# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 12:06:49 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}2-methyl-~{N}4-[(1~{S},2~{S})-2-methylcyclopropyl]-6-(phenylmethyl)pyridine-2,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc(Cc2ccccc2)n1)C(=O)N[C@H]3C[C@@H]3C
#
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
 UL5  UL5  ~{N}2-methyl-~{N}4-[(1~{S},2~{S})-2-methylcyclopropyl]-6-(phenylmethyl)pyridine-2,4-dicarboxamide  ligand  45  24  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UL5
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
 UL5  N1   N  N     0  -0.447  41.3989  17.4946   8.5486
 UL5  C4   C  CR6   0   0.087  44.0896  17.5663   9.1905
 UL5  C5   C  CR16  0  -0.356  43.1692  18.3340   9.8859
 UL5  C6   C  CR6   0   0.283  41.8213  18.2606   9.5441
 UL5  C7   C  CH2   0  -0.602  40.7819  19.0129  10.3289
 UL5  C8   C  CR6   0   0.133  40.3153  18.1895  11.5049
 UL5  C10  C  CR16  0  -0.238  39.0591  16.3219  12.3824
 UL5  C13  C  CR16  0  -0.310  40.7629  18.4687  12.7922
 UL5  C15  C  CH1   0  -0.065  47.6516  16.4781   9.7120
 UL5  C17  C  CH1   0  -0.275  48.1806  15.2295  10.3421
 UL5  O1   O  O     0  -0.463  45.9972  18.7121   9.9981
 UL5  C14  C  C     0   0.529  45.5393  17.6662   9.5688
 UL5  N2   N  NH1   0  -0.654  46.2582  16.5438   9.4137
 UL5  C18  C  CH3   0  -0.661  49.5091  14.6742   9.9065
 UL5  C16  C  CH2   0  -0.477  48.1022  16.4922  11.1423
 UL5  C3   C  CR16  0  -0.358  43.6338  16.7660   8.1487
 UL5  C2   C  CR6   0   0.130  42.2779  16.7729   7.8654
 UL5  C1   C  C     0   0.532  41.7517  15.9351   6.7315
 UL5  O    O  O     0  -0.478  42.4998  15.2423   6.0547
 UL5  N    N  NH1   0  -0.635  40.4346  16.0179   6.5433
 UL5  C    C  CH3   0  -0.515  39.7520  15.2923   5.5010
 UL5  C12  C  CR16  0  -0.238  40.3655  17.6826  13.8668
 UL5  C11  C  CR16  0  -0.267  39.5133  16.6060  13.6648
 UL5  C9   C  CR16  0  -0.292  39.4581  17.1080  11.3112
 UL5  H1   H  HCR6  0   0.275  43.4850  18.9781  10.6960
 UL5  H2   H  HCH2  0   0.276  41.1955  19.9598  10.6793
 UL5  H3   H  HCH2  0   0.278  39.9414  19.2424   9.6722
 UL5  H4   H  HCR6  0   0.253  38.3900  15.4872  12.2164
 UL5  H5   H  HCR6  0   0.250  41.4289  19.3078  12.9566
 UL5  H6   H  HCH1  0   0.266  48.2944  16.9731   8.9892
 UL5  H7   H  HCH1  0   0.260  47.4284  14.4836  10.5819
 UL5  H8   H  HNH1  0   0.412  45.8055  15.7034   9.0900
 UL5  H9   H  HCH3  0   0.231  49.9577  14.0711  10.6969
 UL5  H10  H  HCH3  0   0.231  49.4038  14.0430   9.0228
 UL5  H11  H  HCH3  0   0.225  50.2109  15.4737   9.6647
 UL5  H12  H  HCH2  0   0.256  47.3414  16.5667  11.9085
 UL5  H13  H  HCH2  0   0.250  49.0222  17.0174  11.3689
 UL5  H14  H  HCR6  0   0.278  44.3025  16.1678   7.5445
 UL5  H15  H  HNH1  0   0.408  39.9116  16.6220   7.1585
 UL5  H16  H  HCH3  0   0.252  38.6913  15.5170   5.5626
 UL5  H17  H  HCH3  0   0.240  40.1075  15.5804   4.5109
