# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:39:32 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[[(2~{R})-1-[4-(3-chlorophenyl)phenyl]-4-oxidanyl-4-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)N[C@@H](CC(O)=O)Cc1ccc(cc1)c2cccc(Cl)c2
#
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
 N9Q  N9Q  '4-[[(2~{R})-1-[4-(3-chlorophenyl)phenyl]-4-oxidanyl-4-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butanoic acid'  ligand  45  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N9Q
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
 N9Q  C2   C   CR6    0  -0.020  -4.7704   0.6557  -0.4257
 N9Q  C3   C   CR16   0  -0.270  -3.4843   0.2619  -0.0976
 N9Q  C41  C   CH2    0  -0.567   4.7679  -1.8854   0.6552
 N9Q  C44  C   C      0   0.409   5.7923  -1.0579  -0.1412
 N9Q  C12  C   C      0   0.076  -1.7013  -1.4724  -0.0028
 N9Q  C13  C   C1     0  -0.297  -0.9928  -2.3622  -0.8116
 N9Q  C15  C   C1     0  -0.276   0.2987  -2.7416  -0.4864
 N9Q  C17  C   C      0   0.136   0.9251  -2.2579   0.6588
 N9Q  C18  C   C1     0  -0.294   0.2072  -1.3907   1.4776
 N9Q  C20  C   C1     0  -0.294  -1.0811  -0.9987   1.1524
 N9Q  C22  C   CH2    0  -0.508   2.3580  -2.5846   0.9548
 N9Q  C25  C   CH1    0  -0.067   3.3272  -1.6182   0.2454
 N9Q  CL1  CL  CL     0  -0.130  -5.2599   2.2871  -0.0963
 N9Q  C5   C   CR6    0   0.087  -3.0689  -1.0449  -0.3570
 N9Q  C6   C   CR16   0  -0.305  -3.9708  -1.9270  -0.9541
 N9Q  C8   C   CR16   0  -0.245  -5.2535  -1.5144  -1.2795
 N9Q  C10  C   CR16   0  -0.230  -5.6698  -0.2167  -1.0179
 N9Q  N27  N   NH1    0  -0.636   2.9735  -0.2444   0.5309
 N9Q  O30  O   O      0  -0.495   1.8964   0.2065  -1.4053
 N9Q  C31  C   CH2    0  -0.576   1.7310   1.8118   0.3853
 N9Q  C34  C   CH2    0  -0.580   0.8336   2.6552  -0.4971
 N9Q  C37  C   C      0   0.416   0.3350   3.9628   0.1427
 N9Q  O38  O   OC    -1  -0.632  -0.3480   4.7015  -0.5977
 N9Q  O39  O   O      0  -0.610   0.6333   4.1856   1.3330
 N9Q  O45  O   OC    -1  -0.621   6.7270  -0.5395   0.5030
 N9Q  O46  O   O      0  -0.609   5.6190  -0.9967  -1.3744
 N9Q  H1   H   HCR6   0   0.268  -2.8000   0.9746   0.3441
 N9Q  H2   H   HCH2   0   0.233   4.9799  -2.9482   0.4909
 N9Q  H3   H   HCH2   0   0.206   4.8837  -1.7146   1.7302
 N9Q  H4   H   H      0   0.249  -1.4427  -2.7412  -1.7213
 N9Q  H5   H   H      0   0.242   0.8352  -3.4149  -1.1453
 N9Q  H6   H   H      0   0.246   0.6609  -1.0113   2.3856
 N9Q  H7   H   H      0   0.251  -1.6138  -0.3334   1.8209
 N9Q  H8   H   HCH2   0   0.237   2.5368  -2.5403   2.0335
 N9Q  H9   H   HCH2   0   0.245   2.5924  -3.6032   0.6354
 N9Q  H10  H   HCH1   0   0.245   3.2377  -1.7548  -0.8310
 N9Q  H11  H   HCR6   0   0.259  -3.6763  -2.9501  -1.1487
 N9Q  H12  H   HCR6   0   0.269  -5.9443  -2.2120  -1.7345
