# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:40:08 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: (3alpha,8alpha)-3-hydroxypregn-5-en-20-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[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
 PLO  PLO  (3alpha,8alpha)-3-hydroxypregn-5-en-20-one  ligand  55  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PLO
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
 PLO  C1    C  CH2   0  -0.431   1.5235  -0.6098  -2.7953
 PLO  C2    C  CH2   0  -0.468   1.5838  -0.3923  -4.3018
 PLO  C3    C  CH1   0   0.089   0.2302  -0.6549  -4.9308
 PLO  O3    O  OH1   0  -0.678   0.3338  -0.4466  -6.3249
 PLO  C4    C  CH2   0  -0.547  -0.8171   0.2550  -4.2941
 PLO  C5    C  C     0   0.206  -0.8542   0.1192  -2.7938
 PLO  C6    C  C1    0  -0.328  -2.0090  -0.0877  -2.1627
 PLO  C7    C  CH2   0  -0.452  -2.1697  -0.1888  -0.6821
 PLO  C8    C  CH1   0  -0.241  -0.9281   0.2521   0.0861
 PLO  C9    C  CH1   0  -0.183   0.3341  -0.2773  -0.6108
 PLO  C10   C  CT    0  -0.130   0.4714   0.2497  -2.0624
 PLO  C11   C  CH2   0  -0.447   1.5923  -0.0384   0.2305
 PLO  C12   C  CH2   0  -0.415   1.4774  -0.5455   1.6694
 PLO  C13   C  CT    0  -0.058   0.2583   0.0545   2.3635
 PLO  C14   C  CH1   0  -0.179  -0.9769  -0.2725   1.5115
 PLO  C15   C  CH2   0  -0.445  -2.1528   0.1145   2.4018
 PLO  C16   C  CH2   0  -0.432  -1.6758  -0.2621   3.8215
 PLO  C17   C  CH1   0  -0.346  -0.1822  -0.6274   3.6926
 PLO  C18   C  CH3   0  -0.679   0.4440   1.5592   2.5822
 PLO  C19   C  CH3   0  -0.673   0.8950   1.7275  -2.0968
 PLO  C20   C  C     0   0.403   0.6630  -0.2790   4.8949
 PLO  C21   C  CH3   0  -0.777   1.9094  -1.0992   5.0852
 PLO  O20   O  O     0  -0.407   0.3586   0.5998   5.6728
 PLO  H11   H  HCH2  0   0.221   1.3051  -1.6662  -2.6032
 PLO  H12   H  HCH2  0   0.236   2.5120  -0.4199  -2.3719
 PLO  H21   H  HCH2  0   0.238   2.3351  -1.0593  -4.7333
 PLO  H22   H  HCH2  0   0.221   1.9040   0.6300  -4.5315
 PLO  H3    H  HCH1  0   0.190  -0.0499  -1.6994  -4.7214
 PLO  HO3   H  HOH1  0   0.446  -0.5076  -0.6840  -6.7266
 PLO  H41   H  HCH2  0   0.240  -1.8074   0.0364  -4.7049
 PLO  H42   H  HCH2  0   0.229  -0.5813   1.2878  -4.5787
 PLO  H6    H  H     0   0.221  -2.9137  -0.1901  -2.7569
 PLO  H71   H  HCH2  0   0.223  -2.4176  -1.2257  -0.4182
 PLO  H72   H  HCH2  0   0.239  -3.0373   0.4003  -0.3679
 PLO  H8    H  HCH1  0   0.216  -0.8991   1.3483   0.0953
 PLO  H9    H  HCH1  0   0.206   0.1999  -1.3666  -0.6922
 PLO  H111  H  HCH2  0   0.225   1.8235   1.0291   0.2520
 PLO  H112  H  HCH2  0   0.239   2.4516  -0.5193  -0.2418
 PLO  H121  H  HCH2  0   0.227   2.4021  -0.2995   2.1995
 PLO  H122  H  HCH2  0   0.217   1.3906  -1.6380   1.6756
 PLO  H14   H  HCH1  0   0.213  -0.9940  -1.3707   1.4242
 PLO  H151  H  HCH2  0   0.236  -3.0730  -0.4006   2.1230
 PLO  H152  H  HCH2  0   0.221  -2.3582   1.1858   2.3270
