# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 13:32:44 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: ~{N}2-methyl-~{N}4-[(1~{S},2~{S})-2-methylcyclopropyl]-6-[(~{S})-oxidanyl(phenyl)methyl]pyridine-2,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc(n1)[C@@H](O)c2ccccc2)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
 ULK  ULK  ~{N}2-methyl-~{N}4-[(1~{S},2~{S})-2-methylcyclopropyl]-6-[(~{S})-oxidanyl(phenyl)methyl]pyridine-2,4-dicarboxamide  ligand  46  25  .  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_ULK
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
 ULK  C13  C  CR6   0   0.070  40.3639  18.3700  11.3373
 ULK  C15  C  CR16  0  -0.238  40.4638  17.9123  13.7051
 ULK  C17  C  CR16  0  -0.237  39.1463  16.5091  12.2687
 ULK  C22  C  CH1   0  -0.065  47.6577  16.6338   9.7517
 ULK  C24  C  CH1   0  -0.276  48.1670  15.3978  10.4196
 ULK  C01  C  CH3   0  -0.515  39.8414  15.2997   5.4247
 ULK  N02  N  NH1   0  -0.635  40.5093  16.0586   6.4525
 ULK  O04  O  O     0  -0.477  42.5857  15.2826   6.0101
 ULK  C05  C  CR6   0   0.126  42.3312  16.8663   7.7708
 ULK  C06  C  CR16  0  -0.356  43.6821  16.8734   8.0782
 ULK  C07  C  CR6   0   0.087  44.1178  17.7155   9.0953
 ULK  C08  C  CR16  0  -0.349  43.1850  18.5121   9.7396
 ULK  C09  C  CR6   0   0.247  41.8457  18.4125   9.3789
 ULK  N10  N  N     0  -0.440  41.4386  17.6060   8.4147
 ULK  C11  C  CH1   0  -0.062  40.7962  19.1929  10.1389
 ULK  O12  O  OH1   0  -0.645  39.7430  19.4812   9.2645
 ULK  C14  C  CR16  0  -0.306  40.8300  18.6832  12.6087
 ULK  C16  C  CR16  0  -0.262  39.6209  16.8231  13.5372
 ULK  C18  C  CR16  0  -0.284  39.5150  17.2772  11.1745
 ULK  O20  O  O     0  -0.463  46.0163  18.8950   9.8769
 ULK  N21  N  NH1   0  -0.653  46.2717  16.6950   9.4197
 ULK  C23  C  CH2   0  -0.478  48.0763  16.6777  11.1915
 ULK  C25  C  CH3   0  -0.661  49.5023  14.8269  10.0270
 ULK  H1   H  HCR6  0   0.256  40.8327  18.1676  14.6901
 ULK  H2   H  HCR6  0   0.254  38.4865  15.6620  12.1321
 ULK  H3   H  HCH1  0   0.267  48.3172  17.1120   9.0330
 ULK  H4   H  HCH1  0   0.261  47.4068  14.6599  10.6595
 ULK  H5   H  HCH3  0   0.252  38.7775  15.5117   5.4761
 ULK  H6   H  HCH3  0   0.240  40.1977  15.5677   4.4292
 ULK  H7   H  HCH3  0   0.240  39.9848  14.2273   5.5605
 ULK  H8   H  HNH1  0   0.409  39.9778  16.6821   7.0404
 ULK  H9   H  HCR6  0   0.279  44.3637  16.2534   7.5119
 ULK  H10  H  HCR6  0   0.277  43.4866  19.1961  10.5224
 ULK  H11  H  HCH1  0   0.251  41.2719  20.1110  10.5124
 ULK  H12  H  HOH1  0   0.457  39.0656  19.9550   9.7588
 ULK  H13  H  HCR6  0   0.253  41.4844  19.5365  12.7461
 ULK  H14  H  HCR6  0   0.255  39.3305  16.2231  14.3900
 ULK  H15  H  HCR6  0   0.254  39.1444  17.0204  10.1900
 ULK  H16  H  HNH1  0   0.412  45.8169  15.8407   9.1376
 ULK  H17  H  HCH2  0   0.256  47.2986  16.7712  11.9385
 ULK  H18  H  HCH2  0   0.250  48.9933  17.2036  11.4277
