# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 08:28:14 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-{[(2,6-difluorophenyl)carbonyl]amino}-N-[(3S)-piperidin-3-yl]-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(F)c1C(=O)Nc2c[nH]nc2C(=O)N[C@H]3CCCNC3
#
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
 LZD  LZD  4-{[(2,6-difluorophenyl)carbonyl]amino}-N-[(3S)-piperidin-3-yl]-1H-pyrazole-3-carboxamide  ligand  42  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LZD
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
 LZD  C2    C  CH2   0  -0.314  33.2182   9.4341  65.4517
 LZD  C3    C  CH2   0  -0.450  32.2040   9.4723  66.5910
 LZD  C4    C  CH2   0  -0.453  31.2804   8.2589  66.5364
 LZD  C5    C  CH1   0  -0.073  30.6424   8.1368  65.1570
 LZD  N6    N  NH1   0  -0.654  29.8436   6.9303  65.0802
 LZD  C7    C  C     0   0.564  28.7754   6.7896  64.2890
 LZD  O8    O  O     0  -0.508  28.3058   7.6923  63.5966
 LZD  C9    C  CR5   0   0.060  28.1514   5.4531  64.2826
 LZD  N10   N  N     0  -0.267  28.6110   4.4446  65.0082
 LZD  N11   N  NR15  0  -0.409  27.8193   3.4360  64.7379
 LZD  C12   C  CR15  0  -0.001  26.8407   3.7266  63.8570
 LZD  C13   C  CR5   0   0.127  27.0252   5.0541  63.5302
 LZD  N14   N  NH1   0  -0.710  26.3098   5.8792  62.6758
 LZD  C15   C  C     0   0.521  25.2464   5.4995  61.9445
 LZD  O16   O  O     0  -0.444  24.7738   4.3786  61.9604
 LZD  C17   C  CR6   0  -0.475  24.6600   6.5885  61.1007
 LZD  C18   C  CR6   0   0.584  25.3451   7.1665  60.0429
 LZD  F19   F  F     0  -0.296  26.5992   6.7622  59.8101
 LZD  C20   C  CR16  0  -0.416  24.7828   8.1215  59.2201
 LZD  C21   C  CR16  0  -0.223  23.4770   8.5172  59.4694
 LZD  C22   C  CR16  0  -0.419  22.7486   7.9686  60.5161
 LZD  C23   C  CR6   0   0.568  23.3541   7.0116  61.3028
 LZD  F24   F  F     0  -0.294  22.6750   6.4776  62.3218
 LZD  C25   C  CH2   0  -0.303  31.7236   8.1485  64.0673
 LZD  N26   N  NH1   0  -0.577  32.6140   9.2902  64.1368
 LZD  H2C1  H  HCH2  0   0.238  33.8327  10.3364  65.4568
 LZD  H2C2  H  HCH2  0   0.215  33.9008   8.5906  65.6039
 LZD  H3C1  H  HCH2  0   0.234  32.7195   9.5082  67.5537
 LZD  H3C2  H  HCH2  0   0.220  31.6108  10.3898  66.5181
 LZD  H26   H  HNH1  0   0.342  32.0995  10.1330  63.9104
 LZD  H4C1  H  HCH2  0   0.222  31.8594   7.3521  66.7488
 LZD  H4C2  H  HCH2  0   0.247  30.5057   8.3274  67.3033
 LZD  H5    H  HCH1  0   0.243  29.9766   8.9903  65.0024
 LZD  H6    H  HNH1  0   0.404  30.1714   6.1137  65.5753
 LZD  H251  H  HCH2  0   0.216  32.3222   7.2348  64.1634
 LZD  H252  H  HCH2  0   0.242  31.2556   8.1197  63.0810
 LZD  H12   H  HCR5  0   0.308  26.1199   2.9925  63.5481
 LZD  H20   H  HCR6  0   0.293  25.3522   8.5424  58.4031
