# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:35:01 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 4-[(trans-4-{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbamoyl]amino}cyclohexyl)oxy]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(O[C@@H]2CC[C@H](CC2)NC(=O)NC34CC5CC(CC(C5)C3)C4)cc1
#
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
 AUB  AUB  '4-[(trans-4-{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbamoyl]amino}cyclohexyl)oxy]benzoic acid'  ligand  61  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AUB
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
 AUB  C22  C  CR16   0  -0.280   6.0809  -1.1467  -0.7350
 AUB  C24  C  CR16   0  -0.273   7.3052   0.3553   0.6466
 AUB  C21  C  CR16   0  -0.365   4.9415  -0.3622  -0.6074
 AUB  C25  C  CR16   0  -0.346   6.1833   1.1515   0.7874
 AUB  C23  C  CR6    0  -0.123   7.2805  -0.8102  -0.1192
 AUB  C20  C  CR6    0   0.380   4.9865   0.8036   0.1559
 AUB  C28  C  C      0   0.391   8.5172  -1.6775  -0.2761
 AUB  C26  C  C      0   0.747  -2.6364   0.7826   0.0251
 AUB  C14  C  CH2    0  -0.456   0.5245   2.4539  -0.8959
 AUB  C12  C  CH2    0  -0.441   0.5295   0.1091  -0.0038
 AUB  C15  C  CH2    0  -0.459   1.9123   2.6786  -0.3041
 AUB  C17  C  CH2    0  -0.480   1.9153   0.3422   0.5895
 AUB  C6   C  C      0  -0.417  -6.9694  -2.2605  -0.4237
 AUB  C9   C  CH2    0  -0.416  -7.9226   0.0192  -0.0422
 AUB  C4   C  C      0  -0.417  -6.7767  -1.1825   1.8227
 AUB  C2   C  C      0  -0.462  -5.8845  -0.2657  -1.4577
 AUB  C10  C  C      0  -0.422  -4.7442  -1.4740   0.3962
 AUB  C8   C  C      0  -0.419  -5.6962   0.8151   0.7742
 AUB  C1   C  CR16   0  -0.250  -7.2216  -0.8893  -1.0536
 AUB  C5   C  C      0  -0.254  -6.0806  -2.0945   0.8101
 AUB  C3   C  CR16   0  -0.254  -7.0305   0.1869   1.1882
 AUB  C13  C  CH1    0  -0.044  -0.2617   1.4147  -0.1022
 AUB  C16  C  CH1    0   0.050   2.6808   1.3688  -0.2356
 AUB  C7   C  C      0   0.181  -4.9752  -0.0925  -0.2324
 AUB  N18  N  NH1    0  -0.694  -1.5672   1.2302  -0.6980
 AUB  N11  N  NH1    0  -0.736  -3.7362   0.5016  -0.7198
 AUB  O29  O  O      0  -0.599   8.3925  -2.7152  -0.9568
 AUB  O27  O  O      0  -0.549  -2.5990   0.6857   1.2489
 AUB  O30  O  OC    -1  -0.599   9.5569  -1.2787   0.2856
 AUB  O19  O  O2     0  -0.496   3.9557   1.6552   0.3304
 AUB  H1   H  HCR6   0   0.244   6.0270  -2.0468  -1.3336
 AUB  H2   H  HCR6   0   0.241   8.2219   0.6461   1.1431
 AUB  H3   H  HCR6   0   0.268   4.0363  -0.6780  -1.1083
 AUB  H4   H  HCR6   0   0.251   6.2232   2.0547   1.3847
 AUB  H5   H  HCH2   0   0.248  -0.0263   3.3963  -0.9220
 AUB  H6   H  HCH2   0   0.223   0.6246   2.1175  -1.9346
 AUB  H7   H  HCH2   0   0.218   0.6219  -0.3274  -1.0050
