# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 18:51:45 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)[S](=O)(=O)N2CCCC[C@H]2C(=O)OCCCc3cccnc3
#
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
 4GI  4GI  '3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate'  ligand  53  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GI
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
 4GI  C    C  CR16   0  -0.243  -2.6599   3.2358  -0.0171
 4GI  N    N  N      0  -0.607  -1.8546  -1.6452   0.5406
 4GI  O    O  OS     0  -0.633  -2.9480  -0.7266   2.6312
 4GI  S    S  S      0   1.367  -1.9637  -0.3836   1.6175
 4GI  C1   C  CR16   0  -0.254  -3.8487   3.0396  -0.6971
 4GI  O1   O  OS     0  -0.633  -0.6268   0.0193   2.0304
 4GI  C2   C  CR6    0   0.272  -4.4309   1.7798  -0.6729
 4GI  C3   C  CR16   0  -0.253  -3.8611   0.7207   0.0103
 4GI  C4   C  CR6    0  -0.123  -2.6670   0.9464   0.6716
 4GI  C5   C  CR16   0  -0.215  -2.0590   2.1904   0.6701
 4GI  C6   C  CH2    0  -0.296  -2.6694  -2.8357   0.8507
 4GI  C7   C  CH2    0  -0.438  -2.7995  -3.7204  -0.3741
 4GI  C8   C  CH2    0  -0.453  -1.4311  -4.1193  -0.8958
 4GI  C9   C  CH2    0  -0.448  -0.6249  -2.8694  -1.2021
 4GI  C10  C  CH1    0  -0.133  -0.5166  -1.9436   0.0189
 4GI  C11  C  C      0   0.568   0.1846  -0.6892  -0.4658
 4GI  C12  C  CH2    0  -0.171   2.3044   0.2987  -0.7739
 4GI  C13  C  CH2    0  -0.462   3.7414  -0.0122  -0.4160
 4GI  C14  C  CH2    0  -0.521   4.6761   1.0785  -0.9428
 4GI  H1   H  HCR6   0   0.292  -2.1943   4.2109  -0.0248
 4GI  H2   H  HCR6   0   0.310  -4.3055   3.8566  -1.2356
 4GI  H4   H  HCR6   0   0.312  -4.3309  -0.2533   0.0105
 4GI  H5   H  HCR6   0   0.297  -1.1251   2.3541   1.1885
 4GI  H6   H  HCH2   0   0.245  -2.2170  -3.4048   1.6702
 4GI  H7   H  HCH2   0   0.274  -3.6564  -2.5167   1.1745
 4GI  H8   H  HCH2   0   0.253  -3.3858  -4.5972  -0.0935
 4GI  H9   H  HCH2   0   0.233  -3.3582  -3.1912  -1.1509
 4GI  H10  H  HCH2   0   0.229  -0.9096  -4.7284  -0.1508
 4GI  H11  H  HCH2   0   0.253  -1.5198  -4.7268  -1.7976
 4GI  H12  H  HCH2   0   0.265   0.3864  -3.1282  -1.5207
 4GI  H13  H  HCH2   0   0.247  -1.0986  -2.3206  -2.0202
 4GI  H14  H  HCH1   0   0.281   0.0903  -2.4397   0.7848
 4GI  H15  H  HCH2   0   0.239   2.1814   0.3719  -1.8572
 4GI  H16  H  HCH2   0   0.239   1.9896   1.2476  -0.3329
 4GI  H17  H  HCH2   0   0.247   3.8469  -0.0919   0.6690
 4GI  H18  H  HCH2   0   0.246   4.0293  -0.9772  -0.8414
 4GI  H19  H  HCH2   0   0.254   4.5619   1.1654  -2.0266
 4GI  H20  H  HCH2   0   0.253   4.3877   2.0438  -0.5190
 4GI  C15  C  CR6    0   0.037   6.1093   0.7886  -0.6071
 4GI  C16  C  CR16   0  -0.192   6.8850  -0.0714  -1.3774
 4GI  C17  C  CR16   0  -0.318   8.1912  -0.3351  -0.9977
 4GI  C18  C  CR16   0  -0.075   8.6833   0.2734   0.1477
 4GI  N19  N  N      0  -0.401   7.9602   1.0984   0.8955
 4GI  C20  C  CR16   0  -0.106   6.7105   1.3413   0.5200
 4GI  H21  H  HCR6   0   0.266   6.4716  -0.5276  -2.2692
 4GI  H22  H  HCR6   0   0.270   8.8198  -0.9983  -1.5760
 4GI  H23  H  HCR6   0   0.262   9.7019   0.0893   0.4707