 LZD  H21   H  HCR6  0   0.288  23.0188   9.2665  58.8391
 LZD  H22   H  HCR6  0   0.293  21.7322   8.2788  60.7174
 LZD  H11   H  HNR5  0   0.434  27.9722   2.5454  65.1853
 LZD  H14   H  HNH1  0   0.425  26.6322   6.8383  62.6450

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
 LZD  C2   C3    single    1.526  0.020  1.526
 LZD  C2   N26   single    1.454  0.020  1.454
 LZD  C3   C4    single    1.526  0.020  1.526
 LZD  C4   C5    single    1.525  0.020  1.525
 LZD  C5   N6    single    1.449  0.020  1.449
 LZD  C5   C25   single    1.535  0.020  1.535
 LZD  N6   C7    single    1.337  0.020  1.337
 LZD  C7   O8    double    1.231  0.020  1.231
 LZD  C7   C9    single    1.475  0.020  1.475
 LZD  C9   N10   aromatic  1.325  0.020  1.325
 LZD  C9   C13   aromatic  1.412  0.020  1.412
 LZD  N10  N11   aromatic  1.310  0.020  1.310
 LZD  N11  C12   aromatic  1.348  0.020  1.348
 LZD  C12  C13   aromatic  1.380  0.020  1.380
 LZD  C13  N14   single    1.387  0.020  1.387
 LZD  N14  C15   single    1.345  0.020  1.345
 LZD  C15  O16   double    1.217  0.020  1.217
 LZD  C15  C17   single    1.497  0.020  1.497
 LZD  C17  C18   aromatic  1.387  0.020  1.387
 LZD  C17  C23   aromatic  1.388  0.020  1.388
 LZD  C18  F19   single    1.338  0.020  1.338
 LZD  C18  C20   aromatic  1.380  0.020  1.380
 LZD  C20  C21   aromatic  1.387  0.020  1.387
 LZD  C21  C22   aromatic  1.388  0.020  1.388
 LZD  C22  C23   aromatic  1.379  0.020  1.379
 LZD  C23  F24   single    1.336  0.020  1.336
 LZD  C25  N26   single    1.450  0.020  1.450
 LZD  C2   H2C1  single    0.970  0.020  1.090
 LZD  C2   H2C2  single    0.970  0.020  1.090
 LZD  C3   H3C1  single    0.970  0.020  1.090
 LZD  C3   H3C2  single    0.970  0.020  1.090
 LZD  N26  H26   single    0.890  0.020  1.040
 LZD  C4   H4C1  single    0.970  0.020  1.090
 LZD  C4   H4C2  single    0.970  0.020  1.090
 LZD  C5   H5    single    0.970  0.020  1.090
 LZD  N6   H6    single    0.860  0.020  1.020
 LZD  C25  H251  single    0.970  0.020  1.090
 LZD  C25  H252  single    0.970  0.020  1.090
 LZD  C12  H12   single    0.930  0.020  1.080
 LZD  C20  H20   single    0.930  0.020  1.080
 LZD  C21  H21   single    0.930  0.020  1.080
 LZD  C22  H22   single    0.930  0.020  1.080
 LZD  N11  H11   single    0.860  0.020  1.020
 LZD  N14  H14   single    0.860  0.020  1.020

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
 LZD  H2C2  C2   H2C1  106.56  3.000
 LZD  H2C2  C2   N26   107.95  3.000
 LZD  H2C1  C2   N26   108.65  3.000
 LZD  H2C2  C2   C3    109.25  3.000
 LZD  H2C1  C2   C3    110.49  3.000
 LZD  N26   C2   C3    113.67  3.000
 LZD  H3C2  C3   H3C1  106.66  3.000
 LZD  H3C2  C3   C4    109.63  3.000
 LZD  H3C1  C3   C4    110.07  3.000
 LZD  H3C2  C3   C2    109.35  3.000
