# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:56:00 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@@H]1O[C@@H]1C\C=C/CCCCCCCC(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
 T25  T25  '(9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid'  ligand  52  21  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T25
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
 T25  O1    O  O      0  -0.610   8.8602  -0.1863   1.1598
 T25  C1    C  C      0   0.409   8.6561   0.4181   0.0883
 T25  O2    O  OC    -1  -0.635   9.4613   1.1750  -0.4955
 T25  C2    C  CH2    0  -0.580   7.2988   0.2126  -0.6073
 T25  C3    C  CH2    0  -0.403   6.2460  -0.5459   0.1836
 T25  C4    C  CH2    0  -0.409   4.9470  -0.7316  -0.5919
 T25  C5    C  CH2    0  -0.411   3.8619  -1.4407   0.2076
 T25  C6    C  CH2    0  -0.411   2.5687  -1.6376  -0.5736
 T25  C7    C  CH2    0  -0.413   1.4389  -2.2134   0.2705
 T25  C8    C  CH2    0  -0.491   0.1534  -2.4294  -0.5301
 T25  C9    C  C1     0  -0.206  -0.9683  -2.9276   0.3257
 T25  C10   C  C1     0  -0.214  -2.1327  -2.3276   0.5690
 T25  C11   C  CH2    0  -0.555  -2.6098  -1.0233   0.0037
 T25  C12   C  CH1    0   0.006  -3.8106  -1.2172  -0.8893
 T25  O3    O  O2     0  -0.500  -5.0916  -1.2642  -0.2727
 T25  C13   C  CH1    0   0.004  -4.8089  -0.1847  -1.1591
 T25  C14   C  CH2    0  -0.473  -4.7724   1.2092  -0.6002
 T25  C15   C  CH2    0  -0.417  -6.1600   1.7375  -0.2477
 T25  C16   C  CH2    0  -0.409  -6.1349   3.2013   0.1738
 T25  C17   C  CH2    0  -0.419  -7.5051   3.7419   0.5627
 T25  C18   C  CH3    0  -0.663  -7.4699   5.2165   0.9403
 T25  H21   H  HCH2   0   0.212   6.9052   1.1927  -0.8996
 T25  H22   H  HCH2   0   0.217   7.4866  -0.3064  -1.5560
 T25  H31   H  HCH2   0   0.201   6.6361  -1.5245   0.4762
 T25  H32   H  HCH2   0   0.199   6.0318  -0.0176   1.1185
 T25  H41   H  HCH2   0   0.202   4.5708   0.2459  -0.9155
 T25  H42   H  HCH2   0   0.202   5.1504  -1.2918  -1.5120
 T25  H51   H  HCH2   0   0.207   4.2336  -2.4131   0.5495
 T25  H52   H  HCH2   0   0.204   3.6497  -0.8641   1.1151
 T25  H61   H  HCH2   0   0.207   2.2470  -0.6758  -0.9886
 T25  H62   H  HCH2   0   0.209   2.7555  -2.2904  -1.4332
 T25  H71   H  HCH2   0   0.214   1.7557  -3.1621   0.7165
 T25  H72   H  HCH2   0   0.216   1.2326  -1.5370   1.1061
 T25  H81   H  HCH2   0   0.229  -0.1194  -1.4987  -1.0323
 T25  H82   H  HCH2   0   0.231   0.3502  -3.1597  -1.3225
 T25  H9    H  H      0   0.231  -0.7849  -3.8806   0.8158
 T25  H10   H  H      0   0.237  -2.8318  -2.8282   1.2330
 T25  H111  H  HCH2   0   0.253  -2.8628  -0.3434   0.8208
 T25  H112  H  HCH2   0   0.252  -1.8268  -0.5341  -0.5786
 T25  H12   H  HCH1   0   0.243  -3.6615  -1.9724  -1.6618
 T25  H13   H  HCH1   0   0.239  -5.3374  -0.2569  -2.1111
 T25  H141  H  HCH2   0   0.235  -4.1238   1.2692   0.2768
 T25  H142  H  HCH2   0   0.229  -4.3217   1.8531  -1.3621
 T25  H151  H  HCH2   0   0.216  -6.8272   1.6209  -1.1084
 T25  H152  H  HCH2   0   0.218  -6.5868   1.1295   0.5563
 T25  H161  H  HCH2   0   0.209  -5.4449   3.3263   1.0154
 T25  H162  H  HCH2   0   0.209  -5.7262   3.8057  -0.6438
 T25  H171  H  HCH2   0   0.211  -8.2010   3.5951  -0.2689
 T25  H172  H  HCH2   0   0.211  -7.9009   3.1543   1.3966
 T25  H181  H  HCH3   0   0.216  -7.1204   5.8266   0.1049
 T25  H182  H  HCH3   0   0.226  -8.4565   5.5830   1.2256
 T25  H183  H  HCH3   0   0.216  -6.7949   5.3946   1.7797

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
 T25  C2   C3    single  1.520  0.020  1.520
 T25  C2   C1    single  1.539  0.020  1.539
 T25  C3   C4    single  1.524  0.020  1.524
