# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 29 15:39:36 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](CC[C@@](C)(O)[C@H]1[C@@]2(C)O[C@@H]2CC=C(C)C)OC(=O)NC(=O)CCl
#
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
 TN4  TN4  '(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate'  ligand  57  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TN4
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
 TN4  C1    C   CT    0   0.216  -1.4316  -1.8012  -1.5631
 TN4  C2    C   CH1   0  -0.331  -1.2872  -1.1213  -0.1830
 TN4  C3    C   CH1   0   0.082  -0.3217  -1.9229   0.7015
 TN4  C4    C   CH1   0  -0.024   1.0550  -2.0610   0.0541
 TN4  CL4   CL  CL    0  -0.118   5.9523   3.6087  -0.0873
 TN4  C5    C   CH2   0  -0.459   0.9490  -2.6631  -1.3351
 TN4  C6    C   CH2   0  -0.453  -0.0416  -1.9049  -2.2070
 TN4  C11   C   CH3   0  -0.680  -2.3612  -1.0253  -2.4920
 TN4  O11   O   OH1   0  -0.670  -1.9524  -3.1020  -1.3377
 TN4  C21   C   CT    0   0.276  -2.6075  -0.8405   0.5272
 TN4  C22   C   CH1   0   0.005  -3.2976   0.4072   0.1764
 TN4  C23   C   CH2   0  -0.564  -4.7889   0.6236   0.2495
 TN4  C24   C   C1    0  -0.248  -5.1098   2.0349   0.6424
 TN4  C25   C   C     0   0.081  -5.6166   3.0005  -0.1288
 TN4  C2A   C   CH3   0  -0.710  -3.3844  -2.0140   1.0708
 TN4  O2A   O   O2    0  -0.495  -2.5682   0.3012   1.3852
 TN4  C2B   C   CH3   0  -0.705  -5.8647   4.3758   0.4195
 TN4  C2C   C   CH3   0  -0.718  -5.9823   2.8404  -1.5747
 TN4  O31   O   O2    0  -0.483  -0.2402  -1.3003   1.9566
 TN4  O41   O   O2    0  -0.480   1.6002  -0.7302  -0.0079
 TN4  N42   N   NH1   0  -0.727   3.1882   0.7832  -0.0514
 TN4  C43   C   C     0   0.559   4.4391   1.3534  -0.0372
 TN4  C44   C   CH2   0  -0.596   4.3467   2.8681  -0.0987
 TN4  O4A   O   O     0  -0.454   3.7314  -1.4482   0.0764
 TN4  O4B   O   O     0  -0.395   5.4742   0.7463   0.0187
 TN4  H2    H   HCH1  0   0.255  -0.8368  -0.1408  -0.3772
 TN4  H3    H   HCH1  0   0.227  -0.7061  -2.9469   0.8151
 TN4  H4    H   HCH1  0   0.270   1.7011  -2.6812   0.6805
 TN4  H5    H   HCH2  0   0.256   1.9325  -2.6991  -1.8078
 TN4  H5A   H   HCH2  0   0.246   0.6322  -3.7022  -1.2210
 TN4  H6    H   HCH2  0   0.244  -0.1333  -2.4055  -3.1761
 TN4  H6A   H   HCH2  0   0.235   0.3339  -0.9013  -2.4246
 TN4  H11   H   HCH3  0   0.228  -2.0274   0.0041  -2.6304
 TN4  H11A  H   HCH3  0   0.236  -2.3807  -1.4964  -3.4775
 TN4  H11B  H   HCH3  0   0.241  -3.3841  -1.0039  -2.1162
 TN4  HO11  H   HOH1  0   0.447  -2.0107  -3.5549  -2.1862
 TN4  H22   H   HCH1  0   0.234  -2.8165   1.0446  -0.5682
 TN4  H23   H   HCH2  0   0.248  -5.2132   0.3729  -0.7248
 TN4  H23A  H   HCH2  0   0.253  -5.2409  -0.0635   0.9682
 TN4  H24   H   H     0   0.228  -4.8760   2.2838   1.6745
 TN4  H2A   H   HCH3  0   0.243  -2.7378  -2.7083   1.6075
 TN4  H2AA  H   HCH3  0   0.236  -4.1531  -1.6865   1.7683
 TN4  H2AB  H   HCH3  0   0.241  -3.8673  -2.5687   0.2694
 TN4  H2B   H   HCH3  0   0.232  -5.2967   5.1266  -0.1361
