# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:30:33 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: ~{N}2-methyl-~{N}4-(3-oxidanylcyclobutyl)-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](O)C3
#
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
 UMB  UMB  ~{N}2-methyl-~{N}4-(3-oxidanylcyclobutyl)-6-(phenylmethyl)pyridine-2,4-dicarboxamide  ligand  46  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UMB
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
 UMB  N1   N  N     0  -0.440  41.4786  17.4523   8.6956
 UMB  C4   C  CR6   0   0.081  44.1662  17.5837   9.3428
 UMB  C5   C  CR16  0  -0.367  43.2456  18.4339   9.9370
 UMB  C6   C  CR6   0   0.287  41.9009  18.3303   9.5957
 UMB  C7   C  CH2   0  -0.603  40.8582  19.1842  10.2650
 UMB  C8   C  CR6   0   0.136  40.1331  18.3982  11.3287
 UMB  C10  C  CR16  0  -0.237  38.3208  16.9499  12.0019
 UMB  C13  C  CR16  0  -0.296  40.6437  18.3267  12.6223
 UMB  C15  C  C     0  -0.062  47.7305  16.5098   9.9704
 UMB  C17  C  C     0   0.015  49.2982  15.2472  10.7055
 UMB  O1   O  O     0  -0.469  46.0656  18.7879  10.0834
 UMB  C14  C  C     0   0.534  45.6133  17.7126   9.7227
 UMB  N2   N  NH1   0  -0.650  46.3357  16.5857   9.6349
 UMB  C18  C  C     0  -0.471  48.5183  15.3288   9.3840
 UMB  O2   O  OH1   0  -0.666  50.4901  15.9857  10.5917
 UMB  C16  C  C     0  -0.476  48.1495  16.0295  11.3751
 UMB  C3   C  CR16  0  -0.358  43.7126  16.6745   8.3954
 UMB  C2   C  CR6   0   0.128  42.3569  16.6541   8.1060
 UMB  C1   C  C     0   0.532  41.8365  15.6889   7.0747
 UMB  O    O  O     0  -0.477  42.5948  14.9537   6.4567
 UMB  N    N  NH1   0  -0.635  40.5138  15.7091   6.9094
 UMB  C    C  CH3   0  -0.515  39.8359  14.8484   5.9718
 UMB  C12  C  CR16  0  -0.237  39.9998  17.5785  13.5982
 UMB  C11  C  CR16  0  -0.268  38.8358  16.8860  13.2900
 UMB  C9   C  CR16  0  -0.309  38.9669  17.7003  11.0281
 UMB  H1   H  HCR6  0   0.275  43.5608  19.1661  10.6683
 UMB  H2   H  HCH2  0   0.277  41.3335  20.0612  10.7065
 UMB  H3   H  HCH2  0   0.279  40.1516  19.5384   9.5127
 UMB  H4   H  HCR6  0   0.253  37.4121  16.4162  11.7541
 UMB  H5   H  HCR6  0   0.249  41.5515  18.8650  12.8704
 UMB  H6   H  H     0   0.261  48.2019  17.4597   9.7244
 UMB  H7   H  H     0   0.219  49.4854  14.2415  11.0970
 UMB  H8   H  HNH1  0   0.408  45.8557  15.7116   9.4827
 UMB  H9   H  H     0   0.246  47.8826  14.4499   9.2591
 UMB  H10  H  H     0   0.250  49.0860  15.4892   8.4673
 UMB  H11  H  HOH1  0   0.447  50.8306  16.1419  11.4783
 UMB  H12  H  H     0   0.249  48.4070  16.7816  12.1225
 UMB  H13  H  H     0   0.238  47.4041  15.3515  11.7947
 UMB  H14  H  HCR6  0   0.278  44.3812  16.0089   7.8669
 UMB  H15  H  HNH1  0   0.408  39.9828  16.3605   7.4665
 UMB  H16  H  HCH3  0   0.252  38.7675  15.0265   6.0504
