# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 16:12:01 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-(carbamoylamino)-5-(4-chlorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)Nc1sc(cc1C(=O)N[C@H]2CCCNC2)c3ccc(Cl)cc3
#
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
 C73  C73  2-(carbamoylamino)-5-(4-chlorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-3-carboxamide  ligand  44  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C73
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
 C73  S01   S   S2    0   0.252  -1.3073   2.0734  -0.0282
 C73  C02   C   CR5   0   0.105   0.4151   1.9980   0.0184
 C73  C03   C   CR5   0  -0.057   0.8760   0.6931   0.0394
 C73  C04   C   CR15  0  -0.270  -0.2015  -0.2394   0.0177
 C73  C05   C   CR5   0  -0.216  -1.4305   0.3371  -0.0195
 C73  N06   N   NH1   0  -0.743   1.1968   3.1133   0.0296
 C73  C07   C   C     0   0.694   0.7074   4.3992   0.0292
 C73  N08   N   NH2   0  -0.846   1.6491   5.3543   0.0514
 C73  O09   O   O     0  -0.510  -0.4969   4.6157   0.0047
 C73  C10   C   C     0   0.588   2.3152   0.3769   0.0845
 C73  O11   O   O     0  -0.526   3.1658   1.2721   0.0501
 C73  N12   N   NH1   0  -0.668   2.6509  -0.9190   0.1769
 C73  C13   C   CH1   0  -0.069   4.0162  -1.4028   0.1875
 C73  C14   C   CH2   0  -0.277   4.4688  -1.8030  -1.2166
 C73  N15   N   NH1   0  -0.600   5.8365  -2.2796  -1.1654
 C73  C16   C   CH2   0  -0.292   5.9645  -3.4734  -0.3473
 C73  C17   C   CH2   0  -0.438   5.5666  -3.1534   1.0852
 C73  C18   C   CH2   0  -0.450   4.1530  -2.5832   1.1440
 C73  C19   C   CR6   0   0.163  -2.7354  -0.3148  -0.0578
 C73  C20   C   CR16  0  -0.336  -2.8607  -1.6179  -0.5481
 C73  C21   C   CR16  0  -0.188  -4.0872  -2.2581  -0.5802
 C73  C22   C   CR6   0  -0.060  -5.2157  -1.5883  -0.1310
 C73  C23   C   CR16  0  -0.190  -5.1256  -0.2930   0.3518
 C73  C24   C   CR16  0  -0.332  -3.8898   0.3321   0.3903
 C73  CL25  CL  CL    0  -0.127  -6.7561  -2.3794  -0.1794
 C73  H04   H   HCR5  0   0.266  -0.0773  -1.3132   0.0436
 C73  HN06  H   HNH1  0   0.434   2.1945   2.9128   0.0392
 C73  HN08  H   HNH2  0   0.414   2.6327   5.1535   0.1053
 C73  HN0A  H   HNH2  0   0.413   1.3687   6.3192   0.0764
 C73  HN12  H   HNH1  0   0.405   1.9266  -1.6181   0.1702
 C73  H13   H   HCH1  0   0.247   4.6583  -0.5919   0.5356
 C73  H14   H   HCH2  0   0.187   3.7659  -2.5581  -1.6085
 C73  H14A  H   HCH2  0   0.238   4.4143  -0.9362  -1.8785
 C73  HN15  H   HNH1  0   0.355   6.1632  -2.4693  -2.1034
 C73  H16   H   HCH2  0   0.188   5.3405  -4.3047  -0.7152
 C73  H16A  H   HCH2  0   0.234   7.0010  -3.8145  -0.3830
 C73  H17   H   HCH2  0   0.235   5.6342  -4.0516   1.7019
 C73  H17A  H   HCH2  0   0.220   6.2708  -2.4261   1.4996
 C73  H18   H   HCH2  0   0.245   3.9046  -2.2704   2.1607
 C73  H18A  H   HCH2  0   0.219   3.4328  -3.3622   0.8663
