# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:27:20 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}-[3-oxidanylidene-3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]amino]propyl]-4-(trifluoromethyloxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Oc1ccc(cc1)C(=O)NCCC(=O)N[C@@H]2CCCc3ccccc23
#
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
 MLJ  MLJ  ~{N}-[3-oxidanylidene-3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]amino]propyl]-4-(trifluoromethyloxy)benzamide  ligand  50  29  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MLJ
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
 MLJ  C02   C  CT    0   1.075   7.6617  -0.6752  -1.3054
 MLJ  C06   C  CR6   0   0.317   5.5989   0.1455  -0.5759
 MLJ  C07   C  CR16  0  -0.287   5.5337   0.4556   0.7720
 MLJ  C08   C  CR16  0  -0.267   4.3288   0.3012   1.4371
 MLJ  C09   C  CR6   0  -0.031   3.1956  -0.1408   0.7601
 MLJ  C10   C  CR16  0  -0.286   3.2879  -0.4444  -0.5958
 MLJ  C11   C  CR16  0  -0.284   4.4908  -0.3070  -1.2704
 MLJ  C12   C  C     0   0.538   1.9257  -0.3013   1.5348
 MLJ  C15   C  CH2   0  -0.233  -0.5165  -0.2754   1.4549
 MLJ  C16   C  CH2   0  -0.642  -1.5780  -0.3484   0.3729
 MLJ  C17   C  C     0   0.577  -2.9722  -0.5252   0.9392
 MLJ  C20   C  CH1   0  -0.116  -5.3595  -0.5754   0.3173
 MLJ  C21   C  CH2   0  -0.437  -5.7899  -1.9676  -0.1353
 MLJ  C22   C  CH2   0  -0.456  -7.2935  -2.1288   0.0090
 MLJ  C23   C  CH2   0  -0.497  -8.0097  -1.1653  -0.9249
 MLJ  C24   C  CR6   0   0.072  -7.4643   0.2388  -0.8516
 MLJ  C25   C  CR16  0  -0.301  -8.2218   1.2875  -1.3749
 MLJ  C26   C  CR16  0  -0.255  -7.7644   2.5939  -1.3509
 MLJ  C27   C  CR16  0  -0.261  -6.5242   2.8727  -0.7899
 MLJ  C28   C  CR16  0  -0.287  -5.7626   1.8408  -0.2673
 MLJ  C29   C  CR6   0   0.055  -6.2136   0.5203  -0.2940
 MLJ  F01   F  F     0  -0.275   8.6997  -0.2841  -2.0253
 MLJ  F03   F  F     0  -0.298   7.1444  -1.7676  -1.8693
 MLJ  F04   F  F     0  -0.298   8.0978  -1.0350  -0.0969
 MLJ  N14   N  NH1   0  -0.658   0.7888  -0.1534   0.8383
 MLJ  N19   N  NH1   0  -0.645  -3.9572  -0.3446   0.0415
 MLJ  O05   O  O2    0  -0.522   6.7922   0.3431  -1.2579
 MLJ  O13   O  O     0  -0.486   1.9439  -0.5572   2.7309
 MLJ  O18   O  O     0  -0.497  -3.1722  -0.8106   2.1109
 MLJ  H071  H  HCR6  0   0.287   6.4049   0.8248   1.2961
 MLJ  H081  H  HCR6  0   0.272   4.2730   0.5342   2.4916
 MLJ  H101  H  HCR6  0   0.271   2.4317  -0.8212  -1.1404
 MLJ  H111  H  HCR6  0   0.288   4.5572  -0.5404  -2.3246
 MLJ  H152  H  HCH2  0   0.244  -0.7051   0.5713   2.1211
 MLJ  H151  H  HCH2  0   0.249  -0.5389  -1.1770   2.0661
 MLJ  H161  H  HCH2  0   0.275  -1.5522   0.5508  -0.2497
 MLJ  H162  H  HCH2  0   0.288  -1.3722  -1.1901  -0.2960
 MLJ  H201  H  HCH1  0   0.267  -5.4733  -0.5216   1.4036
 MLJ  H211  H  HCH2  0   0.226  -5.5004  -2.1156  -1.1811
 MLJ  H212  H  HCH2  0   0.245  -5.2541  -2.7143   0.4540
 MLJ  H222  H  HCH2  0   0.244  -7.5925  -3.1542  -0.2139
 MLJ  H221  H  HCH2  0   0.227  -7.5883  -1.9351   1.0454
 MLJ  H231  H  HCH2  0   0.245  -7.9127  -1.5239  -1.9553
 MLJ  H232  H  HCH2  0   0.250  -9.0817  -1.1515  -0.7150
