# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:00:39 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: 2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCO[P](O)(=O)O[P](O)(O)=O)CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C
#
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
 A3C  A3C  '2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate'  ligand  63  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A3C
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
 A3C  C01   C  CH2    0  -0.145   2.2308  -2.2579  -0.9981
 A3C  O01   O  O2     0  -0.621   2.8982  -1.4720  -0.0417
 A3C  C02   C  CH2    0  -0.306   1.4800  -3.3781  -0.3052
 A3C  P02   P  P      0   1.329   3.8919  -0.2670  -0.6109
 A3C  N03   N  NT     0  -0.407   0.4440  -2.9165   0.6011
 A3C  O03   O  O2     0  -0.778   4.2286   0.3108   0.8477
 A3C  P04   P  P      0   1.224   4.8648   1.8901   1.1462
 A3C  O05   O  OP    -1  -0.896   5.6871   1.6400   2.4027
 A3C  O06   O  O      0  -0.837   3.0647   0.6686  -1.4473
 A3C  O07   O  OP    -1  -0.837   5.0920  -0.9209  -1.2421
 A3C  O08   O  O      0  -0.899   5.6747   2.2122  -0.1010
 A3C  O09   O  OP    -1  -0.896   3.6310   2.7525   1.3598
 A3C  C11   C  CH2    0  -0.264  -0.7382  -2.4430  -0.0998
 A3C  C12   C  CH2    0  -0.480  -1.5278  -1.4156   0.7051
 A3C  C13   C  CH3    0  -0.529   0.1029  -3.9321   1.5728
 A3C  C21   C  CH1    0  -0.253  -2.8341  -1.0240   0.0117
 A3C  C22   C  C      0   0.219  -3.9169  -2.0744   0.1224
 A3C  C23   C  CH2    0  -0.491  -5.1224  -1.7895  -0.7219
 A3C  C24   C  CH2    0  -0.439  -5.6914  -0.4087  -0.4060
 A3C  C25   C  CH1    0  -0.162  -4.6127   0.6669  -0.5186
 A3C  C26   C  CT     0  -0.070  -5.1812   2.1137  -0.5181
 A3C  C27   C  CH2    0  -0.399  -4.0157   3.0961  -0.6941
 A3C  C28   C  CH2    0  -0.439  -2.8827   2.8744   0.2925
 A3C  C29   C  CH2    0  -0.418  -2.3389   1.4560   0.1889
 A3C  C30   C  CT     0  -0.052  -3.4069   0.3761   0.4274
 A3C  C31   C  C2     0  -0.628  -3.8697  -3.1465   0.9109
 A3C  C32   C  CH3    0  -0.662  -6.0003   2.4727   0.7259
 A3C  C33   C  CH3    0  -0.656  -6.1025   2.2926  -1.7335
 A3C  C34   C  CH3    0  -0.676  -3.7579   0.3294   1.9175
 A3C  H01   H  HCH2   0   0.194   1.5482  -1.6463  -1.5997
 A3C  H01A  H  HCH2   0   0.193   2.9355  -2.7208  -1.7018
 A3C  H02   H  HCH2   0   0.190   1.0818  -4.0549  -1.0806
 A3C  H02A  H  HCH2   0   0.225   2.2013  -3.9670   0.2678
 A3C  H11   H  HCH2   0   0.228  -0.4298  -1.9557  -1.0272
 A3C  H11A  H  HCH2   0   0.198  -1.3792  -3.2873  -0.4018
 A3C  H12   H  HCH2   0   0.221  -1.7237  -1.7757   1.7177
 A3C  H12A  H  HCH2   0   0.244  -0.8822  -0.5449   0.8201
 A3C  H13   H  HCH3   0   0.232   0.9874  -4.2227   2.1423
 A3C  H13A  H  HCH3   0   0.230  -0.6283  -3.5498   2.2867
 A3C  H13B  H  HCH3   0   0.186  -0.3214  -4.8437   1.1213
 A3C  H21   H  HCH1   0   0.219  -2.6065  -0.9285  -1.0619
 A3C  H23   H  HCH2   0   0.225  -4.8349  -1.8153  -1.7800
 A3C  H23A  H  HCH2   0   0.233  -5.8837  -2.5599  -0.5823
 A3C  H24   H  HCH2   0   0.237  -6.5059  -0.2012  -1.1014
 A3C  H24A  H  HCH2   0   0.221  -6.1336  -0.4187   0.5938
 A3C  H25   H  HCH1   0   0.200  -4.1884   0.5586  -1.5300
 A3C  H27   H  HCH2   0   0.210  -3.6184   2.9844  -1.7108
