# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:38:59 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-[(2-cyclopropylphenyl)methylamino]pyridine-2,4-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(C(O)=O)c(NCc2ccccc2C3CC3)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
 HRR  HRR  "5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid"  ligand  37  23  .  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_HRR
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
 HRR  C10   C  CR6    0   0.295   -6.7059  11.4743  -23.5848
 HRR  C13   C  CR6    0   0.048   -3.3917  10.1181  -24.6628
 HRR  C15   C  CR16   0  -0.255   -1.2267  11.0935  -24.1908
 HRR  C17   C  CR16   0  -0.326   -1.3765   9.0787  -25.4787
 HRR  C20   C  CH2    0  -0.468   -4.0746   6.8371  -25.2406
 HRR  C21   C  CH2    0  -0.496   -3.0521   6.6598  -26.3186
 HRR  C22   C  CR16   0  -0.212   -7.6541  11.0625  -24.5415
 HRR  C2    C  C      0   0.374  -10.8337  12.6683  -23.6229
 HRR  C4    C  CR6    0  -0.002   -9.3712  12.2395  -23.5858
 HRR  C5    C  CR16   0  -0.344   -8.5148  12.6760  -22.5792
 HRR  C6    C  CR6    0  -0.116   -7.1809  12.3028  -22.5399
 HRR  C7    C  C      0   0.437   -6.3011  12.7801  -21.3904
 HRR  C12   C  CH2    0  -0.305   -4.8980  10.1347  -24.5820
 HRR  C14   C  CR16   0  -0.318   -2.6125  11.1150  -24.0863
 HRR  C16   C  CR16   0  -0.251   -0.6053  10.0719  -24.8884
 HRR  C18   C  CR6    0   0.113   -2.7630   9.0803  -25.3730
 HRR  C19   C  CH1    0  -0.324   -3.5887   8.0256  -26.0261
 HRR  N11   N  NH1    0  -0.724   -5.3960  11.1165  -23.6635
 HRR  N23   N  N      0  -0.392   -8.9212  11.4296  -24.5425
 HRR  O1    O  OC    -1  -0.594  -11.1880  13.4834  -22.7450
 HRR  O3    O  O      0  -0.598  -11.5464  12.1784  -24.5179
 HRR  O8    O  OC    -1  -0.565   -6.7929  13.6040  -20.6046
 HRR  O9    O  O      0  -0.595   -5.1448  12.2920  -21.3150
 HRR  H151  H  HCR6   0   0.249   -0.6411  11.8790  -23.7304
 HRR  H171  H  HCR6   0   0.243   -0.8869   8.2918  -26.0384
 HRR  H212  H  HCH2   0   0.253   -3.3547   6.1870  -27.2439
 HRR  H211  H  HCH2   0   0.249   -2.0405   6.4244  -26.0143
 HRR  H221  H  HCR6   0   0.246   -7.3584  10.3954  -25.3446
 HRR  H051  H  HCR6   0   0.234   -8.8985  13.3202  -21.8014
 HRR  H122  H  HCH2   0   0.244   -5.2805  10.3448  -25.5873
 HRR  H121  H  HCH2   0   0.244   -5.2573   9.1247  -24.3403
 HRR  H141  H  HCR6   0   0.236   -3.0813  11.9290  -23.5488
 HRR  H161  H  HCR6   0   0.248    0.4727  10.0475  -24.9830
 HRR  H191  H  HCH1   0   0.272   -4.3026   8.4077  -26.7512
 HRR  H111  H  HNH1   0   0.399   -4.9085  11.2928  -22.7862
 HRR  H201  H  HCH2   0   0.251   -5.0842   6.4879  -25.4154
 HRR  H202  H  HCH2   0   0.248   -3.7418   6.7473  -24.2138

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
 HRR  C21  C19   single    1.496  0.020  1.496
 HRR  C21  C20   single    1.496  0.020  1.496
 HRR  C19  C18   single    1.490  0.020  1.490
 HRR  C19  C20   single    1.505  0.020  1.505
 HRR  C18  C17   aromatic  1.391  0.020  1.391
