# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:13:52 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-[(cyclopropylcarbonyl)amino]-N-(4-phenylpyridin-3-yl)pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cc(ccn1)C(=O)Nc2cnccc2c3ccccc3)C4CC4
#
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
 3UP  3UP  2-[(cyclopropylcarbonyl)amino]-N-(4-phenylpyridin-3-yl)pyridine-4-carboxamide  ligand  45  27  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3UP
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
 3UP  C1   C  CR6   0   0.080  -0.6553   0.1218   0.0845
 3UP  C2   C  CR16  0  -0.437  -1.9345   0.6157   0.2421
 3UP  C3   C  CR6   0   0.554  -3.0188  -0.2246  -0.0370
 3UP  N4   N  N     0  -0.417  -2.8691  -1.4806  -0.4195
 3UP  C5   C  CR16  0  -0.049  -1.6334  -1.9497  -0.5467
 3UP  C6   C  CR16  0  -0.386  -0.4929  -1.2034  -0.3172
 3UP  C7   C  C     0   0.520   0.4934   1.0323   0.3970
 3UP  N8   N  NH1   0  -0.750  -4.2891   0.3132   0.1059
 3UP  N9   N  NH1   0  -0.753   1.6283   0.7719  -0.2908
 3UP  O10  O  O     0  -0.444   0.3860   1.9303   1.2097
 3UP  C11  C  C     0   0.589  -5.5135  -0.2537  -0.1357
 3UP  C12  C  CH1   0  -0.445  -6.6425   0.6756   0.1340
 3UP  O13  O  O     0  -0.450  -5.6779  -1.3899  -0.5289
 3UP  C14  C  CH2   0  -0.463  -7.9198   0.0886   0.6791
 3UP  C15  C  CH2   0  -0.462  -7.8736   0.5553  -0.7274
 3UP  C16  C  CR6   0   0.201   2.8588   1.4197  -0.0885
 3UP  C17  C  CR16  0  -0.077   2.9468   2.8088  -0.0731
 3UP  N18  N  N     0  -0.404   4.0886   3.4629   0.0720
 3UP  C19  C  CR16  0  -0.061   5.2048   2.7522   0.1819
 3UP  C20  C  CR16  0  -0.372   5.2249   1.3687   0.1605
 3UP  C21  C  CR6   0   0.151   4.0292   0.6675   0.0411
 3UP  C22  C  CR6   0   0.038   4.0187  -0.8106   0.0441
 3UP  C23  C  CR16  0  -0.296   3.2170  -1.5179   0.9413
 3UP  C24  C  CR16  0  -0.235   3.2303  -2.9045   0.9514
 3UP  C25  C  CR16  0  -0.259   4.0407  -3.6014   0.0635
 3UP  C26  C  CR16  0  -0.238   4.8443  -2.9048  -0.8285
 3UP  C27  C  CR16  0  -0.289   4.8359  -1.5167  -0.8366
 3UP  H1   H  HCR6  0   0.288  -2.0975   1.6373   0.5604
 3UP  H2   H  HCR6  0   0.274  -1.5466  -2.9871  -0.8481
 3UP  H3   H  HCR6  0   0.265   0.4756  -1.6727  -0.4301
 3UP  H4   H  HNH1  0   0.424  -4.3057   1.2697   0.4239
 3UP  H5   H  HNH1  0   0.425   1.6268   0.0081  -0.9493
 3UP  H6   H  HCH1  0   0.286  -6.3844   1.6723   0.4721
 3UP  H7   H  HCH2  0   0.261  -7.9343  -0.9772   0.8651
 3UP  H8   H  HCH2  0   0.266  -8.4531   0.6851   1.4068
 3UP  H9   H  HCH2  0   0.267  -8.3733   1.4798  -0.9837
 3UP  H10  H  HCH2  0   0.261  -7.8578  -0.1869  -1.5145
 3UP  H11  H  HCR6  0   0.277   2.0550   3.4104  -0.1978
 3UP  H12  H  HCR6  0   0.270   6.1287   3.3081   0.2922
 3UP  H13  H  HCR6  0   0.276   6.1620   0.8378   0.2641
 3UP  H14  H  HCR6  0   0.264   2.5977  -0.9852   1.6523
 3UP  H15  H  HCR6  0   0.264   2.6112  -3.4413   1.6582
 3UP  H16  H  HCR6  0   0.263   4.0481  -4.6835   0.0706
 3UP  H17  H  HCR6  0   0.263   5.4779  -3.4421  -1.5218