 LZD  H3C1  C3   C2    110.19  3.000
 LZD  C4    C3   C2    110.84  3.000
 LZD  H4C2  C4   H4C1  106.88  3.000
 LZD  H4C2  C4   C5    110.09  3.000
 LZD  H4C1  C4   C5    109.26  3.000
 LZD  H4C2  C4   C3    110.75  3.000
 LZD  H4C1  C4   C3    109.33  3.000
 LZD  C5    C4   C3    110.44  3.000
 LZD  H5    C5   C25   108.82  3.000
 LZD  H5    C5   N6    107.86  3.000
 LZD  C25   C5   N6    110.92  3.000
 LZD  H5    C5   C4    108.68  3.000
 LZD  C25   C5   C4    110.29  3.000
 LZD  N6    C5   C4    110.20  3.000
 LZD  H6    N6   C7    117.68  3.000
 LZD  H6    N6   C5    117.93  3.000
 LZD  C7    N6   C5    124.03  3.000
 LZD  C9    C7   O8    120.05  3.000
 LZD  C9    C7   N6    115.85  3.000
 LZD  O8    C7   N6    124.10  3.000
 LZD  C13   C9   N10   110.70  3.000
 LZD  C13   C9   C7    126.57  3.000
 LZD  N10   C9   C7    122.73  3.000
 LZD  N11   N10  C9    105.27  3.000
 LZD  H11   N11  C12   126.17  3.000
 LZD  H11   N11  N10   119.78  3.000
 LZD  C12   N11  N10   114.04  3.000
 LZD  H12   C12  C13   132.79  3.000
 LZD  H12   C12  N11   121.84  3.000
 LZD  C13   C12  N11   105.37  3.000
 LZD  N14   C13  C12   130.51  3.000
 LZD  N14   C13  C9    124.87  3.000
 LZD  C12   C13  C9    104.62  3.000
 LZD  H14   N14  C15   120.18  3.000
 LZD  H14   N14  C13   114.72  3.000
 LZD  C15   N14  C13   125.09  3.000
 LZD  C17   C15  O16   121.69  3.000
 LZD  C17   C15  N14   114.24  3.000
 LZD  O16   C15  N14   124.06  3.000
 LZD  C23   C17  C18   116.69  3.000
 LZD  C23   C17  C15   120.55  3.000
 LZD  C18   C17  C15   122.66  3.000
 LZD  C20   C18  F19   119.16  3.000
 LZD  C20   C18  C17   122.81  3.000
 LZD  F19   C18  C17   118.03  3.000
 LZD  H20   C20  C21   121.37  3.000
 LZD  H20   C20  C18   120.34  3.000
 LZD  C21   C20  C18   118.28  3.000
 LZD  H21   C21  C22   119.41  3.000
 LZD  H21   C21  C20   119.47  3.000
 LZD  C22   C21  C20   121.12  3.000
 LZD  H22   C22  C23   120.36  3.000
 LZD  H22   C22  C21   121.35  3.000
 LZD  C23   C22  C21   118.30  3.000
 LZD  F24   C23  C22   119.30  3.000
 LZD  F24   C23  C17   117.89  3.000
 LZD  C22   C23  C17   122.80  3.000
 LZD  H252  C25  H251  106.92  3.000
 LZD  H252  C25  N26   109.10  3.000
 LZD  H251  C25  N26   108.47  3.000
 LZD  H252  C25  C5    109.82  3.000
 LZD  H251  C25  C5    108.42  3.000
 LZD  N26   C25  C5    113.87  3.000
 LZD  H26   N26  C25   109.42  3.000
 LZD  H26   N26  C2    109.32  3.000
 LZD  C25   N26  C2    112.12  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
 LZD  CONST_01  C12  N11  N10  C9     0.00   0.0  0
 LZD  CONST_02  N11  C12  C13  C9     0.00   0.0  0
 LZD  CONST_03  C12  C13  C9   N10    0.00   0.0  0
 LZD  CONST_04  C13  C12  N11  N10    0.00   0.0  0
 LZD  CONST_05  C13  C9   N10  N11    0.00   0.0  0
