# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 12:25:54 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: ~{N}-cyclopropyl-2-(1-methyl-1,2,3-triazol-4-yl)-6-(phenylmethyl)pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(nn1)c2cc(cc(Cc3ccccc3)n2)C(=O)NC4CC4
#
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
 UM8  UM8  ~{N}-cyclopropyl-2-(1-methyl-1,2,3-triazol-4-yl)-6-(phenylmethyl)pyridine-4-carboxamide  ligand  44  25  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UM8
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
 UM8  N1   N  N     0  -0.325  42.8414  15.3163   6.5327
 UM8  N3   N  N     0  -0.443  42.0236  17.6372   9.2015
 UM8  C4   C  CR16  0  -0.359  44.1430  16.6074   8.8147
 UM8  C5   C  CR6   0   0.078  44.6799  17.2810   9.9024
 UM8  C6   C  CR16  0  -0.364  43.8639  18.1447  10.6193
 UM8  C7   C  CR6   0   0.270  42.5339  18.2853  10.2402
 UM8  C8   C  CH2   0  -0.607  41.5965  19.1618  11.0274
 UM8  C10  C  CR16  0  -0.305  41.3578  18.2829  13.3764
 UM8  C13  C  CR16  0  -0.237  39.0582  16.8886  12.7111
 UM8  C15  C  C     0   0.529  46.1169  17.1483  10.3141
 UM8  C17  C  CH2   0  -0.510  48.8178  14.7772   9.5029
 UM8  O    O  O     0  -0.463  46.6971  18.0735  10.8574
 UM8  N4   N  NH1   0  -0.652  46.6915  15.9622  10.0525
 UM8  C16  C  CH1   0  -0.081  48.0442  15.6797  10.4066
 UM8  C18  C  CH2   0  -0.482  49.1481  16.2366   9.5649
 UM8  C9   C  CR6   0   0.138  40.8675  18.3582  12.0757
 UM8  C14  C  CR16  0  -0.301  39.7121  17.6505  11.7525
 UM8  C12  C  CR16  0  -0.268  39.5533  16.8216  14.0075
 UM8  C11  C  CR16  0  -0.237  40.7056  17.5222  14.3378
 UM8  C3   C  CR6   0   0.204  42.8047  16.8231   8.4975
 UM8  C2   C  CR5   0   0.127  42.1826  16.1597   7.3573
 UM8  C1   C  CR15  0  -0.039  40.8824  16.2455   6.9186
 UM8  N2   N  N     0  -0.089  42.0315  14.8887   5.6314
 UM8  N    N  NR5   0  -0.252  40.8475  15.4392   5.8503
 UM8  C    C  CH3   0  -0.518  39.7207  15.1371   4.9951
 UM8  H1   H  HCR6  0   0.274  44.7394  15.9486   8.1977
 UM8  H2   H  HCR6  0   0.268  44.2486  18.6982  11.4653
 UM8  H3   H  HCH2  0   0.274  42.1597  19.9655  11.5036
 UM8  H4   H  HCH2  0   0.275  40.8823  19.6203  10.3418
 UM8  H6   H  HCR6  0   0.252  38.1581  16.3484  12.4460
 UM8  H7   H  HCH2  0   0.259  48.3189  14.4123   8.6138
 UM8  H8   H  HCH2  0   0.260  49.4943  14.0683   9.9612
 UM8  H9   H  HNH1  0   0.411  46.1156  15.1912   9.7524
 UM8  H10  H  HCH1  0   0.270  48.2320  15.5939  11.4725
 UM8  H11  H  HCH2  0   0.256  50.0557  16.5444  10.0671
 UM8  H12  H  HCH2  0   0.257  48.8693  16.8503   8.7182
 UM8  H13  H  HCR6  0   0.247  39.3183  17.7009  10.7443
 UM8  H14  H  HCR6  0   0.253  39.0415  16.2307  14.7560
 UM8  H15  H  HCR6  0   0.253  41.0970  17.4798  15.3462
 UM8  H16  H  HCR5  0   0.308  40.0264  16.7927   7.2744
 UM8  H17  H  HCH3  0   0.277  40.0512  14.4430   4.2288
 UM8  H18  H  HCH3  0   0.272  38.9223  14.6808   5.5753
 UM8  H19  H  HCH3  0   0.272  39.3527  16.0455   4.5245