 MLJ  H251  H  HCR6  0   0.246  -9.1901   1.0663  -1.8097
 MLJ  H261  H  HCR6  0   0.252  -8.3715   3.3902  -1.7626
 MLJ  H271  H  HCR6  0   0.252  -6.1530   3.8889  -0.7583
 MLJ  H281  H  HCR6  0   0.247  -4.7961   2.0656   0.1667
 MLJ  H141  H  HNH1  0   0.409   0.8337   0.2355  -0.0900
 MLJ  H191  H  HNH1  0   0.399  -3.7014  -0.1671  -0.9184

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
 MLJ  O13  C12   double    1.223  0.020  1.223
 MLJ  C15  C16   single    1.518  0.020  1.518
 MLJ  C15  N14   single    1.449  0.020  1.449
 MLJ  C12  N14   single    1.341  0.020  1.341
 MLJ  C12  C09   single    1.496  0.020  1.496
 MLJ  C08  C09   aromatic  1.392  0.020  1.392
 MLJ  C08  C07   aromatic  1.385  0.020  1.385
 MLJ  C16  C17   single    1.515  0.020  1.515
 MLJ  O18  C17   double    1.222  0.020  1.222
 MLJ  C09  C10   aromatic  1.393  0.020  1.393
 MLJ  C07  C06   aromatic  1.385  0.020  1.385
 MLJ  C17  N19   single    1.345  0.020  1.345
 MLJ  F01  C02   single    1.322  0.020  1.322
 MLJ  C10  C11   aromatic  1.386  0.020  1.386
 MLJ  C06  C11   aromatic  1.384  0.020  1.384
 MLJ  C06  O05   single    1.389  0.020  1.389
 MLJ  F04  C02   single    1.334  0.020  1.334
 MLJ  N19  C20   single    1.448  0.020  1.448
 MLJ  C02  O05   single    1.340  0.020  1.340
 MLJ  C02  F03   single    1.334  0.020  1.334
 MLJ  C20  C21   single    1.526  0.020  1.526
 MLJ  C20  C29   single    1.518  0.020  1.518
 MLJ  C21  C22   single    1.519  0.020  1.519
 MLJ  C28  C29   aromatic  1.396  0.020  1.396
 MLJ  C28  C27   aromatic  1.385  0.020  1.385
 MLJ  C29  C24   aromatic  1.398  0.020  1.398
 MLJ  C22  C23   single    1.521  0.020  1.521
 MLJ  C27  C26   aromatic  1.389  0.020  1.389
 MLJ  C24  C23   single    1.508  0.020  1.508
 MLJ  C24  C25   aromatic  1.396  0.020  1.396
 MLJ  C26  C25   aromatic  1.384  0.020  1.384
 MLJ  C07  H071  single    0.930  0.020  1.080
 MLJ  C08  H081  single    0.930  0.020  1.080
 MLJ  C10  H101  single    0.930  0.020  1.080
 MLJ  C11  H111  single    0.930  0.020  1.080
 MLJ  C15  H152  single    0.970  0.020  1.090
 MLJ  C15  H151  single    0.970  0.020  1.090
 MLJ  C16  H161  single    0.970  0.020  1.090
 MLJ  C16  H162  single    0.970  0.020  1.090
 MLJ  C20  H201  single    0.970  0.020  1.090
 MLJ  C21  H211  single    0.970  0.020  1.090
 MLJ  C21  H212  single    0.970  0.020  1.090
 MLJ  C22  H222  single    0.970  0.020  1.090
 MLJ  C22  H221  single    0.970  0.020  1.090
 MLJ  C23  H231  single    0.970  0.020  1.090
 MLJ  C23  H232  single    0.970  0.020  1.090
 MLJ  C25  H251  single    0.930  0.020  1.080
 MLJ  C26  H261  single    0.930  0.020  1.080
 MLJ  C27  H271  single    0.930  0.020  1.080
 MLJ  C28  H281  single    0.930  0.020  1.080
 MLJ  N14  H141  single    0.860  0.020  1.020
 MLJ  N19  H191  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
 MLJ  O05   C02  F04   112.65  3.000
 MLJ  O05   C02  F03   112.69  3.000
 MLJ  F04   C02  F03   106.79  3.000
 MLJ  F03   C02  F01   108.45  3.000
 MLJ  O05   C02  F01   107.69  3.000
 MLJ  F04   C02  F01   108.44  3.000
 MLJ  O05   C06  C11   119.22  3.000
