# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:50:36 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-oxo-4-{[(9beta,10alpha,13alpha,14beta,17alpha)-3-oxoestr-4-en-17-yl]oxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@H]34)[C@@H]1CC[C@H]2OC(=O)CCC(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
 NTH  NTH  '4-oxo-4-{[(9beta,10alpha,13alpha,14beta,17alpha)-3-oxoestr-4-en-17-yl]oxy}butanoic acid'  ligand  56  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NTH
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
 NTH  C1    C  CH2    0  -0.461  -1.8179  -1.0273  -3.9667
 NTH  C2    C  CH2    0  -0.567  -2.2629  -0.8052  -5.4041
 NTH  C3    C  C      0   0.402  -2.1655   0.6455  -5.7867
 NTH  O3    O  O      0  -0.441  -2.9489   1.1781  -6.5545
 NTH  C4    C  C1     0  -0.461  -1.0165   1.3620  -5.2396
 NTH  C5    C  C      0   0.225  -0.1653   0.8206  -4.3516
 NTH  C6    C  CH2    0  -0.506   1.1052   1.5246  -3.9940
 NTH  C7    C  CH2    0  -0.418   1.3357   1.5804  -2.4890
 NTH  C8    C  CH1    0  -0.234   1.2540   0.1882  -1.8796
 NTH  C9    C  CH1    0  -0.201  -0.1139  -0.4454  -2.1820
 NTH  C10   C  CH1    0  -0.282  -0.4030  -0.5154  -3.6970
 NTH  C11   C  CH2    0  -0.445  -0.2630  -1.8195  -1.5177
 NTH  C12   C  CH2    0  -0.409   0.0277  -1.7958  -0.0137
 NTH  C13   C  CT     0  -0.107   1.3972  -1.1851   0.2636
 NTH  C14   C  CH1    0  -0.183   1.4604   0.2093  -0.3752
 NTH  C15   C  CH2    0  -0.456   2.7488   0.8076   0.1866
 NTH  C16   C  CH2    0  -0.480   2.8596   0.2037   1.6067
 NTH  C17   C  CH1    0   0.064   1.7525  -0.8652   1.7218
 NTH  O17   O  O2     0  -0.474   0.5867  -0.3301   2.3654
 NTH  C18   C  CH3    0  -0.675   2.4988  -2.1271  -0.2435
 NTH  C20   C  C      0   0.603   0.5625  -0.2551   3.6913
 NTH  O20   O  O      0  -0.464   1.4865  -0.5939   4.3915
 NTH  C21   C  CH2    0  -0.586  -0.7464   0.6523   5.6571
 NTH  C22   C  CH2    0  -0.579  -0.7554   0.2745   4.1880
 NTH  C23   C  C      0   0.420  -2.0970   1.1567   6.1974
 NTH  O23   O  O      0  -0.607  -3.0721   1.1562   5.4207
 NTH  O24   O  OC    -1  -0.629  -2.0986   1.5246   7.3902
 NTH  H11   H  HCH2   0   0.233  -2.5128  -0.5176  -3.2909
 NTH  H12   H  HCH2   0   0.253  -1.8849  -2.0900  -3.7351
 NTH  H21   H  HCH2   0   0.262  -3.2793  -1.1666  -5.5674
 NTH  H22   H  HCH2   0   0.263  -1.6114  -1.3660  -6.0851
 NTH  H7    H  H      0   0.249  -0.8207   2.3518  -5.6395
 NTH  H61   H  HCH2   0   0.253   1.1255   2.5224  -4.4351
 NTH  H62   H  HCH2   0   0.251   1.9301   0.9620  -4.4483
 NTH  H71   H  HCH2   0   0.220   0.5918   2.2339  -2.0205
 NTH  H72   H  HCH2   0   0.244   2.3132   2.0250  -2.2908
 NTH  H8    H  HCH1   0   0.214   2.0375  -0.4253  -2.3452
 NTH  H9    H  HCH1   0   0.215  -0.8731   0.2195  -1.7423
 NTH  H10   H  HCH1   0   0.252   0.3209  -1.2164  -4.1417
 NTH  H111  H  HCH2   0   0.217   0.3919  -2.5369  -2.0234
 NTH  H112  H  HCH2   0   0.243  -1.2785  -2.1938  -1.6606
 NTH  H121  H  HCH2   0   0.224  -0.0433  -2.8116   0.3866
 NTH  H122  H  HCH2   0   0.228  -0.7502  -1.2078   0.4793
