# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:58:51 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-chloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1C(=O)Nc2ccnc(NC(=O)C3CC3)c2
#
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
 2TT  2TT  2-chloro-N-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}benzamide  ligand  36  22  .  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_2TT
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
 2TT  C7   C   CR6   0   0.010  -3.4386   0.5105  -0.0556
 2TT  C2   C   CR6   0  -0.081  -4.4327   0.5679  -1.0297
 2TT  C4   C   CR16  0  -0.258  -5.5347   2.3361   0.1541
 2TT  C6   C   CR16  0  -0.276  -3.5104   1.3888   1.0226
 2TT  CL1  CL  CL    0  -0.112  -4.3654  -0.4605  -2.4193
 2TT  C3   C   CR16  0  -0.197  -5.4723   1.4788  -0.9350
 2TT  C5   C   CR16  0  -0.232  -4.5551   2.2932   1.1346
 2TT  C8   C   C     0   0.509  -2.3464  -0.5114  -0.1101
 2TT  O9   O   O     0  -0.427  -2.5813  -1.6968  -0.2054
 2TT  N10  N   NH1   0  -0.739  -1.1007   0.0299  -0.0250
 2TT  C11  C   CR6   0   0.499   0.1289  -0.6146  -0.0071
 2TT  C12  C   CR16  0  -0.391   0.3075  -2.0012  -0.0127
 2TT  C13  C   CR16  0  -0.067   1.6057  -2.4732   0.0044
 2TT  N14  N   N     0  -0.432   2.6987  -1.7193   0.0312
 2TT  C15  C   CR6   0   0.538   2.5201  -0.4085   0.0316
 2TT  N16  N   NH1   0  -0.749   3.6248   0.4352   0.0812
 2TT  C17  C   C     0   0.586   4.9347   0.1582  -0.2025
 2TT  O18  O   O     0  -0.455   5.3429  -0.9259  -0.5667
 2TT  C19  C   CH1   0  -0.442   5.8291   1.3332  -0.0262
 2TT  C20  C   CH2   0  -0.464   7.2392   1.0722   0.4383
 2TT  C21  C   CH2   0  -0.464   6.9973   1.4734  -0.9687
 2TT  C22  C   CR16  0  -0.519   1.2620   0.1897   0.0123
 2TT  H1   H   HCR6  0   0.277  -6.3525   3.0401   0.2284
 2TT  H2   H   HCR6  0   0.282  -2.7518   1.3512   1.7944
 2TT  H3   H   HCR6  0   0.288  -6.2273   1.5200  -1.7079
 2TT  H4   H   HCR6  0   0.273  -4.6017   2.9589   1.9853
 2TT  H5   H   HNH1  0   0.431  -1.0537   1.0388  -0.0227
 2TT  H6   H   HCR6  0   0.292  -0.5132  -2.6964  -0.0290
 2TT  H7   H   HCR6  0   0.267   1.7712  -3.5448   0.0027
 2TT  H8   H   HNH1  0   0.421   3.4130   1.4012   0.2772
 2TT  H9   H   HCH1  0   0.284   5.3694   2.2532   0.3157
 2TT  H10  H   HCH2  0   0.266   7.6670   1.7963   1.1185
 2TT  H11  H   HCH2  0   0.260   7.5099   0.0439   0.6382
 2TT  H12  H   HCH2  0   0.260   7.1035   0.7237  -1.7419
 2TT  H13  H   HCH2  0   0.266   7.2551   2.4792  -1.2716
 2TT  H14  H   HCR6  0   0.294   1.1703   1.2694   0.0077

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
 2TT  C13  N14  aromatic  1.328  0.020  1.328
 2TT  C13  C12  aromatic  1.382  0.020  1.382
 2TT  N14  C15  aromatic  1.323  0.020  1.323
 2TT  C12  C11  aromatic  1.398  0.020  1.398
 2TT  C15  N16  single    1.391  0.020  1.391
 2TT  C15  C22  aromatic  1.393  0.020  1.393
 2TT  C11  C22  aromatic  1.390  0.020  1.390
 2TT  C11  N10  single    1.388  0.020  1.388
 2TT  N16  C17  single    1.369  0.020  1.369
 2TT  O9   C8   double    1.212  0.020  1.212
 2TT  N10  C8   single    1.361  0.020  1.361
 2TT  C8   C7   single    1.497  0.020  1.497
 2TT  C17  C19  single    1.487  0.020  1.487
 2TT  C17  O18  double    1.214  0.020  1.214