 UM8  H5   H  HCR6  0   0.249  42.2554  18.8293  13.6425

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
 UM8  C    N    single    1.447  0.020  1.447
 UM8  N2   N    aromatic  1.324  0.020  1.324
 UM8  N2   N1   aromatic  1.285  0.020  1.285
 UM8  N    C1   aromatic  1.339  0.020  1.339
 UM8  N1   C2   aromatic  1.351  0.020  1.351
 UM8  C1   C2   aromatic  1.375  0.020  1.375
 UM8  C2   C3   single    1.459  0.020  1.459
 UM8  C3   C4   aromatic  1.392  0.020  1.392
 UM8  C3   N3   aromatic  1.330  0.020  1.330
 UM8  C4   C5   aromatic  1.387  0.020  1.387
 UM8  N3   C7   aromatic  1.326  0.020  1.326
 UM8  C18  C17  single    1.498  0.020  1.498
 UM8  C18  C16  single    1.496  0.020  1.496
 UM8  C17  C16  single    1.493  0.020  1.493
 UM8  C5   C15  single    1.501  0.020  1.501
 UM8  C5   C6   aromatic  1.388  0.020  1.388
 UM8  N4   C15  single    1.344  0.020  1.344
 UM8  N4   C16  single    1.427  0.020  1.427
 UM8  C15  O    double    1.220  0.020  1.220
 UM8  C7   C6   aromatic  1.390  0.020  1.390
 UM8  C7   C8   single    1.505  0.020  1.505
 UM8  C8   C9   single    1.509  0.020  1.509
 UM8  C14  C9   aromatic  1.393  0.020  1.393
 UM8  C14  C13  aromatic  1.388  0.020  1.388
 UM8  C9   C10  aromatic  1.392  0.020  1.392
 UM8  C13  C12  aromatic  1.389  0.020  1.389
 UM8  C10  C11  aromatic  1.389  0.020  1.389
 UM8  C12  C11  aromatic  1.388  0.020  1.388
 UM8  C4   H1   single    0.930  0.020  1.080
 UM8  C6   H2   single    0.930  0.020  1.080
 UM8  C8   H3   single    0.970  0.020  1.090
 UM8  C8   H4   single    0.970  0.020  1.090
 UM8  C10  H5   single    0.930  0.020  1.080
 UM8  C13  H6   single    0.930  0.020  1.080
 UM8  C17  H7   single    0.970  0.020  1.090
 UM8  C17  H8   single    0.970  0.020  1.090
 UM8  N4   H9   single    0.860  0.020  1.020
 UM8  C16  H10  single    0.970  0.020  1.090
 UM8  C18  H11  single    0.970  0.020  1.090
 UM8  C18  H12  single    0.970  0.020  1.090
 UM8  C14  H13  single    0.930  0.020  1.080
 UM8  C12  H14  single    0.930  0.020  1.080
 UM8  C11  H15  single    0.930  0.020  1.080
 UM8  C1   H16  single    0.930  0.020  1.080
 UM8  C    H17  single    0.970  0.020  1.090
 UM8  C    H18  single    0.970  0.020  1.090
 UM8  C    H19  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
 UM8  N2   N1   C2   109.17  3.000
 UM8  C3   N3   C7   119.18  3.000
 UM8  H1   C4   C3   119.63  3.000
 UM8  H1   C4   C5   121.97  3.000
 UM8  C3   C4   C5   118.38  3.000
 UM8  C15  C5   C6   118.44  3.000
 UM8  C6   C5   C4   118.66  3.000
 UM8  C15  C5   C4   122.87  3.000
 UM8  H2   C6   C7   120.12  3.000
 UM8  H2   C6   C5   120.89  3.000
 UM8  C7   C6   C5   118.99  3.000
 UM8  C8   C7   C6   120.80  3.000
 UM8  C8   C7   N3   117.03  3.000
 UM8  C6   C7   N3   122.15  3.000
 UM8  H4   C8   H3   107.62  3.000
 UM8  H4   C8   C9   110.13  3.000
 UM8  H3   C8   C9   109.79  3.000
 UM8  H4   C8   C7   108.89  3.000
 UM8  H3   C8   C7   109.62  3.000