 AUB  H8   H  HCH2   0   0.244  -0.0192  -0.6112   0.6060
 AUB  H9   H  HCH2   0   0.248   2.4608   3.4023  -0.9109
 AUB  H10  H  HCH2   0   0.229   1.8226   3.1009   0.7025
 AUB  H11  H  HCH2   0   0.231   1.8214   0.7141   1.6154
 AUB  H12  H  HCH2   0   0.250   2.4603  -0.6029   0.6449
 AUB  H15  H  HCH2   0   0.222  -8.1329   0.9945  -0.4926
 AUB  H16  H  HCH2   0   0.223  -8.8878  -0.4104   0.2442
 AUB  H17  H  H      0   0.222  -7.7234  -1.6313   2.1396
 AUB  H18  H  H      0   0.222  -6.1613  -1.0753   2.7219
 AUB  H19  H  H      0   0.234  -5.3848  -0.9045  -2.1953
 AUB  H20  H  H      0   0.235  -6.0505   0.7089  -1.9302
 AUB  H21  H  H      0   0.236  -4.0868  -1.3867   1.2632
 AUB  H22  H  H      0   0.219  -4.2366  -2.1187  -0.3296
 AUB  H23  H  H      0   0.218  -5.8643   1.7953   0.3150
 AUB  H24  H  H      0   0.236  -5.0685   0.9742   1.6525
 AUB  H25  H  HCR6   0   0.228  -7.8451  -0.9986  -1.9455
 AUB  H26  H  H      0   0.224  -5.8940  -3.0726   1.2634
 AUB  H27  H  HCR6   0   0.224  -7.5235   0.8416   1.9130
 AUB  H28  H  HCH1   0   0.235  -0.4152   1.8020   0.9082
 AUB  H29  H  HCH1   0   0.223   2.8067   0.9966  -1.2612
 AUB  H30  H  HNH1   0   0.380  -1.5839   1.1084  -1.6991
 AUB  H31  H  HNH1   0   0.384  -3.6518   0.5812  -1.7208
 AUB  H13  H  H      0   0.223  -7.9187  -2.7315  -0.1481
 AUB  H14  H  H      0   0.222  -6.4859  -2.9231  -1.1495

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
 AUB  C6   C1   single    1.530  0.020  1.530
 AUB  C6   C5   single    1.530  0.020  1.530
 AUB  C1   C9   single    1.530  0.020  1.530
 AUB  C1   C2   single    1.530  0.020  1.530
 AUB  C9   C3   single    1.529  0.020  1.529
 AUB  C5   C4   single    1.530  0.020  1.530
 AUB  C5   C10  single    1.531  0.020  1.531
 AUB  C4   C3   single    1.530  0.020  1.530
 AUB  C2   C7   single    1.536  0.020  1.536
 AUB  C3   C8   single    1.532  0.020  1.532
 AUB  C10  C7   single    1.535  0.020  1.535
 AUB  C7   C8   single    1.535  0.020  1.535
 AUB  C7   N11  single    1.458  0.020  1.458
 AUB  N11  C26  single    1.358  0.020  1.358
 AUB  O27  C26  double    1.228  0.020  1.228
 AUB  C26  N18  single    1.366  0.020  1.366
 AUB  N18  C13  single    1.447  0.020  1.447
 AUB  C13  C14  single    1.526  0.020  1.526
 AUB  C13  C12  single    1.530  0.020  1.530
 AUB  C14  C15  single    1.525  0.020  1.525
 AUB  C12  C17  single    1.525  0.020  1.525
 AUB  C15  C16  single    1.520  0.020  1.520
 AUB  C17  C16  single    1.523  0.020  1.523
 AUB  C16  O19  single    1.424  0.020  1.424
 AUB  O19  C20  single    1.348  0.020  1.348
 AUB  C20  C21  aromatic  1.394  0.020  1.394
 AUB  C20  C25  aromatic  1.397  0.020  1.397
 AUB  C21  C22  aromatic  1.389  0.020  1.389
 AUB  C25  C24  aromatic  1.383  0.020  1.383
