# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:30:55 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2-[(3S,4R)-4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}-3-fluoropiperidin-1-yl]-1,3-thiazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(C(=O)N[C@@H]2CCN(C[C@@H]2F)c3sc(cn3)C(O)=O)c(Cl)c1Cl
#
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
 07N  07N  '2-[(3S,4R)-4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}-3-fluoropiperidin-1-yl]-1,3-thiazole-5-carboxylic acid'  ligand  40  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_07N
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
 07N  C1    C   CH3    0  -0.728   5.9642   3.0057   0.4536
 07N  CL1   CL  CL     0  -0.117   5.2168  -2.2463   0.5056
 07N  C2    C   CR5    0   0.376   5.3772   1.6466   0.3602
 07N  CL2   CL  CL     0  -0.129   7.5204   0.1207   1.1794
 07N  C3    C   CR5    0  -0.106   5.9366   0.4119   0.6085
 07N  C4    C   CR5    0  -0.071   4.9768  -0.5718   0.3098
 07N  C5    C   CR5    0   0.236   3.8341   0.0764  -0.1069
 07N  N6    N   NR15   0  -0.693   4.1125   1.4157  -0.0570
 07N  C8    C   C      0   0.539   2.5419  -0.4943  -0.5070
 07N  O9    O   O      0  -0.477   2.4534  -1.6518  -0.8892
 07N  N10   N   NH1    0  -0.668   1.4874   0.3477  -0.4369
 07N  C11   C   CH1    0  -0.139   0.1518  -0.0358  -0.8325
 07N  C13   C   CH2    0  -0.453  -0.6105   1.1652  -1.3769
 07N  C14   C   CH2    0  -0.307  -2.0265   0.7712  -1.7636
 07N  N15   N   NT     0  -0.488  -2.7084   0.1361  -0.6469
 07N  C16   C   CH2    0  -0.363  -2.0382  -1.0147  -0.0832
 07N  C17   C   CH1    0   0.196  -0.6159  -0.6806   0.3125
 07N  F19   F   F      0  -0.377  -0.6411   0.2118   1.3840
 07N  C20   C   CR5    0   0.335  -4.0447   0.3034  -0.5054
 07N  N21   N   N      0  -0.472  -4.7375   1.2007  -1.1527
 07N  C22   C   CR15   0  -0.010  -6.0473   1.1649  -0.7731
 07N  C23   C   CR5    0  -0.387  -6.3990   0.2447   0.1566
 07N  S24   S   S2     0   0.146  -4.9870  -0.6642   0.6002
 07N  C25   C   C      0   0.386  -7.7168  -0.0754   0.7858
 07N  O26   O   O      0  -0.605  -7.6999  -1.0049   1.6175
 07N  O27   O   OC    -1  -0.593  -8.6894   0.6103   0.4210
 07N  H1    H   HCH3   0   0.267   6.3727   3.3285  -0.5054
 07N  H1A   H   HCH3   0   0.265   5.2159   3.7358   0.7601
 07N  H1B   H   HCH3   0   0.260   6.7729   3.0243   1.1812
 07N  HN10  H   HNH1   0   0.403   1.5713   1.2008   0.0945
 07N  H11   H   HCH1   0   0.273   0.2366  -0.7870  -1.6222
 07N  H13   H   HCH2   0   0.246  -0.6417   1.9684  -0.6360
 07N  H13A  H   HCH2   0   0.265  -0.0976   1.5540  -2.2576
 07N  H14   H   HCH2   0   0.279  -2.5893   1.6509  -2.0627
 07N  H14A  H   HCH2   0   0.238  -2.0047   0.0878  -2.6227
 07N  H16   H   HCH2   0   0.284  -2.5642  -1.3670   0.8050
 07N  H16A  H   HCH2   0   0.258  -2.0148  -1.8506  -0.7946
 07N  H17   H   HCH1   0   0.248  -0.1138  -1.5913   0.6466
 07N  H22   H   HCR5   0   0.258  -6.7427   1.8604  -1.2238
 07N  HN6   H   HNR5   0   0.425   3.5015   2.1443  -0.3943

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
 07N  C1   C2    single    1.483  0.020  1.483
 07N  C1   H1    single    0.970  0.020  1.090
 07N  C1   H1A   single    0.970  0.020  1.090
 07N  C1   H1B   single    0.970  0.020  1.090
 07N  CL1  C4    single    1.703  0.020  1.703
 07N  C2   C3    aromatic  1.378  0.020  1.378
 07N  C2   N6    aromatic  1.352  0.020  1.352
 07N  CL2  C3    single    1.709  0.020  1.709
