# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:26:22 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-[(1~{R})-1-phenylethyl]pyridine-3,5-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C1=CC(=CN([C@H](C)c2ccccc2)C1=O)C(=O)NC3CC3
#
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
 ULH  ULH  ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-[(1~{R})-1-phenylethyl]pyridine-3,5-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_ULH
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
 ULH  C10  C  CR16  0  -0.165  42.9968  16.6117   8.2606
 ULH  C13  C  CR16  0   0.117  42.3569  18.0195  10.0446
 ULH  C22  C  CR6   0   0.092  40.1552  18.5286  11.7950
 ULH  C01  C  CH3   0  -0.514  39.8991  15.1138   4.8167
 ULH  N05  N  NH1   0  -0.662  40.2419  15.8417   6.0136
 ULH  C07  C  C     0   0.570  41.4838  15.8478   6.5035
 ULH  O08  O  O     0  -0.496  42.4059  15.2372   5.9715
 ULH  C09  C  CR6   0  -0.294  41.7293  16.6383   7.7540
 ULH  C12  C  CR6   0  -0.192  43.3521  17.3190   9.4237
 ULH  N15  N  NR6   0  -0.521  41.0991  18.0525   9.5848
 ULH  C16  C  CH1   0  -0.200  40.1025  18.8698  10.3216
 ULH  C18  C  CH3   0  -0.668  40.2908  20.3360   9.9706
 ULH  C23  C  CR16  0  -0.274  39.8074  17.2373  12.1921
 ULH  C25  C  CR16  0  -0.241  39.8438  16.8728  13.5276
 ULH  C27  C  CR16  0  -0.260  40.2278  17.7991  14.4912
 ULH  C29  C  CR16  0  -0.235  40.5698  19.0857  14.1065
 ULH  C31  C  CR16  0  -0.301  40.5334  19.4492  12.7643
 ULH  C33  C  CR6   0   0.609  40.6972  17.4042   8.4147
 ULH  O34  O  O     0  -0.493  39.5356  17.5145   8.0311
 ULH  C35  C  C     0   0.556  44.7031  17.3488  10.0510
 ULH  O36  O  O     0  -0.476  44.8812  17.9152  11.1198
 ULH  N37  N  NH1   0  -0.678  45.6941  16.7235   9.3899
 ULH  C39  C  CH1   0  -0.078  47.0282  16.6787   9.8925
 ULH  C41  C  CH2   0  -0.512  47.8130  15.4320   9.6446
 ULH  C44  C  CH2   0  -0.481  47.3465  15.7600  11.0293
 ULH  H1   H  HCR6  0   0.271  43.7216  16.0101   7.7267
 ULH  H2   H  HCR6  0   0.328  42.5531  18.5765  10.9510
 ULH  H3   H  HCH3  0   0.247  38.8394  15.2538   4.6231
 ULH  H4   H  HCH3  0   0.236  40.4561  15.4725   3.9499
 ULH  H5   H  HCH3  0   0.236  40.0900  14.0455   4.9237
 ULH  H6   H  HNH1  0   0.416  39.5369  16.3804   6.4972
 ULH  H7   H  HCH1  0   0.304  39.1322  18.5532   9.9433
 ULH  H8   H  HCH3  0   0.255  39.5318  20.9429  10.4628
 ULH  H9   H  HCH3  0   0.240  41.2724  20.7114  10.2630
 ULH  H10  H  HCH3  0   0.262  40.1834  20.4757   8.8957
 ULH  H11  H  HCR6  0   0.259  39.5057  16.5106  11.4462
 ULH  H12  H  HCR6  0   0.258  39.5690  15.8672  13.8187
 ULH  H13  H  HCR6  0   0.258  40.2564  17.5169  15.5356
 ULH  H14  H  HCR6  0   0.258  40.8681  19.8138  14.8495