 C73  H20   H   HCR6  0   0.265  -1.9926  -2.1414  -0.9273
 C73  H21   H   HCR6  0   0.283  -4.1617  -3.2659  -0.9657
 C73  H23   H   HCR6  0   0.283  -6.0062   0.2268   0.7039
 C73  H24   H   HCR6  0   0.263  -3.8371   1.3358   0.7943

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
 C73  S01   C05   aromatic  1.741  0.020  1.741
 C73  S01   C02   aromatic  1.725  0.020  1.725
 C73  C02   N06   single    1.362  0.020  1.362
 C73  C02   C03   aromatic  1.384  0.020  1.384
 C73  C04   C03   aromatic  1.425  0.020  1.425
 C73  C03   C10   single    1.474  0.020  1.474
 C73  C05   C04   aromatic  1.358  0.020  1.358
 C73  C04   H04   single    0.930  0.020  1.080
 C73  C19   C05   single    1.459  0.020  1.459
 C73  C07   N06   single    1.376  0.020  1.376
 C73  N06   HN06  single    0.860  0.020  1.020
 C73  O09   C07   double    1.224  0.020  1.224
 C73  C07   N08   single    1.341  0.020  1.341
 C73  N08   HN08  single    0.860  0.020  1.020
 C73  N08   HN0A  single    0.860  0.020  1.020
 C73  C10   O11   double    1.235  0.020  1.235
 C73  C10   N12   single    1.342  0.020  1.342
 C73  N12   C13   single    1.449  0.020  1.449
 C73  N12   HN12  single    0.860  0.020  1.020
 C73  C13   C18   single    1.525  0.020  1.525
 C73  C13   C14   single    1.529  0.020  1.529
 C73  C13   H13   single    0.970  0.020  1.090
 C73  C14   N15   single    1.449  0.020  1.449
 C73  C14   H14   single    0.970  0.020  1.090
 C73  C14   H14A  single    0.970  0.020  1.090
 C73  N15   C16   single    1.453  0.020  1.453
 C73  N15   HN15  single    0.890  0.020  1.040
 C73  C17   C16   single    1.521  0.020  1.521
 C73  C16   H16   single    0.970  0.020  1.090
 C73  C16   H16A  single    0.970  0.020  1.090
 C73  C18   C17   single    1.525  0.020  1.525
 C73  C17   H17   single    0.970  0.020  1.090
 C73  C17   H17A  single    0.970  0.020  1.090
 C73  C18   H18   single    0.970  0.020  1.090
 C73  C18   H18A  single    0.970  0.020  1.090
 C73  C20   C19   aromatic  1.398  0.020  1.398
 C73  C19   C24   aromatic  1.397  0.020  1.397
 C73  C21   C20   aromatic  1.384  0.020  1.384
 C73  C20   H20   single    0.930  0.020  1.080
 C73  C21   C22   aromatic  1.387  0.020  1.387
 C73  C21   H21   single    0.930  0.020  1.080
 C73  CL25  C22   single    1.732  0.020  1.732
 C73  C22   C23   aromatic  1.385  0.020  1.385
 C73  C23   C24   aromatic  1.385  0.020  1.385
 C73  C23   H23   single    0.930  0.020  1.080
 C73  C24   H24   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
 C73  C05   S01  C02    91.54  3.000
 C73  N06   C02  C03   125.50  3.000
 C73  C03   C02  S01   111.97  3.000
 C73  N06   C02  S01   122.53  3.000
 C73  C10   C03  C04   126.74  3.000
 C73  C10   C03  C02   121.86  3.000
 C73  C04   C03  C02   111.40  3.000
 C73  H04   C04  C05   121.75  3.000
 C73  H04   C04  C03   124.24  3.000
 C73  C05   C04  C03   114.01  3.000