 UM8  C9   C8   C7   110.74  3.000
 UM8  H5   C10  C11  119.68  3.000
 UM8  H5   C10  C9   119.59  3.000
 UM8  C11  C10  C9   120.74  3.000
 UM8  H6   C13  C12  120.05  3.000
 UM8  H6   C13  C14  119.76  3.000
 UM8  C12  C13  C14  120.19  3.000
 UM8  N4   C15  O    123.56  3.000
 UM8  O    C15  C5   120.71  3.000
 UM8  N4   C15  C5   115.73  3.000
 UM8  H8   C17  H7   114.53  3.000
 UM8  H8   C17  C18  118.89  3.000
 UM8  H7   C17  C18  117.64  3.000
 UM8  H8   C17  C16  117.62  3.000
 UM8  H7   C17  C16  117.51  3.000
 UM8  C18  C17  C16   60.01  3.000
 UM8  H9   N4   C16  117.66  3.000
 UM8  H9   N4   C15  119.27  3.000
 UM8  C16  N4   C15  122.14  3.000
 UM8  H10  C16  C18  117.02  3.000
 UM8  H10  C16  N4   115.05  3.000
 UM8  C18  C16  N4   119.10  3.000
 UM8  H10  C16  C17  117.18  3.000
 UM8  N4   C16  C17  117.43  3.000
 UM8  C18  C16  C17   60.14  3.000
 UM8  H12  C18  H11  114.70  3.000
 UM8  H12  C18  C16  117.47  3.000
 UM8  H11  C18  C16  117.63  3.000
 UM8  H12  C18  C17  117.61  3.000
 UM8  H11  C18  C17  118.78  3.000
 UM8  C16  C18  C17   59.85  3.000
 UM8  C14  C9   C10  118.78  3.000
 UM8  C10  C9   C8   120.52  3.000
 UM8  C14  C9   C8   120.68  3.000
 UM8  H13  C14  C9   119.58  3.000
 UM8  H13  C14  C13  119.79  3.000
 UM8  C9   C14  C13  120.62  3.000
 UM8  H14  C12  C11  120.22  3.000
 UM8  H14  C12  C13  120.21  3.000
 UM8  C11  C12  C13  119.57  3.000
 UM8  H15  C11  C12  120.13  3.000
 UM8  H15  C11  C10  119.77  3.000
 UM8  C12  C11  C10  120.10  3.000
 UM8  C2   C3   C4   121.17  3.000
 UM8  C4   C3   N3   122.62  3.000
 UM8  C2   C3   N3   116.21  3.000
 UM8  C1   C2   C3   128.64  3.000
 UM8  C3   C2   N1   123.58  3.000
 UM8  C1   C2   N1   107.78  3.000
 UM8  H16  C1   N    123.31  3.000
 UM8  H16  C1   C2   132.70  3.000
 UM8  N    C1   C2   103.98  3.000
 UM8  N    N2   N1   108.02  3.000
 UM8  C    N    N2   120.80  3.000
 UM8  N2   N    C1   111.04  3.000
 UM8  C    N    C1   128.15  3.000
 UM8  H19  C    H18  109.46  3.000
 UM8  H19  C    H17  109.38  3.000
 UM8  H18  C    H17  109.39  3.000
 UM8  H19  C    N    110.18  3.000
 UM8  H18  C    N    110.13  3.000
 UM8  H17  C    N    108.28  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
 UM8  CONST_01  C1   N    N2   N1      0.00   0.0  0
 UM8  CONST_02  N    C1   C2   N1      0.00   0.0  0
 UM8  CONST_03  C4   C3   C2   N1      0.00   0.0  0
 UM8  CONST_04  N3   C3   C2   N1    180.00   0.0  0
 UM8  CONST_05  C1   C2   C3   N3      0.00   0.0  0
 UM8  CONST_06  C5   C4   C3   N3      0.00   0.0  0
 UM8  CONST_07  C5   C6   C7   N3      0.00   0.0  0
 UM8  CONST_08  C1   C2   C3   C4    180.00   0.0  0
 UM8  CONST_09  C7   N3   C3   C4      0.00   0.0  0
 UM8  CONST_10  C7   C6   C5   C4      0.00   0.0  0
 UM8  CONST_11  C2   C3   C4   C5    180.00   0.0  0
 UM8  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 UM8  CONST_13  C3   N3   C7   C6      0.00   0.0  0
 UM8  CONST_14  C2   C3   N3   C7    180.00   0.0  0
 UM8  CONST_15  C13  C14  C9   C10     0.00   0.0  0