 LZD  CONST_06  C21  C20  C18  C17    0.00   0.0  0
 LZD  CONST_07  C21  C22  C23  C17    0.00   0.0  0
 LZD  CONST_08  C22  C23  C17  C18    0.00   0.0  0
 LZD  CONST_09  C22  C21  C20  C18    0.00   0.0  0
 LZD  CONST_10  C23  C17  C18  C20    0.00   0.0  0
 LZD  CONST_11  C23  C22  C21  C20    0.00   0.0  0
 LZD  CONST_12  N11  N10  C9   C7   180.00   0.0  0
 LZD  CONST_13  C12  C13  C9   C7   180.00   0.0  0
 LZD  CONST_14  N14  C13  C9   N10  180.00   0.0  0
 LZD  CONST_15  N14  C13  C12  N11  180.00   0.0  0
 LZD  CONST_16  C20  C18  C17  C15  180.00   0.0  0
 LZD  CONST_17  C22  C23  C17  C15  180.00   0.0  0
 LZD  CONST_18  F24  C23  C17  C18  180.00   0.0  0
 LZD  CONST_19  C23  C17  C18  F19  180.00   0.0  0
 LZD  CONST_20  C21  C20  C18  F19  180.00   0.0  0
 LZD  CONST_21  F24  C23  C22  C21  180.00   0.0  0
 LZD  CONST_22  H11  N11  N10  C9   180.00   0.0  0
 LZD  CONST_23  H12  C12  C13  C9   180.00   0.0  0
 LZD  CONST_24  H20  C20  C18  C17  180.00   0.0  0
 LZD  CONST_25  H22  C22  C23  C17  180.00   0.0  0
 LZD  CONST_26  H21  C21  C20  C18  180.00   0.0  0
 LZD  CONST_27  C9   C7   N6   C5   180.00   0.0  0
 LZD  CONST_28  C17  C15  N14  C13  180.00   0.0  0
 LZD  CONST_29  C15  N14  C13  C9   180.00   0.0  0
 LZD  CONST_30  C15  N14  C13  C12    0.00   0.0  0
 LZD  CONST_31  H14  N14  C13  C9     0.00   0.0  0
 LZD  CONST_32  O8   C7   N6   C5     0.00   0.0  0
 LZD  CONST_33  O16  C15  N14  C13    0.00   0.0  0
 LZD  CONST_34  H6   N6   C7   C9     0.00   0.0  0
 LZD  Var_01    C5   C4   C3   C2   -53.28  30.0  1
 LZD  Var_02    C5   C25  N26  C2    53.76  30.0  1
 LZD  Var_03    C25  N26  C2   C3   -53.56  30.0  1
 LZD  Var_04    N26  C2   C3   C4    53.82  30.0  1
 LZD  Var_05    N10  C9   C7   N6    -0.13  30.0  2
 LZD  Var_06    C18  C17  C15  N14   65.76  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
 LZD  chir_01  C5  C4  N6  C25  positiv

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
 LZD  plan-1  C7   0.020
 LZD  plan-1  C9   0.020
 LZD  plan-1  N10  0.020
 LZD  plan-1  N11  0.020
 LZD  plan-1  C12  0.020
 LZD  plan-1  C13  0.020
 LZD  plan-1  N14  0.020
 LZD  plan-1  H12  0.020
 LZD  plan-1  H11  0.020
 LZD  plan-2  C15  0.020
 LZD  plan-2  C17  0.020
 LZD  plan-2  C18  0.020
 LZD  plan-2  F19  0.020
 LZD  plan-2  C20  0.020
 LZD  plan-2  C21  0.020
 LZD  plan-2  C22  0.020
 LZD  plan-2  C23  0.020
 LZD  plan-2  F24  0.020
 LZD  plan-2  H20  0.020
 LZD  plan-2  H21  0.020
 LZD  plan-2  H22  0.020
 LZD  plan-3  C13  0.020
 LZD  plan-3  N14  0.020
 LZD  plan-3  C15  0.020
 LZD  plan-3  O16  0.020
 LZD  plan-3  C17  0.020
 LZD  plan-3  H14  0.020
 LZD  plan-4  C5   0.020
 LZD  plan-4  N6   0.020
 LZD  plan-4  C7   0.020
 LZD  plan-4  O8   0.020
 LZD  plan-4  C9   0.020
 LZD  plan-4  H6   0.020