 ULH  H15  H  HCR6  0   0.261  40.8048  20.4592  12.4866
 ULH  H16  H  HNH1  0   0.412  45.5450  16.3853   8.4537
 ULH  H17  H  HCH1  0   0.268  47.5695  17.6190   9.8537
 ULH  H18  H  HCH2  0   0.258  47.3153  14.6228   9.1247
 ULH  H19  H  HCH2  0   0.259  48.8633  15.5380   9.4085
 ULH  H20  H  HCH2  0   0.256  46.5349  15.1729  11.4389
 ULH  H21  H  HCH2  0   0.255  48.0729  16.0964  11.7572

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
 ULH  C01  N05  single    1.442  0.020  1.442
 ULH  O08  C07  double    1.227  0.020  1.227
 ULH  N05  C07  single    1.335  0.020  1.335
 ULH  C07  C09  single    1.500  0.020  1.500
 ULH  C09  C10  double    1.365  0.020  1.365
 ULH  C09  C33  single    1.445  0.020  1.445
 ULH  O34  C33  double    1.228  0.020  1.228
 ULH  C10  C12  single    1.407  0.020  1.407
 ULH  C33  N15  single    1.397  0.020  1.397
 ULH  C12  C35  single    1.490  0.020  1.490
 ULH  C12  C13  double    1.366  0.020  1.366
 ULH  N15  C13  single    1.340  0.020  1.340
 ULH  N15  C16  single    1.485  0.020  1.485
 ULH  N37  C35  single    1.345  0.020  1.345
 ULH  N37  C39  single    1.426  0.020  1.426
 ULH  C41  C39  single    1.494  0.020  1.494
 ULH  C41  C44  single    1.498  0.020  1.498
 ULH  C35  O36  double    1.223  0.020  1.223
 ULH  C39  C44  single    1.496  0.020  1.496
 ULH  C18  C16  single    1.519  0.020  1.519
 ULH  C16  C22  single    1.513  0.020  1.513
 ULH  C22  C23  aromatic  1.395  0.020  1.395
 ULH  C22  C31  aromatic  1.389  0.020  1.389
 ULH  C23  C25  aromatic  1.385  0.020  1.385
 ULH  C31  C29  aromatic  1.391  0.020  1.391
 ULH  C25  C27  aromatic  1.391  0.020  1.391
 ULH  C29  C27  aromatic  1.386  0.020  1.386
 ULH  C10  H1   single    0.930  0.020  1.080
 ULH  C13  H2   single    0.930  0.020  1.080
 ULH  C01  H3   single    0.970  0.020  1.090
 ULH  C01  H4   single    0.970  0.020  1.090
 ULH  C01  H5   single    0.970  0.020  1.090
 ULH  N05  H6   single    0.860  0.020  1.020
 ULH  C16  H7   single    0.970  0.020  1.090
 ULH  C18  H8   single    0.970  0.020  1.090
 ULH  C18  H9   single    0.970  0.020  1.090
 ULH  C18  H10  single    0.970  0.020  1.090
 ULH  C23  H11  single    0.930  0.020  1.080
 ULH  C25  H12  single    0.930  0.020  1.080
 ULH  C27  H13  single    0.930  0.020  1.080
 ULH  C29  H14  single    0.930  0.020  1.080
 ULH  C31  H15  single    0.930  0.020  1.080
 ULH  N37  H16  single    0.860  0.020  1.020
 ULH  C39  H17  single    0.970  0.020  1.090
 ULH  C41  H18  single    0.970  0.020  1.090
 ULH  C41  H19  single    0.970  0.020  1.090
 ULH  C44  H20  single    0.970  0.020  1.090
 ULH  C44  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
 ULH  H1   C10  C12  121.20  3.000
 ULH  H1   C10  C09  116.70  3.000
 ULH  C12  C10  C09  122.10  3.000