 AUB  C22  C23  aromatic  1.390  0.020  1.390
 AUB  C24  C23  aromatic  1.395  0.020  1.395
 AUB  C23  C28  single    1.519  0.020  1.519
 AUB  C28  O29  deloc     1.247  0.020  1.247
 AUB  C28  O30  deloc     1.247  0.020  1.247
 AUB  C22  H1   single    0.930  0.020  1.080
 AUB  C24  H2   single    0.930  0.020  1.080
 AUB  C21  H3   single    0.930  0.020  1.080
 AUB  C25  H4   single    0.930  0.020  1.080
 AUB  C14  H5   single    0.970  0.020  1.090
 AUB  C14  H6   single    0.970  0.020  1.090
 AUB  C12  H7   single    0.970  0.020  1.090
 AUB  C12  H8   single    0.970  0.020  1.090
 AUB  C15  H9   single    0.970  0.020  1.090
 AUB  C15  H10  single    0.970  0.020  1.090
 AUB  C17  H11  single    0.970  0.020  1.090
 AUB  C17  H12  single    0.970  0.020  1.090
 AUB  C6   H13  single    0.970  0.020  1.090
 AUB  C6   H14  single    0.970  0.020  1.090
 AUB  C9   H15  single    0.970  0.020  1.090
 AUB  C9   H16  single    0.970  0.020  1.090
 AUB  C4   H17  single    0.970  0.020  1.090
 AUB  C4   H18  single    0.970  0.020  1.090
 AUB  C2   H19  single    0.970  0.020  1.090
 AUB  C2   H20  single    0.970  0.020  1.090
 AUB  C10  H21  single    0.970  0.020  1.090
 AUB  C10  H22  single    0.970  0.020  1.090
 AUB  C8   H23  single    0.970  0.020  1.090
 AUB  C8   H24  single    0.970  0.020  1.090
 AUB  C1   H25  single    0.970  0.020  1.090
 AUB  C5   H26  single    0.970  0.020  1.090
 AUB  C3   H27  single    0.970  0.020  1.090
 AUB  C13  H28  single    0.970  0.020  1.090
 AUB  C16  H29  single    0.970  0.020  1.090
 AUB  N18  H30  single    0.890  0.020  1.040
 AUB  N11  H31  single    0.860  0.020  1.020

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
 AUB  H1   C22  C23  119.29  3.000
 AUB  H1   C22  C21  118.66  3.000
 AUB  C23  C22  C21  122.04  3.000
 AUB  H2   C24  C23  119.43  3.000
 AUB  H2   C24  C25  119.06  3.000
 AUB  C23  C24  C25  121.51  3.000
 AUB  H3   C21  C20  121.64  3.000
 AUB  H3   C21  C22  118.61  3.000
 AUB  C20  C21  C22  119.74  3.000
 AUB  H4   C25  C20  119.22  3.000
 AUB  H4   C25  C24  120.41  3.000
 AUB  C20  C25  C24  120.37  3.000
 AUB  C28  C23  C24  121.30  3.000
 AUB  C28  C23  C22  121.26  3.000
 AUB  C24  C23  C22  117.44  3.000
 AUB  O19  C20  C25  116.05  3.000
 AUB  C25  C20  C21  118.90  3.000
 AUB  O19  C20  C21  125.05  3.000
 AUB  O30  C28  O29  126.53  3.000
 AUB  O30  C28  C23  116.72  3.000
 AUB  O29  C28  C23  116.75  3.000
 AUB  O27  C26  N11  123.71  3.000
 AUB  O27  C26  N18  121.97  3.000
 AUB  N11  C26  N18  114.29  3.000
 AUB  H6   C14  H5   106.75  3.000
 AUB  H6   C14  C13  109.32  3.000
 AUB  H5   C14  C13  109.90  3.000
 AUB  H6   C14  C15  109.25  3.000
 AUB  H5   C14  C15  109.95  3.000
 AUB  C13  C14  C15  111.55  3.000
 AUB  H8   C12  H7   106.85  3.000