 T25  C5   C4    single  1.523  0.020  1.523
 T25  C5   C6    single  1.524  0.020  1.524
 T25  C1   O1    deloc   1.247  0.020  1.247
 T25  C1   O2    deloc   1.250  0.020  1.250
 T25  C6   C7    single  1.523  0.020  1.523
 T25  C18  C17   single  1.523  0.020  1.523
 T25  C7   C8    single  1.530  0.020  1.530
 T25  C17  C16   single  1.523  0.020  1.523
 T25  C8   C9    single  1.496  0.020  1.496
 T25  C16  C15   single  1.524  0.020  1.524
 T25  C9   C10   double  1.332  0.020  1.332
 T25  C15  C14   single  1.526  0.020  1.526
 T25  C11  C10   single  1.500  0.020  1.500
 T25  C11  C12   single  1.509  0.020  1.509
 T25  C14  C13   single  1.502  0.020  1.502
 T25  C12  C13   single  1.461  0.020  1.461
 T25  C12  O3    single  1.422  0.020  1.422
 T25  C13  O3    single  1.425  0.020  1.425
 T25  C2   H21   single  0.970  0.020  1.090
 T25  C2   H22   single  0.970  0.020  1.090
 T25  C3   H31   single  0.970  0.020  1.090
 T25  C3   H32   single  0.970  0.020  1.090
 T25  C4   H41   single  0.970  0.020  1.090
 T25  C4   H42   single  0.970  0.020  1.090
 T25  C5   H51   single  0.970  0.020  1.090
 T25  C5   H52   single  0.970  0.020  1.090
 T25  C6   H61   single  0.970  0.020  1.090
 T25  C6   H62   single  0.970  0.020  1.090
 T25  C7   H71   single  0.970  0.020  1.090
 T25  C7   H72   single  0.970  0.020  1.090
 T25  C8   H81   single  0.970  0.020  1.090
 T25  C8   H82   single  0.970  0.020  1.090
 T25  C9   H9    single  0.930  0.020  1.080
 T25  C10  H10   single  0.930  0.020  1.080
 T25  C11  H111  single  0.970  0.020  1.090
 T25  C11  H112  single  0.970  0.020  1.090
 T25  C12  H12   single  0.970  0.020  1.090
 T25  C13  H13   single  0.970  0.020  1.090
 T25  C14  H141  single  0.970  0.020  1.090
 T25  C14  H142  single  0.970  0.020  1.090
 T25  C15  H151  single  0.970  0.020  1.090
 T25  C15  H152  single  0.970  0.020  1.090
 T25  C16  H161  single  0.970  0.020  1.090
 T25  C16  H162  single  0.970  0.020  1.090
 T25  C17  H171  single  0.970  0.020  1.090
 T25  C17  H172  single  0.970  0.020  1.090
 T25  C18  H181  single  0.970  0.020  1.090
 T25  C18  H182  single  0.970  0.020  1.090
 T25  C18  H183  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
 T25  C2    C1   O2    115.97  3.000
 T25  O2    C1   O1    126.12  3.000
 T25  C2    C1   O1    117.91  3.000
 T25  H22   C2   H21   104.71  3.000
 T25  H22   C2   C3    109.41  3.000
 T25  H21   C2   C3    109.66  3.000
 T25  H22   C2   C1    107.63  3.000
 T25  H21   C2   C1    108.54  3.000
 T25  C3    C2   C1    116.25  3.000
 T25  H32   C3   H31   105.85  3.000
 T25  H32   C3   C4    109.05  3.000
 T25  H31   C3   C4    109.33  3.000
 T25  H32   C3   C2    109.83  3.000
 T25  H31   C3   C2    109.81  3.000
 T25  C4    C3   C2    112.73  3.000
 T25  H42   C4   H41   105.76  3.000
 T25  H42   C4   C5    109.56  3.000
 T25  H41   C4   C5    109.00  3.000
 T25  H42   C4   C3    109.34  3.000
 T25  H41   C4   C3    109.51  3.000
 T25  C5    C4   C3    113.38  3.000
 T25  H52   C5   H51   105.92  3.000
 T25  H52   C5   C6    109.16  3.000
 T25  H51   C5   C6    109.47  3.000
 T25  H52   C5   C4    109.13  3.000
 T25  H51   C5   C4    109.59  3.000
 T25  C6    C5   C4    113.31  3.000
 T25  H62   C6   H61   106.02  3.000
 T25  H62   C6   C7    109.64  3.000
 T25  H61   C6   C7    108.90  3.000
 T25  H62   C6   C5    109.55  3.000
 T25  H61   C6   C5    109.26  3.000
 T25  C7    C6   C5    113.22  3.000
 T25  H72   C7   H71   106.20  3.000
 T25  H72   C7   C8    109.17  3.000
 T25  H71   C7   C8    109.51  3.000
 T25  H72   C7   C6    109.22  3.000
 T25  H71   C7   C6    109.79  3.000
 T25  C8    C7   C6    112.74  3.000