 N9Q  H13  H   HCR6   0   0.280  -6.6707   0.1054  -1.2698
 N9Q  H14  H   HNH1   0   0.381   3.1254   0.0735   1.4764
 N9Q  H15  H   HCH2   0   0.247   1.2097   1.5512   1.3107
 N9Q  H16  H   HCH2   0   0.251   2.6109   2.3810   0.6999
 N9Q  H17  H   HCH2   0   0.224   1.3431   2.9017  -1.4330
 N9Q  H18  H   HCH2   0   0.226  -0.0445   2.0734  -0.7972
 N9Q  C29  C   C      0   0.576   2.1950   0.5218  -0.2638

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
 N9Q  C8   C10  aromatic  1.388  0.020  1.388
 N9Q  C8   C6   aromatic  1.386  0.020  1.386
 N9Q  C10  C2   aromatic  1.386  0.020  1.386
 N9Q  C6   C5   aromatic  1.396  0.020  1.396
 N9Q  C2   CL1  single    1.735  0.020  1.735
 N9Q  C2   C3   aromatic  1.384  0.020  1.384
 N9Q  C5   C3   aromatic  1.396  0.020  1.396
 N9Q  C5   C12  single    1.476  0.020  1.476
 N9Q  C12  C13  aromatic  1.396  0.020  1.396
 N9Q  C12  C20  aromatic  1.394  0.020  1.394
 N9Q  C13  C15  aromatic  1.385  0.020  1.385
 N9Q  C20  C18  aromatic  1.385  0.020  1.385
 N9Q  C15  C17  aromatic  1.392  0.020  1.392
 N9Q  C18  C17  aromatic  1.392  0.020  1.392
 N9Q  C17  C22  single    1.499  0.020  1.499
 N9Q  C22  C25  single    1.542  0.020  1.542
 N9Q  C25  N27  single    1.447  0.020  1.447
 N9Q  C25  C41  single    1.522  0.020  1.522
 N9Q  O30  C29  double    1.221  0.020  1.221
 N9Q  N27  C29  single    1.351  0.020  1.351
 N9Q  O46  C44  deloc     1.247  0.020  1.247
 N9Q  C29  C31  single    1.517  0.020  1.517
 N9Q  C41  C44  single    1.539  0.020  1.539
 N9Q  C31  C34  single    1.515  0.020  1.515
 N9Q  C44  O45  deloc     1.248  0.020  1.248
 N9Q  O39  C37  deloc     1.247  0.020  1.247
 N9Q  C34  C37  single    1.539  0.020  1.539
 N9Q  C37  O38  deloc     1.249  0.020  1.249
 N9Q  C3   H1   single    0.930  0.020  1.080
 N9Q  C41  H2   single    0.970  0.020  1.090
 N9Q  C41  H3   single    0.970  0.020  1.090
 N9Q  C13  H4   single    0.930  0.020  1.080
 N9Q  C15  H5   single    0.930  0.020  1.080
 N9Q  C18  H6   single    0.930  0.020  1.080
 N9Q  C20  H7   single    0.930  0.020  1.080
 N9Q  C22  H8   single    0.970  0.020  1.090
 N9Q  C22  H9   single    0.970  0.020  1.090
 N9Q  C25  H10  single    0.970  0.020  1.090
 N9Q  C6   H11  single    0.930  0.020  1.080
 N9Q  C8   H12  single    0.930  0.020  1.080
 N9Q  C10  H13  single    0.930  0.020  1.080
 N9Q  N27  H14  single    0.860  0.020  1.020
 N9Q  C31  H15  single    0.970  0.020  1.090
 N9Q  C31  H16  single    0.970  0.020  1.090
 N9Q  C34  H17  single    0.970  0.020  1.090
 N9Q  C34  H18  single    0.970  0.020  1.090

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
 N9Q  C10  C2   CL1  119.34  3.000
 N9Q  CL1  C2   C3   118.99  3.000
 N9Q  C10  C2   C3   121.67  3.000
 N9Q  H1   C3   C5   120.29  3.000
 N9Q  H1   C3   C2   119.78  3.000