 A3C  H27A  H  HCH2   0   0.217  -4.3951   4.1209  -0.6249
 A3C  H28   H  HCH2   0   0.229  -2.0762   3.5855   0.0951
 A3C  H28A  H  HCH2   0   0.212  -3.2177   3.0826   1.3129
 A3C  H29   H  HCH2   0   0.212  -1.9109   1.3149  -0.8120
 A3C  H29A  H  HCH2   0   0.226  -1.5155   1.3390   0.8969
 A3C  H31   H  H      0   0.223  -3.0233  -3.3837   1.5422
 A3C  H31A  H  H      0   0.227  -4.6976  -3.8446   0.9476
 A3C  H32   H  HCH3   0   0.227  -5.4068   2.5239   1.6366
 A3C  H32A  H  HCH3   0   0.222  -6.4661   3.4524   0.5946
 A3C  H32B  H  HCH3   0   0.226  -6.8020   1.7527   0.8972
 A3C  H33   H  HCH3   0   0.224  -7.0522   1.7662  -1.6249
 A3C  H33A  H  HCH3   0   0.224  -6.3376   3.3502  -1.8748
 A3C  H33B  H  HCH3   0   0.219  -5.6257   1.9373  -2.6501
 A3C  H34   H  HCH3   0   0.232  -4.0635   1.2952   2.3127
 A3C  H34A  H  HCH3   0   0.229  -4.5520  -0.3835   2.1382
 A3C  H34B  H  HCH3   0   0.233  -2.8840   0.0199   2.4945

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
 A3C  O01  C01   single  1.406  0.020  1.406
 A3C  C01  C02   single  1.516  0.020  1.516
 A3C  C01  H01   single  0.970  0.020  1.090
 A3C  C01  H01A  single  0.970  0.020  1.090
 A3C  P02  O01   single  1.662  0.020  1.662
 A3C  C02  N03   single  1.452  0.020  1.452
 A3C  C02  H02   single  0.970  0.020  1.090
 A3C  C02  H02A  single  0.970  0.020  1.090
 A3C  O06  P02   deloc   1.503  0.020  1.503
 A3C  O07  P02   deloc   1.505  0.020  1.505
 A3C  P02  O03   single  1.605  0.020  1.605
 A3C  C11  N03   single  1.454  0.020  1.454
 A3C  N03  C13   single  1.446  0.020  1.446
 A3C  P04  O03   single  1.729  0.020  1.729
 A3C  O08  P04   deloc   1.522  0.020  1.522
 A3C  O09  P04   deloc   1.520  0.020  1.520
 A3C  P04  O05   deloc   1.522  0.020  1.522
 A3C  C11  C12   single  1.525  0.020  1.525
 A3C  C11  H11   single  0.970  0.020  1.090
 A3C  C11  H11A  single  0.970  0.020  1.090
 A3C  C12  C21   single  1.530  0.020  1.530
 A3C  C12  H12   single  0.970  0.020  1.090
 A3C  C12  H12A  single  0.970  0.020  1.090
 A3C  C13  H13   single  0.970  0.020  1.090
 A3C  C13  H13A  single  0.970  0.020  1.090
 A3C  C13  H13B  single  0.970  0.020  1.090
 A3C  C30  C21   single  1.569  0.020  1.569
 A3C  C21  C22   single  1.513  0.020  1.513
 A3C  C21  H21   single  0.970  0.020  1.090
 A3C  C22  C23   single  1.499  0.020  1.499
 A3C  C22  C31   double  1.332  0.020  1.332
 A3C  C24  C23   single  1.527  0.020  1.527
 A3C  C23  H23   single  0.970  0.020  1.090
 A3C  C23  H23A  single  0.970  0.020  1.090
 A3C  C25  C24   single  1.527  0.020  1.527
 A3C  C24  H24   single  0.970  0.020  1.090
 A3C  C24  H24A  single  0.970  0.020  1.090
 A3C  C26  C25   single  1.555  0.020  1.555
 A3C  C30  C25   single  1.560  0.020  1.560
 A3C  C25  H25   single  0.970  0.020  1.090
 A3C  C27  C26   single  1.534  0.020  1.534
 A3C  C33  C26   single  1.536  0.020  1.536
 A3C  C26  C32   single  1.532  0.020  1.532
 A3C  C28  C27   single  1.519  0.020  1.519
 A3C  C27  H27   single  0.970  0.020  1.090
 A3C  C27  H27A  single  0.970  0.020  1.090
 A3C  C28  C29   single  1.523  0.020  1.523
 A3C  C28  H28   single  0.970  0.020  1.090
 A3C  C28  H28A  single  0.970  0.020  1.090
 A3C  C29  C30   single  1.537  0.020  1.537