 T25  H82   C8   H81   106.28  3.000
 T25  H82   C8   C9    109.05  3.000
 T25  H81   C8   C9    111.07  3.000
 T25  H82   C8   C7    108.77  3.000
 T25  H81   C8   C7    109.29  3.000
 T25  C9    C8   C7    112.19  3.000
 T25  H9    C9   C10   117.37  3.000
 T25  H9    C9   C8    115.04  3.000
 T25  C10   C9   C8    127.57  3.000
 T25  H10   C10  C11   115.24  3.000
 T25  H10   C10  C9    117.81  3.000
 T25  C11   C10  C9    126.93  3.000
 T25  H112  C11  H111  106.63  3.000
 T25  H112  C11  C12   108.22  3.000
 T25  H111  C11  C12   109.77  3.000
 T25  H112  C11  C10   111.27  3.000
 T25  H111  C11  C10   109.45  3.000
 T25  C12   C11  C10   111.38  3.000
 T25  H12   C12  C13   116.86  3.000
 T25  H12   C12  O3    114.03  3.000
 T25  C13   C12  O3     59.22  3.000
 T25  H12   C12  C11   113.54  3.000
 T25  O3    C12  C11   117.67  3.000
 T25  C13   C12  C11   124.20  3.000
 T25  C13   O3   C12    61.75  3.000
 T25  H13   C13  C14   113.44  3.000
 T25  H13   C13  O3    113.36  3.000
 T25  C14   C13  O3    118.44  3.000
 T25  H13   C13  C12   116.44  3.000
 T25  O3    C13  C12    59.03  3.000
 T25  C14   C13  C12   124.77  3.000
 T25  H142  C14  H141  106.38  3.000
 T25  H142  C14  C15   109.36  3.000
 T25  H141  C14  C15   109.60  3.000
 T25  H142  C14  C13   107.27  3.000
 T25  H141  C14  C13   111.35  3.000
 T25  C15   C14  C13   112.65  3.000
 T25  H152  C15  H151  106.29  3.000
 T25  H152  C15  C16   109.68  3.000
 T25  H151  C15  C16   109.25  3.000
 T25  H152  C15  C14   109.39  3.000
 T25  H151  C15  C14   109.61  3.000
 T25  C16   C15  C14   112.43  3.000
 T25  H162  C16  H161  105.98  3.000
 T25  H162  C16  C17   109.28  3.000
 T25  H161  C16  C17   109.26  3.000
 T25  H162  C16  C15   109.25  3.000
 T25  H161  C16  C15   109.42  3.000
 T25  C17   C16  C15   113.38  3.000
 T25  H172  C17  H171  106.09  3.000
 T25  H172  C17  C18   109.84  3.000
 T25  H171  C17  C18   109.45  3.000
 T25  H172  C17  C16   109.23  3.000
 T25  H171  C17  C16   109.29  3.000
 T25  C18   C17  C16   112.72  3.000
 T25  H183  C18  H182  107.66  3.000
 T25  H183  C18  H181  107.41  3.000
 T25  H182  C18  H181  107.58  3.000
 T25  H183  C18  C17   111.28  3.000
 T25  H182  C18  C17   111.68  3.000
 T25  H181  C18  C17   111.03  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
 T25  Var_01  O3    C13  C12  C11  -104.40  30.0  1
 T25  Var_02  C14   C13  O3   C12  -115.55  30.0  1
 T25  Var_03  C13   C12  C11  C10   154.76  30.0  3
 T25  Var_04  C15   C14  C13  C12  -142.76  30.0  1
 T25  Var_05  C12   C11  C10  C9    114.65  30.0  1
 T25  Var_06  C16   C15  C14  C13  -173.72  30.0  2
 T25  Var_07  C11   C10  C9   C8      2.04   0.0  2
 T25  Var_08  C3    C2   C1   O1      8.98  30.0  2
 T25  Var_09  C4    C3   C2   C1   -178.65  30.0  3
 T25  Var_10  C5    C4   C3   C2   -177.67  30.0  3
 T25  Var_11  C6    C5   C4   C3   -179.44  30.0  2
 T25  Var_12  C7    C6   C5   C4   -173.96  30.0  3
 T25  Var_13  C8    C7   C6   C5   -179.00  30.0  3
 T25  Var_14  C9    C8   C7   C6   -177.02  30.0  3
 T25  Var_15  C10   C9   C8   C7    118.04  30.0  3
 T25  Var_16  C17   C16  C15  C14  -178.62  30.0  1
 T25  Var_17  C18   C17  C16  C15  -178.25  30.0  1
 T25  Var_18  H181  C18  C17  C16    60.53  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
 T25  chir_01  C12  C11  C13  O3   both
 T25  chir_02  C13  O3   C12  C14  both

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
 T25  plan-1  O1   0.020
 T25  plan-1  C1   0.020
 T25  plan-1  O2   0.020
 T25  plan-1  C2   0.020
 T25  plan-2  C8   0.020
 T25  plan-2  C9   0.020
 T25  plan-2  C10  0.020
 T25  plan-2  C11  0.020
 T25  plan-2  H9   0.020
 T25  plan-2  H10  0.020