 UM8  CONST_16  C13  C12  C11  C10     0.00   0.0  0
 UM8  CONST_17  C12  C13  C14  C9      0.00   0.0  0
 UM8  CONST_18  C12  C11  C10  C9      0.00   0.0  0
 UM8  CONST_19  C11  C10  C9   C14     0.00   0.0  0
 UM8  CONST_20  C11  C12  C13  C14     0.00   0.0  0
 UM8  CONST_21  N2   N1   C2   C3    180.00   0.0  0
 UM8  CONST_22  N    C1   C2   C3    180.00   0.0  0
 UM8  CONST_23  N    N2   N1   C2      0.00   0.0  0
 UM8  CONST_24  N2   N    C1   C2      0.00   0.0  0
 UM8  CONST_25  N2   N1   C2   C1      0.00   0.0  0
 UM8  CONST_26  C    N    N2   N1    180.00   0.0  0
 UM8  CONST_27  C8   C7   C6   C5    180.00   0.0  0
 UM8  CONST_28  C15  C5   C6   C7    180.00   0.0  0
 UM8  CONST_29  C3   N3   C7   C8    180.00   0.0  0
 UM8  CONST_30  C13  C14  C9   C8    180.00   0.0  0
 UM8  CONST_31  C11  C10  C9   C8    180.00   0.0  0
 UM8  CONST_32  C3   C4   C5   C15   180.00   0.0  0
 UM8  CONST_33  C    N    C1   C2    180.00   0.0  0
 UM8  CONST_34  H16  C1   C2   N1    180.00   0.0  0
 UM8  CONST_35  H1   C4   C3   N3    180.00   0.0  0
 UM8  CONST_36  H2   C6   C7   N3    180.00   0.0  0
 UM8  CONST_37  H13  C14  C9   C10   180.00   0.0  0
 UM8  CONST_38  H14  C12  C11  C10   180.00   0.0  0
 UM8  CONST_39  H15  C11  C12  C13   180.00   0.0  0
 UM8  CONST_40  H6   C13  C14  C9    180.00   0.0  0
 UM8  CONST_41  H5   C10  C9   C14   180.00   0.0  0
 UM8  CONST_42  C16  N4   C15  C5    180.00   0.0  0
 UM8  CONST_43  C16  N4   C15  O       0.00   0.0  0
 UM8  CONST_44  H9   N4   C15  C5      0.00   0.0  0
 UM8  Var_01    C9   C8   C7   N3     85.67  30.0  2
 UM8  Var_02    C14  C9   C8   C7    -84.20  30.0  2
 UM8  Var_03    N4   C16  C18  C17  -106.76  30.0  1
 UM8  Var_04    H7   C17  C18  C16   107.45  30.0  1
 UM8  Var_05    N4   C15  C5   C4    -30.60  30.0  2
 UM8  Var_06    C18  C16  N4   C15   -77.33  30.0  3
 UM8  Var_07    H17  C    N    C1   -179.80  30.0  2

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
 UM8  chir_01  C16  C18  C17  N4  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
 UM8  plan-1  N1   0.020
 UM8  plan-1  C3   0.020
 UM8  plan-1  C2   0.020
 UM8  plan-1  C1   0.020
 UM8  plan-1  N2   0.020
 UM8  plan-1  N    0.020
 UM8  plan-1  C    0.020
 UM8  plan-1  H16  0.020
 UM8  plan-2  C8   0.020
 UM8  plan-2  C10  0.020
 UM8  plan-2  C13  0.020
 UM8  plan-2  C9   0.020
 UM8  plan-2  C14  0.020
 UM8  plan-2  C12  0.020
 UM8  plan-2  C11  0.020
 UM8  plan-2  H6   0.020
 UM8  plan-2  H13  0.020
 UM8  plan-2  H14  0.020
 UM8  plan-2  H15  0.020
 UM8  plan-2  H5   0.020
 UM8  plan-3  N3   0.020
 UM8  plan-3  C4   0.020
 UM8  plan-3  C5   0.020
 UM8  plan-3  C6   0.020
 UM8  plan-3  C7   0.020
 UM8  plan-3  C8   0.020
 UM8  plan-3  C15  0.020
 UM8  plan-3  C3   0.020
 UM8  plan-3  C2   0.020
 UM8  plan-3  H1   0.020
 UM8  plan-3  H2   0.020
 UM8  plan-4  C5   0.020
 UM8  plan-4  C15  0.020
 UM8  plan-4  O    0.020
 UM8  plan-4  N4   0.020
 UM8  plan-4  C16  0.020
 UM8  plan-4  H9   0.020

