# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 06:57:50 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{N}-(4-pyrimidin-2-ylphenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccc(cc1)c2ncccn2
#
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
 9Z2  9Z2  ~{N}-(4-pyrimidin-2-ylphenyl)propanamide  ligand  30  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9Z2
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
 9Z2  N1   N  N     0  -0.426  -3.5341  -1.0771   0.0033
 9Z2  C2   C  CH3   0  -0.659   6.3754   0.6502   0.0651
 9Z2  C4   C  CR16  0  -0.301   0.8637   0.9154  -0.0402
 9Z2  C5   C  CR16  0  -0.271  -0.5165   1.0250  -0.0624
 9Z2  C6   C  CR16  0  -0.335   0.6336  -1.4749   0.0883
 9Z2  O    O  O     0  -0.461   3.7102   1.5205  -0.0894
 9Z2  C    C  C     0   0.552   3.8635   0.3184   0.0065
 9Z2  C1   C  CH2   0  -0.588   5.2258  -0.3402   0.0611
 9Z2  C3   C  CR6   0   0.376   1.4602  -0.3466   0.0369
 9Z2  C7   C  CR16  0  -0.268  -0.7397  -1.3503   0.0643
 9Z2  C8   C  CR6   0  -0.024  -1.3445  -0.0943  -0.0110
 9Z2  C9   C  CR6   0   0.394  -2.8118   0.0408  -0.0321
 9Z2  N2   N  N     0  -0.426  -3.3197   1.2706  -0.0833
 9Z2  C12  C  CR16  0  -0.013  -4.6389   1.3845  -0.0982
 9Z2  C11  C  CR16  0  -0.360  -5.4775   0.2832  -0.0633
 9Z2  C10  C  CR16  0  -0.012  -4.8522  -0.9513  -0.0125
 9Z2  H1   H  HCH3  0   0.231   6.3778   1.2680  -0.8318
 9Z2  H2   H  HCH3  0   0.230   6.3345   1.3103   0.9306
 9Z2  H3   H  HCH3  0   0.237   7.3235   0.1151   0.1008
 9Z2  H4   H  HCR6  0   0.282   1.4634   1.8092  -0.0817
 9Z2  H5   H  HCR6  0   0.255  -0.9562   2.0115  -0.1213
 9Z2  H6   H  HCR6  0   0.271   1.0761  -2.4625   0.1491
 9Z2  H7   H  HCH2  0   0.275   5.3105  -1.0191  -0.7929
 9Z2  H8   H  HCH2  0   0.272   5.2679  -0.9793   0.9478
 9Z2  H9   H  HNH1  0   0.418   3.0981  -1.5432   0.1502
 9Z2  H10  H  HCR6  0   0.258  -1.3527  -2.2400   0.1056
 9Z2  H11  H  HCR6  0   0.276  -5.0408   2.3908  -0.1386
 9Z2  H12  H  HCR6  0   0.285  -6.5528   0.3808  -0.0744
 9Z2  H13  H  HCR6  0   0.276  -5.4306  -1.8681   0.0167
 9Z2  N    N  NH1   0  -0.744   2.8325  -0.5724   0.0707

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
 9Z2  O    C    double    1.216  0.020  1.216
 9Z2  C2   C1   single    1.517  0.020  1.517
 9Z2  C1   C    single    1.514  0.020  1.514
 9Z2  C    N    single    1.364  0.020  1.364
 9Z2  C4   C5   aromatic  1.385  0.020  1.385
 9Z2  C4   C3   aromatic  1.398  0.020  1.398
 9Z2  C5   C8   aromatic  1.393  0.020  1.393
 9Z2  N    C3   single    1.391  0.020  1.391
 9Z2  N1   C10  aromatic  1.324  0.020  1.324
 9Z2  N1   C9   aromatic  1.331  0.020  1.331