 UL5  H18  H  HCH3  0   0.240  39.8814  14.2150   5.6102
 UL5  H19  H  HCR6  0   0.253  40.7219  17.9140  14.8625
 UL5  H20  H  HCR6  0   0.253  39.2016  15.9937  14.5010
 UL5  H21  H  HCR6  0   0.249  39.1031  16.8785  10.3133

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
 UL5  C    N    single    1.442  0.020  1.442
 UL5  O    C1   double    1.224  0.020  1.224
 UL5  N    C1   single    1.333  0.020  1.333
 UL5  C1   C2   single    1.505  0.020  1.505
 UL5  C2   C3   aromatic  1.385  0.020  1.385
 UL5  C2   N1   aromatic  1.327  0.020  1.327
 UL5  C3   C4   aromatic  1.391  0.020  1.391
 UL5  N1   C6   aromatic  1.325  0.020  1.325
 UL5  C4   C14  single    1.502  0.020  1.502
 UL5  C4   C5   aromatic  1.386  0.020  1.386
 UL5  C18  C17  single    1.504  0.020  1.504
 UL5  C6   C5   aromatic  1.392  0.020  1.392
 UL5  C6   C7   single    1.504  0.020  1.504
 UL5  N2   C14  single    1.342  0.020  1.342
 UL5  N2   C15  single    1.427  0.020  1.427
 UL5  C17  C15  single    1.495  0.020  1.495
 UL5  C17  C16  single    1.497  0.020  1.497
 UL5  C14  O1   double    1.220  0.020  1.220
 UL5  C15  C16  single    1.500  0.020  1.500
 UL5  C7   C8   single    1.510  0.020  1.510
 UL5  C9   C8   aromatic  1.394  0.020  1.394
 UL5  C9   C10  aromatic  1.387  0.020  1.387
 UL5  C8   C13  aromatic  1.391  0.020  1.391
 UL5  C10  C11  aromatic  1.390  0.020  1.390
 UL5  C13  C12  aromatic  1.389  0.020  1.389
 UL5  C11  C12  aromatic  1.388  0.020  1.388
 UL5  C5   H1   single    0.930  0.020  1.080
 UL5  C7   H2   single    0.970  0.020  1.090
 UL5  C7   H3   single    0.970  0.020  1.090
 UL5  C10  H4   single    0.930  0.020  1.080
 UL5  C13  H5   single    0.930  0.020  1.080
 UL5  C15  H6   single    0.970  0.020  1.090
 UL5  C17  H7   single    0.970  0.020  1.090
 UL5  N2   H8   single    0.860  0.020  1.020
 UL5  C18  H9   single    0.970  0.020  1.090
 UL5  C18  H10  single    0.970  0.020  1.090
 UL5  C18  H11  single    0.970  0.020  1.090
 UL5  C16  H12  single    0.970  0.020  1.090
 UL5  C16  H13  single    0.970  0.020  1.090
 UL5  C3   H14  single    0.930  0.020  1.080
 UL5  N    H15  single    0.860  0.020  1.020
 UL5  C    H16  single    0.970  0.020  1.090
 UL5  C    H17  single    0.970  0.020  1.090
 UL5  C    H18  single    0.970  0.020  1.090
 UL5  C12  H19  single    0.930  0.020  1.080
 UL5  C11  H20  single    0.930  0.020  1.080
 UL5  C9   H21  single    0.930  0.020  1.080

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
 UL5  C2   N1   C6   119.34  3.000
 UL5  C3   C4   C14  122.92  3.000
 UL5  C14  C4   C5   118.56  3.000
 UL5  C3   C4   C5   118.50  3.000
 UL5  H1   C5   C6   119.85  3.000
 UL5  H1   C5   C4   120.77  3.000
 UL5  C6   C5   C4   119.38  3.000
 UL5  C7   C6   C5   120.96  3.000
 UL5  C7   C6   N1   117.44  3.000
 UL5  C5   C6   N1   121.56  3.000
 UL5  H3   C7   H2   107.63  3.000
 UL5  H3   C7   C8   110.21  3.000