 AUB  H8   C12  C13  109.82  3.000
 AUB  H7   C12  C13  108.94  3.000
 AUB  H8   C12  C17  109.89  3.000
 AUB  H7   C12  C17  109.85  3.000
 AUB  C13  C12  C17  111.37  3.000
 AUB  H10  C15  H9   107.23  3.000
 AUB  H10  C15  C16  109.40  3.000
 AUB  H9   C15  C16  110.00  3.000
 AUB  H10  C15  C14  109.81  3.000
 AUB  H9   C15  C14  109.81  3.000
 AUB  C16  C15  C14  110.52  3.000
 AUB  H12  C17  H11  106.80  3.000
 AUB  H12  C17  C16  111.09  3.000
 AUB  H11  C17  C16  108.76  3.000
 AUB  H12  C17  C12  109.93  3.000
 AUB  H11  C17  C12  109.77  3.000
 AUB  C16  C17  C12  110.42  3.000
 AUB  H14  C6   H13  106.82  3.000
 AUB  H14  C6   C5   110.10  3.000
 AUB  H13  C6   C5   110.33  3.000
 AUB  H14  C6   C1   110.01  3.000
 AUB  H13  C6   C1   110.26  3.000
 AUB  C5   C6   C1   109.30  3.000
 AUB  H16  C9   H15  106.74  3.000
 AUB  H16  C9   C3   110.30  3.000
 AUB  H15  C9   C3   110.21  3.000
 AUB  H16  C9   C1   110.12  3.000
 AUB  H15  C9   C1   110.19  3.000
 AUB  C3   C9   C1   109.26  3.000
 AUB  H18  C4   H17  106.76  3.000
 AUB  H18  C4   C3   110.25  3.000
 AUB  H17  C4   C3   110.09  3.000
 AUB  H18  C4   C5   110.25  3.000
 AUB  H17  C4   C5   109.92  3.000
 AUB  C3   C4   C5   109.53  3.000
 AUB  H20  C2   H19  107.29  3.000
 AUB  H20  C2   C7   109.48  3.000
 AUB  H19  C2   C7   109.43  3.000
 AUB  H20  C2   C1   110.13  3.000
 AUB  H19  C2   C1   109.79  3.000
 AUB  C7   C2   C1   110.65  3.000
 AUB  H22  C10  H21  107.12  3.000
 AUB  H22  C10  C7   109.15  3.000
 AUB  H21  C10  C7   110.11  3.000
 AUB  H22  C10  C5   110.19  3.000
 AUB  H21  C10  C5   110.09  3.000
 AUB  C7   C10  C5   110.13  3.000
 AUB  H24  C8   H23  107.17  3.000
 AUB  H24  C8   C7   110.11  3.000
 AUB  H23  C8   C7   109.04  3.000
 AUB  H24  C8   C3   110.08  3.000
 AUB  H23  C8   C3   110.28  3.000
 AUB  C7   C8   C3   110.11  3.000
 AUB  H25  C1   C2   108.88  3.000
 AUB  H25  C1   C9   109.72  3.000
 AUB  C2   C1   C9   109.46  3.000
 AUB  H25  C1   C6   109.88  3.000
 AUB  C2   C1   C6   109.27  3.000
 AUB  C9   C1   C6   109.61  3.000
 AUB  H26  C5   C10  109.00  3.000
 AUB  H26  C5   C4   109.64  3.000
 AUB  C10  C5   C4   109.55  3.000
 AUB  H26  C5   C6   109.65  3.000
 AUB  C10  C5   C6   109.47  3.000
 AUB  C4   C5   C6   109.52  3.000
 AUB  H27  C3   C8   109.03  3.000
 AUB  H27  C3   C4   109.61  3.000
 AUB  C8   C3   C4   109.55  3.000
 AUB  H27  C3   C9   109.62  3.000
 AUB  C8   C3   C9   109.62  3.000
 AUB  C4   C3   C9   109.40  3.000
 AUB  H28  C13  N18  107.41  3.000
 AUB  H28  C13  C12  108.40  3.000
 AUB  N18  C13  C12  112.60  3.000
 AUB  H28  C13  C14  108.17  3.000
 AUB  C12  C13  C14  110.38  3.000
 AUB  N18  C13  C14  109.73  3.000
 AUB  H29  C16  O19  109.68  3.000
 AUB  H29  C16  C17  109.57  3.000