 ULK  H19  H  HCH3  0   0.231  49.9272  14.2366  10.8399
 ULK  H20  H  HCH3  0   0.231  49.4165  14.1791   9.1537
 ULK  H21  H  HCH3  0   0.225  50.2149  15.6174   9.7874
 ULK  C19  C  C     0   0.530  45.5597  17.8296   9.4974
 ULK  C03  C  C     0   0.531  41.8248  15.9894   6.6574

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
 ULK  C01  N02  single    1.442  0.020  1.442
 ULK  O04  C03  double    1.224  0.020  1.224
 ULK  N02  C03  single    1.333  0.020  1.333
 ULK  C03  C05  single    1.505  0.020  1.505
 ULK  C05  C06  aromatic  1.385  0.020  1.385
 ULK  C05  N10  aromatic  1.326  0.020  1.326
 ULK  C06  C07  aromatic  1.390  0.020  1.390
 ULK  N10  C09  aromatic  1.321  0.020  1.321
 ULK  O12  C11  single    1.399  0.020  1.399
 ULK  C07  C19  single    1.501  0.020  1.501
 ULK  C07  C08  aromatic  1.386  0.020  1.386
 ULK  C09  C08  aromatic  1.391  0.020  1.391
 ULK  C09  C11  single    1.513  0.020  1.513
 ULK  C25  C24  single    1.504  0.020  1.504
 ULK  N21  C19  single    1.342  0.020  1.342
 ULK  N21  C22  single    1.426  0.020  1.426
 ULK  C24  C22  single    1.494  0.020  1.494
 ULK  C24  C23  single    1.497  0.020  1.497
 ULK  C19  O20  double    1.220  0.020  1.220
 ULK  C11  C13  single    1.517  0.020  1.517
 ULK  C22  C23  single    1.500  0.020  1.500
 ULK  C18  C13  aromatic  1.393  0.020  1.393
 ULK  C18  C17  aromatic  1.387  0.020  1.387
 ULK  C13  C14  aromatic  1.390  0.020  1.390
 ULK  C17  C16  aromatic  1.390  0.020  1.390
 ULK  C14  C15  aromatic  1.389  0.020  1.389
 ULK  C16  C15  aromatic  1.387  0.020  1.387
 ULK  C15  H1   single    0.930  0.020  1.080
 ULK  C17  H2   single    0.930  0.020  1.080
 ULK  C22  H3   single    0.970  0.020  1.090
 ULK  C24  H4   single    0.970  0.020  1.090
 ULK  C01  H5   single    0.970  0.020  1.090
 ULK  C01  H6   single    0.970  0.020  1.090
 ULK  C01  H7   single    0.970  0.020  1.090
 ULK  N02  H8   single    0.860  0.020  1.020
 ULK  C06  H9   single    0.930  0.020  1.080
 ULK  C08  H10  single    0.930  0.020  1.080
 ULK  C11  H11  single    0.970  0.020  1.090
 ULK  O12  H12  single    0.850  0.020  0.980
 ULK  C14  H13  single    0.930  0.020  1.080
 ULK  C16  H14  single    0.930  0.020  1.080
 ULK  C18  H15  single    0.930  0.020  1.080
 ULK  N21  H16  single    0.860  0.020  1.020
 ULK  C23  H17  single    0.970  0.020  1.090
 ULK  C23  H18  single    0.970  0.020  1.090
 ULK  C25  H19  single    0.970  0.020  1.090
 ULK  C25  H20  single    0.970  0.020  1.090
 ULK  C25  H21  single    0.970  0.020  1.090

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
 ULK  C18  C13  C14  119.20  3.000
 ULK  C14  C13  C11  120.33  3.000
 ULK  C18  C13  C11  120.46  3.000
 ULK  H1   C15  C16  120.15  3.000
 ULK  H1   C15  C14  119.83  3.000
 ULK  C16  C15  C14  120.01  3.000
 ULK  H2   C17  C18  119.73  3.000
 ULK  H2   C17  C16  120.00  3.000