 ULH  H2   C13  N15  116.43  3.000
 ULH  H2   C13  C12  120.84  3.000
 ULH  N15  C13  C12  122.72  3.000
 ULH  C31  C22  C23  118.86  3.000
 ULH  C31  C22  C16  122.64  3.000
 ULH  C23  C22  C16  118.50  3.000
 ULH  H5   C01  H4   108.10  3.000
 ULH  H5   C01  H3   108.33  3.000
 ULH  H4   C01  H3   108.31  3.000
 ULH  H5   C01  N05  111.80  3.000
 ULH  H4   C01  N05  111.85  3.000
 ULH  H3   C01  N05  108.34  3.000
 ULH  H6   N05  C07  118.09  3.000
 ULH  H6   N05  C01  120.03  3.000
 ULH  C07  N05  C01  121.87  3.000
 ULH  C09  C07  O08  120.05  3.000
 ULH  C09  C07  N05  117.43  3.000
 ULH  O08  C07  N05  122.52  3.000
 ULH  C33  C09  C07  122.94  3.000
 ULH  C33  C09  C10  120.25  3.000
 ULH  C07  C09  C10  116.82  3.000
 ULH  C35  C12  C13  117.32  3.000
 ULH  C13  C12  C10  116.71  3.000
 ULH  C35  C12  C10  125.95  3.000
 ULH  C33  N15  C16  118.56  3.000
 ULH  C16  N15  C13  118.26  3.000
 ULH  C33  N15  C13  123.11  3.000
 ULH  H7   C16  C18  108.11  3.000
 ULH  H7   C16  N15  105.42  3.000
 ULH  C18  C16  N15  109.48  3.000
 ULH  H7   C16  C22  107.69  3.000
 ULH  C18  C16  C22  115.99  3.000
 ULH  N15  C16  C22  109.62  3.000
 ULH  H10  C18  H9   108.01  3.000
 ULH  H10  C18  H8   107.81  3.000
 ULH  H9   C18  H8   108.30  3.000
 ULH  H10  C18  C16  109.85  3.000
 ULH  H9   C18  C16  112.44  3.000
 ULH  H8   C18  C16  110.30  3.000
 ULH  H11  C23  C25  119.63  3.000
 ULH  H11  C23  C22  119.60  3.000
 ULH  C25  C23  C22  120.77  3.000
 ULH  H12  C25  C27  120.17  3.000
 ULH  H12  C25  C23  119.82  3.000
 ULH  C27  C25  C23  120.01  3.000
 ULH  H13  C27  C29  120.23  3.000
 ULH  H13  C27  C25  120.15  3.000
 ULH  C29  C27  C25  119.62  3.000
 ULH  H14  C29  C31  119.59  3.000
 ULH  H14  C29  C27  120.14  3.000
 ULH  C31  C29  C27  120.27  3.000
 ULH  H15  C31  C29  119.02  3.000
 ULH  H15  C31  C22  120.51  3.000
 ULH  C29  C31  C22  120.47  3.000
 ULH  O34  C33  N15  119.48  3.000
 ULH  N15  C33  C09  115.06  3.000
 ULH  O34  C33  C09  125.46  3.000
 ULH  N37  C35  O36  122.52  3.000
 ULH  O36  C35  C12  120.63  3.000
 ULH  N37  C35  C12  116.86  3.000
 ULH  H16  N37  C39  117.11  3.000
 ULH  H16  N37  C35  120.27  3.000
 ULH  C39  N37  C35  122.03  3.000
 ULH  H17  C39  C44  116.94  3.000
 ULH  H17  C39  C41  117.06  3.000
 ULH  C44  C39  C41   60.12  3.000
 ULH  H17  C39  N37  115.25  3.000
 ULH  C44  C39  N37  119.08  3.000
 ULH  C41  C39  N37  117.33  3.000
 ULH  H19  C41  H18  114.50  3.000
 ULH  H19  C41  C44  118.87  3.000
 ULH  H18  C41  C44  117.67  3.000
 ULH  H19  C41  C39  117.68  3.000
 ULH  H18  C41  C39  117.50  3.000
 ULH  C44  C41  C39   60.01  3.000
 ULH  H21  C44  H20  114.68  3.000
 ULH  H21  C44  C41  118.75  3.000
 ULH  H20  C44  C41  117.70  3.000
