# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:15:42 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 6-[3-(1-adamantyl)-4-oxidanyl-phenyl]naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2cc(ccc2c1)c3ccc(O)c(c3)C45CC6CC(CC(C6)C4)C5
#
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
 E9T  E9T  '6-[3-(1-adamantyl)-4-oxidanyl-phenyl]naphthalene-2-carboxylic acid'  ligand  56  30  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9T
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
 E9T  C4   C  CR16  0  -0.292   2.7635   1.1539  -1.0801
 E9T  C5   C  CR66  0   0.122   3.8512   0.5163  -0.4386
 E9T  C6   C  CR66  0   0.154   3.6295  -0.7293   0.2013
 E9T  C7   C  CR16  0  -0.306   4.7154  -1.3615   0.8532
 E9T  C8   C  CR16  0  -0.266   5.9553  -0.7898   0.8696
 E9T  C9   C  CR6   0  -0.091   6.1781   0.4529   0.2265
 E9T  C10  C  CR16  0  -0.322   5.1395   1.0840  -0.4146
 E9T  C11  C  C     0   0.536   7.5063   1.1116   0.2213
 E9T  C15  C  CH2   0  -0.416  -5.3359   2.3895  -0.9216
 E9T  C1   C  CR16  0  -0.312   1.5226   0.5860  -1.0762
 E9T  C2   C  CR6   0   0.100   1.2841  -0.6580  -0.4339
 E9T  C3   C  CR16  0  -0.393   2.3362  -1.2922   0.1864
 E9T  O12  O  O     0  -0.440   7.7369   2.1613  -0.3314
 E9T  O13  O  OH1   0  -0.595   8.4244   0.4287   0.8911
 E9T  C16  C  CH1   0  -0.248  -5.8400   0.9522  -1.0331
 E9T  C17  C  CH2   0  -0.409  -4.6563   0.0070  -1.2559
 E9T  C19  C  CH2   0  -0.435  -3.1995   1.5297   0.0528
 E9T  C20  C  CH1   0  -0.242  -4.3737   2.4871   0.2610
 E9T  C21  C  CH2   0  -0.415  -6.5719   0.5699   0.2561
 E9T  C22  C  CH1   0  -0.249  -5.6131   0.6845   1.4435
 E9T  C23  C  CH2   0  -0.408  -4.4308  -0.2668   1.2393
 E9T  C24  C  CH2   0  -0.415  -5.1062   2.1218   1.5518
 E9T  C25  C  CR6   0   0.139  -2.5019  -0.8908  -0.2619
 E9T  C26  C  CR6   0   0.303  -2.6653  -2.2850  -0.3808
 E9T  C27  C  CR16  0  -0.365  -1.5586  -3.1218  -0.5104
 E9T  C28  C  CR16  0  -0.323  -0.2738  -2.6125  -0.5298
 E9T  C29  C  CR6   0   0.111  -0.0693  -1.2414  -0.4292
 E9T  C30  C  CR16  0  -0.411  -1.1923  -0.4218  -0.3022
 E9T  H1   H  HCR6  0   0.261   2.9286   2.0987  -1.5833
 E9T  H2   H  HCR6  0   0.261   4.5504  -2.3111   1.3470
 E9T  H3   H  HCR6  0   0.267   6.7635  -1.2950   1.3792
 E9T  H4   H  HCR6  0   0.265   5.3014   2.0346  -0.9076
 E9T  H6   H  HCH2  0   0.220  -6.1754   3.0788  -0.7850
 E9T  H7   H  HCR6  0   0.258   0.7102   1.0821  -1.5917
 E9T  H8   H  HCR6  0   0.255   2.1769  -2.2317   0.7027
 E9T  H9   H  HOH1  0   0.488   9.2723   0.8964   0.8606
 E9T  H11  H  HCH1  0   0.221  -6.5246   0.8649  -1.8826
 E9T  H12  H  HCH2  0   0.241  -5.0282  -1.0074  -1.4011
 E9T  H13  H  HCH2  0   0.220  -4.1288   0.2859  -2.1742
 E9T  H14  H  HCH2  0   0.229  -2.5074   1.6349   0.8946
 E9T  H15  H  HCH2  0   0.227  -2.6513   1.8247  -0.8483