 4GI  H25  H  HCR6   0   0.255   6.1423   2.0215   1.1484
 4GI  N1   N  N      1   0.332  -5.6829   1.5592  -1.3864
 4GI  O4   O  O     -1  -0.368  -6.1742   2.4968  -1.9659
 4GI  O5   O  O      0  -0.370  -6.1613   0.4510  -1.3579
 4GI  O2   O  O      0  -0.433  -0.3705   0.2098  -1.0425
 4GI  O3   O  O2     0  -0.450   1.4858  -0.7636  -0.2633

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
 4GI  C14  C13  single    1.530  0.020  1.530
 4GI  C13  C12  single    1.513  0.020  1.513
 4GI  C12  O3   single    1.435  0.020  1.435
 4GI  O3   C11  single    1.319  0.020  1.319
 4GI  O2   C11  double    1.204  0.020  1.204
 4GI  C6   C7   single    1.517  0.020  1.517
 4GI  C6   N    single    1.476  0.020  1.476
 4GI  C11  C10  single    1.517  0.020  1.517
 4GI  C2   C1   aromatic  1.388  0.020  1.388
 4GI  C2   C3   aromatic  1.383  0.020  1.383
 4GI  C7   C8   single    1.518  0.020  1.518
 4GI  C1   C    aromatic  1.384  0.020  1.384
 4GI  C3   C4   aromatic  1.383  0.020  1.383
 4GI  C8   C9   single    1.519  0.020  1.519
 4GI  N    C10  single    1.467  0.020  1.467
 4GI  N    S    single    1.662  0.020  1.662
 4GI  C10  C9   single    1.536  0.020  1.536
 4GI  C    C5   aromatic  1.388  0.020  1.388
 4GI  C4   C5   aromatic  1.385  0.020  1.385
 4GI  C4   S    single    1.777  0.020  1.777
 4GI  S    O    double    1.454  0.020  1.454
 4GI  S    O1   double    1.456  0.020  1.456
 4GI  C    H1   single    0.930  0.020  1.080
 4GI  C1   H2   single    0.930  0.020  1.080
 4GI  C3   H4   single    0.930  0.020  1.080
 4GI  C5   H5   single    0.930  0.020  1.080
 4GI  C6   H6   single    0.970  0.020  1.090
 4GI  C6   H7   single    0.970  0.020  1.090
 4GI  C7   H8   single    0.970  0.020  1.090
 4GI  C7   H9   single    0.970  0.020  1.090
 4GI  C8   H10  single    0.970  0.020  1.090
 4GI  C8   H11  single    0.970  0.020  1.090
 4GI  C9   H12  single    0.970  0.020  1.090
 4GI  C9   H13  single    0.970  0.020  1.090
 4GI  C10  H14  single    0.970  0.020  1.090
 4GI  C12  H15  single    0.970  0.020  1.090
 4GI  C12  H16  single    0.970  0.020  1.090
 4GI  C13  H17  single    0.970  0.020  1.090
 4GI  C13  H18  single    0.970  0.020  1.090
 4GI  C14  H19  single    0.970  0.020  1.090
 4GI  C14  H20  single    0.970  0.020  1.090
 4GI  C14  C15  single    1.500  0.020  1.500
 4GI  C15  C16  aromatic  1.391  0.020  1.391
 4GI  C16  C17  aromatic  1.386  0.020  1.386
 4GI  C17  C18  aromatic  1.387  0.020  1.387
 4GI  C18  N19  aromatic  1.328  0.020  1.328
 4GI  N19  C20  aromatic  1.327  0.020  1.327
 4GI  C20  C15  aromatic  1.392  0.020  1.392
 4GI  C16  H21  single    0.930  0.020  1.080
 4GI  C17  H22  single    0.930  0.020  1.080
 4GI  C18  H23  single    0.930  0.020  1.080
 4GI  C20  H25  single    0.930  0.020  1.080
 4GI  C2   N1   single    1.458  0.020  1.458
 4GI  N1   O4   single    1.207  0.020  1.207
 4GI  N1   O5   double    1.207  0.020  1.207

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
 4GI  H1   C    C5   119.78  3.000
 4GI  H1   C    C1   119.65  3.000
 4GI  C5   C    C1   120.57  3.000
 4GI  C10  N    C6   114.47  3.000
 4GI  C10  N    S    116.40  3.000
 4GI  C6   N    S    116.10  3.000