 HRR  C18  C13   aromatic  1.406  0.020  1.406
 HRR  C17  C16   aromatic  1.389  0.020  1.389
 HRR  C12  C13   single    1.509  0.020  1.509
 HRR  C12  N11   single    1.434  0.020  1.434
 HRR  C13  C14   aromatic  1.390  0.020  1.390
 HRR  C22  N23   aromatic  1.319  0.020  1.319
 HRR  C22  C10   aromatic  1.409  0.020  1.409
 HRR  N23  C4    aromatic  1.332  0.020  1.332
 HRR  C16  C15   aromatic  1.384  0.020  1.384
 HRR  O3   C2    deloc     1.245  0.020  1.245
 HRR  C14  C15   aromatic  1.390  0.020  1.390
 HRR  N11  C10   single    1.360  0.020  1.360
 HRR  C10  C6    aromatic  1.416  0.020  1.416
 HRR  C4   C2    single    1.525  0.020  1.525
 HRR  C4   C5    aromatic  1.392  0.020  1.392
 HRR  C2   O1    deloc     1.249  0.020  1.249
 HRR  C6   C5    aromatic  1.386  0.020  1.386
 HRR  C6   C7    single    1.524  0.020  1.524
 HRR  O9   C7    deloc     1.257  0.020  1.257
 HRR  C7   O8    deloc     1.240  0.020  1.240
 HRR  C15  H151  single    0.930  0.020  1.080
 HRR  C17  H171  single    0.930  0.020  1.080
 HRR  C20  H201  single    0.970  0.020  1.090
 HRR  C20  H202  single    0.970  0.020  1.090
 HRR  C21  H212  single    0.970  0.020  1.090
 HRR  C21  H211  single    0.970  0.020  1.090
 HRR  C22  H221  single    0.930  0.020  1.080
 HRR  C5   H051  single    0.930  0.020  1.080
 HRR  C12  H122  single    0.970  0.020  1.090
 HRR  C12  H121  single    0.970  0.020  1.090
 HRR  C14  H141  single    0.930  0.020  1.080
 HRR  C16  H161  single    0.930  0.020  1.080
 HRR  C19  H191  single    0.970  0.020  1.090
 HRR  N11  H111  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
 HRR  N11   C10  C6    121.32  3.000
 HRR  C6    C10  C22   116.53  3.000
 HRR  N11   C10  C22   122.15  3.000
 HRR  C18   C13  C14   119.21  3.000
 HRR  C14   C13  C12   121.97  3.000
 HRR  C18   C13  C12   118.79  3.000
 HRR  H151  C15  C16   120.46  3.000
 HRR  H151  C15  C14   119.75  3.000
 HRR  C16   C15  C14   119.79  3.000
 HRR  H171  C17  C18   119.41  3.000
 HRR  H171  C17  C16   119.23  3.000
 HRR  C18   C17  C16   121.36  3.000
 HRR  H202  C20  H201  114.39  3.000
 HRR  H202  C20  C19   117.46  3.000
 HRR  H201  C20  C19   118.13  3.000
 HRR  H202  C20  C21   117.59  3.000
 HRR  H201  C20  C21   118.86  3.000
 HRR  C19   C20  C21    59.80  3.000
 HRR  H211  C21  H212  113.99  3.000
 HRR  H211  C21  C19   118.61  3.000
 HRR  H212  C21  C19   117.75  3.000
 HRR  H211  C21  C20   117.51  3.000
 HRR  H212  C21  C20   118.47  3.000
 HRR  C19   C21  C20    60.39  3.000
 HRR  H221  C22  N23   115.61  3.000
 HRR  H221  C22  C10   119.93  3.000
 HRR  N23   C22  C10   124.45  3.000
 HRR  O3    C2   O1    126.86  3.000
 HRR  O1    C2   C4    116.01  3.000
 HRR  O3    C2   C4    117.14  3.000
 HRR  N23   C4   C5    120.15  3.000
 HRR  C5    C4   C2    121.31  3.000
 HRR  N23   C4   C2    118.54  3.000
 HRR  H051  C5   C6    118.82  3.000
 HRR  H051  C5   C4    119.29  3.000
 HRR  C6    C5   C4    121.89  3.000
 HRR  C7    C6   C5    119.51  3.000
 HRR  C7    C6   C10   123.12  3.000
 HRR  C5    C6   C10   117.37  3.000