 ULK  C18  C17  C16  120.27  3.000
 ULK  H3   C22  C23  116.91  3.000
 ULK  H3   C22  N21  114.65  3.000
 ULK  C23  C22  N21  119.56  3.000
 ULK  H3   C22  C24  116.92  3.000
 ULK  C23  C22  C24   60.01  3.000
 ULK  N21  C22  C24  118.07  3.000
 ULK  H4   C24  C25  114.90  3.000
 ULK  H4   C24  C23  115.11  3.000
 ULK  C25  C24  C23  120.84  3.000
 ULK  H4   C24  C22  114.96  3.000
 ULK  C23  C24  C22   60.19  3.000
 ULK  C25  C24  C22  119.98  3.000
 ULK  H7   C01  H6   108.20  3.000
 ULK  H7   C01  H5   108.36  3.000
 ULK  H6   C01  H5   108.37  3.000
 ULK  H7   C01  N02  111.60  3.000
 ULK  H6   C01  N02  111.71  3.000
 ULK  H5   C01  N02  108.50  3.000
 ULK  H8   N02  C03  117.56  3.000
 ULK  H8   N02  C01  119.80  3.000
 ULK  C03  N02  C01  122.64  3.000
 ULK  N10  C05  C06  123.07  3.000
 ULK  N10  C05  C03  117.24  3.000
 ULK  C06  C05  C03  119.68  3.000
 ULK  H9   C06  C07  122.19  3.000
 ULK  H9   C06  C05  119.69  3.000
 ULK  C07  C06  C05  118.09  3.000
 ULK  C19  C07  C08  118.58  3.000
 ULK  C08  C07  C06  118.52  3.000
 ULK  C19  C07  C06  122.88  3.000
 ULK  H10  C08  C09  120.08  3.000
 ULK  H10  C08  C07  120.80  3.000
 ULK  C09  C08  C07  119.12  3.000
 ULK  C11  C09  N10  117.89  3.000
 ULK  C11  C09  C08  120.06  3.000
 ULK  N10  C09  C08  121.99  3.000
 ULK  C09  N10  C05  119.17  3.000
 ULK  H11  C11  O12  111.47  3.000
 ULK  H11  C11  C09  107.54  3.000
 ULK  O12  C11  C09  108.34  3.000
 ULK  H11  C11  C13  107.94  3.000
 ULK  C09  C11  C13  108.36  3.000
 ULK  O12  C11  C13  113.02  3.000
 ULK  H12  O12  C11  108.07  3.000
 ULK  H13  C14  C15  119.72  3.000
 ULK  H13  C14  C13  119.72  3.000
 ULK  C15  C14  C13  120.56  3.000
 ULK  H14  C16  C17  120.14  3.000
 ULK  H14  C16  C15  120.19  3.000
 ULK  C17  C16  C15  119.67  3.000
 ULK  H15  C18  C17  119.67  3.000
 ULK  H15  C18  C13  120.05  3.000
 ULK  C17  C18  C13  120.28  3.000
 ULK  H16  N21  C19  119.56  3.000
 ULK  H16  N21  C22  117.85  3.000
 ULK  C19  N21  C22  122.57  3.000
 ULK  H18  C23  H17  114.57  3.000
 ULK  H18  C23  C24  118.44  3.000
 ULK  H17  C23  C24  118.24  3.000
 ULK  H18  C23  C22  117.37  3.000
 ULK  H17  C23  C22  117.67  3.000
 ULK  C24  C23  C22   59.81  3.000
 ULK  H21  C25  H20  107.81  3.000
 ULK  H21  C25  H19  107.54  3.000
 ULK  H20  C25  H19  107.81  3.000
 ULK  H21  C25  C24  111.23  3.000
 ULK  H20  C25  C24  111.38  3.000
 ULK  H19  C25  C24  110.89  3.000
 ULK  N21  C19  O20  123.92  3.000
 ULK  O20  C19  C07  120.62  3.000
 ULK  N21  C19  C07  115.46  3.000
 ULK  C05  C03  O04  121.24  3.000
 ULK  C05  C03  N02  114.55  3.000
 ULK  O04  C03  N02  124.21  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
 ULK  CONST_01  C16  C17  C18  C13    0.00   0.0  0
 ULK  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 ULK  CONST_03  C18  C13  C14  C15    0.00   0.0  0
 ULK  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 ULK  CONST_05  C14  C13  C18  C17    0.00   0.0  0