 NTH  H14   H  HCH1   0   0.221   0.6207   0.7819   0.0446
 NTH  H151  H  HCH2   0   0.225   3.6081   0.5241  -0.4266
 NTH  H152  H  HCH2   0   0.239   2.7251   1.8975   0.2088
 NTH  H161  H  HCH2   0   0.244   3.8361  -0.2530   1.7703
 NTH  H162  H  HCH2   0   0.252   2.7480   0.9642   2.3792
 NTH  H17   H  HCH1   0   0.246   2.0806  -1.7529   2.2682
 NTH  H181  H  HCH3   0   0.239   2.4420  -2.3007  -1.3168
 NTH  H182  H  HCH3   0   0.240   3.5029  -1.7580  -0.0314
 NTH  H183  H  HCH3   0   0.234   2.4051  -3.0989   0.2459
 NTH  H221  H  HCH2   0   0.233  -0.4353  -0.2031   6.2636
 NTH  H222  H  HCH2   0   0.230   0.0073   1.4237   5.8420
 NTH  H211  H  HCH2   0   0.258  -1.0514   1.1221   3.5663
 NTH  H212  H  HCH2   0   0.267  -1.5084  -0.4966   3.9976

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
 NTH  C1   C2    single  1.521  0.020  1.521
 NTH  C1   C10   single  1.529  0.020  1.529
 NTH  C1   H11   single  0.970  0.020  1.090
 NTH  C1   H12   single  0.970  0.020  1.090
 NTH  C2   C3    single  1.503  0.020  1.503
 NTH  C2   H21   single  0.970  0.020  1.090
 NTH  C2   H22   single  0.970  0.020  1.090
 NTH  C3   O3    double  1.219  0.020  1.219
 NTH  C3   C4    single  1.460  0.020  1.460
 NTH  C4   C5    double  1.344  0.020  1.344
 NTH  C4   H7    single  0.930  0.020  1.080
 NTH  C5   C6    single  1.496  0.020  1.496
 NTH  C5   C10   single  1.507  0.020  1.507
 NTH  C6   C7    single  1.524  0.020  1.524
 NTH  C6   H61   single  0.970  0.020  1.090
 NTH  C6   H62   single  0.970  0.020  1.090
 NTH  C7   C8    single  1.522  0.020  1.522
 NTH  C7   H71   single  0.970  0.020  1.090
 NTH  C7   H72   single  0.970  0.020  1.090
 NTH  C8   C9    single  1.537  0.020  1.537
 NTH  C8   C14   single  1.519  0.020  1.519
 NTH  C8   H8    single  0.970  0.020  1.090
 NTH  C9   C10   single  1.544  0.020  1.544
 NTH  C9   C11   single  1.534  0.020  1.534
 NTH  C9   H9    single  0.970  0.020  1.090
 NTH  C10  H10   single  0.970  0.020  1.090
 NTH  C11  C12   single  1.532  0.020  1.532
 NTH  C11  H111  single  0.970  0.020  1.090
 NTH  C11  H112  single  0.970  0.020  1.090
 NTH  C12  C13   single  1.525  0.020  1.525
 NTH  C12  H121  single  0.970  0.020  1.090
 NTH  C12  H122  single  0.970  0.020  1.090
 NTH  C13  C14   single  1.535  0.020  1.535
 NTH  C13  C17   single  1.534  0.020  1.534
 NTH  C13  C18   single  1.536  0.020  1.536
 NTH  C14  C15   single  1.528  0.020  1.528
 NTH  C14  H14   single  0.970  0.020  1.090
 NTH  C15  C16   single  1.547  0.020  1.547
 NTH  C15  H151  single  0.970  0.020  1.090
 NTH  C15  H152  single  0.970  0.020  1.090
 NTH  C16  C17   single  1.543  0.020  1.543
 NTH  C16  H161  single  0.970  0.020  1.090
 NTH  C16  H162  single  0.970  0.020  1.090
 NTH  C17  O17   single  1.435  0.020  1.435
 NTH  C17  H17   single  0.970  0.020  1.090
 NTH  O17  C20   single  1.328  0.020  1.328
 NTH  C18  H181  single  0.970  0.020  1.090
 NTH  C18  H182  single  0.970  0.020  1.090
 NTH  C18  H183  single  0.970  0.020  1.090
 NTH  C20  O20   double  1.208  0.020  1.208