 PLO  H161  H  HCH2  0   0.239  -2.2365  -1.1068   4.2233
 PLO  H162  H  HCH2  0   0.234  -1.8162   0.5640   4.5182
 PLO  H17   H  HCH1  0   0.252  -0.0818  -1.7067   3.5301
 PLO  H181  H  HCH3  0   0.237   0.4742   2.1148   1.6451
 PLO  H182  H  HCH3  0   0.240  -0.3562   1.9937   3.1819
 PLO  H183  H  HCH3  0   0.230   1.3849   1.7623   3.0984
 PLO  H191  H  HCH3  0   0.235   0.8420   2.1325  -3.1073
 PLO  H192  H  HCH3  0   0.232   0.2464   2.3434  -1.4715
 PLO  H193  H  HCH3  0   0.229   1.9215   1.8639  -1.7538
 PLO  H211  H  HCH3  0   0.256   2.5161  -0.7260   5.9077
 PLO  H212  H  HCH3  0   0.267   1.6294  -2.1353   5.2895
 PLO  H213  H  HCH3  0   0.264   2.5076  -1.1165   4.1738

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
 PLO  C1   C2    single  1.523  0.020  1.523
 PLO  C1   C10   single  1.544  0.020  1.544
 PLO  C1   H11   single  0.970  0.020  1.090
 PLO  C1   H12   single  0.970  0.020  1.090
 PLO  C2   C3    single  1.515  0.020  1.515
 PLO  C2   H21   single  0.970  0.020  1.090
 PLO  C2   H22   single  0.970  0.020  1.090
 PLO  C3   O3    single  1.413  0.020  1.413
 PLO  C3   C4    single  1.527  0.020  1.527
 PLO  C3   H3    single  0.970  0.020  1.090
 PLO  O3   HO3   single  0.850  0.020  0.980
 PLO  C4   C5    single  1.507  0.020  1.507
 PLO  C4   H41   single  0.970  0.020  1.090
 PLO  C4   H42   single  0.970  0.020  1.090
 PLO  C5   C6    double  1.332  0.020  1.332
 PLO  C5   C10   single  1.520  0.020  1.520
 PLO  C6   C7    single  1.493  0.020  1.493
 PLO  C6   H6    single  0.930  0.020  1.080
 PLO  C7   C8    single  1.525  0.020  1.525
 PLO  C7   H71   single  0.970  0.020  1.090
 PLO  C7   H72   single  0.970  0.020  1.090
 PLO  C8   C9    single  1.536  0.020  1.536
 PLO  C8   C14   single  1.520  0.020  1.520
 PLO  C8   H8    single  0.970  0.020  1.090
 PLO  C9   C10   single  1.550  0.020  1.550
 PLO  C9   C11   single  1.532  0.020  1.532
 PLO  C9   H9    single  0.970  0.020  1.090
 PLO  C10  C19   single  1.538  0.020  1.538
 PLO  C11  C12   single  1.530  0.020  1.530
 PLO  C11  H111  single  0.970  0.020  1.090
 PLO  C11  H112  single  0.970  0.020  1.090
 PLO  C12  C13   single  1.526  0.020  1.526
 PLO  C12  H121  single  0.970  0.020  1.090
 PLO  C12  H122  single  0.970  0.020  1.090
 PLO  C13  C14   single  1.536  0.020  1.536
 PLO  C13  C17   single  1.557  0.020  1.557
 PLO  C13  C18   single  1.532  0.020  1.532
 PLO  C14  C15   single  1.525  0.020  1.525
 PLO  C14  H14   single  0.970  0.020  1.090
 PLO  C15  C16   single  1.544  0.020  1.544
 PLO  C15  H151  single  0.970  0.020  1.090
 PLO  C15  H152  single  0.970  0.020  1.090
 PLO  C16  C17   single  1.543  0.020  1.543
 PLO  C16  H161  single  0.970  0.020  1.090
 PLO  C16  H162  single  0.970  0.020  1.090
 PLO  C17  C20   single  1.510  0.020  1.510
 PLO  C17  H17   single  0.970  0.020  1.090
 PLO  C18  H181  single  0.970  0.020  1.090
 PLO  C18  H182  single  0.970  0.020  1.090