 UL5  H2   C7   C8   109.90  3.000
 UL5  H3   C7   C6   108.88  3.000
 UL5  H2   C7   C6   109.86  3.000
 UL5  C8   C7   C6   110.32  3.000
 UL5  C9   C8   C13  118.83  3.000
 UL5  C13  C8   C7   120.80  3.000
 UL5  C9   C8   C7   120.34  3.000
 UL5  H4   C10  C9   119.76  3.000
 UL5  H4   C10  C11  120.07  3.000
 UL5  C9   C10  C11  120.17  3.000
 UL5  H5   C13  C12  119.77  3.000
 UL5  H5   C13  C8   119.56  3.000
 UL5  C12  C13  C8   120.67  3.000
 UL5  H6   C15  C16  116.90  3.000
 UL5  H6   C15  N2   114.69  3.000
 UL5  C16  C15  N2   119.50  3.000
 UL5  H6   C15  C17  116.84  3.000
 UL5  C16  C15  C17   59.98  3.000
 UL5  N2   C15  C17  118.17  3.000
 UL5  H7   C17  C16  115.15  3.000
 UL5  H7   C17  C18  114.96  3.000
 UL5  C16  C17  C18  120.82  3.000
 UL5  H7   C17  C15  114.93  3.000
 UL5  C16  C17  C15   60.16  3.000
 UL5  C18  C17  C15  119.91  3.000
 UL5  N2   C14  O1   123.84  3.000
 UL5  O1   C14  C4   120.54  3.000
 UL5  N2   C14  C4   115.62  3.000
 UL5  H8   N2   C14  119.60  3.000
 UL5  H8   N2   C15  117.87  3.000
 UL5  C14  N2   C15  122.53  3.000
 UL5  H11  C18  H10  107.85  3.000
 UL5  H11  C18  H9   107.53  3.000
 UL5  H10  C18  H9   107.86  3.000
 UL5  H11  C18  C17  111.21  3.000
 UL5  H10  C18  C17  111.28  3.000
 UL5  H9   C18  C17  110.94  3.000
 UL5  H13  C16  H12  114.55  3.000
 UL5  H13  C16  C17  118.44  3.000
 UL5  H12  C16  C17  118.24  3.000
 UL5  H13  C16  C15  117.34  3.000
 UL5  H12  C16  C15  117.68  3.000
 UL5  C17  C16  C15   59.86  3.000
 UL5  H14  C3   C2   119.58  3.000
 UL5  H14  C3   C4   122.28  3.000
 UL5  C2   C3   C4   118.11  3.000
 UL5  C1   C2   C3   119.58  3.000
 UL5  C3   C2   N1   123.09  3.000
 UL5  C1   C2   N1   117.34  3.000
 UL5  N    C1   O    124.13  3.000
 UL5  N    C1   C2   114.66  3.000
 UL5  O    C1   C2   121.21  3.000
 UL5  H15  N    C    119.80  3.000
 UL5  H15  N    C1   117.62  3.000
 UL5  C    N    C1   122.58  3.000
 UL5  H18  C    H17  108.25  3.000
 UL5  H18  C    H16  108.33  3.000
 UL5  H17  C    H16  108.37  3.000
 UL5  H18  C    N    111.63  3.000
 UL5  H17  C    N    111.65  3.000
 UL5  H16  C    N    108.50  3.000
 UL5  H19  C12  C11  120.12  3.000
 UL5  H19  C12  C13  119.75  3.000
 UL5  C11  C12  C13  120.12  3.000
 UL5  H20  C11  C12  120.21  3.000
 UL5  H20  C11  C10  120.21  3.000
 UL5  C12  C11  C10  119.58  3.000
 UL5  H21  C9   C10  119.78  3.000
 UL5  H21  C9   C8   119.59  3.000
 UL5  C10  C9   C8   120.62  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
 UL5  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 UL5  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 UL5  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 UL5  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 UL5  CONST_05  C3   C2   N1   C6      0.00   0.0  0
 UL5  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 UL5  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 UL5  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 UL5  CONST_09  C13  C8   C9   C10     0.00   0.0  0