 C73  C19   C05  C04   128.34  3.000
 C73  C19   C05  S01   120.58  3.000
 C73  C04   C05  S01   111.07  3.000
 C73  HN06  N06  C07   122.20  3.000
 C73  HN06  N06  C02   113.67  3.000
 C73  C07   N06  C02   124.13  3.000
 C73  O09   C07  N08   124.41  3.000
 C73  N08   C07  N06   114.57  3.000
 C73  O09   C07  N06   121.02  3.000
 C73  HN0A  N08  HN08  117.60  3.000
 C73  HN0A  N08  C07   119.22  3.000
 C73  HN08  N08  C07   123.06  3.000
 C73  N12   C10  O11   121.97  3.000
 C73  N12   C10  C03   116.97  3.000
 C73  O11   C10  C03   121.06  3.000
 C73  HN12  N12  C13   116.50  3.000
 C73  HN12  N12  C10   119.35  3.000
 C73  C13   N12  C10   123.98  3.000
 C73  H13   C13  C18   108.80  3.000
 C73  H13   C13  C14   108.26  3.000
 C73  C18   C13  C14   110.30  3.000
 C73  H13   C13  N12   107.98  3.000
 C73  C14   C13  N12   111.09  3.000
 C73  C18   C13  N12   110.34  3.000
 C73  H14A  C14  H14   107.22  3.000
 C73  H14A  C14  N15   109.25  3.000
 C73  H14   C14  N15   112.87  3.000
 C73  H14A  C14  C13   109.53  3.000
 C73  H14   C14  C13   108.46  3.000
 C73  N15   C14  C13   109.46  3.000
 C73  HN15  N15  C16   109.86  3.000
 C73  HN15  N15  C14   109.50  3.000
 C73  C16   N15  C14   111.92  3.000
 C73  H16A  C16  H16   106.90  3.000
 C73  H16A  C16  C17   110.17  3.000
 C73  H16   C16  C17   108.95  3.000
 C73  H16A  C16  N15   108.79  3.000
 C73  H16   C16  N15   112.44  3.000
 C73  C17   C16  N15   109.55  3.000
 C73  H17A  C17  H17   107.05  3.000
 C73  H17A  C17  C18   109.47  3.000
 C73  H17   C17  C18   110.07  3.000
 C73  H17A  C17  C16   109.16  3.000
 C73  H17   C17  C16   110.05  3.000
 C73  C18   C17  C16   110.94  3.000
 C73  H18A  C18  H18   106.84  3.000
 C73  H18A  C18  C17   109.47  3.000
 C73  H18   C18  C17   110.71  3.000
 C73  H18A  C18  C13   109.39  3.000
 C73  H18   C18  C13   109.98  3.000
 C73  C17   C18  C13   110.38  3.000
 C73  C24   C19  C20   118.04  3.000
 C73  C24   C19  C05   121.58  3.000
 C73  C20   C19  C05   120.38  3.000
 C73  H20   C20  C21   118.62  3.000
 C73  H20   C20  C19   120.12  3.000
 C73  C21   C20  C19   121.25  3.000
 C73  H21   C21  C22   120.61  3.000
 C73  H21   C21  C20   120.03  3.000
 C73  C22   C21  C20   119.36  3.000
 C73  CL25  C22  C23   119.64  3.000
 C73  C23   C22  C21   120.76  3.000
 C73  CL25  C22  C21   119.60  3.000
 C73  H23   C23  C24   120.02  3.000
 C73  H23   C23  C22   120.66  3.000
 C73  C24   C23  C22   119.31  3.000
 C73  H24   C24  C23   118.15  3.000
 C73  H24   C24  C19   120.56  3.000
 C73  C23   C24  C19   121.28  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
 C73  CONST_01  C03   C04  C05  S01    0.00   0.0  0
 C73  CONST_04  C04   C03  C02  S01    0.00   0.0  0
 C73  CONST_05  C04   C05  S01  C02    0.00   0.0  0
 C73  CONST_06  C19   C05  S01  C02  180.00   0.0  0
 C73  CONST_07  C05   C04  C03  C02    0.00   0.0  0
 C73  CONST_08  C05   S01  C02  C03    0.00   0.0  0