 PLO  C18  H183  single  0.970  0.020  1.090
 PLO  C19  H191  single  0.970  0.020  1.090
 PLO  C19  H192  single  0.970  0.020  1.090
 PLO  C19  H193  single  0.970  0.020  1.090
 PLO  C20  C21   single  1.504  0.020  1.504
 PLO  C20  O20   double  1.212  0.020  1.212
 PLO  C21  H211  single  0.970  0.020  1.090
 PLO  C21  H212  single  0.970  0.020  1.090
 PLO  C21  H213  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
 PLO  H12   C1   H11   106.27  3.000
 PLO  H12   C1   C10   109.64  3.000
 PLO  H11   C1   C10   108.53  3.000
 PLO  H12   C1   C2    108.83  3.000
 PLO  H11   C1   C2    108.60  3.000
 PLO  C10   C1   C2    114.65  3.000
 PLO  H22   C2   H21   106.60  3.000
 PLO  H22   C2   C3    109.62  3.000
 PLO  H21   C2   C3    110.13  3.000
 PLO  H22   C2   C1    110.61  3.000
 PLO  H21   C2   C1    109.29  3.000
 PLO  C3    C2   C1    110.51  3.000
 PLO  H3    C3   C4    108.14  3.000
 PLO  H3    C3   O3    110.24  3.000
 PLO  C4    C3   O3    111.95  3.000
 PLO  H3    C3   C2    108.22  3.000
 PLO  C4    C3   C2    109.66  3.000
 PLO  O3    C3   C2    108.56  3.000
 PLO  HO3   O3   C3    108.14  3.000
 PLO  H42   C4   H41   106.57  3.000
 PLO  H42   C4   C5    110.39  3.000
 PLO  H41   C4   C5    109.48  3.000
 PLO  H42   C4   C3    107.79  3.000
 PLO  H41   C4   C3    110.20  3.000
 PLO  C5    C4   C3    112.24  3.000
 PLO  C10   C5   C6    122.79  3.000
 PLO  C10   C5   C4    116.74  3.000
 PLO  C6    C5   C4    120.47  3.000
 PLO  H6    C6   C7    116.49  3.000
 PLO  H6    C6   C5    118.50  3.000
 PLO  C7    C6   C5    125.01  3.000
 PLO  H72   C7   H71   105.08  3.000
 PLO  H72   C7   C8    110.19  3.000
 PLO  H71   C7   C8    109.61  3.000
 PLO  H72   C7   C6    109.48  3.000
 PLO  H71   C7   C6    109.06  3.000
 PLO  C8    C7   C6    113.10  3.000
 PLO  H8    C8   C14   109.76  3.000
 PLO  H8    C8   C9    109.07  3.000
 PLO  C14   C8   C9    109.45  3.000
 PLO  H8    C8   C7    108.34  3.000
 PLO  C14   C8   C7    110.27  3.000
 PLO  C9    C8   C7    109.93  3.000
 PLO  H9    C9   C11   107.16  3.000
 PLO  H9    C9   C10   106.14  3.000
 PLO  C11   C9   C10   112.85  3.000
 PLO  H9    C9   C8    105.93  3.000
 PLO  C11   C9   C8    111.83  3.000
 PLO  C10   C9   C8    112.36  3.000
 PLO  C19   C10  C9    111.84  3.000
 PLO  C19   C10  C5    108.18  3.000
 PLO  C9    C10  C5    110.13  3.000
 PLO  C19   C10  C1    109.68  3.000
 PLO  C9    C10  C1    108.40  3.000
 PLO  C5    C10  C1    108.56  3.000
 PLO  H112  C11  H111  105.80  3.000
 PLO  H112  C11  C12   108.66  3.000
 PLO  H111  C11  C12   108.74  3.000
 PLO  H112  C11  C9    109.87  3.000
 PLO  H111  C11  C9    109.69  3.000
 PLO  C12   C11  C9    113.77  3.000
 PLO  H122  C12  H121  106.76  3.000
 PLO  H122  C12  C13   109.04  3.000
 PLO  H121  C12  C13   111.50  3.000
 PLO  H122  C12  C11   109.97  3.000
 PLO  H121  C12  C11   108.53  3.000
 PLO  C13   C12  C11   110.95  3.000