 ULH  H21  C44  C39  117.59  3.000
 ULH  H20  C44  C39  117.47  3.000
 ULH  C41  C44  C39   59.88  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
 ULH  CONST_01  C27  C25  C23  C22     0.00   0.0  0
 ULH  CONST_02  C27  C29  C31  C22     0.00   0.0  0
 ULH  CONST_03  C29  C31  C22  C23     0.00   0.0  0
 ULH  CONST_04  C29  C27  C25  C23     0.00   0.0  0
 ULH  CONST_05  C31  C22  C23  C25     0.00   0.0  0
 ULH  CONST_06  C31  C29  C27  C25     0.00   0.0  0
 ULH  CONST_07  C09  C33  N15  C13     0.00   0.0  0
 ULH  CONST_08  C25  C23  C22  C16   180.00   0.0  0
 ULH  CONST_09  C29  C31  C22  C16   180.00   0.0  0
 ULH  CONST_10  O34  C33  N15  C13   180.00   0.0  0
 ULH  CONST_11  C16  N15  C33  C09   180.00   0.0  0
 ULH  CONST_12  H12  C25  C23  C22   180.00   0.0  0
 ULH  CONST_13  H14  C29  C31  C22   180.00   0.0  0
 ULH  CONST_14  H15  C31  C22  C23   180.00   0.0  0
 ULH  CONST_15  H13  C27  C25  C23   180.00   0.0  0
 ULH  CONST_16  H11  C23  C25  C27   180.00   0.0  0
 ULH  CONST_17  C39  N37  C35  C12   180.00   0.0  0
 ULH  CONST_18  O34  C33  N15  C16     0.00   0.0  0
 ULH  CONST_19  C09  C07  N05  C01   180.00   0.0  0
 ULH  CONST_20  C39  N37  C35  O36     0.00   0.0  0
 ULH  CONST_21  H6   N05  C07  C09     0.00   0.0  0
 ULH  CONST_22  H16  N37  C35  C12     0.00   0.0  0
 ULH  CONST_23  O08  C07  N05  C01     0.00   0.0  0
 ULH  Var_01    C44  C41  C39  N37  -109.52  30.0  1
 ULH  Var_02    H20  C44  C41  C39   107.32  30.0  1
 ULH  Var_03    O08  C07  C09  C10    -1.32  30.0  2
 ULH  Var_04    N37  C35  C12  C10     5.27  30.0  2
 ULH  Var_05    C41  C39  N37  C35   144.46  30.0  3
 ULH  Var_06    H3   C01  N05  C07   179.62  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
 ULH  chir_01  C16  N15  C18  C22  positiv
 ULH  chir_02  C39  N37  C41  C44  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
 ULH  plan-1  C22  0.020
 ULH  plan-1  C16  0.020
 ULH  plan-1  C23  0.020
 ULH  plan-1  C25  0.020
 ULH  plan-1  C27  0.020
 ULH  plan-1  C29  0.020
 ULH  plan-1  C31  0.020
 ULH  plan-1  H11  0.020
 ULH  plan-1  H12  0.020
 ULH  plan-1  H13  0.020
 ULH  plan-1  H14  0.020
 ULH  plan-1  H15  0.020
 ULH  plan-2  C10  0.020
 ULH  plan-2  C13  0.020
 ULH  plan-2  C07  0.020
 ULH  plan-2  C09  0.020
 ULH  plan-2  C12  0.020
 ULH  plan-2  N15  0.020
 ULH  plan-2  C16  0.020
 ULH  plan-2  C33  0.020
 ULH  plan-2  O34  0.020
 ULH  plan-2  C35  0.020
 ULH  plan-2  H1   0.020
 ULH  plan-2  H2   0.020
 ULH  plan-3  C12  0.020
 ULH  plan-3  C35  0.020
 ULH  plan-3  O36  0.020
 ULH  plan-3  N37  0.020
 ULH  plan-3  C39  0.020
 ULH  plan-3  H16  0.020
 ULH  plan-4  C01  0.020
 ULH  plan-4  N05  0.020
 ULH  plan-4  C07  0.020
 ULH  plan-4  O08  0.020
 ULH  plan-4  C09  0.020
 ULH  plan-4  H6   0.020