 E9T  H16  H  HCH1  0   0.222  -3.9814   3.5061   0.3338
 E9T  H17  H  HCH2  0   0.221  -7.4344   1.2281   0.4051
 E9T  H18  H  HCH2  0   0.220  -6.9620  -0.4505   0.1819
 E9T  H19  H  HCH1  0   0.221  -6.1322   0.4053   2.3653
 E9T  H20  H  HCH2  0   0.240  -4.7961  -1.2938   1.2220
 E9T  H21  H  HCH2  0   0.220  -3.7388  -0.1905   2.0847
 E9T  H22  H  HCH2  0   0.220  -4.4319   2.2207   2.4093
 E9T  H23  H  HCH2  0   0.220  -5.9391   2.8118   1.7238
 E9T  H24  H  HCR6  0   0.268  -1.7081  -4.1922  -0.6039
 E9T  H25  H  HCR6  0   0.256   0.5619  -3.2910  -0.6455
 E9T  H26  H  HCR6  0   0.255  -1.0229   0.6399  -0.2009
 E9T  O14  O  OH1   0  -0.627  -3.9063  -2.8119  -0.3657
 E9T  C18  C  CT    0  -0.152  -3.6747   0.0685  -0.0653
 E9T  H5   H  HCH2  0   0.220  -4.8302   2.6860  -1.8461
 E9T  H10  H  HOH1  0   0.474  -3.8599  -3.7726  -0.4297

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
 E9T  O12  C11  double    1.209  0.020  1.209
 E9T  C8   C7   aromatic  1.366  0.020  1.366
 E9T  C8   C9   aromatic  1.417  0.020  1.417
 E9T  C11  C9   single    1.483  0.020  1.483
 E9T  C11  O13  single    1.326  0.020  1.326
 E9T  C7   C6   aromatic  1.416  0.020  1.416
 E9T  C9   C10  aromatic  1.374  0.020  1.374
 E9T  C10  C5   aromatic  1.408  0.020  1.408
 E9T  C6   C5   aromatic  1.418  0.020  1.418
 E9T  C6   C3   aromatic  1.411  0.020  1.411
 E9T  C5   C4   aromatic  1.415  0.020  1.415
 E9T  C3   C2   aromatic  1.376  0.020  1.376
 E9T  C4   C1   aromatic  1.365  0.020  1.365
 E9T  C2   C1   aromatic  1.420  0.020  1.420
 E9T  C2   C29  single    1.474  0.020  1.474
 E9T  C28  C29  aromatic  1.390  0.020  1.390
 E9T  C28  C27  aromatic  1.382  0.020  1.382
 E9T  C29  C30  aromatic  1.396  0.020  1.396
 E9T  C27  C26  aromatic  1.393  0.020  1.393
 E9T  C30  C25  aromatic  1.392  0.020  1.392
 E9T  C26  C25  aromatic  1.409  0.020  1.409
 E9T  C26  O14  single    1.348  0.020  1.348
 E9T  C25  C18  single    1.528  0.020  1.528
 E9T  C17  C18  single    1.544  0.020  1.544
 E9T  C17  C16  single    1.531  0.020  1.531
 E9T  C19  C18  single    1.541  0.020  1.541
 E9T  C19  C20  single    1.529  0.020  1.529
 E9T  C18  C23  single    1.545  0.020  1.545
 E9T  C15  C16  single    1.527  0.020  1.527
 E9T  C15  C20  single    1.528  0.020  1.528
 E9T  C16  C21  single    1.531  0.020  1.531
 E9T  C20  C24  single    1.528  0.020  1.528
 E9T  C23  C22  single    1.531  0.020  1.531
 E9T  C21  C22  single    1.530  0.020  1.530
 E9T  C24  C22  single    1.528  0.020  1.528
 E9T  C4   H1   single    0.930  0.020  1.080
 E9T  C7   H2   single    0.930  0.020  1.080
 E9T  C8   H3   single    0.930  0.020  1.080
 E9T  C10  H4   single    0.930  0.020  1.080
 E9T  C15  H5   single    0.970  0.020  1.090
 E9T  C15  H6   single    0.970  0.020  1.090
 E9T  C1   H7   single    0.930  0.020  1.080