 PLO  C18   C13  C17   110.03  3.000
 PLO  C18   C13  C14   112.70  3.000
 PLO  C17   C13  C14    98.79  3.000
 PLO  C18   C13  C12   110.75  3.000
 PLO  C17   C13  C12   116.23  3.000
 PLO  C14   C13  C12   107.85  3.000
 PLO  H14   C14  C15   106.69  3.000
 PLO  H14   C14  C13   105.59  3.000
 PLO  C15   C14  C13   104.02  3.000
 PLO  H14   C14  C8    105.69  3.000
 PLO  C15   C14  C8    119.00  3.000
 PLO  C13   C14  C8    114.90  3.000
 PLO  H152  C15  H151  106.66  3.000
 PLO  H152  C15  C16   111.09  3.000
 PLO  H151  C15  C16   112.36  3.000
 PLO  H152  C15  C14   110.70  3.000
 PLO  H151  C15  C14   112.42  3.000
 PLO  C16   C15  C14   103.69  3.000
 PLO  H162  C16  H161  106.58  3.000
 PLO  H162  C16  C17   110.95  3.000
 PLO  H161  C16  C17   110.18  3.000
 PLO  H162  C16  C15   111.29  3.000
 PLO  H161  C16  C15   111.64  3.000
 PLO  C17   C16  C15   106.26  3.000
 PLO  H17   C17  C20   107.09  3.000
 PLO  H17   C17  C16   109.52  3.000
 PLO  C20   C17  C16   114.87  3.000
 PLO  H17   C17  C13   106.18  3.000
 PLO  C20   C17  C13   114.84  3.000
 PLO  C16   C17  C13   103.97  3.000
 PLO  H183  C18  H182  107.35  3.000
 PLO  H183  C18  H181  106.72  3.000
 PLO  H182  C18  H181  106.87  3.000
 PLO  H183  C18  C13   110.77  3.000
 PLO  H182  C18  C13   112.40  3.000
 PLO  H181  C18  C13   112.42  3.000
 PLO  H193  C19  H192  107.98  3.000
 PLO  H193  C19  H191  106.91  3.000
 PLO  H192  C19  H191  107.02  3.000
 PLO  H193  C19  C10   111.85  3.000
 PLO  H192  C19  C10   111.46  3.000
 PLO  H191  C19  C10   111.38  3.000
 PLO  O20   C20  C21   121.48  3.000
 PLO  O20   C20  C17   122.51  3.000
 PLO  C21   C20  C17   116.01  3.000
 PLO  H213  C21  H212  106.37  3.000
 PLO  H213  C21  H211  109.35  3.000
 PLO  H212  C21  H211  109.07  3.000
 PLO  H213  C21  C20   110.96  3.000
 PLO  H212  C21  C20   109.18  3.000
 PLO  H211  C21  C20   111.76  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
 PLO  Var_01  C7    C6   C5   C4   -177.72   0.0  0
 PLO  Var_02  C10   C1   C2   C3    -57.19  30.0  1
 PLO  Var_03  C6    C5   C4   C3   -129.54  30.0  1
 PLO  Var_04  C8    C7   C6   C5     11.92  30.0  1
 PLO  Var_05  C13   C12  C11  C9    -55.09  30.0  1
 PLO  Var_06  C17   C16  C15  C14     8.88  30.0  1
 PLO  Var_07  H211  C21  C20  C17   174.15  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
 PLO  chir_01  C3   C2   O3   C4   positiv
 PLO  chir_02  C8   C7   C9   C14  positiv
 PLO  chir_03  C9   C11  C10  C8   positiv
 PLO  chir_04  C10  C9   C5   C1   positiv
 PLO  chir_05  C13  C14  C17  C12  negativ
 PLO  chir_06  C14  C8   C13  C15  negativ
 PLO  chir_07  C17  C13  C16  C20  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
 PLO  plan-1  C17  0.020
 PLO  plan-1  C20  0.020
 PLO  plan-1  C21  0.020
 PLO  plan-1  O20  0.020
 PLO  plan-2  C4   0.020
 PLO  plan-2  C5   0.020
 PLO  plan-2  C6   0.020
 PLO  plan-2  C7   0.020
 PLO  plan-2  C10  0.020
 PLO  plan-2  H6   0.020