 3UP  H18  H  HCR6  0   0.261   5.4591  -0.9784  -1.5403

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
 3UP  C5   N4   aromatic  1.328  0.020  1.328
 3UP  C5   C6   aromatic  1.382  0.020  1.382
 3UP  N4   C3   aromatic  1.321  0.020  1.321
 3UP  C6   C1   aromatic  1.394  0.020  1.394
 3UP  C3   N8   single    1.387  0.020  1.387
 3UP  C3   C2   aromatic  1.400  0.020  1.400
 3UP  N8   C11  single    1.371  0.020  1.371
 3UP  C1   C2   aromatic  1.380  0.020  1.380
 3UP  C1   C7   single    1.499  0.020  1.499
 3UP  O10  C7   double    1.216  0.020  1.216
 3UP  C12  C11  single    1.487  0.020  1.487
 3UP  C12  C14  single    1.508  0.020  1.508
 3UP  C12  C15  single    1.507  0.020  1.507
 3UP  C7   N9   single    1.352  0.020  1.352
 3UP  C11  O13  double    1.213  0.020  1.213
 3UP  C14  C15  single    1.483  0.020  1.483
 3UP  N9   C16  single    1.405  0.020  1.405
 3UP  C17  C16  aromatic  1.392  0.020  1.392
 3UP  C17  N18  aromatic  1.324  0.020  1.324
 3UP  C16  C21  aromatic  1.397  0.020  1.397
 3UP  C23  C24  aromatic  1.387  0.020  1.387
 3UP  C23  C22  aromatic  1.396  0.020  1.396
 3UP  C24  C25  aromatic  1.389  0.020  1.389
 3UP  N18  C19  aromatic  1.328  0.020  1.328
 3UP  C21  C22  single    1.478  0.020  1.478
 3UP  C21  C20  aromatic  1.391  0.020  1.391
 3UP  C22  C27  aromatic  1.394  0.020  1.394
 3UP  C25  C26  aromatic  1.388  0.020  1.388
 3UP  C19  C20  aromatic  1.384  0.020  1.384
 3UP  C27  C26  aromatic  1.388  0.020  1.388
 3UP  C2   H1   single    0.930  0.020  1.080
 3UP  C5   H2   single    0.930  0.020  1.080
 3UP  C6   H3   single    0.930  0.020  1.080
 3UP  N8   H4   single    0.860  0.020  1.020
 3UP  N9   H5   single    0.860  0.020  1.020
 3UP  C12  H6   single    0.970  0.020  1.090
 3UP  C14  H7   single    0.970  0.020  1.090
 3UP  C14  H8   single    0.970  0.020  1.090
 3UP  C15  H9   single    0.970  0.020  1.090
 3UP  C15  H10  single    0.970  0.020  1.090
 3UP  C17  H11  single    0.930  0.020  1.080
 3UP  C19  H12  single    0.930  0.020  1.080
 3UP  C20  H13  single    0.930  0.020  1.080
 3UP  C23  H14  single    0.930  0.020  1.080
 3UP  C24  H15  single    0.930  0.020  1.080
 3UP  C25  H16  single    0.930  0.020  1.080
 3UP  C26  H17  single    0.930  0.020  1.080
 3UP  C27  H18  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
 3UP  C7   C1   C6   123.25  3.000
 3UP  C7   C1   C2   117.97  3.000
 3UP  C6   C1   C2   118.75  3.000
 3UP  H1   C2   C3   120.57  3.000
 3UP  H1   C2   C1   120.73  3.000
 3UP  C3   C2   C1   118.70  3.000
 3UP  N8   C3   N4   120.15  3.000
 3UP  N8   C3   C2   117.14  3.000
 3UP  N4   C3   C2   122.72  3.000
 3UP  C5   N4   C3   117.97  3.000
 3UP  H2   C5   C6   119.80  3.000
 3UP  H2   C5   N4   116.06  3.000
 3UP  C6   C5   N4   124.14  3.000
 3UP  H3   C6   C5   119.15  3.000
 3UP  H3   C6   C1   123.13  3.000
 3UP  C5   C6   C1   117.70  3.000
 3UP  O10  C7   N9   123.80  3.000
 3UP  N9   C7   C1   114.85  3.000
 3UP  O10  C7   C1   121.35  3.000
 3UP  H4   N8   C11  115.67  3.000
 3UP  H4   N8   C3   114.56  3.000