 E9T  C3   H8   single    0.930  0.020  1.080
 E9T  O13  H9   single    0.850  0.020  0.980
 E9T  O14  H10  single    0.850  0.020  0.980
 E9T  C16  H11  single    0.970  0.020  1.090
 E9T  C17  H12  single    0.970  0.020  1.090
 E9T  C17  H13  single    0.970  0.020  1.090
 E9T  C19  H14  single    0.970  0.020  1.090
 E9T  C19  H15  single    0.970  0.020  1.090
 E9T  C20  H16  single    0.970  0.020  1.090
 E9T  C21  H17  single    0.970  0.020  1.090
 E9T  C21  H18  single    0.970  0.020  1.090
 E9T  C22  H19  single    0.970  0.020  1.090
 E9T  C23  H20  single    0.970  0.020  1.090
 E9T  C23  H21  single    0.970  0.020  1.090
 E9T  C24  H22  single    0.970  0.020  1.090
 E9T  C24  H23  single    0.970  0.020  1.090
 E9T  C27  H24  single    0.930  0.020  1.080
 E9T  C28  H25  single    0.930  0.020  1.080
 E9T  C30  H26  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
 E9T  H1   C4   C1   120.20  3.000
 E9T  H1   C4   C5   119.12  3.000
 E9T  C1   C4   C5   120.68  3.000
 E9T  C10  C5   C6   119.32  3.000
 E9T  C6   C5   C4   118.71  3.000
 E9T  C10  C5   C4   121.97  3.000
 E9T  C3   C6   C7   122.00  3.000
 E9T  C3   C6   C5   119.29  3.000
 E9T  C7   C6   C5   118.70  3.000
 E9T  H2   C7   C8   120.00  3.000
 E9T  H2   C7   C6   119.00  3.000
 E9T  C8   C7   C6   121.01  3.000
 E9T  H3   C8   C9   120.43  3.000
 E9T  H3   C8   C7   119.28  3.000
 E9T  C9   C8   C7   120.30  3.000
 E9T  C11  C9   C10  118.13  3.000
 E9T  C10  C9   C8   119.73  3.000
 E9T  C11  C9   C8   122.15  3.000
 E9T  H4   C10  C9   120.17  3.000
 E9T  H4   C10  C5   118.88  3.000
 E9T  C9   C10  C5   120.95  3.000
 E9T  O13  C11  O12  123.11  3.000
 E9T  O13  C11  C9   112.94  3.000
 E9T  O12  C11  C9   123.95  3.000
 E9T  H6   C15  H5   106.80  3.000
 E9T  H6   C15  C20  110.25  3.000
 E9T  H5   C15  C20  110.21  3.000
 E9T  H6   C15  C16  110.40  3.000
 E9T  H5   C15  C16  110.23  3.000
 E9T  C20  C15  C16  108.94  3.000
 E9T  H7   C1   C2   119.39  3.000
 E9T  H7   C1   C4   119.36  3.000
 E9T  C2   C1   C4   121.23  3.000
 E9T  C29  C2   C3   121.21  3.000
 E9T  C29  C2   C1   120.16  3.000
 E9T  C3   C2   C1   118.63  3.000
 E9T  H8   C3   C2   120.12  3.000
 E9T  H8   C3   C6   118.40  3.000
 E9T  C2   C3   C6   121.46  3.000
 E9T  H9   O13  C11  109.96  3.000
 E9T  H11  C16  C21  109.55  3.000
 E9T  H11  C16  C17  108.75  3.000
 E9T  C21  C16  C17  109.75  3.000
 E9T  H11  C16  C15  109.77  3.000
 E9T  C21  C16  C15  109.35  3.000
 E9T  C17  C16  C15  109.66  3.000
 E9T  H13  C17  H12  106.83  3.000
 E9T  H13  C17  C18  109.28  3.000
 E9T  H12  C17  C18  110.89  3.000
 E9T  H13  C17  C16  109.70  3.000
 E9T  H12  C17  C16  109.28  3.000
 E9T  C18  C17  C16  110.77  3.000
 E9T  H15  C19  H14  106.88  3.000
 E9T  H15  C19  C20  109.13  3.000
 E9T  H14  C19  C20  108.70  3.000
 E9T  H15  C19  C18  110.29  3.000
 E9T  H14  C19  C18  110.18  3.000