 9Z2  C3   C6   aromatic  1.400  0.020  1.400
 9Z2  C10  C11  aromatic  1.385  0.020  1.385
 9Z2  C8   C9   single    1.474  0.020  1.474
 9Z2  C8   C7   aromatic  1.396  0.020  1.396
 9Z2  C9   N2   aromatic  1.332  0.020  1.332
 9Z2  C6   C7   aromatic  1.379  0.020  1.379
 9Z2  C11  C12  aromatic  1.385  0.020  1.385
 9Z2  N2   C12  aromatic  1.324  0.020  1.324
 9Z2  C2   H1   single    0.970  0.020  1.090
 9Z2  C2   H2   single    0.970  0.020  1.090
 9Z2  C2   H3   single    0.970  0.020  1.090
 9Z2  C4   H4   single    0.930  0.020  1.080
 9Z2  C5   H5   single    0.930  0.020  1.080
 9Z2  C6   H6   single    0.930  0.020  1.080
 9Z2  C1   H7   single    0.970  0.020  1.090
 9Z2  C1   H8   single    0.970  0.020  1.090
 9Z2  N    H9   single    0.860  0.020  1.020
 9Z2  C7   H10  single    0.930  0.020  1.080
 9Z2  C12  H11  single    0.930  0.020  1.080
 9Z2  C11  H12  single    0.930  0.020  1.080
 9Z2  C10  H13  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
 9Z2  C10  N1   C9   117.39  3.000
 9Z2  H3   C2   H2   107.72  3.000
 9Z2  H3   C2   H1   107.68  3.000
 9Z2  H2   C2   H1   108.10  3.000
 9Z2  H3   C2   C1   109.81  3.000
 9Z2  H2   C2   C1   111.67  3.000
 9Z2  H1   C2   C1   111.70  3.000
 9Z2  H4   C4   C3   120.91  3.000
 9Z2  H4   C4   C5   119.24  3.000
 9Z2  C3   C4   C5   119.85  3.000
 9Z2  H5   C5   C8   119.54  3.000
 9Z2  H5   C5   C4   118.58  3.000
 9Z2  C8   C5   C4   121.88  3.000
 9Z2  H6   C6   C7   119.33  3.000
 9Z2  H6   C6   C3   119.70  3.000
 9Z2  C7   C6   C3   120.97  3.000
 9Z2  N    C    C1   113.22  3.000
 9Z2  N    C    O    123.66  3.000
 9Z2  C1   C    O    123.12  3.000
 9Z2  H8   C1   H7   105.49  3.000
 9Z2  H8   C1   C    108.55  3.000
 9Z2  H7   C1   C    108.14  3.000
 9Z2  H8   C1   C2   110.49  3.000
 9Z2  H7   C1   C2   110.39  3.000
 9Z2  C    C1   C2   113.44  3.000
 9Z2  N    C3   C6   116.80  3.000
 9Z2  C6   C3   C4   118.54  3.000
 9Z2  N    C3   C4   124.66  3.000
 9Z2  H10  C7   C8   119.79  3.000
 9Z2  H10  C7   C6   119.31  3.000
 9Z2  C8   C7   C6   120.90  3.000
 9Z2  C9   C8   C7   120.97  3.000
 9Z2  C7   C8   C5   117.86  3.000
 9Z2  C9   C8   C5   121.17  3.000
 9Z2  N2   C9   C8   117.71  3.000
 9Z2  N2   C9   N1   124.72  3.000
 9Z2  C8   C9   N1   117.57  3.000
 9Z2  C12  N2   C9   117.38  3.000
 9Z2  H11  C12  C11  120.96  3.000
 9Z2  H11  C12  N2   116.72  3.000
 9Z2  C11  C12  N2   122.32  3.000
 9Z2  H12  C11  C10  122.05  3.000
 9Z2  H12  C11  C12  122.07  3.000
 9Z2  C10  C11  C12  115.88  3.000
 9Z2  H13  C10  C11  120.92  3.000
 9Z2  H13  C10  N1   116.76  3.000
 9Z2  C11  C10  N1   122.32  3.000
 9Z2  H9   N    C3   114.68  3.000
 9Z2  H9   N    C    115.64  3.000
