# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:22:15 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R,3R)-2-(2-chlorophenyl)-1-[2-(4-chlorophenyl)ethyl]-6-oxidanylidene-piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCC(=O)N(CCc2ccc(Cl)cc2)[C@H]1c3ccccc3Cl
#
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
 SVQ  SVQ  '(2R,3R)-2-(2-chlorophenyl)-1-[2-(4-chlorophenyl)ethyl]-6-oxidanylidene-piperidine-3-carboxylic acid'  ligand  44  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SVQ
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
 SVQ  CL2   CL  CL     0  -0.125  -2.2729   0.2026  -2.6496
 SVQ  C25   C   CR6    0  -0.115  -1.8782   1.4537  -1.5082
 SVQ  C24   C   CR16   0  -0.198  -1.7892   2.7485  -1.9993
 SVQ  C23   C   CR16   0  -0.279  -1.4855   3.7913  -1.1378
 SVQ  C22   C   CR16   0  -0.231  -1.2714   3.5305   0.2072
 SVQ  C21   C   CR16   0  -0.312  -1.3577   2.2291   0.6766
 SVQ  C20   C   CR6    0   0.198  -1.6613   1.1592  -0.1634
 SVQ  C14   C   CH1    0  -0.098  -1.7794  -0.2234   0.4449
 SVQ  C13   C   CH1    0  -0.383  -3.2524  -0.6125   0.5711
 SVQ  C17   C   C      0   0.434  -3.9403   0.1518   1.7260
 SVQ  O19   O   O      0  -0.595  -3.2874   0.3043   2.7771
 SVQ  O18   O   OC    -1  -0.607  -5.1161   0.5077   1.5210
 SVQ  C12   C   CH2    0  -0.452  -3.3738  -2.1152   0.7779
 SVQ  C11   C   CH2    0  -0.558  -2.7649  -2.8154  -0.4215
 SVQ  C10   C   C      0   0.542  -1.3238  -2.4332  -0.6437
 SVQ  O15   O   O      0  -0.513  -0.5386  -3.2204  -1.1610
 SVQ  N9    N   NT     0  -0.468  -0.9383  -1.1976  -0.2538
 SVQ  C8    C   CH2    0  -0.305   0.4709  -0.8590  -0.3344
 SVQ  C7    C   CH2    0  -0.530   1.2428  -1.2598   0.9272
 SVQ  C2    C   CR6    0   0.145   2.6748  -0.8220   0.8319
 SVQ  C3    C   CR16   0  -0.314   3.0841   0.4069   1.3425
 SVQ  C4    C   CR16   0  -0.196   4.3953   0.8415   1.2131
 SVQ  C5    C   CR6    0  -0.057   5.3103   0.0329   0.5582
 SVQ  CL1   CL  CL     0  -0.135   6.9546   0.5634   0.3948
 SVQ  C6    C   CR16   0  -0.196   4.9335  -1.1945   0.0358
 SVQ  C1    C   CR16   0  -0.311   3.6179  -1.6105   0.1769
 SVQ  H24   H   HCR6   0   0.277  -1.9600   2.9392  -3.0504
 SVQ  H23   H   HCR6   0   0.267  -1.4184   4.8005  -1.5219
 SVQ  H22   H   HCR6   0   0.261  -1.0351   4.3361   0.8897
 SVQ  H21   H   HCR6   0   0.258  -1.1925   2.0291   1.7277
 SVQ  H14   H   HCH1   0   0.262  -1.3979  -0.1446   1.4677
 SVQ  H13   H   HCH1   0   0.227  -3.7745  -0.3682  -0.3573
 SVQ  H121  H   HCH2   0   0.231  -2.8616  -2.4156   1.6969
 SVQ  H122  H   HCH2   0   0.249  -4.4225  -2.3981   0.8873
 SVQ  H111  H   HCH2   0   0.265  -2.8087  -3.9011  -0.3296
 SVQ  H112  H   HCH2   0   0.259  -3.3253  -2.5507  -1.3245
 SVQ  H81C  H   HCH2   0   0.263   0.9105  -1.3389  -1.2069
 SVQ  H82C  H   HCH2   0   0.259   0.5658   0.2167  -0.4904
 SVQ  H71C  H   HCH2   0   0.253   0.7729  -0.8075   1.8042
