plan-3  N10   0.020
 HRL  plan-4  C15   0.020
 HRL  plan-4  C14   0.020
 HRL  plan-4  O16   0.020
 HRL  plan-4  O17   0.020
 HRL  plan-5  C20   0.020
 HRL  plan-5  C19   0.020
 HRL  plan-5  O21   0.020
 HRL  plan-5  O22   0.020

