# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 21:10:44 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 1-(5-carboxypentyl)-5-[(2,6-dichlorobenzyl)oxy]-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCn1c(cc2cc(OCc3c(Cl)cccc3Cl)ccc12)C(O)=O
#
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
 669  669  '1-(5-carboxypentyl)-5-[(2,6-dichlorobenzyl)oxy]-1H-indole-2-carboxylic acid'  ligand  51  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_669
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
 669  O01   O   OH1   0  -0.598   8.8356  -3.7583  -0.8461
 669  C02   C   C     0   0.550   8.0073  -3.0438  -0.0885
 669  O03   O   O     0  -0.446   8.0208  -3.0878   1.1166
 669  C04   C   CH2   0  -0.580   7.0820  -2.1959  -0.9162
 669  C05   C   CH2   0  -0.419   6.0682  -1.4152  -0.0963
 669  C06   C   CH2   0  -0.427   5.1692  -0.5584  -0.9794
 669  C07   C   CH2   0  -0.432   4.1061   0.1837  -0.1809
 669  C08   C   CH2   0  -0.315   3.2639   1.0859  -1.0737
 669  N09   N   NR5   0  -0.584   2.1430   1.6910  -0.3750
 669  C10   C   CR5   0   0.202   2.0990   2.8275   0.4071
 669  C11   C   CR15  0  -0.394   0.8435   2.9766   0.9445
 669  C12   C   CR56  0   0.087   0.0650   1.8827   0.4977
 669  C13   C   CR16  0  -0.448  -1.2656   1.5007   0.7065
 669  C14   C   CR6   0   0.387  -1.7248   0.3434   0.1113
 669  O15   O   O2    0  -0.473  -3.0130   0.0016   0.3645
 669  C16   C   CH2   0  -0.258  -3.6201  -0.9880  -0.4441
 669  C17   C   CR6   0   0.265  -5.0886  -0.9550  -0.1442
 669  C18   C   CR6   0  -0.134  -5.7261  -1.9098   0.6472
 669  CL9   CL  CL    0  -0.116  -4.8224  -3.2154   1.3436
 669  C20   C   CR16  0  -0.181  -7.0856  -1.8613   0.9173
 669  C21   C   CR16  0  -0.284  -7.8419  -0.8256   0.3973
 669  C22   C   CR16  0  -0.186  -7.2480   0.1542  -0.3818
 669  C23   C   CR6   0  -0.113  -5.8891   0.0786  -0.6346
 669  CL4   CL  CL    0  -0.109  -5.1726   1.3236  -1.6011
 669  C25   C   CR16  0  -0.382  -0.8689  -0.4365  -0.6958
 669  C26   C   CR16  0  -0.298   0.4420  -0.0690  -0.9169
 669  C27   C   CR56  0   0.355   0.9102   1.1005  -0.3174
 669  C28   C   C     0   0.515   3.1847   3.7795   0.6755
 669  O29   O   OH1   0  -0.593   4.3523   3.4559   0.1414
 669  O30   O   O     0  -0.438   3.0146   4.7733   1.3426
 669  H01   H   HOH1  0   0.478   9.4215  -4.2892  -0.2860
 669  H041  H   HCH2  0   0.278   7.6954  -1.5168  -1.5177
 669  H042  H   HCH2  0   0.275   6.5755  -2.8461  -1.6368
 669  H051  H   HCH2  0   0.229   5.4535  -2.1060   0.4866
 669  H052  H   HCH2  0   0.229   6.5840  -0.7740   0.6228
 669  H061  H   HCH2  0   0.223   5.7820   0.1592  -1.5351
 669  H062  H   HCH2  0   0.222   4.6825  -1.1908  -1.7295
 669  H071  H   HCH2  0   0.229   3.4535  -0.5385   0.3193
 669  H072  H   HCH2  0   0.232   4.5762   0.7804   0.6049
 669  H081  H   HCH2  0   0.273   3.8706   1.8614  -1.5332
 669  H082  H   HCH2  0   0.258   2.8487   0.5065  -1.8991
 669  H11   H   HCR5  0   0.263   0.5271   3.7835   1.5857
 669  H13   H   HCR6  0   0.257  -1.9254   2.0971   1.3245
 669  H161  H   HCH2  0   0.249  -3.4554  -0.7827  -1.5066
 669  H162  H   HCH2  0   0.250  -3.2056  -1.9767  -0.2377
 669  H20   H   HCR6  0   0.288  -7.5468  -2.6228   1.5301
 669  H21   H   HCR6  0   0.283  -8.9024  -0.7790   0.6034
 669  H22   H   HCR6  0   0.289  -7.8344   0.9675  -0.7858