 A3C  C29  H29   single  0.970  0.020  1.090
 A3C  C29  H29A  single  0.970  0.020  1.090
 A3C  C30  C34   single  1.532  0.020  1.532
 A3C  C31  H31   single  0.930  0.020  1.080
 A3C  C31  H31A  single  0.930  0.020  1.080
 A3C  C32  H32   single  0.970  0.020  1.090
 A3C  C32  H32A  single  0.970  0.020  1.090
 A3C  C32  H32B  single  0.970  0.020  1.090
 A3C  C33  H33   single  0.970  0.020  1.090
 A3C  C33  H33A  single  0.970  0.020  1.090
 A3C  C33  H33B  single  0.970  0.020  1.090
 A3C  C34  H34   single  0.970  0.020  1.090
 A3C  C34  H34A  single  0.970  0.020  1.090
 A3C  C34  H34B  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
 A3C  H01A  C01  H01   106.44  3.000
 A3C  H01A  C01  C02   107.41  3.000
 A3C  H01   C01  C02   110.77  3.000
 A3C  H01A  C01  O01   111.52  3.000
 A3C  H01   C01  O01   110.91  3.000
 A3C  C02   C01  O01   109.70  3.000
 A3C  P02   O01  C01   117.12  3.000
 A3C  H02A  C02  H02   106.02  3.000
 A3C  H02A  C02  N03   108.35  3.000
 A3C  H02   C02  N03   112.09  3.000
 A3C  H02A  C02  C01   108.10  3.000
 A3C  H02   C02  C01   108.10  3.000
 A3C  N03   C02  C01   113.81  3.000
 A3C  O07   P02  O06   118.41  3.000
 A3C  O07   P02  O03   111.74  3.000
 A3C  O06   P02  O03   113.40  3.000
 A3C  O03   P02  O01    94.31  3.000
 A3C  O07   P02  O01   107.77  3.000
 A3C  O06   P02  O01   108.22  3.000
 A3C  C13   N03  C11   111.15  3.000
 A3C  C13   N03  C02   111.37  3.000
 A3C  C11   N03  C02   112.52  3.000
 A3C  P04   O03  P02   124.28  3.000
 A3C  O09   P04  O08   115.28  3.000
 A3C  O09   P04  O05   114.56  3.000
 A3C  O08   P04  O05   115.07  3.000
 A3C  O05   P04  O03   101.03  3.000
 A3C  O09   P04  O03   104.11  3.000
 A3C  O08   P04  O03   104.34  3.000
 A3C  H11A  C11  H11   105.86  3.000
 A3C  H11A  C11  C12   111.07  3.000
 A3C  H11   C11  C12   107.09  3.000
 A3C  H11A  C11  N03   110.83  3.000
 A3C  H11   C11  N03   108.97  3.000
 A3C  C12   C11  N03   112.71  3.000
 A3C  H12A  C12  H12   105.76  3.000
 A3C  H12A  C12  C21   110.43  3.000
 A3C  H12   C12  C21   110.58  3.000
 A3C  H12A  C12  C11   106.68  3.000
 A3C  H12   C12  C11   111.10  3.000
 A3C  C21   C12  C11   112.04  3.000
 A3C  H13B  C13  H13A  107.44  3.000
 A3C  H13B  C13  H13   107.79  3.000
 A3C  H13A  C13  H13   107.16  3.000
 A3C  H13B  C13  N03   113.34  3.000
 A3C  H13A  C13  N03   110.59  3.000
 A3C  H13   C13  N03   110.27  3.000
 A3C  H21   C21  C30   104.86  3.000
 A3C  H21   C21  C22   106.22  3.000
 A3C  C30   C21  C22   109.82  3.000
 A3C  H21   C21  C12   106.71  3.000
 A3C  C22   C21  C12   113.59  3.000
 A3C  C30   C21  C12   114.84  3.000
 A3C  C31   C22  C23   121.00  3.000
 A3C  C31   C22  C21   125.24  3.000
 A3C  C23   C22  C21   113.73  3.000
 A3C  H23A  C23  H23   106.83  3.000
 A3C  H23A  C23  C24   110.60  3.000
 A3C  H23   C23  C24   108.58  3.000
 A3C  H23A  C23  C22   110.77  3.000
 A3C  H23   C23  C22   109.16  3.000
 A3C  C24   C23  C22   110.80  3.000
 A3C  H24A  C24  H24   106.42  3.000
 A3C  H24A  C24  C25   111.07  3.000
 A3C  H24   C24  C25   110.27  3.000
 A3C  H24A  C24  C23   109.37  3.000
 A3C  H24   C24  C23   108.57  3.000
 A3C  C25   C24  C23   111.01  3.000
 A3C  H25   C25  C30   103.92  3.000
 A3C  H25   C25  C26   103.45  3.000