 N9Q  C5   C3   C2   119.92  3.000
 N9Q  H3   C41  H2   106.15  3.000
 N9Q  H3   C41  C25  109.71  3.000
 N9Q  H2   C41  C25  108.24  3.000
 N9Q  H3   C41  C44  110.73  3.000
 N9Q  H2   C41  C44  108.36  3.000
 N9Q  C25  C41  C44  113.36  3.000
 N9Q  O46  C44  O45  126.46  3.000
 N9Q  O45  C44  C41  117.05  3.000
 N9Q  O46  C44  C41  116.47  3.000
 N9Q  C5   C12  C20  120.84  3.000
 N9Q  C20  C12  C13  118.10  3.000
 N9Q  C5   C12  C13  121.06  3.000
 N9Q  H4   C13  C15  119.26  3.000
 N9Q  H4   C13  C12  119.93  3.000
 N9Q  C15  C13  C12  120.79  3.000
 N9Q  H5   C15  C17  119.55  3.000
 N9Q  H5   C15  C13  119.27  3.000
 N9Q  C17  C15  C13  121.18  3.000
 N9Q  C22  C17  C18  120.83  3.000
 N9Q  C22  C17  C15  121.12  3.000
 N9Q  C18  C17  C15  117.93  3.000
 N9Q  H6   C18  C20  119.15  3.000
 N9Q  H6   C18  C17  119.67  3.000
 N9Q  C20  C18  C17  121.18  3.000
 N9Q  H7   C20  C18  119.09  3.000
 N9Q  H7   C20  C12  120.09  3.000
 N9Q  C18  C20  C12  120.80  3.000
 N9Q  H9   C22  H8   106.90  3.000
 N9Q  H9   C22  C25  108.36  3.000
 N9Q  H8   C22  C25  109.00  3.000
 N9Q  H9   C22  C17  110.51  3.000
 N9Q  H8   C22  C17  110.00  3.000
 N9Q  C25  C22  C17  111.93  3.000
 N9Q  H10  C25  N27  107.10  3.000
 N9Q  H10  C25  C22  108.94  3.000
 N9Q  N27  C25  C22  110.53  3.000
 N9Q  H10  C25  C41  108.79  3.000
 N9Q  N27  C25  C41  110.18  3.000
 N9Q  C22  C25  C41  111.18  3.000
 N9Q  C6   C5   C12  121.22  3.000
 N9Q  C12  C5   C3   120.16  3.000
 N9Q  C6   C5   C3   118.62  3.000
 N9Q  H11  C6   C8   119.40  3.000
 N9Q  H11  C6   C5   119.90  3.000
 N9Q  C8   C6   C5   120.68  3.000
 N9Q  H12  C8   C10  119.38  3.000
 N9Q  H12  C8   C6   119.84  3.000
 N9Q  C10  C8   C6   120.77  3.000
 N9Q  H13  C10  C8   120.81  3.000
 N9Q  H13  C10  C2   120.86  3.000
 N9Q  C8   C10  C2   118.33  3.000
 N9Q  H14  N27  C29  117.34  3.000
 N9Q  H14  N27  C25  116.56  3.000
 N9Q  C29  N27  C25  124.29  3.000
 N9Q  H16  C31  H15  105.31  3.000
 N9Q  H16  C31  C34  110.74  3.000
 N9Q  H15  C31  C34  110.07  3.000
 N9Q  H16  C31  C29  108.63  3.000
 N9Q  H15  C31  C29  107.77  3.000
 N9Q  C34  C31  C29  113.91  3.000
 N9Q  H18  C34  H17  105.00  3.000
 N9Q  H18  C34  C37  107.79  3.000
 N9Q  H17  C34  C37  108.37  3.000
 N9Q  H18  C34  C31  109.80  3.000
 N9Q  H17  C34  C31  110.36  3.000
 N9Q  C37  C34  C31  115.01  3.000
 N9Q  O39  C37  O38  126.21  3.000
 N9Q  O38  C37  C34  115.68  3.000
 N9Q  O39  C37  C34  118.11  3.000
 N9Q  C31  C29  O30  123.01  3.000
 N9Q  C31  C29  N27  114.01  3.000
 N9Q  O30  C29  N27  122.98  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
 N9Q  CONST_01  C6   C8   C10  C2      0.00   0.0  0
 N9Q  CONST_02  C6   C5   C3   C2      0.00   0.0  0
 N9Q  CONST_03  C12  C5   C3   C2    180.00   0.0  0
 N9Q  CONST_04  C8   C10  C2   C3      0.00   0.0  0