 NTH  C20  C22   single  1.505  0.020  1.505
 NTH  C21  C22   single  1.517  0.020  1.517
 NTH  C21  C23   single  1.540  0.020  1.540
 NTH  C21  H221  single  0.970  0.020  1.090
 NTH  C21  H222  single  0.970  0.020  1.090
 NTH  C22  H211  single  0.970  0.020  1.090
 NTH  C22  H212  single  0.970  0.020  1.090
 NTH  C23  O23   deloc   1.247  0.020  1.247
 NTH  C23  O24   deloc   1.248  0.020  1.248

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
 NTH  H12   C1   H11   106.48  3.000
 NTH  H12   C1   C10   110.24  3.000
 NTH  H11   C1   C10   108.82  3.000
 NTH  H12   C1   C2    108.98  3.000
 NTH  H11   C1   C2    109.24  3.000
 NTH  C10   C1   C2    112.87  3.000
 NTH  H22   C2   H21   106.92  3.000
 NTH  H22   C2   C3    107.27  3.000
 NTH  H21   C2   C3    109.99  3.000
 NTH  H22   C2   C1    109.78  3.000
 NTH  H21   C2   C1    111.45  3.000
 NTH  C3    C2   C1    111.25  3.000
 NTH  C4    C3   O3    121.81  3.000
 NTH  C4    C3   C2    115.41  3.000
 NTH  O3    C3   C2    122.69  3.000
 NTH  H7    C4   C5    119.77  3.000
 NTH  H7    C4   C3    116.83  3.000
 NTH  C5    C4   C3    123.24  3.000
 NTH  C10   C5   C6    116.58  3.000
 NTH  C10   C5   C4    122.98  3.000
 NTH  C6    C5   C4    120.42  3.000
 NTH  H62   C6   H61   106.71  3.000
 NTH  H62   C6   C7    108.31  3.000
 NTH  H61   C6   C7    111.29  3.000
 NTH  H62   C6   C5    107.36  3.000
 NTH  H61   C6   C5    110.45  3.000
 NTH  C7    C6   C5    112.45  3.000
 NTH  H72   C7   H71   106.70  3.000
 NTH  H72   C7   C8    110.36  3.000
 NTH  H71   C7   C8    109.75  3.000
 NTH  H72   C7   C6    109.24  3.000
 NTH  H71   C7   C6    109.97  3.000
 NTH  C8    C7   C6    110.73  3.000
 NTH  H8    C8   C14   109.31  3.000
 NTH  H8    C8   C9    108.72  3.000
 NTH  C14   C8   C9    108.75  3.000
 NTH  H8    C8   C7    107.63  3.000
 NTH  C14   C8   C7    112.13  3.000
 NTH  C9    C8   C7    110.24  3.000
 NTH  H9    C9   C11   107.52  3.000
 NTH  H9    C9   C10   106.87  3.000
 NTH  C11   C9   C10   111.48  3.000
 NTH  H9    C9   C8    106.62  3.000
 NTH  C11   C9   C8    111.75  3.000
 NTH  C10   C9   C8    112.23  3.000
 NTH  H10   C10  C9    107.57  3.000
 NTH  H10   C10  C5    106.58  3.000
 NTH  C9    C10  C5    110.89  3.000
 NTH  H10   C10  C1    108.90  3.000
 NTH  C9    C10  C1    111.20  3.000
 NTH  C5    C10  C1    111.49  3.000
 NTH  H112  C11  H111  105.74  3.000
 NTH  H112  C11  C12   108.08  3.000
 NTH  H111  C11  C12   110.49  3.000
 NTH  H112  C11  C9    109.93  3.000
 NTH  H111  C11  C9    109.19  3.000
 NTH  C12   C11  C9    113.14  3.000
 NTH  H122  C12  H121  106.76  3.000
 NTH  H122  C12  C13   109.98  3.000
 NTH  H121  C12  C13   111.32  3.000
 NTH  H122  C12  C11   108.43  3.000
 NTH  H121  C12  C11   109.42  3.000
 NTH  C13   C12  C11   110.80  3.000
 NTH  C18   C13  C17   106.00  3.000
 NTH  C18   C13  C14   112.97  3.000
 NTH  C17   C13  C14   101.34  3.000
 NTH  C18   C13  C12   109.79  3.000
 NTH  C17   C13  C12   117.66  3.000
 NTH  C14   C13  C12   108.97  3.000
 NTH  H14   C14  C15   107.44  3.000