 TN4  H2BA  H   HCH3  0   0.232  -6.9183   4.6504   0.3216
 TN4  H2BB  H   HCH3  0   0.237  -5.5915   4.4578   1.4713
 TN4  H2C   H   HCH3  0   0.237  -5.8266   1.8345  -1.9595
 TN4  H2CA  H   HCH3  0   0.236  -7.0313   3.1007  -1.7353
 TN4  H2CB  H   HCH3  0   0.238  -5.3966   3.5251  -2.1932
 TN4  H31   H   HCH3  0   0.238   0.1449  -1.5760   3.9233
 TN4  H31A  H   HCH3  0   0.207  -0.4792  -3.0180   3.1026
 TN4  H31B  H   HCH3  0   0.207   1.2036  -2.5157   2.8673
 TN4  HN42  H   HNH1  0   0.434   2.3898   1.4019  -0.0997
 TN4  H44   H   HCH2  0   0.329   3.7832   3.2431   0.7562
 TN4  H44A  H   HCH2  0   0.329   3.8272   3.1756  -1.0070
 TN4  C31   C   CH3   0  -0.410   0.1796  -2.1483   2.9969
 TN4  C41   C   C     0   0.779   2.9123  -0.5718   0.0118

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
 TN4  O11  C1    single  1.419  0.020  1.419
 TN4  C11  C1    single  1.526  0.020  1.526
 TN4  C1   C2    single  1.545  0.020  1.545
 TN4  C1   C6    single  1.535  0.020  1.535
 TN4  C21  C2    single  1.525  0.020  1.525
 TN4  C2   C3    single  1.535  0.020  1.535
 TN4  C2   H2    single  0.970  0.020  1.090
 TN4  C3   O31   single  1.403  0.020  1.403
 TN4  C3   C4    single  1.528  0.020  1.528
 TN4  C3   H3    single  0.970  0.020  1.090
 TN4  C4   C5    single  1.518  0.020  1.518
 TN4  C4   O41   single  1.439  0.020  1.439
 TN4  C4   H4    single  0.970  0.020  1.090
 TN4  C44  CL4   single  1.768  0.020  1.768
 TN4  C6   C5    single  1.522  0.020  1.522
 TN4  C5   H5    single  0.970  0.020  1.090
 TN4  C5   H5A   single  0.970  0.020  1.090
 TN4  C6   H6    single  0.970  0.020  1.090
 TN4  C6   H6A   single  0.970  0.020  1.090
 TN4  C11  H11   single  0.970  0.020  1.090
 TN4  C11  H11A  single  0.970  0.020  1.090
 TN4  C11  H11B  single  0.970  0.020  1.090
 TN4  O11  HO11  single  0.850  0.020  0.980
 TN4  C2A  C21   single  1.509  0.020  1.509
 TN4  C22  C21   single  1.468  0.020  1.468
 TN4  C21  O2A   single  1.429  0.020  1.429
 TN4  C23  C22   single  1.509  0.020  1.509
 TN4  C22  O2A   single  1.416  0.020  1.416
 TN4  C22  H22   single  0.970  0.020  1.090
 TN4  C24  C23   single  1.500  0.020  1.500
 TN4  C23  H23   single  0.970  0.020  1.090
 TN4  C23  H23A  single  0.970  0.020  1.090
 TN4  C25  C24   double  1.336  0.020  1.336
 TN4  C24  H24   single  0.930  0.020  1.080
 TN4  C2B  C25   single  1.501  0.020  1.501
 TN4  C25  C2C   single  1.500  0.020  1.500
 TN4  C2A  H2A   single  0.970  0.020  1.090
 TN4  C2A  H2AA  single  0.970  0.020  1.090
 TN4  C2A  H2AB  single  0.970  0.020  1.090
 TN4  C2B  H2B   single  0.970  0.020  1.090
 TN4  C2B  H2BA  single  0.970  0.020  1.090
 TN4  C2B  H2BB  single  0.970  0.020  1.090
 TN4  C2C  H2C   single  0.970  0.020  1.090
 TN4  C2C  H2CA  single  0.970  0.020  1.090
 TN4  C2C  H2CB  single  0.970  0.020  1.090
 TN4  O31  C31   single  1.406  0.020  1.406
 TN4  C31  H31   single  0.970  0.020  1.090
 TN4  C31  H31A  single  0.970  0.020  1.090
 TN4  C31  H31B  single  0.970  0.020  1.090
 TN4  O41  C41   single  1.322  0.020  1.322