 2TT  C19  C20  single    1.507  0.020  1.507
 2TT  C19  C21  single    1.508  0.020  1.508
 2TT  CL1  C2   single    1.730  0.020  1.730
 2TT  C7   C2   aromatic  1.393  0.020  1.393
 2TT  C7   C6   aromatic  1.393  0.020  1.393
 2TT  C2   C3   aromatic  1.385  0.020  1.385
 2TT  C20  C21  single    1.483  0.020  1.483
 2TT  C6   C5   aromatic  1.386  0.020  1.386
 2TT  C3   C4   aromatic  1.387  0.020  1.387
 2TT  C5   C4   aromatic  1.387  0.020  1.387
 2TT  C4   H1   single    0.930  0.020  1.080
 2TT  C6   H2   single    0.930  0.020  1.080
 2TT  C3   H3   single    0.930  0.020  1.080
 2TT  C5   H4   single    0.930  0.020  1.080
 2TT  N10  H5   single    0.860  0.020  1.020
 2TT  C12  H6   single    0.930  0.020  1.080
 2TT  C13  H7   single    0.930  0.020  1.080
 2TT  N16  H8   single    0.860  0.020  1.020
 2TT  C19  H9   single    0.970  0.020  1.090
 2TT  C20  H10  single    0.970  0.020  1.090
 2TT  C20  H11  single    0.970  0.020  1.090
 2TT  C21  H12  single    0.970  0.020  1.090
 2TT  C21  H13  single    0.970  0.020  1.090
 2TT  C22  H14  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
 2TT  C8   C7   C6   119.76  3.000
 2TT  C6   C7   C2   118.60  3.000
 2TT  C8   C7   C2   121.56  3.000
 2TT  C3   C2   CL1  118.35  3.000
 2TT  C3   C2   C7   120.98  3.000
 2TT  CL1  C2   C7   120.63  3.000
 2TT  H1   C4   C5   120.38  3.000
 2TT  H1   C4   C3   119.35  3.000
 2TT  C5   C4   C3   120.27  3.000
 2TT  H2   C6   C5   119.53  3.000
 2TT  H2   C6   C7   119.60  3.000
 2TT  C5   C6   C7   120.85  3.000
 2TT  H3   C3   C4   120.41  3.000
 2TT  H3   C3   C2   120.01  3.000
 2TT  C4   C3   C2   119.58  3.000
 2TT  H4   C5   C6   119.85  3.000
 2TT  H4   C5   C4   120.45  3.000
 2TT  C6   C5   C4   119.70  3.000
 2TT  N10  C8   O9   124.84  3.000
 2TT  N10  C8   C7   113.21  3.000
 2TT  O9   C8   C7   121.95  3.000
 2TT  H5   N10  C11  115.00  3.000
 2TT  H5   N10  C8   116.11  3.000
 2TT  C11  N10  C8   128.81  3.000
 2TT  C22  C11  C12  118.03  3.000
 2TT  C22  C11  N10  116.97  3.000
 2TT  C12  C11  N10  125.00  3.000
 2TT  H6   C12  C13  119.76  3.000
 2TT  H6   C12  C11  122.93  3.000
 2TT  C13  C12  C11  117.31  3.000
 2TT  H7   C13  N14  115.82  3.000
 2TT  H7   C13  C12  118.75  3.000
 2TT  N14  C13  C12  125.43  3.000
 2TT  C15  N14  C13  116.83  3.000
 2TT  C22  C15  N16  117.21  3.000
 2TT  C22  C15  N14  123.18  3.000
 2TT  N16  C15  N14  119.59  3.000
 2TT  H8   N16  C17  115.80  3.000
 2TT  H8   N16  C15  114.91  3.000
 2TT  C17  N16  C15  129.06  3.000
 2TT  C19  C17  O18  122.60  3.000
 2TT  O18  C17  N16  124.37  3.000
 2TT  C19  C17  N16  113.03  3.000
 2TT  H9   C19  C21  116.55  3.000
 2TT  H9   C19  C20  116.52  3.000
 2TT  C21  C19  C20   58.93  3.000
 2TT  H9   C19  C17  116.94  3.000
 2TT  C21  C19  C17  117.73  3.000
 2TT  C20  C19  C17  117.53  3.000
 2TT  H11  C20  H10  114.91  3.000
 2TT  H11  C20  C21  118.24  3.000
 2TT  H10  C20  C21  118.69  3.000
 2TT  H11  C20  C19  117.10  3.000
 2TT  H10  C20  C19  116.60  3.000
 2TT  C21  C20  C19   60.54  3.000
 2TT  H13  C21  H12  114.88  3.000
 2TT  H13  C21  C20  118.58  3.000
 2TT  H12  C21  C20  118.33  3.000
 2TT  H13  C21  C19  116.50  3.000
 2TT  H12  C21  C19  117.28  3.000
 2TT  C20  C21  C19   60.53  3.000