 4GI  C4   S    O1   107.89  3.000
 4GI  O1   S    O    119.28  3.000
 4GI  C4   S    O    106.24  3.000
 4GI  O1   S    N    109.48  3.000
 4GI  O    S    N    108.49  3.000
 4GI  C4   S    N    104.42  3.000
 4GI  H2   C1   C2   121.19  3.000
 4GI  H2   C1   C    120.08  3.000
 4GI  C2   C1   C    118.72  3.000
 4GI  N1   C2   C3   118.66  3.000
 4GI  N1   C2   C1   119.28  3.000
 4GI  C3   C2   C1   122.06  3.000
 4GI  H4   C3   C4   121.46  3.000
 4GI  H4   C3   C2   120.71  3.000
 4GI  C4   C3   C2   117.82  3.000
 4GI  C5   C4   C3   121.67  3.000
 4GI  C5   C4   S    119.94  3.000
 4GI  C3   C4   S    118.29  3.000
 4GI  H5   C5   C4   121.00  3.000
 4GI  H5   C5   C    119.85  3.000
 4GI  C4   C5   C    119.15  3.000
 4GI  H7   C6   H6   107.74  3.000
 4GI  H7   C6   C7   109.51  3.000
 4GI  H6   C6   C7   109.66  3.000
 4GI  H7   C6   N    109.11  3.000
 4GI  H6   C6   N    110.39  3.000
 4GI  C7   C6   N    110.39  3.000
 4GI  H9   C7   H8   107.27  3.000
 4GI  H9   C7   C8   110.10  3.000
 4GI  H8   C7   C8   111.20  3.000
 4GI  H9   C7   C6   109.58  3.000
 4GI  H8   C7   C6   107.89  3.000
 4GI  C8   C7   C6   110.71  3.000
 4GI  H11  C8   H10  106.95  3.000
 4GI  H11  C8   C9   109.56  3.000
 4GI  H10  C8   C9   110.02  3.000
 4GI  H11  C8   C7   110.92  3.000
 4GI  H10  C8   C7   109.99  3.000
 4GI  C9   C8   C7   109.37  3.000
 4GI  H13  C9   H12  107.59  3.000
 4GI  H13  C9   C10  108.83  3.000
 4GI  H12  C9   C10  108.04  3.000
 4GI  H13  C9   C8   109.52  3.000
 4GI  H12  C9   C8   110.83  3.000
 4GI  C10  C9   C8   111.91  3.000
 4GI  H14  C10  C11  109.98  3.000
 4GI  H14  C10  C9   108.77  3.000
 4GI  C11  C10  C9   106.08  3.000
 4GI  H14  C10  N    110.41  3.000
 4GI  C9   C10  N    109.94  3.000
 4GI  C11  C10  N    111.54  3.000
 4GI  C10  C11  O3   111.13  3.000
 4GI  C10  C11  O2   123.89  3.000
 4GI  O3   C11  O2   124.80  3.000
 4GI  H16  C12  H15  108.03  3.000
 4GI  H16  C12  C13  110.89  3.000
 4GI  H15  C12  C13  110.80  3.000
 4GI  H16  C12  O3   109.57  3.000
 4GI  H15  C12  O3   109.76  3.000
 4GI  C13  C12  O3   107.79  3.000
 4GI  H18  C13  H17  107.25  3.000
 4GI  H18  C13  C14  109.54  3.000
 4GI  H17  C13  C14  109.56  3.000
 4GI  H18  C13  C12  109.85  3.000
 4GI  H17  C13  C12  109.96  3.000
 4GI  C14  C13  C12  110.63  3.000
 4GI  C15  C14  H20  109.63  3.000
 4GI  C15  C14  H19  109.69  3.000
 4GI  H20  C14  H19  106.66  3.000
 4GI  C15  C14  C13  111.64  3.000
 4GI  H20  C14  C13  109.57  3.000
 4GI  H19  C14  C13  109.52  3.000
 4GI  C20  C15  C16  116.94  3.000
 4GI  C20  C15  C14  121.14  3.000
 4GI  C16  C15  C14  121.89  3.000
 4GI  H21  C16  C17  120.33  3.000
 4GI  H21  C16  C15  120.22  3.000
 4GI  C17  C16  C15  119.45  3.000
 4GI  H22  C17  C18  120.29  3.000
 4GI  H22  C17  C16  121.21  3.000
 4GI  C18  C17  C16  118.50  3.000
 4GI  H23  C18  N19  116.70  3.000
 4GI  H23  C18  C17  120.31  3.000
 4GI  N19  C18  C17  122.99  3.000
 4GI  C20  N19  C18  117.85  3.000
 4GI  H25  C20  N19  116.32  3.000
 4GI  H25  C20  C15  119.42  3.000
 4GI  N19  C20  C15  124.27  3.000
 4GI  O5   N1   O4   124.27  3.000
 4GI  O5   N1   C2   117.88  3.000