 E9T  C20  C19  C18  111.54  3.000
 E9T  H16  C20  C24  109.77  3.000
 E9T  H16  C20  C19  108.46  3.000
 E9T  C24  C20  C19  109.47  3.000
 E9T  H16  C20  C15  109.68  3.000
 E9T  C24  C20  C15  109.68  3.000
 E9T  C19  C20  C15  109.76  3.000
 E9T  H18  C21  H17  106.78  3.000
 E9T  H18  C21  C22  110.21  3.000
 E9T  H17  C21  C22  110.05  3.000
 E9T  H18  C21  C16  110.24  3.000
 E9T  H17  C21  C16  109.94  3.000
 E9T  C22  C21  C16  109.58  3.000
 E9T  H19  C22  C24  109.74  3.000
 E9T  H19  C22  C23  108.67  3.000
 E9T  C24  C22  C23  109.74  3.000
 E9T  H19  C22  C21  109.71  3.000
 E9T  C24  C22  C21  109.47  3.000
 E9T  C23  C22  C21  109.49  3.000
 E9T  H21  C23  H20  106.84  3.000
 E9T  H21  C23  C22  109.98  3.000
 E9T  H20  C23  C22  109.19  3.000
 E9T  H21  C23  C18  109.12  3.000
 E9T  H20  C23  C18  110.80  3.000
 E9T  C22  C23  C18  110.84  3.000
 E9T  H23  C24  H22  106.76  3.000
 E9T  H23  C24  C22  110.58  3.000
 E9T  H22  C24  C22  110.16  3.000
 E9T  H23  C24  C20  110.28  3.000
 E9T  H22  C24  C20  110.15  3.000
 E9T  C22  C24  C20  108.90  3.000
 E9T  C30  C25  C26  116.12  3.000
 E9T  C26  C25  C18  122.90  3.000
 E9T  C30  C25  C18  120.97  3.000
 E9T  C27  C26  C25  120.66  3.000
 E9T  C25  C26  O14  119.51  3.000
 E9T  C27  C26  O14  119.83  3.000
 E9T  H24  C27  C28  119.37  3.000
 E9T  H24  C27  C26  119.41  3.000
 E9T  C28  C27  C26  121.22  3.000
 E9T  H25  C28  C29  120.82  3.000
 E9T  H25  C28  C27  119.22  3.000
 E9T  C29  C28  C27  119.94  3.000
 E9T  C30  C29  C28  117.86  3.000
 E9T  C30  C29  C2   120.44  3.000
 E9T  C28  C29  C2   121.69  3.000
 E9T  H26  C30  C29  117.36  3.000
 E9T  H26  C30  C25  118.44  3.000
 E9T  C29  C30  C25  124.18  3.000
 E9T  H10  O14  C26  110.14  3.000
 E9T  C25  C18  C23  110.37  3.000
 E9T  C23  C18  C19  106.98  3.000
 E9T  C25  C18  C19  111.62  3.000
 E9T  C23  C18  C17  109.35  3.000
 E9T  C19  C18  C17  107.03  3.000
 E9T  C25  C18  C17  111.33  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
 E9T  CONST_01  C9   C10  C5   C4   180.00   0.0  0
 E9T  CONST_02  C7   C6   C5   C4   180.00   0.0  0
 E9T  CONST_03  C3   C6   C5   C4     0.00   0.0  0
 E9T  CONST_04  C3   C2   C1   C4     0.00   0.0  0
 E9T  CONST_05  C29  C2   C1   C4   180.00   0.0  0
 E9T  CONST_06  C8   C9   C10  C5     0.00   0.0  0
 E9T  CONST_07  C8   C7   C6   C5     0.00   0.0  0
 E9T  CONST_08  C2   C3   C6   C5     0.00   0.0  0
 E9T  CONST_09  C2   C1   C4   C5     0.00   0.0  0
 E9T  CONST_10  C9   C8   C7   C6     0.00   0.0  0
 E9T  CONST_11  C9   C10  C5   C6     0.00   0.0  0
 E9T  CONST_12  C1   C4   C5   C6     0.00   0.0  0
 E9T  CONST_13  C1   C2   C3   C6     0.00   0.0  0
 E9T  CONST_14  C29  C2   C3   C6   180.00   0.0  0
 E9T  CONST_15  C10  C9   C8   C7     0.00   0.0  0
 E9T  CONST_16  C10  C5   C6   C7     0.00   0.0  0