 2TT  H14  C22  C15  120.28  3.000
 2TT  H14  C22  C11  120.51  3.000
 2TT  C15  C22  C11  119.21  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
 2TT  CONST_01  C4   C3   C2   C7      0.00   0.0  0
 2TT  CONST_02  C4   C5   C6   C7      0.00   0.0  0
 2TT  CONST_03  C5   C6   C7   C2      0.00   0.0  0
 2TT  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2TT  CONST_05  C3   C2   C7   C6      0.00   0.0  0
 2TT  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 2TT  CONST_07  N14  C13  C12  C11     0.00   0.0  0
 2TT  CONST_08  N14  C15  C22  C11     0.00   0.0  0
 2TT  CONST_09  C15  N14  C13  C12     0.00   0.0  0
 2TT  CONST_10  C15  C22  C11  C12     0.00   0.0  0
 2TT  CONST_11  C22  C15  N14  C13     0.00   0.0  0
 2TT  CONST_12  C22  C11  C12  C13     0.00   0.0  0
 2TT  CONST_13  CL1  C2   C3   C4    180.00   0.0  0
 2TT  CONST_14  CL1  C2   C7   C6    180.00   0.0  0
 2TT  CONST_15  C8   C7   C2   C3    180.00   0.0  0
 2TT  CONST_16  C8   C7   C6   C5    180.00   0.0  0
 2TT  CONST_17  C13  C12  C11  N10   180.00   0.0  0
 2TT  CONST_18  C15  C22  C11  N10   180.00   0.0  0
 2TT  CONST_19  N16  C15  C22  C11   180.00   0.0  0
 2TT  CONST_20  N16  C15  N14  C13   180.00   0.0  0
 2TT  CONST_21  H3   C3   C2   C7    180.00   0.0  0
 2TT  CONST_22  H4   C5   C6   C7    180.00   0.0  0
 2TT  CONST_23  H2   C6   C7   C2    180.00   0.0  0
 2TT  CONST_24  H1   C4   C3   C2    180.00   0.0  0
 2TT  CONST_25  H7   C13  C12  C11   180.00   0.0  0
 2TT  CONST_26  H14  C22  C11  C12   180.00   0.0  0
 2TT  CONST_27  H6   C12  C13  N14   180.00   0.0  0
 2TT  CONST_28  C11  N10  C8   C7    180.00   0.0  0
 2TT  CONST_29  C19  C17  N16  C15   180.00   0.0  0
 2TT  CONST_30  C12  C11  N10  C8      0.00   0.0  0
 2TT  CONST_31  C22  C11  N10  C8    180.00   0.0  0
 2TT  CONST_34  H5   N10  C11  C12   180.00   0.0  0
 2TT  CONST_35  H8   N16  C15  N14   180.00   0.0  0
 2TT  CONST_36  C11  N10  C8   O9      0.00   0.0  0
 2TT  CONST_37  O18  C17  N16  C15     0.00   0.0  0
 2TT  Var_01    C21  C20  C19  C17   107.37  30.0  1
 2TT  Var_02    H12  C21  C20  C19  -107.06  30.0  1
 2TT  Var_03    O9   C8   C7   C2    -53.52  30.0  2
 2TT  Var_04    C20  C19  C17  N16   147.16  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
 2TT  chir_01  C19  C17  C20  C21  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
 2TT  plan-1  C7   0.020
 2TT  plan-1  C2   0.020
 2TT  plan-1  C4   0.020
 2TT  plan-1  C6   0.020
 2TT  plan-1  CL1  0.020
 2TT  plan-1  C3   0.020
 2TT  plan-1  C5   0.020
 2TT  plan-1  C8   0.020
 2TT  plan-1  H1   0.020
 2TT  plan-1  H2   0.020
 2TT  plan-1  H3   0.020
 2TT  plan-1  H4   0.020
 2TT  plan-2  N10  0.020
 2TT  plan-2  C11  0.020
 2TT  plan-2  C12  0.020
 2TT  plan-2  C13  0.020
 2TT  plan-2  N14  0.020
 2TT  plan-2  C15  0.020
 2TT  plan-2  N16  0.020
 2TT  plan-2  C22  0.020
 2TT  plan-2  H6   0.020
 2TT  plan-2  H7   0.020
 2TT  plan-2  H14  0.020
 2TT  plan-3  C15  0.020
 2TT  plan-3  N16  0.020
 2TT  plan-3  C17  0.020
 2TT  plan-3  O18  0.020
 2TT  plan-3  C19  0.020
 2TT  plan-3  H8   0.020
 2TT  plan-4  C7   0.020
 2TT  plan-4  C8   0.020
 2TT  plan-4  O9   0.020
 2TT  plan-4  N10  0.020
 2TT  plan-4  C11  0.020
 2TT  plan-4  H5   0.020