 MLJ  O05   C06  C07   119.13  3.000
 MLJ  C11   C06  C07   121.61  3.000
 MLJ  H071  C07  C08   120.40  3.000
 MLJ  H071  C07  C06   120.68  3.000
 MLJ  C08   C07  C06   118.91  3.000
 MLJ  H081  C08  C09   120.04  3.000
 MLJ  H081  C08  C07   119.29  3.000
 MLJ  C09   C08  C07   120.67  3.000
 MLJ  C12   C09  C10   122.48  3.000
 MLJ  C10   C09  C08   119.26  3.000
 MLJ  C12   C09  C08   118.24  3.000
 MLJ  H101  C10  C11   118.43  3.000
 MLJ  H101  C10  C09   120.89  3.000
 MLJ  C11   C10  C09   120.65  3.000
 MLJ  H111  C11  C10   120.41  3.000
 MLJ  H111  C11  C06   120.70  3.000
 MLJ  C10   C11  C06   118.89  3.000
 MLJ  O13   C12  N14   122.92  3.000
 MLJ  N14   C12  C09   116.01  3.000
 MLJ  O13   C12  C09   121.07  3.000
 MLJ  H151  C15  H152  107.18  3.000
 MLJ  H151  C15  N14   109.08  3.000
 MLJ  H152  C15  N14   110.45  3.000
 MLJ  H151  C15  C16   110.23  3.000
 MLJ  H152  C15  C16   110.55  3.000
 MLJ  N14   C15  C16   109.32  3.000
 MLJ  H162  C16  H161  106.25  3.000
 MLJ  H162  C16  C17   108.16  3.000
 MLJ  H161  C16  C17   109.29  3.000
 MLJ  H162  C16  C15   109.95  3.000
 MLJ  H161  C16  C15   110.47  3.000
 MLJ  C17   C16  C15   112.51  3.000
 MLJ  O18   C17  N19   123.46  3.000
 MLJ  N19   C17  C16   114.13  3.000
 MLJ  O18   C17  C16   122.41  3.000
 MLJ  H201  C20  N19   106.39  3.000
 MLJ  H201  C20  C29   107.82  3.000
 MLJ  N19   C20  C29   110.69  3.000
 MLJ  H201  C20  C21   108.07  3.000
 MLJ  C29   C20  C21   112.36  3.000
 MLJ  N19   C20  C21   111.23  3.000
 MLJ  H212  C21  H211  107.05  3.000
 MLJ  H212  C21  C22   111.22  3.000
 MLJ  H211  C21  C22   109.75  3.000
 MLJ  H212  C21  C20   109.00  3.000
 MLJ  H211  C21  C20   109.39  3.000
 MLJ  C22   C21  C20   110.35  3.000
 MLJ  H221  C22  H222  106.61  3.000
 MLJ  H221  C22  C23   110.02  3.000
 MLJ  H222  C22  C23   109.93  3.000
 MLJ  H221  C22  C21   109.73  3.000
 MLJ  H222  C22  C21   110.58  3.000
 MLJ  C23   C22  C21   109.91  3.000
 MLJ  H232  C23  H231  105.77  3.000
 MLJ  H232  C23  C24   109.50  3.000
 MLJ  H231  C23  C24   108.57  3.000
 MLJ  H232  C23  C22   110.62  3.000
 MLJ  H231  C23  C22   109.18  3.000
 MLJ  C24   C23  C22   112.93  3.000
 MLJ  C29   C24  C25   118.94  3.000
 MLJ  C25   C24  C23   119.03  3.000
 MLJ  C29   C24  C23   122.03  3.000
 MLJ  H251  C25  C26   119.65  3.000
 MLJ  H251  C25  C24   118.80  3.000
 MLJ  C26   C25  C24   121.55  3.000
 MLJ  H261  C26  C27   120.43  3.000
 MLJ  H261  C26  C25   120.14  3.000
 MLJ  C27   C26  C25   119.43  3.000
 MLJ  H271  C27  C28   120.00  3.000
 MLJ  H271  C27  C26   120.42  3.000
 MLJ  C28   C27  C26   119.58  3.000
 MLJ  H281  C28  C29   119.50  3.000
 MLJ  H281  C28  C27   119.16  3.000
 MLJ  C29   C28  C27   121.34  3.000
 MLJ  C28   C29  C24   119.16  3.000
 MLJ  C24   C29  C20   121.25  3.000
 MLJ  C28   C29  C20   119.57  3.000
 MLJ  H141  N14  C15   117.70  3.000
 MLJ  H141  N14  C12   118.90  3.000
 MLJ  C15   N14  C12   122.22  3.000
 MLJ  H191  N19  C20   117.05  3.000
 MLJ  H191  N19  C17   118.22  3.000
 MLJ  C20   N19  C17   124.12  3.000
 MLJ  C06   O05  C02   117.84  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