 SVQ  H72C  H   HCH2   0   0.258   1.1837  -2.3425   1.0554
 SVQ  H3    H   HCR6   0   0.256   2.3723   1.0395   1.8597
 SVQ  H1    H   HCR6   0   0.259   3.3249  -2.5707  -0.2307
 SVQ  H4    H   HCR6   0   0.278   4.6971   1.7966   1.6209
 SVQ  H6    H   HCR6   0   0.278   5.6532  -1.8213  -0.4733

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
 SVQ  CL2  C25   single    1.739  0.020  1.739
 SVQ  C25  C24   aromatic  1.388  0.020  1.388
 SVQ  C25  C20   aromatic  1.394  0.020  1.394
 SVQ  C24  C23   aromatic  1.386  0.020  1.386
 SVQ  C23  C22   aromatic  1.387  0.020  1.387
 SVQ  C22  C21   aromatic  1.386  0.020  1.386
 SVQ  C21  C20   aromatic  1.394  0.020  1.394
 SVQ  C20  C14   single    1.515  0.020  1.515
 SVQ  C14  C13   single    1.529  0.020  1.529
 SVQ  C14  N9    single    1.464  0.020  1.464
 SVQ  C13  C17   single    1.546  0.020  1.546
 SVQ  C13  C12   single    1.522  0.020  1.522
 SVQ  C17  O19   deloc     1.247  0.020  1.247
 SVQ  C17  O18   deloc     1.246  0.020  1.246
 SVQ  C12  C11   single    1.516  0.020  1.516
 SVQ  C11  C10   single    1.507  0.020  1.507
 SVQ  C10  O15   double    1.226  0.020  1.226
 SVQ  C10  N9    single    1.352  0.020  1.352
 SVQ  N9   C8    single    1.452  0.020  1.452
 SVQ  C8   C7    single    1.532  0.020  1.532
 SVQ  C7   C2    single    1.501  0.020  1.501
 SVQ  C2   C3    aromatic  1.392  0.020  1.392
 SVQ  C2   C1    aromatic  1.393  0.020  1.393
 SVQ  C3   C4    aromatic  1.387  0.020  1.387
 SVQ  C4   C5    aromatic  1.386  0.020  1.386
 SVQ  C5   CL1   single    1.735  0.020  1.735
 SVQ  C5   C6    aromatic  1.386  0.020  1.386
 SVQ  C6   C1    aromatic  1.387  0.020  1.387
 SVQ  C24  H24   single    0.930  0.020  1.080
 SVQ  C23  H23   single    0.930  0.020  1.080
 SVQ  C22  H22   single    0.930  0.020  1.080
 SVQ  C21  H21   single    0.930  0.020  1.080
 SVQ  C14  H14   single    0.970  0.020  1.090
 SVQ  C13  H13   single    0.970  0.020  1.090
 SVQ  C12  H121  single    0.970  0.020  1.090
 SVQ  C12  H122  single    0.970  0.020  1.090
 SVQ  C11  H111  single    0.970  0.020  1.090
 SVQ  C11  H112  single    0.970  0.020  1.090
 SVQ  C8   H81C  single    0.970  0.020  1.090
 SVQ  C8   H82C  single    0.970  0.020  1.090
 SVQ  C7   H71C  single    0.970  0.020  1.090
 SVQ  C7   H72C  single    0.970  0.020  1.090
 SVQ  C3   H3    single    0.930  0.020  1.080
 SVQ  C1   H1    single    0.930  0.020  1.080
 SVQ  C4   H4    single    0.930  0.020  1.080
 SVQ  C6   H6    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
 SVQ  C20   C25  C24   121.91  3.000
 SVQ  C20   C25  CL2   121.11  3.000
 SVQ  C24   C25  CL2   116.98  3.000
 SVQ  H24   C24  C23   120.39  3.000
 SVQ  H24   C24  C25   119.88  3.000
 SVQ  C23   C24  C25   119.73  3.000
 SVQ  H23   C23  C22   120.67  3.000
 SVQ  H23   C23  C24   119.64  3.000
 SVQ  C22   C23  C24   119.68  3.000