 C73  CONST_09  C19   C05  C04  C03  180.00   0.0  0
 C73  CONST_12  C21   C20  C19  C05  180.00   0.0  0
 C73  CONST_13  C23   C24  C19  C05  180.00   0.0  0
 C73  CONST_14  C22   C21  C20  C19    0.00   0.0  0
 C73  CONST_15  C22   C23  C24  C19    0.00   0.0  0
 C73  CONST_16  C23   C24  C19  C20    0.00   0.0  0
 C73  CONST_17  C23   C22  C21  C20    0.00   0.0  0
 C73  CONST_18  C24   C19  C20  C21    0.00   0.0  0
 C73  CONST_19  C24   C23  C22  C21    0.00   0.0  0
 C73  CONST_20  C10   C03  C02  S01  180.00   0.0  0
 C73  CONST_21  N06   C02  C03  C04  180.00   0.0  0
 C73  CONST_22  N06   C02  S01  C05  180.00   0.0  0
 C73  CONST_23  C10   C03  C04  C05  180.00   0.0  0
 C73  CONST_24  CL25  C22  C21  C20  180.00   0.0  0
 C73  CONST_25  CL25  C22  C23  C24  180.00   0.0  0
 C73  CONST_26  H04   C04  C05  S01  180.00   0.0  0
 C73  CONST_27  H20   C20  C19  C05    0.00   0.0  0
 C73  CONST_28  H24   C24  C19  C05    0.00   0.0  0
 C73  CONST_29  H21   C21  C20  C19  180.00   0.0  0
 C73  CONST_30  H23   C23  C24  C19  180.00   0.0  0
 C73  CONST_31  N12   C10  C03  C02  180.00   0.0  0
 C73  CONST_32  C13   N12  C10  C03  180.00   0.0  0
 C73  CONST_33  C07   N06  C02  S01    0.00   0.0  0
 C73  CONST_34  C07   N06  C02  C03  180.00   0.0  0
 C73  CONST_35  HN06  N06  C02  S01  180.00   0.0  0
 C73  CONST_36  O09   C07  N06  C02    0.00   0.0  0
 C73  CONST_37  C13   N12  C10  O11    0.00   0.0  0
 C73  CONST_38  N08   C07  N06  C02  180.00   0.0  0
 C73  CONST_39  HN12  N12  C10  C03    0.00   0.0  0
 C73  CONST_40  HN08  N08  C07  O09  180.00   0.0  0
 C73  CONST_41  HN0A  N08  C07  O09    0.00   0.0  0
 C73  Var_01    C16   C17  C18  C13  -52.84  30.0  1
 C73  Var_02    C16   N15  C14  C13   62.76  30.0  1
 C73  Var_03    C17   C16  N15  C14  -62.20  30.0  1
 C73  Var_04    C18   C17  C16  N15   56.43  30.0  1

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
 C73  chir_01  C13  N12  C18  C14  negativ

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
 C73  plan-1  C05   0.020
 C73  plan-1  C19   0.020
 C73  plan-1  C20   0.020
 C73  plan-1  C21   0.020
 C73  plan-1  C22   0.020
 C73  plan-1  C23   0.020
 C73  plan-1  C24   0.020
 C73  plan-1  CL25  0.020
 C73  plan-1  H20   0.020
 C73  plan-1  H21   0.020
 C73  plan-1  H23   0.020
 C73  plan-1  H24   0.020
 C73  plan-2  S01   0.020
 C73  plan-2  C02   0.020
 C73  plan-2  C03   0.020
 C73  plan-2  C04   0.020
 C73  plan-2  C05   0.020
 C73  plan-2  N06   0.020
 C73  plan-2  C10   0.020
 C73  plan-2  O11   0.020
 C73  plan-2  N12   0.020
 C73  plan-2  C13   0.020
 C73  plan-2  C19   0.020
 C73  plan-2  H04   0.020
 C73  plan-2  HN12  0.020
 C73  plan-3  C02   0.020
 C73  plan-3  N06   0.020
 C73  plan-3  C07   0.020
 C73  plan-3  N08   0.020
 C73  plan-3  O09   0.020
 C73  plan-3  HN06  0.020
 C73  plan-3  HN08  0.020
 C73  plan-3  HN0A  0.020