 HRR  O9    C7   O8    125.77  3.000
 HRR  O8    C7   C6    117.20  3.000
 HRR  O9    C7   C6    117.03  3.000
 HRR  H121  C12  H122  105.30  3.000
 HRR  H121  C12  N11   112.02  3.000
 HRR  H122  C12  N11   109.58  3.000
 HRR  H121  C12  C13   109.16  3.000
 HRR  H122  C12  C13   107.55  3.000
 HRR  N11   C12  C13   112.87  3.000
 HRR  H141  C14  C15   118.74  3.000
 HRR  H141  C14  C13   120.16  3.000
 HRR  C15   C14  C13   121.09  3.000
 HRR  H161  C16  C17   119.97  3.000
 HRR  H161  C16  C15   120.51  3.000
 HRR  C17   C16  C15   119.51  3.000
 HRR  C19   C18  C17   121.22  3.000
 HRR  C17   C18  C13   119.02  3.000
 HRR  C19   C18  C13   119.74  3.000
 HRR  H191  C19  C18   114.04  3.000
 HRR  H191  C19  C21   115.22  3.000
 HRR  C18   C19  C21   122.21  3.000
 HRR  H191  C19  C20   114.44  3.000
 HRR  C18   C19  C20   120.59  3.000
 HRR  C21   C19  C20    59.80  3.000
 HRR  H111  N11  C12   120.26  3.000
 HRR  H111  N11  C10   111.43  3.000
 HRR  C12   N11  C10   123.49  3.000
 HRR  C4    N23  C22   119.56  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
 HRR  CONST_01  C4    N23  C22  C10     0.00   0.0  0
 HRR  CONST_02  C4    C5   C6   C10     0.00   0.0  0
 HRR  CONST_03  C16   C17  C18  C13     0.00   0.0  0
 HRR  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 HRR  CONST_05  C18   C17  C16  C15     0.00   0.0  0
 HRR  CONST_06  C18   C13  C14  C15     0.00   0.0  0
 HRR  CONST_07  C14   C13  C18  C17     0.00   0.0  0
 HRR  CONST_08  C14   C15  C16  C17     0.00   0.0  0
 HRR  CONST_09  C5    C4   N23  C22     0.00   0.0  0
 HRR  CONST_10  C5    C6   C10  C22     0.00   0.0  0
 HRR  CONST_11  N23   C22  C10  C6      0.00   0.0  0
 HRR  CONST_12  N23   C4   C5   C6      0.00   0.0  0
 HRR  CONST_13  C19   C18  C13  C14   180.00   0.0  0
 HRR  CONST_14  C19   C18  C17  C16   180.00   0.0  0
 HRR  CONST_15  C12   C13  C14  C15   180.00   0.0  0
 HRR  CONST_16  C12   C13  C18  C17   180.00   0.0  0
 HRR  CONST_17  C2    C4   N23  C22   180.00   0.0  0
 HRR  CONST_18  C7    C6   C10  C22   180.00   0.0  0
 HRR  CONST_19  C6    C5   C4   C2    180.00   0.0  0
 HRR  CONST_20  C7    C6   C5   C4    180.00   0.0  0
 HRR  CONST_21  N11   C10  C6   C5    180.00   0.0  0
 HRR  CONST_22  C19   C18  C13  C12     0.00   0.0  0
 HRR  CONST_23  N23   C22  C10  N11   180.00   0.0  0
 HRR  CONST_24  H051  C5   C6   C10   180.00   0.0  0
 HRR  CONST_25  H171  C17  C18  C13   180.00   0.0  0
 HRR  CONST_26  H151  C15  C14  C13   180.00   0.0  0
 HRR  CONST_27  H171  C17  C16  C15   180.00   0.0  0
 HRR  CONST_28  H151  C15  C16  C17   180.00   0.0  0
 HRR  CONST_29  H221  C22  N23  C4    180.00   0.0  0
 HRR  CONST_30  H221  C22  C10  C6    180.00   0.0  0
 HRR  CONST_31  H161  C16  C15  C14   180.00   0.0  0
 HRR  CONST_32  H141  C14  C15  C16   180.00   0.0  0
 HRR  CONST_33  H161  C16  C17  C18   180.00   0.0  0
 HRR  CONST_34  H141  C14  C13  C18   180.00   0.0  0
 HRR  CONST_35  H171  C17  C18  C19     0.00   0.0  0
 HRR  CONST_36  H051  C5   C4   N23   180.00   0.0  0