 SVQ  H22   C22  C21   119.94  3.000
 SVQ  H22   C22  C23   120.37  3.000
 SVQ  C21   C22  C23   119.69  3.000
 SVQ  H21   C21  C20   118.46  3.000
 SVQ  H21   C21  C22   119.52  3.000
 SVQ  C20   C21  C22   122.02  3.000
 SVQ  C14   C20  C21   118.40  3.000
 SVQ  C14   C20  C25   124.61  3.000
 SVQ  C21   C20  C25   116.95  3.000
 SVQ  H14   C14  N9    107.07  3.000
 SVQ  H14   C14  C13   106.09  3.000
 SVQ  N9    C14  C13   115.06  3.000
 SVQ  H14   C14  C20   106.39  3.000
 SVQ  N9    C14  C20   111.76  3.000
 SVQ  C13   C14  C20   109.91  3.000
 SVQ  H13   C13  C12   107.35  3.000
 SVQ  H13   C13  C17   108.14  3.000
 SVQ  C12   C13  C17   110.56  3.000
 SVQ  H13   C13  C14   109.47  3.000
 SVQ  C12   C13  C14   109.84  3.000
 SVQ  C17   C13  C14   111.37  3.000
 SVQ  O18   C17  O19   126.74  3.000
 SVQ  O18   C17  C13   115.99  3.000
 SVQ  O19   C17  C13   117.20  3.000
 SVQ  H122  C12  H121  107.11  3.000
 SVQ  H122  C12  C11   110.20  3.000
 SVQ  H121  C12  C11   110.47  3.000
 SVQ  H122  C12  C13   110.26  3.000
 SVQ  H121  C12  C13   110.36  3.000
 SVQ  C11   C12  C13   108.45  3.000
 SVQ  H112  C11  H111  106.83  3.000
 SVQ  H112  C11  C10   107.84  3.000
 SVQ  H111  C11  C10   107.65  3.000
 SVQ  H112  C11  C12   109.58  3.000
 SVQ  H111  C11  C12   112.15  3.000
 SVQ  C10   C11  C12   112.54  3.000
 SVQ  N9    C10  O15   121.72  3.000
 SVQ  N9    C10  C11   117.51  3.000
 SVQ  O15   C10  C11   120.77  3.000
 SVQ  C8    N9   C10   118.30  3.000
 SVQ  C8    N9   C14   115.40  3.000
 SVQ  C10   N9   C14   125.58  3.000
 SVQ  H82C  C8   H81C  106.55  3.000
 SVQ  H82C  C8   C7    109.38  3.000
 SVQ  H81C  C8   C7    109.95  3.000
 SVQ  H82C  C8   N9    108.81  3.000
 SVQ  H81C  C8   N9    109.50  3.000
 SVQ  C7    C8   N9    112.48  3.000
 SVQ  H72C  C7   H71C  107.03  3.000
 SVQ  H72C  C7   C2    110.39  3.000
 SVQ  H71C  C7   C2    109.91  3.000
 SVQ  H72C  C7   C8    109.19  3.000
 SVQ  H71C  C7   C8    109.62  3.000
 SVQ  C2    C7   C8    110.62  3.000
 SVQ  C1    C2   C3    118.23  3.000
 SVQ  C1    C2   C7    120.73  3.000
 SVQ  C3    C2   C7    120.98  3.000
 SVQ  H3    C3   C4    118.84  3.000
 SVQ  H3    C3   C2    119.82  3.000
 SVQ  C4    C3   C2    121.34  3.000
 SVQ  H4    C4   C5    120.62  3.000
 SVQ  H4    C4   C3    120.35  3.000
 SVQ  C5    C4   C3    119.04  3.000
 SVQ  C6    C5   CL1   119.52  3.000
 SVQ  C6    C5   C4    121.02  3.000
 SVQ  CL1   C5   C4    119.46  3.000
 SVQ  H6    C6   C1    120.35  3.000
 SVQ  H6    C6   C5    120.64  3.000
 SVQ  C1    C6   C5    119.02  3.000
 SVQ  H1    C1   C6    118.95  3.000
 SVQ  H1    C1   C2    119.70  3.000
 SVQ  C6    C1   C2    121.35  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
 SVQ  CONST_01  C22  C23  C24  C25     0.00   0.0  0
 SVQ  CONST_02  C22  C21  C20  C25     0.00   0.0  0
 SVQ  CONST_03  C21  C20  C25  C24     0.00   0.0  0