 UMB  H17  H  HCH3  0   0.240  40.1435  15.0488   4.9446
 UMB  H18  H  HCH3  0   0.240  40.0257  13.7960   6.1850
 UMB  H19  H  HCR6  0   0.253  40.4066  17.5379  14.6005
 UMB  H20  H  HCR6  0   0.253  38.3312  16.3036  14.0500
 UMB  H21  H  HCR6  0   0.248  38.5571  17.7497  10.0264

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
 UMB  C    N    single    1.442  0.020  1.442
 UMB  O    C1   double    1.224  0.020  1.224
 UMB  N    C1   single    1.333  0.020  1.333
 UMB  C1   C2   single    1.505  0.020  1.505
 UMB  C2   C3   aromatic  1.386  0.020  1.386
 UMB  C2   N1   aromatic  1.325  0.020  1.325
 UMB  C3   C4   aromatic  1.389  0.020  1.389
 UMB  N1   C6   aromatic  1.326  0.020  1.326
 UMB  C4   C14  single    1.502  0.020  1.502
 UMB  C4   C5   aromatic  1.387  0.020  1.387
 UMB  N2   C14  single    1.341  0.020  1.341
 UMB  N2   C15  single    1.437  0.020  1.437
 UMB  C18  C15  single    1.536  0.020  1.536
 UMB  C18  C17  single    1.537  0.020  1.537
 UMB  C6   C5   aromatic  1.391  0.020  1.391
 UMB  C6   C7   single    1.505  0.020  1.505
 UMB  C14  O1   double    1.221  0.020  1.221
 UMB  C15  C16  single    1.542  0.020  1.542
 UMB  C7   C8   single    1.508  0.020  1.508
 UMB  C17  O2   single    1.407  0.020  1.407
 UMB  C17  C16  single    1.543  0.020  1.543
 UMB  C9   C8   aromatic  1.392  0.020  1.392
 UMB  C9   C10  aromatic  1.389  0.020  1.389
 UMB  C8   C13  aromatic  1.393  0.020  1.393
 UMB  C10  C11  aromatic  1.389  0.020  1.389
 UMB  C13  C12  aromatic  1.388  0.020  1.388
 UMB  C11  C12  aromatic  1.389  0.020  1.389
 UMB  C5   H1   single    0.930  0.020  1.080
 UMB  C7   H2   single    0.970  0.020  1.090
 UMB  C7   H3   single    0.970  0.020  1.090
 UMB  C10  H4   single    0.930  0.020  1.080
 UMB  C13  H5   single    0.930  0.020  1.080
 UMB  C15  H6   single    0.970  0.020  1.090
 UMB  C17  H7   single    0.970  0.020  1.090
 UMB  N2   H8   single    0.860  0.020  1.020
 UMB  C18  H9   single    0.970  0.020  1.090
 UMB  C18  H10  single    0.970  0.020  1.090
 UMB  O2   H11  single    0.850  0.020  0.980
 UMB  C16  H12  single    0.970  0.020  1.090
 UMB  C16  H13  single    0.970  0.020  1.090
 UMB  C3   H14  single    0.930  0.020  1.080
 UMB  N    H15  single    0.860  0.020  1.020
 UMB  C    H16  single    0.970  0.020  1.090
 UMB  C    H17  single    0.970  0.020  1.090
 UMB  C    H18  single    0.970  0.020  1.090
 UMB  C12  H19  single    0.930  0.020  1.080
 UMB  C11  H20  single    0.930  0.020  1.080
 UMB  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
 UMB  C2   N1   C6   119.31  3.000
 UMB  C3   C4   C14  122.91  3.000
 UMB  C14  C4   C5   118.60  3.000
 UMB  C3   C4   C5   118.47  3.000
 UMB  H1   C5   C6   119.86  3.000
 UMB  H1   C5   C4   120.73  3.000
 UMB  C6   C5   C4   119.40  3.000
 UMB  C7   C6   C5   121.22  3.000
 UMB  C7   C6   N1   117.18  3.000