 669  H25   H   HCR6  0   0.283  -1.2224  -1.3504  -1.1534
 669  H26   H   HCR6  0   0.271   1.0706  -0.6913  -1.5398
 669  H29   H   HOH1  0   0.491   5.0157   4.1251   0.3693

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
 669  O01  C02   single    1.331  0.020  1.331
 669  O01  H01   single    0.850  0.020  0.980
 669  C02  O03   double    1.206  0.020  1.206
 669  C02  C04   single    1.503  0.020  1.503
 669  C04  C05   single    1.520  0.020  1.520
 669  C04  H041  single    0.970  0.020  1.090
 669  C04  H042  single    0.970  0.020  1.090
 669  C05  C06   single    1.524  0.020  1.524
 669  C05  H051  single    0.970  0.020  1.090
 669  C05  H052  single    0.970  0.020  1.090
 669  C06  C07   single    1.523  0.020  1.523
 669  C06  H061  single    0.970  0.020  1.090
 669  C06  H062  single    0.970  0.020  1.090
 669  C07  C08   single    1.523  0.020  1.523
 669  C07  H071  single    0.970  0.020  1.090
 669  C07  H072  single    0.970  0.020  1.090
 669  C08  N09   single    1.453  0.020  1.453
 669  C08  H081  single    0.970  0.020  1.090
 669  C08  H082  single    0.970  0.020  1.090
 669  N09  C10   aromatic  1.380  0.020  1.380
 669  N09  C27   aromatic  1.368  0.020  1.368
 669  C10  C11   aromatic  1.374  0.020  1.374
 669  C10  C28   single    1.469  0.020  1.469
 669  C11  C12   aromatic  1.415  0.020  1.415
 669  C11  H11   single    0.930  0.020  1.080
 669  C12  C13   aromatic  1.400  0.020  1.400
 669  C12  C27   aromatic  1.411  0.020  1.411
 669  C13  C14   aromatic  1.380  0.020  1.380
 669  C13  H13   single    0.930  0.020  1.080
 669  C14  O15   single    1.357  0.020  1.357
 669  C14  C25   aromatic  1.411  0.020  1.411
 669  O15  C16   single    1.415  0.020  1.415
 669  C16  C17   single    1.499  0.020  1.499
 669  C16  H161  single    0.970  0.020  1.090
 669  C16  H162  single    0.970  0.020  1.090
 669  C17  C18   aromatic  1.394  0.020  1.394
 669  C17  C23   aromatic  1.396  0.020  1.396
 669  C18  CL9   single    1.734  0.020  1.734
 669  C18  C20   aromatic  1.387  0.020  1.387
 669  C20  C21   aromatic  1.384  0.020  1.384
 669  C20  H20   single    0.930  0.020  1.080
 669  C21  C22   aromatic  1.386  0.020  1.386
 669  C21  H21   single    0.930  0.020  1.080
 669  C22  C23   aromatic  1.384  0.020  1.384
 669  C22  H22   single    0.930  0.020  1.080
 669  C23  CL4   single    1.731  0.020  1.731
 669  C25  C26   aromatic  1.379  0.020  1.379
 669  C25  H25   single    0.930  0.020  1.080
 669  C26  C27   aromatic  1.395  0.020  1.395
 669  C26  H26   single    0.930  0.020  1.080
 669  C28  O29   single    1.324  0.020  1.324
 669  C28  O30   double    1.209  0.020  1.209
 669  O29  H29   single    0.850  0.020  0.980

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
 669  H01   O01  C02   109.97  3.000
 669  C04   C02  O03   125.28  3.000
 669  C04   C02  O01   111.87  3.000
 669  O03   C02  O01   122.85  3.000
 669  H042  C04  H041  105.42  3.000
 669  H042  C04  C05   110.58  3.000
 669  H041  C04  C05   110.58  3.000
 669  H042  C04  C02   108.19  3.000
 669  H041  C04  C02   107.90  3.000
 669  C05   C04  C02   113.79  3.000
 669  H052  C05  H051  106.58  3.000
 669  H052  C05  C06   109.27  3.000
 669  H051  C05  C06   109.43  3.000
 669  H052  C05  C04   109.97  3.000
 669  H051  C05  C04   109.77  3.000
 669  C06   C05  C04   111.70  3.000