 E9T  CONST_17  C2   C3   C6   C7   180.00   0.0  0
 E9T  CONST_18  C3   C6   C7   C8   180.00   0.0  0
 E9T  CONST_19  C3   C6   C5   C10  180.00   0.0  0
 E9T  CONST_20  C1   C4   C5   C10  180.00   0.0  0
 E9T  CONST_23  C27  C28  C29  C2   180.00   0.0  0
 E9T  CONST_24  C25  C30  C29  C2   180.00   0.0  0
 E9T  CONST_27  C28  C29  C30  C25    0.00   0.0  0
 E9T  CONST_28  C28  C27  C26  C25    0.00   0.0  0
 E9T  CONST_29  C29  C28  C27  C26    0.00   0.0  0
 E9T  CONST_30  C29  C30  C25  C26    0.00   0.0  0
 E9T  CONST_31  C30  C29  C28  C27    0.00   0.0  0
 E9T  CONST_32  C30  C25  C26  C27    0.00   0.0  0
 E9T  CONST_33  C29  C30  C25  C18  180.00   0.0  0
 E9T  CONST_34  C27  C26  C25  C18  180.00   0.0  0
 E9T  CONST_35  C11  C9   C10  C5   180.00   0.0  0
 E9T  CONST_36  C11  C9   C8   C7   180.00   0.0  0
 E9T  CONST_37  C28  C27  C26  O14  180.00   0.0  0
 E9T  CONST_38  C30  C25  C26  O14  180.00   0.0  0
 E9T  CONST_39  C18  C25  C26  O14    0.00   0.0  0
 E9T  CONST_40  H4   C10  C5   C4     0.00   0.0  0
 E9T  CONST_41  H2   C7   C6   C5   180.00   0.0  0
 E9T  CONST_42  H8   C3   C6   C5   180.00   0.0  0
 E9T  CONST_43  H7   C1   C4   C5   180.00   0.0  0
 E9T  CONST_44  H3   C8   C7   C6   180.00   0.0  0
 E9T  CONST_45  H1   C4   C5   C6   180.00   0.0  0
 E9T  CONST_46  H25  C28  C29  C2     0.00   0.0  0
 E9T  CONST_47  H26  C30  C29  C2     0.00   0.0  0
 E9T  CONST_48  H24  C27  C26  C25  180.00   0.0  0
 E9T  CONST_49  H9   O13  C11  C9   180.00   0.0  0
 E9T  Var_01    C25  C18  C17  C16  178.89  30.0  3
 E9T  Var_02    C30  C25  C18  C17  120.23  30.0  3
 E9T  Var_03    C20  C19  C18  C17   58.42  30.0  3
 E9T  Var_04    C22  C23  C18  C17  -56.94  30.0  3
 E9T  Var_05    O12  C11  C9   C8   178.97  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
 E9T  chir_01  C16  C17  C15  C21  positiv
 E9T  chir_02  C20  C24  C15  C19  positiv
 E9T  chir_03  C22  C24  C21  C23  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
 E9T  plan-1  C2   0.020
 E9T  plan-1  C25  0.020
 E9T  plan-1  C26  0.020
 E9T  plan-1  C27  0.020
 E9T  plan-1  C28  0.020
 E9T  plan-1  C29  0.020
 E9T  plan-1  C30  0.020
 E9T  plan-1  H24  0.020
 E9T  plan-1  H25  0.020
 E9T  plan-1  H26  0.020
 E9T  plan-1  O14  0.020
 E9T  plan-1  C18  0.020
 E9T  plan-2  C4   0.020
 E9T  plan-2  C5   0.020
 E9T  plan-2  C6   0.020
 E9T  plan-2  C7   0.020
 E9T  plan-2  C8   0.020
 E9T  plan-2  C9   0.020
 E9T  plan-2  C10  0.020
 E9T  plan-2  C11  0.020
 E9T  plan-2  C1   0.020
 E9T  plan-2  C2   0.020
 E9T  plan-2  C3   0.020
 E9T  plan-2  C29  0.020
 E9T  plan-2  H1   0.020
 E9T  plan-2  H2   0.020
 E9T  plan-2  H3   0.020
 E9T  plan-2  H4   0.020
 E9T  plan-2  H7   0.020
 E9T  plan-2  H8   0.020
 E9T  plan-3  C9   0.020
 E9T  plan-3  C11  0.020
 E9T  plan-3  O12  0.020
 E9T  plan-3  O13  0.020
 E9T  plan-3  H9   0.020