 N9Q  CONST_05  C8   C6   C5   C3      0.00   0.0  0
 N9Q  CONST_08  C8   C6   C5   C12   180.00   0.0  0
 N9Q  CONST_09  C17  C15  C13  C12     0.00   0.0  0
 N9Q  CONST_10  C17  C18  C20  C12     0.00   0.0  0
 N9Q  CONST_12  C18  C20  C12  C13     0.00   0.0  0
 N9Q  CONST_13  C18  C17  C15  C13     0.00   0.0  0
 N9Q  CONST_14  C5   C12  C13  C15   180.00   0.0  0
 N9Q  CONST_15  C20  C12  C13  C15     0.00   0.0  0
 N9Q  CONST_16  C20  C18  C17  C15     0.00   0.0  0
 N9Q  CONST_17  C5   C12  C20  C18   180.00   0.0  0
 N9Q  CONST_19  C10  C8   C6   C5      0.00   0.0  0
 N9Q  CONST_20  C10  C2   C3   C5      0.00   0.0  0
 N9Q  CONST_21  C22  C17  C15  C13   180.00   0.0  0
 N9Q  CONST_22  C22  C17  C18  C20   180.00   0.0  0
 N9Q  CONST_23  C8   C10  C2   CL1   180.00   0.0  0
 N9Q  CONST_24  C5   C3   C2   CL1   180.00   0.0  0
 N9Q  CONST_25  H12  C8   C10  C2    180.00   0.0  0
 N9Q  CONST_26  H13  C10  C2   C3    180.00   0.0  0
 N9Q  CONST_27  H11  C6   C5   C3    180.00   0.0  0
 N9Q  CONST_28  H1   C3   C5   C12     0.00   0.0  0
 N9Q  CONST_29  H5   C15  C13  C12   180.00   0.0  0
 N9Q  CONST_30  H6   C18  C20  C12   180.00   0.0  0
 N9Q  CONST_31  H7   C20  C12  C13   180.00   0.0  0
 N9Q  CONST_32  H4   C13  C15  C17   180.00   0.0  0
 N9Q  CONST_33  O30  C29  N27  C25     0.00   0.0  0
 N9Q  CONST_34  C31  C29  N27  C25   180.00   0.0  0
 N9Q  CONST_35  H14  N27  C29  O30   180.00   0.0  0
 N9Q  Var_01    C25  C22  C17  C15    84.88  30.0  2
 N9Q  Var_02    O46  C44  C41  C25   -44.77  30.0  3
 N9Q  Var_03    C37  C34  C31  C29   179.34  30.0  3
 N9Q  Var_04    C34  C31  C29  N27  -178.75  30.0  3
 N9Q  Var_05    O39  C37  C34  C31    -4.07  30.0  3

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
 N9Q  chir_01  C25  C22  N27  C41  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
 N9Q  plan-1  C12  0.020
 N9Q  plan-1  C13  0.020
 N9Q  plan-1  C15  0.020
 N9Q  plan-1  C17  0.020
 N9Q  plan-1  C18  0.020
 N9Q  plan-1  C20  0.020
 N9Q  plan-1  C22  0.020
 N9Q  plan-1  C5   0.020
 N9Q  plan-1  H4   0.020
 N9Q  plan-1  H5   0.020
 N9Q  plan-1  H6   0.020
 N9Q  plan-1  H7   0.020
 N9Q  plan-2  C2   0.020
 N9Q  plan-2  C3   0.020
 N9Q  plan-2  C12  0.020
 N9Q  plan-2  CL1  0.020
 N9Q  plan-2  C5   0.020
 N9Q  plan-2  C6   0.020
 N9Q  plan-2  C8   0.020
 N9Q  plan-2  C10  0.020
 N9Q  plan-2  H1   0.020
 N9Q  plan-2  H11  0.020
 N9Q  plan-2  H12  0.020
 N9Q  plan-2  H13  0.020
 N9Q  plan-3  C25  0.020
 N9Q  plan-3  N27  0.020
 N9Q  plan-3  O30  0.020
 N9Q  plan-3  C31  0.020
 N9Q  plan-3  H14  0.020
 N9Q  plan-3  C29  0.020
 N9Q  plan-4  C41  0.020
 N9Q  plan-4  C44  0.020
 N9Q  plan-4  O45  0.020
 N9Q  plan-4  O46  0.020
 N9Q  plan-5  C34  0.020
 N9Q  plan-5  C37  0.020
 N9Q  plan-5  O38  0.020
 N9Q  plan-5  O39  0.020