 SVQ  CONST_04  C21  C22  C23  C24     0.00   0.0  0
 SVQ  CONST_05  C20  C25  C24  C23     0.00   0.0  0
 SVQ  CONST_06  C20  C21  C22  C23     0.00   0.0  0
 SVQ  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 SVQ  CONST_08  C5   C6   C1   C2      0.00   0.0  0
 SVQ  CONST_09  C6   C1   C2   C3      0.00   0.0  0
 SVQ  CONST_10  C6   C5   C4   C3      0.00   0.0  0
 SVQ  CONST_11  C1   C2   C3   C4      0.00   0.0  0
 SVQ  CONST_12  C1   C6   C5   C4      0.00   0.0  0
 SVQ  CONST_13  C14  C20  C25  C24   180.00   0.0  0
 SVQ  CONST_14  C14  C20  C21  C22   180.00   0.0  0
 SVQ  CONST_15  C11  C10  N9   C14     0.00   0.0  0
 SVQ  CONST_16  C23  C24  C25  CL2   180.00   0.0  0
 SVQ  CONST_17  C21  C20  C25  CL2   180.00   0.0  0
 SVQ  CONST_18  C14  C20  C25  CL2     0.00   0.0  0
 SVQ  CONST_19  C4   C3   C2   C7    180.00   0.0  0
 SVQ  CONST_20  C6   C1   C2   C7    180.00   0.0  0
 SVQ  CONST_21  CL1  C5   C4   C3    180.00   0.0  0
 SVQ  CONST_22  C1   C6   C5   CL1   180.00   0.0  0
 SVQ  CONST_23  O15  C10  N9   C14   180.00   0.0  0
 SVQ  CONST_24  C8   N9   C10  C11   180.00   0.0  0
 SVQ  CONST_25  H23  C23  C24  C25   180.00   0.0  0
 SVQ  CONST_26  H21  C21  C20  C25   180.00   0.0  0
 SVQ  CONST_27  H22  C22  C23  C24   180.00   0.0  0
 SVQ  CONST_28  H24  C24  C23  C22   180.00   0.0  0
 SVQ  CONST_29  H4   C4   C3   C2    180.00   0.0  0
 SVQ  CONST_30  H6   C6   C1   C2    180.00   0.0  0
 SVQ  CONST_31  H1   C1   C2   C3    180.00   0.0  0
 SVQ  CONST_32  H3   C3   C4   C5    180.00   0.0  0
 SVQ  CONST_33  C8   N9   C10  O15     0.00   0.0  0
 SVQ  Var_01    C10  C11  C12  C13    57.71  30.0  1
 SVQ  Var_02    N9   C10  C11  C12   -29.53  30.0  1
 SVQ  Var_03    C7   C8   N9   C14    83.57  30.0  3
 SVQ  Var_04    C2   C7   C8   N9   -176.79  30.0  3
 SVQ  Var_05    C3   C2   C7   C8     92.71  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
 SVQ  chir_01  C14  C20  C13  N9   negativ
 SVQ  chir_02  C13  C14  C17  C12  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
 SVQ  plan-1  CL2  0.020
 SVQ  plan-1  C25  0.020
 SVQ  plan-1  C24  0.020
 SVQ  plan-1  C23  0.020
 SVQ  plan-1  C22  0.020
 SVQ  plan-1  C21  0.020
 SVQ  plan-1  C20  0.020
 SVQ  plan-1  C14  0.020
 SVQ  plan-1  H24  0.020
 SVQ  plan-1  H23  0.020
 SVQ  plan-1  H22  0.020
 SVQ  plan-1  H21  0.020
 SVQ  plan-2  C7   0.020
 SVQ  plan-2  C2   0.020
 SVQ  plan-2  C3   0.020
 SVQ  plan-2  C4   0.020
 SVQ  plan-2  C5   0.020
 SVQ  plan-2  CL1  0.020
 SVQ  plan-2  C6   0.020
 SVQ  plan-2  C1   0.020
 SVQ  plan-2  H3   0.020
 SVQ  plan-2  H1   0.020
 SVQ  plan-2  H4   0.020
 SVQ  plan-2  H6   0.020
 SVQ  plan-3  C13  0.020
 SVQ  plan-3  C17  0.020
 SVQ  plan-3  O19  0.020
 SVQ  plan-3  O18  0.020
 SVQ  plan-4  C14  0.020
 SVQ  plan-4  C11  0.020
 SVQ  plan-4  C10  0.020
 SVQ  plan-4  O15  0.020
 SVQ  plan-4  N9   0.020
 SVQ  plan-4  C8   0.020