 ULK  CONST_06  C14  C15  C16  C17    0.00   0.0  0
 ULK  CONST_07  C08  C07  C06  C05    0.00   0.0  0
 ULK  CONST_08  C08  C09  N10  C05    0.00   0.0  0
 ULK  CONST_09  C09  N10  C05  C06    0.00   0.0  0
 ULK  CONST_10  C09  C08  C07  C06    0.00   0.0  0
 ULK  CONST_11  N10  C05  C06  C07    0.00   0.0  0
 ULK  CONST_12  N10  C09  C08  C07    0.00   0.0  0
 ULK  CONST_13  C11  C13  C14  C15  180.00   0.0  0
 ULK  CONST_14  C11  C13  C18  C17  180.00   0.0  0
 ULK  CONST_15  C07  C06  C05  C03  180.00   0.0  0
 ULK  CONST_16  C09  N10  C05  C03  180.00   0.0  0
 ULK  CONST_17  C19  C07  C06  C05  180.00   0.0  0
 ULK  CONST_18  C11  C09  N10  C05  180.00   0.0  0
 ULK  CONST_19  C11  C09  C08  C07  180.00   0.0  0
 ULK  CONST_20  C19  C07  C08  C09  180.00   0.0  0
 ULK  CONST_21  H2   C17  C18  C13  180.00   0.0  0
 ULK  CONST_22  H1   C15  C14  C13  180.00   0.0  0
 ULK  CONST_23  H10  C08  C07  C06  180.00   0.0  0
 ULK  CONST_24  H9   C06  C07  C08  180.00   0.0  0
 ULK  CONST_25  H15  C18  C13  C14  180.00   0.0  0
 ULK  CONST_26  H14  C16  C15  C14  180.00   0.0  0
 ULK  CONST_27  H13  C14  C15  C16  180.00   0.0  0
 ULK  CONST_28  C07  C19  N21  C22  180.00   0.0  0
 ULK  CONST_29  O20  C19  N21  C22    0.00   0.0  0
 ULK  CONST_30  C05  C03  N02  C01  180.00   0.0  0
 ULK  CONST_31  H8   N02  C03  C05    0.00   0.0  0
 ULK  CONST_32  H16  N21  C19  C07    0.00   0.0  0
 ULK  CONST_33  O04  C03  N02  C01    0.00   0.0  0
 ULK  Var_01    C25  C24  C23  C22  109.19  30.0  1
 ULK  Var_02    N21  C22  C23  C24  107.30  30.0  1
 ULK  Var_03    C19  N21  C22  C24  143.93  30.0  1
 ULK  Var_04    C06  C05  C03  N02  179.77  30.0  2
 ULK  Var_05    N21  C19  C07  C06  -34.94  30.0  2
 ULK  Var_06    H19  C25  C24  C22  155.30  30.0  3
 ULK  Var_07    H5   C01  N02  C03  178.73  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
 ULK  chir_03  C11  O12  C09  C13  positiv
 ULK  chir_04  C22  N21  C24  C23  both
 ULK  chir_05  C24  C25  C22  C23  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
 ULK  plan-1  C05  0.020
 ULK  plan-1  C06  0.020
 ULK  plan-1  C07  0.020
 ULK  plan-1  C08  0.020
 ULK  plan-1  C09  0.020
 ULK  plan-1  N10  0.020
 ULK  plan-1  C11  0.020
 ULK  plan-1  H9   0.020
 ULK  plan-1  H10  0.020
 ULK  plan-1  C19  0.020
 ULK  plan-1  C03  0.020
 ULK  plan-2  C13  0.020
 ULK  plan-2  C15  0.020
 ULK  plan-2  C17  0.020
 ULK  plan-2  C11  0.020
 ULK  plan-2  C14  0.020
 ULK  plan-2  C16  0.020
 ULK  plan-2  C18  0.020
 ULK  plan-2  H1   0.020
 ULK  plan-2  H2   0.020
 ULK  plan-2  H13  0.020
 ULK  plan-2  H14  0.020
 ULK  plan-2  H15  0.020
 ULK  plan-3  C01  0.020
 ULK  plan-3  N02  0.020
 ULK  plan-3  O04  0.020
 ULK  plan-3  C05  0.020
 ULK  plan-3  H8   0.020
 ULK  plan-3  C03  0.020
 ULK  plan-4  C22  0.020
 ULK  plan-4  C07  0.020
 ULK  plan-4  O20  0.020
 ULK  plan-4  N21  0.020
 ULK  plan-4  H16  0.020
 ULK  plan-4  C19  0.020