 TN4  C41  O4A   double  1.201  0.020  1.201
 TN4  C41  N42   single  1.384  0.020  1.384
 TN4  N42  C43   single  1.375  0.020  1.375
 TN4  N42  HN42  single  0.860  0.020  1.020
 TN4  C43  C44   single  1.519  0.020  1.519
 TN4  C43  O4B   double  1.201  0.020  1.201
 TN4  C44  H44   single  0.970  0.020  1.090
 TN4  C44  H44A  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
 TN4  O11   C1   C11   109.83  3.000
 TN4  C11   C1   C6    109.30  3.000
 TN4  O11   C1   C6    109.69  3.000
 TN4  C6    C1   C2    108.64  3.000
 TN4  C11   C1   C2    112.14  3.000
 TN4  O11   C1   C2    107.20  3.000
 TN4  H2    C2   C21   105.88  3.000
 TN4  H2    C2   C3    108.10  3.000
 TN4  C21   C2   C3    111.86  3.000
 TN4  H2    C2   C1    105.88  3.000
 TN4  C3    C2   C1    110.09  3.000
 TN4  C21   C2   C1    114.58  3.000
 TN4  H3    C3   O31   109.94  3.000
 TN4  H3    C3   C4    105.94  3.000
 TN4  O31   C3   C4    111.52  3.000
 TN4  H3    C3   C2    109.02  3.000
 TN4  C4    C3   C2    111.70  3.000
 TN4  O31   C3   C2    108.67  3.000
 TN4  H4    C4   O41   108.99  3.000
 TN4  H4    C4   C5    109.92  3.000
 TN4  O41   C4   C5    110.72  3.000
 TN4  H4    C4   C3    109.95  3.000
 TN4  O41   C4   C3    106.02  3.000
 TN4  C5    C4   C3    111.15  3.000
 TN4  H5A   C5   H5    105.98  3.000
 TN4  H5A   C5   C6    110.18  3.000
 TN4  H5    C5   C6    110.78  3.000
 TN4  H5A   C5   C4    107.58  3.000
 TN4  H5    C5   C4    110.27  3.000
 TN4  C6    C5   C4    111.85  3.000
 TN4  H6A   C6   H6    105.80  3.000
 TN4  H6A   C6   C5    110.35  3.000
 TN4  H6    C6   C5    109.50  3.000
 TN4  H6A   C6   C1    109.42  3.000
 TN4  H6    C6   C1    109.05  3.000
 TN4  C5    C6   C1    112.50  3.000
 TN4  H11B  C11  H11A  107.62  3.000
 TN4  H11B  C11  H11   108.20  3.000
 TN4  H11A  C11  H11   107.34  3.000
 TN4  H11B  C11  C1    111.82  3.000
 TN4  H11A  C11  C1    109.92  3.000
 TN4  H11   C11  C1    111.75  3.000
 TN4  HO11  O11  C1    108.25  3.000
 TN4  O2A   C21  C2A   114.79  3.000
 TN4  O2A   C21  C22    58.49  3.000
 TN4  C2A   C21  C22   120.33  3.000
 TN4  O2A   C21  C2    113.76  3.000
 TN4  C22   C21  C2    116.87  3.000
 TN4  C2A   C21  C2    118.06  3.000
 TN4  H22   C22  O2A   113.51  3.000
 TN4  H22   C22  C23   112.63  3.000
 TN4  O2A   C22  C23   118.59  3.000
 TN4  H22   C22  C21   116.87  3.000
 TN4  O2A   C22  C21    59.36  3.000
 TN4  C23   C22  C21   125.09  3.000
 TN4  H23A  C23  H23   106.37  3.000
 TN4  H23A  C23  C24   109.34  3.000
 TN4  H23   C23  C24   111.51  3.000
 TN4  H23A  C23  C22   110.53  3.000
 TN4  H23   C23  C22   107.93  3.000
 TN4  C24   C23  C22   111.05  3.000
 TN4  H24   C24  C25   117.66  3.000
 TN4  H24   C24  C23   114.71  3.000
 TN4  C25   C24  C23   127.61  3.000
 TN4  C2C   C25  C2B   114.18  3.000
 TN4  C2C   C25  C24   124.88  3.000
 TN4  C2B   C25  C24   120.94  3.000
 TN4  H2AB  C2A  H2AA  108.18  3.000
 TN4  H2AB  C2A  H2A   107.53  3.000
 TN4  H2AA  C2A  H2A   107.16  3.000
 TN4  H2AB  C2A  C21   111.09  3.000
 TN4  H2AA  C2A  C21   111.13  3.000