 UMB  C5   C6   N1   121.57  3.000
 UMB  H3   C7   H2   107.47  3.000
 UMB  H3   C7   C8   110.12  3.000
 UMB  H2   C7   C8   110.06  3.000
 UMB  H3   C7   C6   109.04  3.000
 UMB  H2   C7   C6   109.53  3.000
 UMB  C8   C7   C6   110.55  3.000
 UMB  C9   C8   C13  118.82  3.000
 UMB  C13  C8   C7   120.37  3.000
 UMB  C9   C8   C7   120.78  3.000
 UMB  H4   C10  C9   119.76  3.000
 UMB  H4   C10  C11  120.06  3.000
 UMB  C9   C10  C11  120.18  3.000
 UMB  H5   C13  C12  119.68  3.000
 UMB  H5   C13  C8   119.61  3.000
 UMB  C12  C13  C8   120.71  3.000
 UMB  H6   C15  C16  111.09  3.000
 UMB  H6   C15  C18  111.26  3.000
 UMB  C16  C15  C18   88.22  3.000
 UMB  H6   C15  N2   108.76  3.000
 UMB  C16  C15  N2   119.53  3.000
 UMB  C18  C15  N2   116.71  3.000
 UMB  H7   C17  C16  115.96  3.000
 UMB  H7   C17  O2   111.48  3.000
 UMB  C16  C17  O2   113.56  3.000
 UMB  H7   C17  C18  116.29  3.000
 UMB  C16  C17  C18   88.19  3.000
 UMB  O2   C17  C18  109.43  3.000
 UMB  N2   C14  O1   124.03  3.000
 UMB  O1   C14  C4   120.48  3.000
 UMB  N2   C14  C4   115.49  3.000
 UMB  H8   N2   C14  118.79  3.000
 UMB  H8   N2   C15  116.84  3.000
 UMB  C14  N2   C15  123.50  3.000
 UMB  H10  C18  H9   108.99  3.000
 UMB  H10  C18  C17  117.81  3.000
 UMB  H9   C18  C17  110.56  3.000
 UMB  H10  C18  C15  118.36  3.000
 UMB  H9   C18  C15  111.35  3.000
 UMB  C17  C18  C15   88.44  3.000
 UMB  H11  O2   C17  108.08  3.000
 UMB  H13  C16  H12  109.02  3.000
 UMB  H13  C16  C17  111.12  3.000
 UMB  H12  C16  C17  118.11  3.000
 UMB  H13  C16  C15  110.98  3.000
 UMB  H12  C16  C15  118.25  3.000
 UMB  C17  C16  C15   87.99  3.000
 UMB  H14  C3   C2   119.57  3.000
 UMB  H14  C3   C4   122.30  3.000
 UMB  C2   C3   C4   118.12  3.000
 UMB  C1   C2   C3   119.38  3.000
 UMB  C3   C2   N1   123.12  3.000
 UMB  C1   C2   N1   117.51  3.000
 UMB  N    C1   O    124.15  3.000
 UMB  N    C1   C2   114.73  3.000
 UMB  O    C1   C2   121.13  3.000
 UMB  H15  N    C    119.82  3.000
 UMB  H15  N    C1   117.63  3.000
 UMB  C    N    C1   122.55  3.000
 UMB  H18  C    H17  108.20  3.000
 UMB  H18  C    H16  108.39  3.000
 UMB  H17  C    H16  108.38  3.000
 UMB  H18  C    N    111.54  3.000
 UMB  H17  C    N    111.72  3.000
 UMB  H16  C    N    108.51  3.000
 UMB  H19  C12  C11  120.11  3.000
 UMB  H19  C12  C13  119.79  3.000
 UMB  C11  C12  C13  120.10  3.000
 UMB  H20  C11  C12  120.21  3.000
 UMB  H20  C11  C10  120.21  3.000
 UMB  C12  C11  C10  119.58  3.000
 UMB  H21  C9   C10  119.80  3.000
 UMB  H21  C9   C8   119.59  3.000
 UMB  C10  C9   C8   120.61  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
 UMB  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 UMB  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 UMB  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 UMB  CONST_04  C2   N1   C6   C5     0.00   0.0  0