 NTH  H14   C14  C13   106.42  3.000
 NTH  C15   C14  C13   103.73  3.000
 NTH  H14   C14  C8    106.36  3.000
 NTH  C15   C14  C8    118.97  3.000
 NTH  C13   C14  C8    113.21  3.000
 NTH  H152  C15  H151  106.72  3.000
 NTH  H152  C15  C16   111.91  3.000
 NTH  H151  C15  C16   110.94  3.000
 NTH  H152  C15  C14   112.38  3.000
 NTH  H151  C15  C14   110.80  3.000
 NTH  C16   C15  C14   104.19  3.000
 NTH  H162  C16  H161  106.12  3.000
 NTH  H162  C16  C17   110.92  3.000
 NTH  H161  C16  C17   109.95  3.000
 NTH  H162  C16  C15   111.77  3.000
 NTH  H161  C16  C15   111.43  3.000
 NTH  C17   C16  C15   106.70  3.000
 NTH  H17   C17  O17   108.82  3.000
 NTH  H17   C17  C16   112.61  3.000
 NTH  O17   C17  C16   110.97  3.000
 NTH  H17   C17  C13   112.05  3.000
 NTH  O17   C17  C13   108.41  3.000
 NTH  C16   C17  C13   103.87  3.000
 NTH  C20   O17  C17   118.92  3.000
 NTH  H183  C18  H182  107.03  3.000
 NTH  H183  C18  H181  107.18  3.000
 NTH  H182  C18  H181  107.08  3.000
 NTH  H183  C18  C13   109.65  3.000
 NTH  H182  C18  C13   112.87  3.000
 NTH  H181  C18  C13   112.70  3.000
 NTH  C22   C20  O20   125.27  3.000
 NTH  C22   C20  O17   111.43  3.000
 NTH  O20   C20  O17   123.29  3.000
 NTH  H222  C21  H221  105.18  3.000
 NTH  H222  C21  C23   108.29  3.000
 NTH  H221  C21  C23   108.13  3.000
 NTH  H222  C21  C22   110.08  3.000
 NTH  H221  C21  C22   110.12  3.000
 NTH  C23   C21  C22   114.60  3.000
 NTH  H212  C22  H211  105.15  3.000
 NTH  H212  C22  C21   110.37  3.000
 NTH  H211  C22  C21   111.08  3.000
 NTH  H212  C22  C20   107.29  3.000
 NTH  H211  C22  C20   108.82  3.000
 NTH  C21   C22  C20   113.71  3.000
 NTH  O24   C23  O23   126.48  3.000
 NTH  O24   C23  C21   115.66  3.000
 NTH  O23   C23  C21   117.86  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
 NTH  Var_01  C4   C3   C2   C1     37.49  30.0  1
 NTH  Var_02  C5   C4   C3   C2     -6.25  30.0  1
 NTH  Var_03  C10  C1   C2   C3    -56.10  30.0  1
 NTH  Var_04  C6   C5   C4   C3    170.39  30.0  1
 NTH  Var_05  C7   C6   C5   C4    132.69  30.0  1
 NTH  Var_06  C8   C7   C6   C5     53.39  30.0  1
 NTH  Var_07  C13  C12  C11  C9    -53.86  30.0  1
 NTH  Var_08  C17  C16  C15  C14     8.08  30.0  1
 NTH  Var_09  O20  C20  O17  C17     1.38  30.0  3
 NTH  Var_10  C21  C22  C20  O17  -168.04  30.0  3
 NTH  Var_11  C23  C21  C22  C20  -178.24  30.0  1
 NTH  Var_12  O23  C23  C21  C22     3.06  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
 NTH  chir_01  C8   C7   C9   C14  positiv
 NTH  chir_02  C9   C8   C10  C11  negativ
 NTH  chir_03  C10  C9   C5   C1   positiv
 NTH  chir_04  C13  C17  C14  C12  positiv
 NTH  chir_05  C14  C15  C13  C8   positiv
 NTH  chir_06  C17  O17  C16  C13  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
 NTH  plan-1  C2   0.020
 NTH  plan-1  C3   0.020
 NTH  plan-1  O3   0.020
 NTH  plan-1  C4   0.020
 NTH  plan-2  C21  0.020
 NTH  plan-2  C23  0.020
 NTH  plan-2  O23  0.020
 NTH  plan-2  O24  0.020
 NTH  plan-3  O17  0.020
 NTH  plan-3  C20  0.020
 NTH  plan-3  O20  0.020
 NTH  plan-3  C22  0.020