 AUB  O19  C16  C17  111.73  3.000
 AUB  H29  C16  C15  107.93  3.000
 AUB  O19  C16  C15  107.29  3.000
 AUB  C17  C16  C15  110.55  3.000
 AUB  N11  C7   C8   112.17  3.000
 AUB  N11  C7   C10  112.07  3.000
 AUB  C8   C7   C10  109.52  3.000
 AUB  N11  C7   C2   106.40  3.000
 AUB  C8   C7   C2   108.17  3.000
 AUB  C10  C7   C2   108.32  3.000
 AUB  H30  N18  C13  116.05  3.000
 AUB  H30  N18  C26  118.21  3.000
 AUB  C13  N18  C26  122.00  3.000
 AUB  H31  N11  C7   115.81  3.000
 AUB  H31  N11  C26  117.44  3.000
 AUB  C7   N11  C26  126.11  3.000
 AUB  C16  O19  C20  120.39  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
 AUB  CONST_01  C25  C20  C21  C22    0.00   0.0  0
 AUB  CONST_02  C25  C24  C23  C22    0.00   0.0  0
 AUB  CONST_03  C21  C20  C25  C24    0.00   0.0  0
 AUB  CONST_04  C21  C22  C23  C24    0.00   0.0  0
 AUB  CONST_05  C20  C21  C22  C23    0.00   0.0  0
 AUB  CONST_06  C20  C25  C24  C23    0.00   0.0  0
 AUB  CONST_07  O19  C20  C21  C22  180.00   0.0  0
 AUB  CONST_08  O19  C20  C25  C24  180.00   0.0  0
 AUB  CONST_09  C28  C23  C22  C21  180.00   0.0  0
 AUB  CONST_10  C28  C23  C24  C25  180.00   0.0  0
 AUB  CONST_11  H2   C24  C23  C22  180.00   0.0  0
 AUB  CONST_12  H1   C22  C23  C24  180.00   0.0  0
 AUB  CONST_13  H4   C25  C20  C21  180.00   0.0  0
 AUB  CONST_14  H3   C21  C20  C25  180.00   0.0  0
 AUB  CONST_15  O27  C26  N18  C13    0.00   0.0  0
 AUB  CONST_16  O27  C26  N11  C7     0.00   0.0  0
 AUB  CONST_17  N11  C26  N18  C13  180.00   0.0  0
 AUB  CONST_18  N18  C26  N11  C7   180.00   0.0  0
 AUB  CONST_19  H31  N11  C26  O27  180.00   0.0  0
 AUB  CONST_20  H30  N18  C26  O27  180.00   0.0  0
 AUB  Var_01    C16  C15  C14  C13   56.67  30.0  1
 AUB  Var_02    C16  C17  C12  C13  -56.85  30.0  1
 AUB  Var_03    O29  C28  C23  C22   -1.54  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
 AUB  chir_01  C1   C6   C9   C2   negativ
 AUB  chir_02  C5   C6   C4   C10  positiv
 AUB  chir_03  C3   C9   C4   C8   negativ
 AUB  chir_04  C13  N18  C14  C12  positiv
 AUB  chir_05  C16  O19  C15  C17  positiv
 AUB  chir_06  C7   C10  C8   N11  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
 AUB  plan-1  C22  0.020
 AUB  plan-1  C24  0.020
 AUB  plan-1  C21  0.020
 AUB  plan-1  C25  0.020
 AUB  plan-1  C23  0.020
 AUB  plan-1  C20  0.020
 AUB  plan-1  C28  0.020
 AUB  plan-1  O19  0.020
 AUB  plan-1  H1   0.020
 AUB  plan-1  H2   0.020
 AUB  plan-1  H3   0.020
 AUB  plan-1  H4   0.020
 AUB  plan-2  C26  0.020
 AUB  plan-2  C13  0.020
 AUB  plan-2  C7   0.020
 AUB  plan-2  N18  0.020
 AUB  plan-2  N11  0.020
 AUB  plan-2  O27  0.020
 AUB  plan-2  H30  0.020
 AUB  plan-2  H31  0.020
 AUB  plan-3  C23  0.020
 AUB  plan-3  C28  0.020
 AUB  plan-3  O29  0.020
 AUB  plan-3  O30  0.020