 TN4  H2A   C2A  C21   111.55  3.000
 TN4  C22   O2A  C21    62.15  3.000
 TN4  H2BB  C2B  H2BA  108.01  3.000
 TN4  H2BB  C2B  H2B   107.98  3.000
 TN4  H2BA  C2B  H2B   106.42  3.000
 TN4  H2BB  C2B  C25   112.33  3.000
 TN4  H2BA  C2B  C25   110.89  3.000
 TN4  H2B   C2B  C25   110.96  3.000
 TN4  H2CB  C2C  H2CA  106.39  3.000
 TN4  H2CB  C2C  H2C   107.60  3.000
 TN4  H2CA  C2C  H2C   107.80  3.000
 TN4  H2CB  C2C  C25   110.36  3.000
 TN4  H2CA  C2C  C25   110.50  3.000
 TN4  H2C   C2C  C25   113.86  3.000
 TN4  C31   O31  C3    114.29  3.000
 TN4  C41   O41  C4    119.08  3.000
 TN4  HN42  N42  C43   117.72  3.000
 TN4  HN42  N42  C41   116.34  3.000
 TN4  C43   N42  C41   125.94  3.000
 TN4  O4B   C43  C44   123.94  3.000
 TN4  O4B   C43  N42   125.09  3.000
 TN4  C44   C43  N42   110.97  3.000
 TN4  H44A  C44  H44   108.05  3.000
 TN4  H44A  C44  C43   110.12  3.000
 TN4  H44   C44  C43   110.03  3.000
 TN4  H44A  C44  CL4   108.66  3.000
 TN4  H44   C44  CL4   108.67  3.000
 TN4  C43   C44  CL4   111.23  3.000
 TN4  H31B  C31  H31A  107.88  3.000
 TN4  H31B  C31  H31   107.85  3.000
 TN4  H31A  C31  H31   108.40  3.000
 TN4  H31B  C31  O31   113.18  3.000
 TN4  H31A  C31  O31   111.74  3.000
 TN4  H31   C31  O31   107.63  3.000
 TN4  O4A   C41  N42   125.50  3.000
 TN4  N42   C41  O41   108.33  3.000
 TN4  O4A   C41  O41   126.17  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
 TN4  CONST_01  C44   C43  N42  C41   180.00   0.0  0
 TN4  CONST_02  O4B   C43  N42  C41     0.00   0.0  0
 TN4  CONST_03  HN42  N42  C43  C44     0.00   0.0  0
 TN4  Var_01    C4    C5   C6   C1    -55.17  30.0  1
 TN4  Var_02    O2A   C22  C21  C2   -102.66  30.0  1
 TN4  Var_03    C2A   C21  O2A  C22  -111.67  30.0  1
 TN4  Var_04    C24   C23  C22  C21   145.74  30.0  1
 TN4  Var_05    H2A   C2A  C21  C2     45.60  30.0  3
 TN4  Var_06    O4A   C41  O41  C4      0.10  30.0  3
 TN4  Var_07    C25   C24  C23  C22   108.26  30.0  1
 TN4  Var_08    H31   C31  O31  C3   -176.55  30.0  3
 TN4  Var_09    C2B   C25  C24  C23  -179.22   0.0  2
 TN4  Var_10    N42   C43  C44  CL4  -179.78  30.0  2
 TN4  Var_11    C43   N42  C41  O41   179.14  30.0  2
 TN4  Var_12    H2B   C2B  C25  C24   120.70  30.0  3
 TN4  Var_13    H2C   C2C  C25  C24     1.74  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
 TN4  chir_01  C1   C11  C2   C6   positiv
 TN4  chir_02  C2   C1   C21  C3   negativ
 TN4  chir_03  C3   O31  C4   C2   positiv
 TN4  chir_04  C4   O41  C5   C3   positiv
 TN4  chir_05  C21  C2A  C22  O2A  both
 TN4  chir_06  C22  O2A  C21  C23  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
 TN4  plan-1  N42   0.020
 TN4  plan-1  C43   0.020
 TN4  plan-1  C44   0.020
 TN4  plan-1  O4B   0.020
 TN4  plan-1  HN42  0.020
 TN4  plan-1  C41   0.020
 TN4  plan-2  C23   0.020
 TN4  plan-2  C24   0.020
 TN4  plan-2  C25   0.020
 TN4  plan-2  C2B   0.020
 TN4  plan-2  C2C   0.020
 TN4  plan-2  H24   0.020
 TN4  plan-3  O41   0.020
 TN4  plan-3  N42   0.020
 TN4  plan-3  O4A   0.020
 TN4  plan-3  C41   0.020