 UL5  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 UL5  CONST_11  C9   C8   C13  C12     0.00   0.0  0
 UL5  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 UL5  CONST_13  C1   C2   C3   C4    180.00   0.0  0
 UL5  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 UL5  CONST_15  C1   C2   N1   C6    180.00   0.0  0
 UL5  CONST_16  C14  C4   C5   C6    180.00   0.0  0
 UL5  CONST_17  C2   N1   C6   C7    180.00   0.0  0
 UL5  CONST_18  C10  C9   C8   C7    180.00   0.0  0
 UL5  CONST_19  C12  C13  C8   C7    180.00   0.0  0
 UL5  CONST_20  C2   C3   C4   C14   180.00   0.0  0
 UL5  CONST_21  H14  C3   C2   N1    180.00   0.0  0
 UL5  CONST_22  H1   C5   C6   N1    180.00   0.0  0
 UL5  CONST_23  H4   C10  C9   C8    180.00   0.0  0
 UL5  CONST_24  H19  C12  C13  C8    180.00   0.0  0
 UL5  CONST_25  H21  C9   C8   C13   180.00   0.0  0
 UL5  CONST_26  H20  C11  C12  C13   180.00   0.0  0
 UL5  CONST_27  H5   C13  C12  C11   180.00   0.0  0
 UL5  CONST_28  C15  N2   C14  C4    180.00   0.0  0
 UL5  CONST_29  O1   C14  N2   C15     0.00   0.0  0
 UL5  CONST_30  C    N    C1   C2    180.00   0.0  0
 UL5  CONST_31  H8   N2   C14  C4      0.00   0.0  0
 UL5  CONST_32  H15  N    C1   C2      0.00   0.0  0
 UL5  CONST_33  C    N    C1   O       0.00   0.0  0
 UL5  Var_01    C8   C7   C6   N1     90.78  30.0  2
 UL5  Var_02    C9   C8   C7   C6    -74.88  30.0  2
 UL5  Var_03    C18  C17  C16  C15   109.09  30.0  1
 UL5  Var_04    N2   C15  C16  C17   107.43  30.0  1
 UL5  Var_05    O    C1   C2   N1   -179.99  30.0  2
 UL5  Var_06    N2   C14  C4   C5    147.86  30.0  2
 UL5  Var_07    C14  N2   C15  C17   141.96  30.0  1
 UL5  Var_08    H9   C18  C17  C15   155.11  30.0  3
 UL5  Var_09    H16  C    N    C1    179.34  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
 UL5  chir_01  C15  N2   C17  C16  both
 UL5  chir_02  C17  C18  C15  C16  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
 UL5  plan-1  N1   0.020
 UL5  plan-1  C4   0.020
 UL5  plan-1  C5   0.020
 UL5  plan-1  C6   0.020
 UL5  plan-1  C7   0.020
 UL5  plan-1  C14  0.020
 UL5  plan-1  C3   0.020
 UL5  plan-1  C2   0.020
 UL5  plan-1  C1   0.020
 UL5  plan-1  H1   0.020
 UL5  plan-1  H14  0.020
 UL5  plan-2  C7   0.020
 UL5  plan-2  C8   0.020
 UL5  plan-2  C10  0.020
 UL5  plan-2  C13  0.020
 UL5  plan-2  C12  0.020
 UL5  plan-2  C11  0.020
 UL5  plan-2  C9   0.020
 UL5  plan-2  H4   0.020
 UL5  plan-2  H5   0.020
 UL5  plan-2  H19  0.020
 UL5  plan-2  H20  0.020
 UL5  plan-2  H21  0.020
 UL5  plan-3  C2   0.020
 UL5  plan-3  C1   0.020
 UL5  plan-3  O    0.020
 UL5  plan-3  N    0.020
 UL5  plan-3  C    0.020
 UL5  plan-3  H15  0.020
 UL5  plan-4  C4   0.020
 UL5  plan-4  C15  0.020
 UL5  plan-4  O1   0.020
 UL5  plan-4  C14  0.020
 UL5  plan-4  N2   0.020
 UL5  plan-4  H8   0.020