 MLJ  CONST_01  C09   C08  C07  C06     0.00   0.0  0
 MLJ  CONST_02  C09   C10  C11  C06     0.00   0.0  0
 MLJ  CONST_03  C10   C09  C08  C07     0.00   0.0  0
 MLJ  CONST_04  C10   C11  C06  C07     0.00   0.0  0
 MLJ  CONST_05  C11   C10  C09  C08     0.00   0.0  0
 MLJ  CONST_06  C11   C06  C07  C08     0.00   0.0  0
 MLJ  CONST_07  C27   C28  C29  C24     0.00   0.0  0
 MLJ  CONST_08  C27   C26  C25  C24     0.00   0.0  0
 MLJ  CONST_09  C28   C29  C24  C25     0.00   0.0  0
 MLJ  CONST_10  C28   C27  C26  C25     0.00   0.0  0
 MLJ  CONST_11  C29   C28  C27  C26     0.00   0.0  0
 MLJ  CONST_12  C29   C24  C25  C26     0.00   0.0  0
 MLJ  CONST_13  C12   C09  C08  C07   180.00   0.0  0
 MLJ  CONST_14  O05   C06  C07  C08   180.00   0.0  0
 MLJ  CONST_15  O05   C06  C11  C10   180.00   0.0  0
 MLJ  CONST_16  C12   C09  C10  C11   180.00   0.0  0
 MLJ  CONST_17  H081  C08  C07  C06   180.00   0.0  0
 MLJ  CONST_18  H101  C10  C11  C06   180.00   0.0  0
 MLJ  CONST_19  H111  C11  C06  C07   180.00   0.0  0
 MLJ  CONST_20  H071  C07  C08  C09   180.00   0.0  0
 MLJ  CONST_21  H281  C28  C29  C20     0.00   0.0  0
 MLJ  CONST_22  H251  C25  C24  C23     0.00   0.0  0
 MLJ  CONST_23  H261  C26  C25  C24   180.00   0.0  0
 MLJ  CONST_24  H271  C27  C26  C25   180.00   0.0  0
 MLJ  CONST_25  C15   N14  C12  C09   180.00   0.0  0
 MLJ  CONST_26  C20   N19  C17  C16   180.00   0.0  0
 MLJ  CONST_27  O18   C17  N19  C20     0.00   0.0  0
 MLJ  CONST_28  H141  N14  C12  C09     0.00   0.0  0
 MLJ  CONST_29  O13   C12  N14  C15     0.00   0.0  0
 MLJ  CONST_30  H191  N19  C17  C16     0.00   0.0  0
 MLJ  Var_01    C23   C22  C21  C20    64.36  30.0  1
 MLJ  Var_02    C24   C23  C22  C21   -47.51  30.0  1
 MLJ  Var_03    C29   C24  C23  C22    17.33  30.0  1
 MLJ  Var_04    C07   C06  O05  C02    90.59  30.0  2
 MLJ  Var_05    O13   C12  C09  C08   -28.14  30.0  2
 MLJ  Var_06    F01   C02  O05  C06   178.40  30.0  3
 MLJ  Var_07    C16   C15  N14  C12  -168.16  30.0  1
 MLJ  Var_08    O18   C17  C16  C15   -11.98  30.0  3
 MLJ  Var_09    N14   C15  C16  C17   178.04  30.0  1

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
 MLJ  chir_01  C20  N19  C21  C29  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
 MLJ  plan-1  C06   0.020
 MLJ  plan-1  C07   0.020
 MLJ  plan-1  C08   0.020
 MLJ  plan-1  C09   0.020
 MLJ  plan-1  C10   0.020
 MLJ  plan-1  C11   0.020
 MLJ  plan-1  C12   0.020
 MLJ  plan-1  O05   0.020
 MLJ  plan-1  H071  0.020
 MLJ  plan-1  H081  0.020
 MLJ  plan-1  H101  0.020
 MLJ  plan-1  H111  0.020
 MLJ  plan-2  C20   0.020
 MLJ  plan-2  C23   0.020
 MLJ  plan-2  C24   0.020
 MLJ  plan-2  C25   0.020
 MLJ  plan-2  C26   0.020
 MLJ  plan-2  C27   0.020
 MLJ  plan-2  C28   0.020
 MLJ  plan-2  C29   0.020
 MLJ  plan-2  H251  0.020
 MLJ  plan-2  H261  0.020
 MLJ  plan-2  H271  0.020
 MLJ  plan-2  H281  0.020
 MLJ  plan-3  C09   0.020
 MLJ  plan-3  C12   0.020
 MLJ  plan-3  C15   0.020
 MLJ  plan-3  N14   0.020
 MLJ  plan-3  O13   0.020
 MLJ  plan-3  H141  0.020
 MLJ  plan-4  C16   0.020
 MLJ  plan-4  C17   0.020
 MLJ  plan-4  C20   0.020
 MLJ  plan-4  N19   0.020
 MLJ  plan-4  O18   0.020
 MLJ  plan-4  H191  0.020