 669  H062  C06  H061  106.23  3.000
 669  H062  C06  C07   109.29  3.000
 669  H061  C06  C07   109.72  3.000
 669  H062  C06  C05   109.54  3.000
 669  H061  C06  C05   109.41  3.000
 669  C07   C06  C05   112.46  3.000
 669  H072  C07  H071  106.75  3.000
 669  H072  C07  C08   109.63  3.000
 669  H071  C07  C08   109.21  3.000
 669  H072  C07  C06   110.05  3.000
 669  H071  C07  C06   109.53  3.000
 669  C08   C07  C06   111.55  3.000
 669  H082  C08  H081  105.77  3.000
 669  H082  C08  N09   106.95  3.000
 669  H081  C08  N09   109.68  3.000
 669  H082  C08  C07   109.84  3.000
 669  H081  C08  C07   111.21  3.000
 669  N09   C08  C07   113.04  3.000
 669  C27   N09  C10   107.62  3.000
 669  C27   N09  C08   122.39  3.000
 669  C10   N09  C08   129.80  3.000
 669  C28   C10  C11   122.26  3.000
 669  C28   C10  N09   127.85  3.000
 669  C11   C10  N09   109.89  3.000
 669  H11   C11  C12   127.22  3.000
 669  H11   C11  C10   125.60  3.000
 669  C12   C11  C10   107.18  3.000
 669  C27   C12  C13   120.28  3.000
 669  C27   C12  C11   106.34  3.000
 669  C13   C12  C11   133.37  3.000
 669  H13   C13  C14   120.34  3.000
 669  H13   C13  C12   120.92  3.000
 669  C14   C13  C12   118.73  3.000
 669  C25   C14  O15   122.91  3.000
 669  C25   C14  C13   120.55  3.000
 669  O15   C14  C13   116.53  3.000
 669  C16   O15  C14   118.48  3.000
 669  H162  C16  H161  107.24  3.000
 669  H162  C16  C17   110.73  3.000
 669  H161  C16  C17   109.72  3.000
 669  H162  C16  O15   111.25  3.000
 669  H161  C16  O15   111.04  3.000
 669  C17   C16  O15   106.89  3.000
 669  C23   C17  C18   116.37  3.000
 669  C23   C17  C16   120.51  3.000
 669  C18   C17  C16   123.11  3.000
 669  C20   C18  CL9   117.32  3.000
 669  C20   C18  C17   122.32  3.000
 669  CL9   C18  C17   120.35  3.000
 669  H20   C20  C21   120.47  3.000
 669  H20   C20  C18   120.27  3.000
 669  C21   C20  C18   119.26  3.000
 669  H21   C21  C22   119.80  3.000
 669  H21   C21  C20   119.78  3.000
 669  C22   C21  C20   120.42  3.000
 669  H22   C22  C23   120.36  3.000
 669  H22   C22  C21   120.64  3.000
 669  C23   C22  C21   119.00  3.000
 669  CL4   C23  C22   117.96  3.000
 669  CL4   C23  C17   119.41  3.000
 669  C22   C23  C17   122.62  3.000
 669  H25   C25  C26   117.91  3.000
 669  H25   C25  C14   120.71  3.000
 669  C26   C25  C14   121.38  3.000
 669  H26   C26  C27   122.32  3.000
 669  H26   C26  C25   119.42  3.000
 669  C27   C26  C25   118.26  3.000
 669  C26   C27  C12   120.80  3.000
 669  C26   C27  N09   130.25  3.000
 669  C12   C27  N09   108.96  3.000
 669  O30   C28  O29   123.20  3.000
 669  O30   C28  C10   121.98  3.000
 669  O29   C28  C10   114.82  3.000
 669  H29   O29  C28   109.87  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
 669  CONST_01  C12  C11  C10  N09     0.00   0.0  0
 669  CONST_02  C11  C12  C27  N09     0.00   0.0  0
 669  CONST_03  C13  C12  C27  N09   180.00   0.0  0
 669  CONST_04  C25  C26  C27  N09   180.00   0.0  0
 669  CONST_05  C12  C27  N09  C10     0.00   0.0  0
 669  CONST_06  C26  C27  N09  C10   180.00   0.0  0
 669  CONST_07  C13  C12  C11  C10   180.00   0.0  0
 669  CONST_08  C27  C12  C11  C10     0.00   0.0  0
 669  CONST_09  C27  N09  C10  C11     0.00   0.0  0
 669  CONST_10  C14  C13  C12  C11   180.00   0.0  0
 669  CONST_11  C26  C27  C12  C11   180.00   0.0  0