 4GI  O4   N1   C2   117.84  3.000
 4GI  C12  O3   C11  117.80  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
 4GI  CONST_01  C3   C2   C1   C       0.00   0.0  0
 4GI  CONST_02  C3   C4   C5   C       0.00   0.0  0
 4GI  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 4GI  CONST_04  C4   C5   C    C1      0.00   0.0  0
 4GI  CONST_05  C5   C    C1   C2      0.00   0.0  0
 4GI  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 4GI  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 4GI  CONST_08  C18  N19  C20  C15     0.00   0.0  0
 4GI  CONST_09  N19  C20  C15  C16     0.00   0.0  0
 4GI  CONST_10  N19  C18  C17  C16     0.00   0.0  0
 4GI  CONST_11  C20  C15  C16  C17     0.00   0.0  0
 4GI  CONST_12  C20  N19  C18  C17     0.00   0.0  0
 4GI  CONST_13  N1   C2   C1   C     180.00   0.0  0
 4GI  CONST_14  S    C4   C5   C     180.00   0.0  0
 4GI  CONST_15  C2   C3   C4   S     180.00   0.0  0
 4GI  CONST_16  N1   C2   C3   C4    180.00   0.0  0
 4GI  CONST_17  C17  C16  C15  C14   180.00   0.0  0
 4GI  CONST_18  N19  C20  C15  C14   180.00   0.0  0
 4GI  CONST_19  H4   C3   C2   C1    180.00   0.0  0
 4GI  CONST_20  H5   C5   C    C1    180.00   0.0  0
 4GI  CONST_21  H1   C    C1   C2    180.00   0.0  0
 4GI  CONST_22  H2   C1   C2   C3    180.00   0.0  0
 4GI  CONST_23  H22  C17  C16  C15   180.00   0.0  0
 4GI  CONST_24  H25  C20  C15  C16   180.00   0.0  0
 4GI  CONST_25  H23  C18  C17  C16   180.00   0.0  0
 4GI  CONST_26  H21  C16  C17  C18   180.00   0.0  0
 4GI  CONST_27  O4   N1   C2   C1      0.00   0.0  0
 4GI  CONST_28  O5   N1   C2   C1    180.00   0.0  0
 4GI  CONST_29  O4   N1   C2   C3    180.00   0.0  0
 4GI  CONST_30  O5   N1   C2   C3      0.00   0.0  0
 4GI  Var_01    C8   C7   C6   N      56.72  30.0  1
 4GI  Var_02    C9   C8   C7   C6    -57.04  30.0  1
 4GI  Var_03    C10  N    C6   C7    -56.41  30.0  1
 4GI  Var_04    C10  C9   C8   C7     55.81  30.0  1
 4GI  Var_05    C3   C4   S    N      54.52  30.0  2
 4GI  Var_06    C6   N    S    C4   -116.46  30.0  2
 4GI  Var_07    C16  C15  C14  C13    82.41  30.0  2
 4GI  Var_08    C15  C14  C13  C12  -179.67  30.0  1
 4GI  Var_09    C14  C13  C12  O3    179.51  30.0  2
 4GI  Var_10    C13  C12  O3   C11   179.91  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
 4GI  chir_01  C10  C11  N  C9  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
 4GI  plan-1  C    0.020
 4GI  plan-1  S    0.020
 4GI  plan-1  C1   0.020
 4GI  plan-1  C2   0.020
 4GI  plan-1  C3   0.020
 4GI  plan-1  C4   0.020
 4GI  plan-1  C5   0.020
 4GI  plan-1  H1   0.020
 4GI  plan-1  H2   0.020
 4GI  plan-1  H4   0.020
 4GI  plan-1  H5   0.020
 4GI  plan-1  N1   0.020
 4GI  plan-2  C14  0.020
 4GI  plan-2  C15  0.020
 4GI  plan-2  C16  0.020
 4GI  plan-2  C17  0.020
 4GI  plan-2  C18  0.020
 4GI  plan-2  N19  0.020
 4GI  plan-2  C20  0.020
 4GI  plan-2  H21  0.020
 4GI  plan-2  H22  0.020
 4GI  plan-2  H23  0.020
 4GI  plan-2  H25  0.020
 4GI  plan-3  C2   0.020
 4GI  plan-3  N1   0.020
 4GI  plan-3  O4   0.020
 4GI  plan-3  O5   0.020
 4GI  plan-4  C10  0.020
 4GI  plan-4  C11  0.020
 4GI  plan-4  O2   0.020
 4GI  plan-4  O3   0.020