 A3C  C30   C25  C26   117.12  3.000
 A3C  H25   C25  C24   105.68  3.000
 A3C  C30   C25  C24   111.71  3.000
 A3C  C26   C25  C24   113.40  3.000
 A3C  C33   C26  C32   107.13  3.000
 A3C  C32   C26  C27   110.44  3.000
 A3C  C33   C26  C27   106.88  3.000
 A3C  C32   C26  C25   114.45  3.000
 A3C  C33   C26  C25   109.12  3.000
 A3C  C27   C26  C25   108.55  3.000
 A3C  H27A  C27  H27   106.21  3.000
 A3C  H27A  C27  C28   110.74  3.000
 A3C  H27   C27  C28   108.48  3.000
 A3C  H27A  C27  C26   109.19  3.000
 A3C  H27   C27  C26   108.43  3.000
 A3C  C28   C27  C26   113.50  3.000
 A3C  H28A  C28  H28   105.70  3.000
 A3C  H28A  C28  C29   110.50  3.000
 A3C  H28   C28  C29   109.28  3.000
 A3C  H28A  C28  C27   110.47  3.000
 A3C  H28   C28  C27   109.76  3.000
 A3C  C29   C28  C27   110.99  3.000
 A3C  H29A  C29  H29   106.46  3.000
 A3C  H29A  C29  C30   110.36  3.000
 A3C  H29   C29  C30   108.79  3.000
 A3C  H29A  C29  C28   108.96  3.000
 A3C  H29   C29  C28   108.73  3.000
 A3C  C30   C29  C28   113.31  3.000
 A3C  C34   C30  C29   109.36  3.000
 A3C  C34   C30  C25   114.74  3.000
 A3C  C29   C30  C25   108.18  3.000
 A3C  C34   C30  C21   108.32  3.000
 A3C  C29   C30  C21   109.40  3.000
 A3C  C25   C30  C21   106.73  3.000
 A3C  H31A  C31  H31   115.89  3.000
 A3C  H31A  C31  C22   120.77  3.000
 A3C  H31   C31  C22   123.34  3.000
 A3C  H32B  C32  H32A  107.30  3.000
 A3C  H32B  C32  H32   107.48  3.000
 A3C  H32A  C32  H32   106.91  3.000
 A3C  H32B  C32  C26   111.45  3.000
 A3C  H32A  C32  C26   109.90  3.000
 A3C  H32   C32  C26   113.51  3.000
 A3C  H33B  C33  H33A  107.47  3.000
 A3C  H33B  C33  H33   107.84  3.000
 A3C  H33A  C33  H33   107.01  3.000
 A3C  H33B  C33  C26   111.37  3.000
 A3C  H33A  C33  C26   110.14  3.000
 A3C  H33   C33  C26   112.78  3.000
 A3C  H34B  C34  H34A  106.90  3.000
 A3C  H34B  C34  H34   106.53  3.000
 A3C  H34A  C34  H34   107.62  3.000
 A3C  H34B  C34  C30   109.84  3.000
 A3C  H34A  C34  C30   112.58  3.000
 A3C  H34   C34  C30   113.02  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
 A3C  Var_01  C24  C23  C22  C21   -55.14  30.0  1
 A3C  Var_02  C25  C24  C23  C22    53.44  30.0  1
 A3C  Var_03  C28  C27  C26  C25   -52.00  30.0  1
 A3C  Var_04  C29  C28  C27  C26    57.49  30.0  1
 A3C  Var_05  C30  C29  C28  C27   -57.82  30.0  1
 A3C  Var_06  H31  C31  C22  C21    -1.54   0.0  2
 A3C  Var_07  H33  C33  C26  C25    72.81  30.0  3
 A3C  Var_08  H32  C32  C26  C25    67.43  30.0  3
 A3C  Var_09  C21  C12  C11  N03  -174.74  30.0  3
 A3C  Var_10  O06  P02  O01  C01    59.09  30.0  2
 A3C  Var_11  C11  N03  C02  C01    75.41  30.0  3
 A3C  Var_12  N03  C02  C01  O01    62.35  30.0  3
 A3C  Var_13  C12  C11  N03  C02  -153.87  30.0  1
 A3C  Var_14  O08  P04  O03  P02   -29.51  30.0  3
 A3C  Var_15  H13  C13  N03  C02    57.96  30.0  3
 A3C  Var_16  H01  C01  O01  P02   -62.59  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
 A3C  chir_02  C21  C12  C30  C22  positiv
 A3C  chir_03  C25  C30  C26  C24  positiv
 A3C  chir_04  C30  C25  C29  C21  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
 A3C  plan-1  C21   0.020
 A3C  plan-1  C22   0.020
 A3C  plan-1  C23   0.020
 A3C  plan-1  C31   0.020
 A3C  plan-1  H31   0.020
 A3C  plan-1  H31A  0.020