 3UP  C11  N8   C3   129.77  3.000
 3UP  H5   N9   C16  116.38  3.000
 3UP  H5   N9   C7   118.47  3.000
 3UP  C16  N9   C7   124.95  3.000
 3UP  O13  C11  C12  122.76  3.000
 3UP  O13  C11  N8   124.43  3.000
 3UP  C12  C11  N8   112.81  3.000
 3UP  H6   C12  C15  116.50  3.000
 3UP  H6   C12  C14  116.55  3.000
 3UP  C15  C12  C14   58.91  3.000
 3UP  H6   C12  C11  116.78  3.000
 3UP  C15  C12  C11  117.81  3.000
 3UP  C14  C12  C11  117.74  3.000
 3UP  H8   C14  H7   114.90  3.000
 3UP  H8   C14  C15  118.69  3.000
 3UP  H7   C14  C15  118.27  3.000
 3UP  H8   C14  C12  116.50  3.000
 3UP  H7   C14  C12  117.19  3.000
 3UP  C15  C14  C12   60.53  3.000
 3UP  H10  C15  H9   114.87  3.000
 3UP  H10  C15  C14  118.34  3.000
 3UP  H9   C15  C14  118.65  3.000
 3UP  H10  C15  C12  117.29  3.000
 3UP  H9   C15  C12  116.39  3.000
 3UP  C14  C15  C12   60.56  3.000
 3UP  C21  C16  C17  118.90  3.000
 3UP  C21  C16  N9   119.91  3.000
 3UP  C17  C16  N9   121.13  3.000
 3UP  H11  C17  N18  116.64  3.000
 3UP  H11  C17  C16  120.07  3.000
 3UP  N18  C17  C16  123.28  3.000
 3UP  C19  N18  C17  118.01  3.000
 3UP  H12  C19  C20  120.13  3.000
 3UP  H12  C19  N18  116.77  3.000
 3UP  C20  C19  N18  123.10  3.000
 3UP  H13  C20  C21  120.35  3.000
 3UP  H13  C20  C19  120.11  3.000
 3UP  C21  C20  C19  119.52  3.000
 3UP  C22  C21  C20  120.66  3.000
 3UP  C20  C21  C16  117.16  3.000
 3UP  C22  C21  C16  122.18  3.000
 3UP  C27  C22  C23  119.10  3.000
 3UP  C27  C22  C21  120.08  3.000
 3UP  C23  C22  C21  120.81  3.000
 3UP  H14  C23  C24  119.51  3.000
 3UP  H14  C23  C22  120.08  3.000
 3UP  C24  C23  C22  120.39  3.000
 3UP  H15  C24  C25  120.15  3.000
 3UP  H15  C24  C23  119.69  3.000
 3UP  C25  C24  C23  120.16  3.000
 3UP  H16  C25  C26  120.14  3.000
 3UP  H16  C25  C24  120.09  3.000
 3UP  C26  C25  C24  119.77  3.000
 3UP  H17  C26  C27  119.76  3.000
 3UP  H17  C26  C25  120.10  3.000
 3UP  C27  C26  C25  120.14  3.000
 3UP  H18  C27  C26  119.82  3.000
 3UP  H18  C27  C22  119.74  3.000
 3UP  C26  C27  C22  120.43  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
 3UP  CONST_01  N4   C5   C6   C1      0.00   0.0  0
 3UP  CONST_02  N4   C3   C2   C1      0.00   0.0  0
 3UP  CONST_03  C5   N4   C3   C2      0.00   0.0  0
 3UP  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 3UP  CONST_05  C6   C5   N4   C3      0.00   0.0  0
 3UP  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 3UP  CONST_07  C19  N18  C17  C16     0.00   0.0  0
 3UP  CONST_10  C19  C20  C21  C16     0.00   0.0  0
 3UP  CONST_11  C22  C21  C16  C17   180.00   0.0  0
 3UP  CONST_12  C20  C21  C16  C17     0.00   0.0  0
 3UP  CONST_13  C20  C19  N18  C17     0.00   0.0  0
 3UP  CONST_14  C21  C16  C17  N18     0.00   0.0  0
 3UP  CONST_15  C21  C20  C19  N18     0.00   0.0  0
 3UP  CONST_16  C22  C21  C20  C19   180.00   0.0  0
 3UP  CONST_19  C24  C23  C22  C21   180.00   0.0  0
 3UP  CONST_20  C26  C27  C22  C21   180.00   0.0  0
 3UP  CONST_21  C25  C24  C23  C22     0.00   0.0  0
 3UP  CONST_22  C25  C26  C27  C22     0.00   0.0  0