 HRR  CONST_37  C12   N11  C10  C22     0.00   0.0  0
 HRR  CONST_38  C12   N11  C10  C6    180.00   0.0  0
 HRR  CONST_39  H111  N11  C10  C22   180.00   0.0  0
 HRR  Var_01    C21   C19  C18  C13  -155.49  30.0  1
 HRR  Var_02    C20   C19  C18  C13   -84.04  30.0  1
 HRR  Var_03    C21   C19  C18  C17    26.10  30.0  1
 HRR  Var_04    C20   C19  C18  C17    97.55  30.0  1
 HRR  Var_05    C18   C19  C21  C20   109.23  30.0  1
 HRR  Var_06    H191  C19  C18  C13    58.16  30.0  1
 HRR  Var_07    H191  C19  C18  C17  -120.25  30.0  1
 HRR  Var_08    H191  C19  C21  C20  -104.78  30.0  1
 HRR  Var_09    H212  C21  C19  C20   108.70  30.0  1
 HRR  Var_10    H211  C21  C19  C20  -107.18  30.0  1
 HRR  Var_11    H201  C20  C19  C21  -108.80  30.0  1
 HRR  Var_12    H202  C20  C19  C21   107.55  30.0  1
 HRR  Var_13    H212  C21  C19  C18  -142.07  30.0  1
 HRR  Var_14    H211  C21  C19  C18     2.06  30.0  1
 HRR  Var_15    H201  C20  C19  C18   139.35  30.0  1
 HRR  Var_16    H202  C20  C19  C18    -4.31  30.0  1
 HRR  Var_17    C13   C12  N11  C10   168.55  30.0  2
 HRR  Var_18    O9    C7   C6   C10    -7.46  30.0  2
 HRR  Var_19    O8    C7   C6   C10   173.28  30.0  2
 HRR  Var_20    O3    C2   C4   C5   -176.43  30.0  2
 HRR  Var_21    O1    C2   C4   C5      3.73  30.0  2
 HRR  Var_22    O9    C7   C6   C5    172.00  30.0  2
 HRR  Var_23    O8    C7   C6   C5     -7.26  30.0  2
 HRR  Var_24    N11   C12  C13  C14   -10.82  30.0  3
 HRR  Var_25    N11   C12  C13  C18   170.86  30.0  3
 HRR  Var_26    O3    C2   C4   N23     3.49  30.0  2
 HRR  Var_27    O1    C2   C4   N23  -176.35  30.0  2
 HRR  Var_28    H122  C12  C13  C14   110.17  30.0  3
 HRR  Var_29    H121  C12  C13  C14  -136.08  30.0  3
 HRR  Var_30    H122  C12  C13  C18   -68.15  30.0  3
 HRR  Var_31    H121  C12  C13  C18    45.60  30.0  3
 HRR  Var_32    H122  C12  N11  C10    48.72  30.0  2
 HRR  Var_33    H121  C12  N11  C10   -67.76  30.0  2
 HRR  Var_34    H111  N11  C12  C13   -38.19  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HRR  chir_01  C19  C21  C18  C20  both

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
 HRR  plan-1  C10   0.020
 HRR  plan-1  C22   0.020
 HRR  plan-1  C2    0.020
 HRR  plan-1  C4    0.020
 HRR  plan-1  C5    0.020
 HRR  plan-1  C6    0.020
 HRR  plan-1  C7    0.020
 HRR  plan-1  N11   0.020
 HRR  plan-1  N23   0.020
 HRR  plan-1  H221  0.020
 HRR  plan-1  H051  0.020
 HRR  plan-2  C13   0.020
 HRR  plan-2  C15   0.020
 HRR  plan-2  C17   0.020
 HRR  plan-2  C12   0.020
 HRR  plan-2  C14   0.020
 HRR  plan-2  C16   0.020
 HRR  plan-2  C18   0.020
 HRR  plan-2  C19   0.020
 HRR  plan-2  H151  0.020
 HRR  plan-2  H171  0.020
 HRR  plan-2  H141  0.020
 HRR  plan-2  H161  0.020
 HRR  plan-3  C10   0.020
 HRR  plan-3  C12   0.020
 HRR  plan-3  N11   0.020
 HRR  plan-3  H111  0.020
 HRR  plan-4  C2    0.020
 HRR  plan-4  C4    0.020
 HRR  plan-4  O1    0.020
 HRR  plan-4  O3    0.020
 HRR  plan-5  C6    0.020
 HRR  plan-5  C7    0.020
 HRR  plan-5  O8    0.020
 HRR  plan-5  O9    0.020