 07N  C3   C4    aromatic  1.406  0.020  1.406
 07N  C4   C5    aromatic  1.378  0.020  1.378
 07N  C5   N6    aromatic  1.369  0.020  1.369
 07N  C5   C8    single    1.468  0.020  1.468
 07N  N10  C8    single    1.351  0.020  1.351
 07N  C8   O9    double    1.222  0.020  1.222
 07N  N10  C11   single    1.445  0.020  1.445
 07N  N10  HN10  single    0.860  0.020  1.020
 07N  C17  C11   single    1.522  0.020  1.522
 07N  C11  C13   single    1.523  0.020  1.523
 07N  C11  H11   single    0.970  0.020  1.090
 07N  C13  C14   single    1.520  0.020  1.520
 07N  C13  H13   single    0.970  0.020  1.090
 07N  C13  H13A  single    0.970  0.020  1.090
 07N  N15  C14   single    1.454  0.020  1.454
 07N  C14  H14   single    0.970  0.020  1.090
 07N  C14  H14A  single    0.970  0.020  1.090
 07N  C20  N15   single    1.354  0.020  1.354
 07N  C16  N15   single    1.446  0.020  1.446
 07N  C17  C16   single    1.514  0.020  1.514
 07N  C16  H16   single    0.970  0.020  1.090
 07N  C16  H16A  single    0.970  0.020  1.090
 07N  F19  C17   single    1.395  0.020  1.395
 07N  C17  H17   single    0.970  0.020  1.090
 07N  N21  C20   aromatic  1.305  0.020  1.305
 07N  C20  S24   aromatic  1.745  0.020  1.745
 07N  C22  N21   aromatic  1.364  0.020  1.364
 07N  C22  C23   aromatic  1.355  0.020  1.355
 07N  C22  H22   single    0.930  0.020  1.080
 07N  C23  C25   single    1.495  0.020  1.495
 07N  C23  S24   aromatic  1.737  0.020  1.737
 07N  O26  C25   deloc     1.247  0.020  1.247
 07N  C25  O27   deloc     1.245  0.020  1.245
 07N  N6   HN6   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
 07N  H1B   C1   H1A  108.12  3.000
 07N  H1B   C1   H1   107.72  3.000
 07N  H1A   C1   H1   107.83  3.000
 07N  H1B   C1   C2   110.60  3.000
 07N  H1A   C1   C2   111.09  3.000
 07N  H1    C1   C2   111.34  3.000
 07N  N6    C2   C3   106.41  3.000
 07N  N6    C2   C1   123.11  3.000
 07N  C3    C2   C1   130.46  3.000
 07N  C4    C3   CL2  125.76  3.000
 07N  C4    C3   C2   108.14  3.000
 07N  CL2   C3   C2   126.10  3.000
 07N  C5    C4   C3   107.52  3.000
 07N  C5    C4   CL1  127.88  3.000
 07N  C3    C4   CL1  124.55  3.000
 07N  C8    C5   N6   124.69  3.000
 07N  C8    C5   C4   129.00  3.000
 07N  N6    C5   C4   106.29  3.000
 07N  HN6   N6   C5   124.84  3.000
 07N  HN6   N6   C2   123.13  3.000
 07N  C5    N6   C2   111.63  3.000
 07N  N10   C8   O9   123.36  3.000
 07N  O9    C8   C5   121.13  3.000
 07N  N10   C8   C5   115.50  3.000
 07N  HN10  N10  C11  116.47  3.000
 07N  HN10  N10  C8   119.31  3.000
 07N  C11   N10  C8   122.81  3.000
 07N  H11   C11  C17  106.94  3.000
 07N  H11   C11  C13  108.81  3.000
 07N  C17   C11  C13  110.52  3.000
 07N  H11   C11  N10  107.97  3.000
 07N  C13   C11  N10  110.56  3.000
 07N  C17   C11  N10  111.89  3.000
 07N  H13A  C13  H13  107.38  3.000
 07N  H13A  C13  C14  108.97  3.000
 07N  H13   C13  C14  109.65  3.000
 07N  H13A  C13  C11  109.53  3.000
 07N  H13   C13  C11  110.57  3.000
 07N  C14   C13  C11  110.66  3.000
 07N  H14A  C14  H14  107.39  3.000
 07N  H14A  C14  N15  109.78  3.000
 07N  H14   C14  N15  108.80  3.000
 07N  H14A  C14  C13  109.99  3.000
 07N  H14   C14  C13  110.05  3.000
 07N  N15   C14  C13  110.77  3.000
 07N  C20   N15  C16  120.99  3.000
 07N  C16   N15  C14  115.44  3.000
 07N  C20   N15  C14  119.27  3.000
 07N  H16A  C16  H16  106.98  3.000
 07N  H16A  C16  C17  108.51  3.000
 07N  H16   C16  C17  108.15  3.000
 07N  H16A  C16  N15  111.29  3.000