 9Z2  C3   N    C    129.68  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
 9Z2  CONST_01  C12  C11  C10  N1    0.00   0.0  0
 9Z2  CONST_02  C5   C8   C9   N1  180.00   0.0  0
 9Z2  CONST_03  C7   C8   C9   N1    0.00   0.0  0
 9Z2  CONST_04  C12  N2   C9   N1    0.00   0.0  0
 9Z2  CONST_05  C9   C8   C5   C4  180.00   0.0  0
 9Z2  CONST_06  C7   C8   C5   C4    0.00   0.0  0
 9Z2  CONST_07  C7   C6   C3   C4    0.00   0.0  0
 9Z2  CONST_08  C6   C3   C4   C5    0.00   0.0  0
 9Z2  CONST_09  N2   C9   C8   C5    0.00   0.0  0
 9Z2  CONST_10  C6   C7   C8   C5    0.00   0.0  0
 9Z2  CONST_11  C9   C8   C7   C6  180.00   0.0  0
 9Z2  CONST_12  C8   C5   C4   C3    0.00   0.0  0
 9Z2  CONST_13  C8   C7   C6   C3    0.00   0.0  0
 9Z2  CONST_14  N2   C9   C8   C7  180.00   0.0  0
 9Z2  CONST_15  C10  N1   C9   C8  180.00   0.0  0
 9Z2  CONST_16  C12  N2   C9   C8  180.00   0.0  0
 9Z2  CONST_17  C11  C10  N1   C9    0.00   0.0  0
 9Z2  CONST_18  C11  C12  N2   C9    0.00   0.0  0
 9Z2  CONST_19  C10  N1   C9   N2    0.00   0.0  0
 9Z2  CONST_20  C10  C11  C12  N2    0.00   0.0  0
 9Z2  CONST_21  N    C3   C4   C5  180.00   0.0  0
 9Z2  CONST_22  C7   C6   C3   N   180.00   0.0  0
 9Z2  CONST_23  H12  C11  C10  N1  180.00   0.0  0
 9Z2  CONST_24  H6   C6   C3   C4  180.00   0.0  0
 9Z2  CONST_25  H10  C7   C8   C5  180.00   0.0  0
 9Z2  CONST_26  H4   C4   C3   C6  180.00   0.0  0
 9Z2  CONST_27  H5   C5   C4   C3  180.00   0.0  0
 9Z2  CONST_28  H13  C10  N1   C9  180.00   0.0  0
 9Z2  CONST_29  H11  C12  N2   C9  180.00   0.0  0
 9Z2  CONST_30  C    N    C3   C4    0.00   0.0  0
 9Z2  CONST_31  C    N    C3   C6  180.00   0.0  0
 9Z2  CONST_32  H9   N    C3   C4  180.00   0.0  0
 9Z2  CONST_33  C3   N    C    O     0.00   0.0  0
 9Z2  CONST_34  C3   N    C    C1  180.00   0.0  0
 9Z2  Var_01    O    C    C1   C2    3.32  30.0  3
 9Z2  Var_02    H1   C2   C1   C   -60.36  30.0  3

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
 9Z2  plan-1  N1   0.020
 9Z2  plan-1  C8   0.020
 9Z2  plan-1  C9   0.020
 9Z2  plan-1  N2   0.020
 9Z2  plan-1  C12  0.020
 9Z2  plan-1  C11  0.020
 9Z2  plan-1  C10  0.020
 9Z2  plan-1  H11  0.020
 9Z2  plan-1  H12  0.020
 9Z2  plan-1  H13  0.020
 9Z2  plan-2  C4   0.020
 9Z2  plan-2  C5   0.020
 9Z2  plan-2  C6   0.020
 9Z2  plan-2  C3   0.020
 9Z2  plan-2  C7   0.020
 9Z2  plan-2  C8   0.020
 9Z2  plan-2  C9   0.020
 9Z2  plan-2  H4   0.020
 9Z2  plan-2  H5   0.020
 9Z2  plan-2  H6   0.020
 9Z2  plan-2  H10  0.020
 9Z2  plan-2  N    0.020
 9Z2  plan-3  O    0.020
 9Z2  plan-3  C    0.020
 9Z2  plan-3  C1   0.020
 9Z2  plan-3  C3   0.020
 9Z2  plan-3  H9   0.020
 9Z2  plan-3  N    0.020