 UMB  CONST_05  C3   C2   N1   C6     0.00   0.0  0
 UMB  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 UMB  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 UMB  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 UMB  CONST_09  C13  C8   C9   C10    0.00   0.0  0
 UMB  CONST_10  C13  C12  C11  C10    0.00   0.0  0
 UMB  CONST_11  C9   C8   C13  C12    0.00   0.0  0
 UMB  CONST_12  C9   C10  C11  C12    0.00   0.0  0
 UMB  CONST_13  C1   C2   C3   C4   180.00   0.0  0
 UMB  CONST_14  C7   C6   C5   C4   180.00   0.0  0
 UMB  CONST_15  C1   C2   N1   C6   180.00   0.0  0
 UMB  CONST_16  C14  C4   C5   C6   180.00   0.0  0
 UMB  CONST_17  C2   N1   C6   C7   180.00   0.0  0
 UMB  CONST_18  C10  C9   C8   C7   180.00   0.0  0
 UMB  CONST_19  C12  C13  C8   C7   180.00   0.0  0
 UMB  CONST_20  C2   C3   C4   C14  180.00   0.0  0
 UMB  CONST_21  H14  C3   C2   N1   180.00   0.0  0
 UMB  CONST_22  H1   C5   C6   N1   180.00   0.0  0
 UMB  CONST_23  H4   C10  C9   C8   180.00   0.0  0
 UMB  CONST_24  H19  C12  C13  C8   180.00   0.0  0
 UMB  CONST_25  H21  C9   C8   C13  180.00   0.0  0
 UMB  CONST_26  H20  C11  C12  C13  180.00   0.0  0
 UMB  CONST_27  H5   C13  C12  C11  180.00   0.0  0
 UMB  CONST_28  C15  N2   C14  C4   180.00   0.0  0
 UMB  CONST_29  O1   C14  N2   C15    0.00   0.0  0
 UMB  CONST_30  C    N    C1   C2   180.00   0.0  0
 UMB  CONST_31  H8   N2   C14  C4     0.00   0.0  0
 UMB  CONST_32  H15  N    C1   C2     0.00   0.0  0
 UMB  CONST_33  C    N    C1   O      0.00   0.0  0
 UMB  Var_01    C8   C7   C6   N1    77.53  30.0  2
 UMB  Var_02    C9   C8   C7   C6   -91.44  30.0  2
 UMB  Var_03    O    C1   C2   N1   177.47  30.0  2
 UMB  Var_04    N2   C14  C4   C5   151.20  30.0  2
 UMB  Var_05    H16  C    N    C1   177.88  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
 UMB  chir_01  C15  N2  C18  C16  positiv
 UMB  chir_02  C17  O2  C16  C18  negativ

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
 UMB  plan-1  N1   0.020
 UMB  plan-1  C4   0.020
 UMB  plan-1  C5   0.020
 UMB  plan-1  C6   0.020
 UMB  plan-1  C7   0.020
 UMB  plan-1  C14  0.020
 UMB  plan-1  C3   0.020
 UMB  plan-1  C2   0.020
 UMB  plan-1  C1   0.020
 UMB  plan-1  H1   0.020
 UMB  plan-1  H14  0.020
 UMB  plan-2  C7   0.020
 UMB  plan-2  C8   0.020
 UMB  plan-2  C10  0.020
 UMB  plan-2  C13  0.020
 UMB  plan-2  C12  0.020
 UMB  plan-2  C11  0.020
 UMB  plan-2  C9   0.020
 UMB  plan-2  H4   0.020
 UMB  plan-2  H5   0.020
 UMB  plan-2  H19  0.020
 UMB  plan-2  H20  0.020
 UMB  plan-2  H21  0.020
 UMB  plan-3  C2   0.020
 UMB  plan-3  C1   0.020
 UMB  plan-3  O    0.020
 UMB  plan-3  N    0.020
 UMB  plan-3  C    0.020
 UMB  plan-3  H15  0.020
 UMB  plan-4  C4   0.020
 UMB  plan-4  C15  0.020
 UMB  plan-4  O1   0.020
 UMB  plan-4  C14  0.020
 UMB  plan-4  N2   0.020
 UMB  plan-4  H8   0.020