 07N  H16   C16  N15  110.55  3.000
 07N  C17   C16  N15  111.21  3.000
 07N  H17   C17  F19  107.86  3.000
 07N  H17   C17  C16  109.14  3.000
 07N  F19   C17  C16  108.97  3.000
 07N  H17   C17  C11  110.58  3.000
 07N  F19   C17  C11  108.42  3.000
 07N  C16   C17  C11  111.77  3.000
 07N  S24   C20  N21  114.12  3.000
 07N  S24   C20  N15  122.04  3.000
 07N  N21   C20  N15  123.83  3.000
 07N  C22   N21  C20  110.70  3.000
 07N  H22   C22  C23  123.76  3.000
 07N  H22   C22  N21  118.97  3.000
 07N  C23   C22  N21  117.26  3.000
 07N  C25   C23  S24  119.81  3.000
 07N  S24   C23  C22  108.64  3.000
 07N  C25   C23  C22  131.55  3.000
 07N  C23   S24  C20   89.26  3.000
 07N  O27   C25  O26  128.06  3.000
 07N  O27   C25  C23  116.58  3.000
 07N  O26   C25  C23  115.35  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
 07N  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 07N  CONST_02  C4   C5   N6   C2     0.00   0.0  0
 07N  CONST_03  C5   N6   C2   C3     0.00   0.0  0
 07N  CONST_04  N6   C5   C4   C3     0.00   0.0  0
 07N  CONST_05  N6   C2   C3   C4     0.00   0.0  0
 07N  CONST_06  C23  C22  N21  C20    0.00   0.0  0
 07N  CONST_07  C22  C23  S24  C20    0.00   0.0  0
 07N  CONST_08  C23  S24  C20  N21    0.00   0.0  0
 07N  CONST_09  S24  C23  C22  N21    0.00   0.0  0
 07N  CONST_10  S24  C20  N21  C22    0.00   0.0  0
 07N  CONST_11  C22  N21  C20  N15  180.00   0.0  0
 07N  CONST_12  C23  S24  C20  N15  180.00   0.0  0
 07N  CONST_13  C4   C3   C2   C1   180.00   0.0  0
 07N  CONST_14  C5   N6   C2   C1   180.00   0.0  0
 07N  CONST_15  C2   C3   C4   CL1  180.00   0.0  0
 07N  CONST_16  N6   C5   C4   CL1  180.00   0.0  0
 07N  CONST_17  C8   C5   N6   C2   180.00   0.0  0
 07N  CONST_18  N6   C2   C3   CL2  180.00   0.0  0
 07N  CONST_19  C5   C4   C3   CL2  180.00   0.0  0
 07N  CONST_20  C8   C5   C4   C3   180.00   0.0  0
 07N  CONST_21  C25  C23  S24  C20  180.00   0.0  0
 07N  CONST_22  C25  C23  C22  N21  180.00   0.0  0
 07N  CONST_23  HN6  N6   C2   C3   180.00   0.0  0
 07N  CONST_24  H22  C22  N21  C20  180.00   0.0  0
 07N  CONST_25  C11  N10  C8   C5   180.00   0.0  0
 07N  CONST_26  C11  N10  C8   O9     0.00   0.0  0
 07N  Var_01    N15  C14  C13  C11   54.40  30.0  1
 07N  Var_02    C20  N15  C14  C13  147.44  30.0  1
 07N  Var_03    N21  C20  N15  C14  -13.59  30.0  2
 07N  Var_04    C17  C16  N15  C14   54.28  30.0  1
 07N  Var_05    N10  C8   C5   C4   158.69  30.0  2
 07N  Var_06    O26  C25  C23  C22  179.56  30.0  2
 07N  Var_07    H1   C1   C2   C3    92.85  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
 07N  chir_01  C11  N10  C17  C13  negativ
 07N  chir_02  C17  F19  C16  C11  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
 07N  plan-1  C1    0.020
 07N  plan-1  CL1   0.020
 07N  plan-1  C2    0.020
 07N  plan-1  CL2   0.020
 07N  plan-1  C3    0.020
 07N  plan-1  C4    0.020
 07N  plan-1  C5    0.020
 07N  plan-1  N6    0.020
 07N  plan-1  C8    0.020
 07N  plan-1  HN6   0.020
 07N  plan-2  N15   0.020
 07N  plan-2  C20   0.020
 07N  plan-2  N21   0.020
 07N  plan-2  C22   0.020
 07N  plan-2  C23   0.020
 07N  plan-2  S24   0.020
 07N  plan-2  C25   0.020
 07N  plan-2  H22   0.020
 07N  plan-3  C5    0.020
 07N  plan-3  C8    0.020
 07N  plan-3  O9    0.020
 07N  plan-3  N10   0.020
 07N  plan-3  C11   0.020
 07N  plan-3  HN10  0.020
 07N  plan-4  C23   0.020
 07N  plan-4  C25   0.020
 07N  plan-4  O26   0.020
 07N  plan-4  O27   0.020