 3UP  CONST_23  C26  C25  C24  C23     0.00   0.0  0
 3UP  CONST_24  C26  C27  C22  C23     0.00   0.0  0
 3UP  CONST_25  C27  C22  C23  C24     0.00   0.0  0
 3UP  CONST_26  C27  C26  C25  C24     0.00   0.0  0
 3UP  CONST_27  N8   C3   C2   C1    180.00   0.0  0
 3UP  CONST_28  C7   C1   C2   C3    180.00   0.0  0
 3UP  CONST_29  N8   C3   N4   C5    180.00   0.0  0
 3UP  CONST_30  C7   C1   C6   C5    180.00   0.0  0
 3UP  CONST_31  N18  C17  C16  N9    180.00   0.0  0
 3UP  CONST_32  C22  C21  C16  N9      0.00   0.0  0
 3UP  CONST_33  C20  C21  C16  N9    180.00   0.0  0
 3UP  CONST_34  H2   C5   C6   C1    180.00   0.0  0
 3UP  CONST_35  H3   C6   C1   C2    180.00   0.0  0
 3UP  CONST_36  H1   C2   C3   N4    180.00   0.0  0
 3UP  CONST_37  H13  C20  C21  C16   180.00   0.0  0
 3UP  CONST_38  H12  C19  N18  C17   180.00   0.0  0
 3UP  CONST_39  H11  C17  N18  C19   180.00   0.0  0
 3UP  CONST_40  H14  C23  C22  C21     0.00   0.0  0
 3UP  CONST_41  H18  C27  C22  C21     0.00   0.0  0
 3UP  CONST_42  H15  C24  C23  C22   180.00   0.0  0
 3UP  CONST_43  H17  C26  C27  C22   180.00   0.0  0
 3UP  CONST_44  H16  C25  C24  C23   180.00   0.0  0
 3UP  CONST_45  C16  N9   C7   C1    180.00   0.0  0
 3UP  CONST_46  C12  C11  N8   C3    180.00   0.0  0
 3UP  CONST_47  C11  N8   C3   C2    180.00   0.0  0
 3UP  CONST_48  C11  N8   C3   N4      0.00   0.0  0
 3UP  CONST_51  H4   N8   C3   C2      0.00   0.0  0
 3UP  CONST_53  O13  C11  N8   C3      0.00   0.0  0
 3UP  CONST_54  C16  N9   C7   O10     0.00   0.0  0
 3UP  Var_01    C15  C14  C12  C11  -107.36  30.0  1
 3UP  Var_02    H9   C15  C14  C12  -105.86  30.0  1
 3UP  Var_03    O10  C7   C1   C2     27.89  30.0  2
 3UP  Var_04    C14  C12  C11  N8   -145.65  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
 3UP  chir_01  C12  C11  C14  C15  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
 3UP  plan-1  C1   0.020
 3UP  plan-1  C2   0.020
 3UP  plan-1  C3   0.020
 3UP  plan-1  N4   0.020
 3UP  plan-1  C5   0.020
 3UP  plan-1  C6   0.020
 3UP  plan-1  C7   0.020
 3UP  plan-1  N8   0.020
 3UP  plan-1  H1   0.020
 3UP  plan-1  H2   0.020
 3UP  plan-1  H3   0.020
 3UP  plan-2  N9   0.020
 3UP  plan-2  C16  0.020
 3UP  plan-2  C17  0.020
 3UP  plan-2  N18  0.020
 3UP  plan-2  C19  0.020
 3UP  plan-2  C20  0.020
 3UP  plan-2  C21  0.020
 3UP  plan-2  C22  0.020
 3UP  plan-2  H11  0.020
 3UP  plan-2  H12  0.020
 3UP  plan-2  H13  0.020
 3UP  plan-3  C21  0.020
 3UP  plan-3  C22  0.020
 3UP  plan-3  C23  0.020
 3UP  plan-3  C24  0.020
 3UP  plan-3  C25  0.020
 3UP  plan-3  C26  0.020
 3UP  plan-3  C27  0.020
 3UP  plan-3  H14  0.020
 3UP  plan-3  H15  0.020
 3UP  plan-3  H16  0.020
 3UP  plan-3  H17  0.020
 3UP  plan-3  H18  0.020
 3UP  plan-4  C3   0.020
 3UP  plan-4  N8   0.020
 3UP  plan-4  C11  0.020
 3UP  plan-4  C12  0.020
 3UP  plan-4  O13  0.020
 3UP  plan-4  H4   0.020
 3UP  plan-5  C1   0.020
 3UP  plan-5  C7   0.020
 3UP  plan-5  N9   0.020
 3UP  plan-5  O10  0.020
 3UP  plan-5  C16  0.020
 3UP  plan-5  H5   0.020