 669  CONST_12  C25  C14  C13  C12     0.00   0.0  0
 669  CONST_13  C25  C26  C27  C12     0.00   0.0  0
 669  CONST_14  C26  C27  C12  C13     0.00   0.0  0
 669  CONST_15  C26  C25  C14  C13     0.00   0.0  0
 669  CONST_16  C27  C12  C13  C14     0.00   0.0  0
 669  CONST_17  C27  C26  C25  C14     0.00   0.0  0
 669  CONST_18  C21  C20  C18  C17     0.00   0.0  0
 669  CONST_19  C21  C22  C23  C17     0.00   0.0  0
 669  CONST_20  C22  C23  C17  C18     0.00   0.0  0
 669  CONST_21  C22  C21  C20  C18     0.00   0.0  0
 669  CONST_22  C23  C17  C18  C20     0.00   0.0  0
 669  CONST_23  C23  C22  C21  C20     0.00   0.0  0
 669  CONST_24  C11  C10  N09  C08   180.00   0.0  0
 669  CONST_25  C12  C27  N09  C08   180.00   0.0  0
 669  CONST_26  C26  C27  N09  C08     0.00   0.0  0
 669  CONST_27  C28  C10  C11  C12   180.00   0.0  0
 669  CONST_28  O15  C14  C13  C12   180.00   0.0  0
 669  CONST_29  C26  C25  C14  O15   180.00   0.0  0
 669  CONST_30  C20  C18  C17  C16   180.00   0.0  0
 669  CONST_31  C22  C23  C17  C16   180.00   0.0  0
 669  CONST_32  CL4  C23  C17  C18   180.00   0.0  0
 669  CONST_33  C23  C17  C18  CL9   180.00   0.0  0
 669  CONST_34  C21  C20  C18  CL9   180.00   0.0  0
 669  CONST_35  CL4  C23  C22  C21   180.00   0.0  0
 669  CONST_36  C28  C10  N09  C27   180.00   0.0  0
 669  CONST_37  H11  C11  C10  N09   180.00   0.0  0
 669  CONST_38  H26  C26  C27  N09     0.00   0.0  0
 669  CONST_39  H13  C13  C12  C11     0.00   0.0  0
 669  CONST_40  H25  C25  C14  C13   180.00   0.0  0
 669  CONST_41  H20  C20  C18  C17   180.00   0.0  0
 669  CONST_42  H22  C22  C23  C17   180.00   0.0  0
 669  CONST_43  H21  C21  C20  C18   180.00   0.0  0
 669  CONST_44  H29  O29  C28  C10   180.00   0.0  0
 669  CONST_45  H01  O01  C02  O03     0.00   0.0  0
 669  Var_01    C10  N09  C08  C07    83.72  30.0  2
 669  Var_02    O29  C28  C10  N09    -3.29  30.0  2
 669  Var_03    C17  C16  O15  C14  -168.24  30.0  3
 669  Var_04    C18  C17  C16  O15  -103.86  30.0  2
 669  Var_05    C25  C14  O15  C16   -15.13  30.0  1
 669  Var_06    N09  C08  C07  C06   173.32  30.0  3
 669  Var_07    C05  C04  C02  O01   177.01  30.0  3
 669  Var_08    C06  C05  C04  C02   179.19  30.0  3
 669  Var_09    C07  C06  C05  C04   177.44  30.0  3
 669  Var_10    C08  C07  C06  C05   177.19  30.0  3

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
 669  plan-1  C16  0.020
 669  plan-1  C17  0.020
 669  plan-1  C18  0.020
 669  plan-1  CL9  0.020
 669  plan-1  C20  0.020
 669  plan-1  C21  0.020
 669  plan-1  C22  0.020
 669  plan-1  C23  0.020
 669  plan-1  CL4  0.020
 669  plan-1  H20  0.020
 669  plan-1  H21  0.020
 669  plan-1  H22  0.020
 669  plan-2  C08  0.020
 669  plan-2  N09  0.020
 669  plan-2  C10  0.020
 669  plan-2  C11  0.020
 669  plan-2  C12  0.020
 669  plan-2  C13  0.020
 669  plan-2  C14  0.020
 669  plan-2  O15  0.020
 669  plan-2  C25  0.020
 669  plan-2  C26  0.020
 669  plan-2  C27  0.020
 669  plan-2  C28  0.020
 669  plan-2  H11  0.020
 669  plan-2  H13  0.020
 669  plan-2  H25  0.020
 669  plan-2  H26  0.020
 669  plan-3  O01  0.020
 669  plan-3  C02  0.020
 669  plan-3  O03  0.020
 669  plan-3  C04  0.020
 669  plan-3  H01  0.020
 669  plan-4  C10  0.020
 669  plan-4  C28  0.020
 669  plan-4  O29  0.020
 669  plan-4  O30  0.020
 669  plan-4  H29  0.020

