# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 13:36:25 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[(4S,4aS,6S,8aR)-10-aminohexahydro-3H-4,8a-(epithiomethenoazeno)isochromen-6(1H)-yl]-3-chlorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=N[C@]23CC[C@@H](C[C@@H]2[C@@H](COC3)S1)NC(=O)c4cccc(Cl)c4
#
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
 4RX  4RX  N-[(4S,4aS,6S,8aR)-10-aminohexahydro-3H-4,8a-(epithiomethenoazeno)isochromen-6(1H)-yl]-3-chlorobenzamide  ligand  44  24  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4RX
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
 4RX  C7   C   CH1   0  -0.058   0.2182  -1.1590   0.1930
 4RX  C6   C   CH2   0  -0.413   1.0577  -0.0387   0.7991
 4RX  C5   C   CH1   0  -0.264   2.5241  -0.4508   0.8438
 4RX  C4   C   CT    0   0.028   3.0748  -0.8465  -0.5344
 4RX  C2   C   C     0   0.267   3.2978   1.4498  -1.1451
 4RX  C15  C   CR16  0  -0.247  -5.9026  -1.3475  -0.3063
 4RX  C14  C   CR16  0  -0.262  -4.6157  -1.8505  -0.2031
 4RX  C16  C   CR16  0  -0.212  -6.1705  -0.0227   0.0081
 4RX  C18  C   CR16  0  -0.253  -3.8316   0.3059   0.5226
 4RX  C13  C   CR6   0  -0.041  -3.5707  -1.0228   0.1977
 4RX  C17  C   CR6   0  -0.022  -5.1268   0.7876   0.4254
 4RX  C11  C   C     0   0.540  -2.1977  -1.6147   0.3043
 4RX  C8   C   CH2   0  -0.429   0.7403  -1.5493  -1.1890
 4RX  C9   C   CH2   0  -0.417   2.2064  -1.9585  -1.1227
 4RX  C21  C   CH2   0  -0.155   4.8724  -0.0062   1.5316
 4RX  C23  C   CH2   0  -0.137   4.5061  -1.3626  -0.3368
 4RX  C20  C   CH1   0  -0.407   3.4663   0.5747   1.4603
 4RX  N3   N   N     0  -0.395   3.1128   0.2439  -1.4822
 4RX  N24  N   NH2   0  -0.807   3.2964   2.4530  -2.0773
 4RX  N10  N   NH1   0  -0.659  -1.1752  -0.7593   0.1474
 4RX  O12  O   O     0  -0.487  -2.0517  -2.8091   0.5254
 4RX  O22  O   O2    0  -0.472   5.3343  -0.3948   0.2629
 4RX  S1   S   S2    0   0.008   3.4483   2.1161   0.4960
 4RX  CL1  CL  CL    0  -0.120  -5.4461   2.4378   0.8451
 4RX  H1   H   HCH1  0   0.244   0.2808  -2.0312   0.8481
 4RX  H2   H   HCH2  0   0.231   0.9270   0.8766   0.2143
 4RX  H3   H   HCH2  0   0.250   0.7101   0.1793   1.8128
 4RX  H4   H   HCH1  0   0.257   2.5901  -1.3418   1.4819
 4RX  H6   H   HCR6  0   0.267  -4.4217  -2.8867  -0.4444
 4RX  H7   H   HCR6  0   0.287  -7.1759   0.3686  -0.0660
 4RX  H8   H   HCR6  0   0.280  -3.0471   0.9634   0.8738
 4RX  H9   H   HCH2  0   0.243   0.1392  -2.3696  -1.5876
 4RX  H10  H   HCH2  0   0.223   0.6217  -0.7025  -1.8716
 4RX  H11  H   HCH2  0   0.237   2.5718  -2.2132  -2.1208
 4RX  H12  H   HCH2  0   0.224   2.3035  -2.8590  -0.5070
 4RX  H13  H   HCH2  0   0.252   5.5773   0.7258   1.9270
 4RX  H14  H   HCH2  0   0.221   4.8526  -0.8622   2.2231
 4RX  H15  H   HCH2  0   0.203   4.4796  -2.2807   0.2694
 4RX  H16  H   HCH2  0   0.238   4.9492  -1.6110  -1.3034
 4RX  H17  H   HCH1  0   0.307   3.1392   0.8579   2.4638
 4RX  H18  H   HNH2  0   0.391   3.8498   3.2718  -1.8793
 4RX  H19  H   HNH2  0   0.384   3.3894   2.1350  -3.0302
 4RX  H20  H   HNH1  0   0.403  -1.3688   0.1667  -0.2006
 4RX  H5   H   HCR6  0   0.275  -6.7105  -1.9900  -0.6297

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
 4RX  O12  C11  double    1.223  0.020  1.223
 4RX  C11  C13  single    1.499  0.020  1.499
 4RX  C11  N10  single    1.342  0.020  1.342
 4RX  C14  C15  aromatic  1.386  0.020  1.386
 4RX  C14  C13  aromatic  1.392  0.020  1.392
 4RX  C8   C9   single    1.524  0.020  1.524
 4RX  C8   C7   single    1.528  0.020  1.528
 4RX  C9   C4   single    1.529  0.020  1.529
 4RX  C15  C16  aromatic  1.388  0.020  1.388
 4RX  C13  C18  aromatic  1.393  0.020  1.393
 4RX  C7   N10  single    1.450  0.020  1.450
 4RX  C7   C6   single    1.526  0.020  1.526
 4RX  C16  C17  aromatic  1.386  0.020  1.386
 4RX  C18  C17  aromatic  1.385  0.020  1.385
 4RX  C23  C4   single    1.534  0.020  1.534
 4RX  C23  O22  single    1.408  0.020  1.408
 4RX  C4   C5   single    1.536  0.020  1.536
 4RX  C4   N3   single    1.445  0.020  1.445
 4RX  C6   C5   single    1.524  0.020  1.524
 4RX  C5   C20  single    1.523  0.020  1.523
 4RX  C17  CL1  single    1.732  0.020  1.732
 4RX  N3   C2   double    1.266  0.020  1.266
 4RX  O22  C21  single    1.405  0.020  1.405
 4RX  C21  C20  single    1.523  0.020  1.523
 4RX  C20  S1   single    1.818  0.020  1.818
 4RX  C2   S1   single    1.778  0.020  1.778
 4RX  C2   N24  single    1.370  0.020  1.370
 4RX  C7   H1   single    0.970  0.020  1.090
 4RX  C6   H2   single    0.970  0.020  1.090
 4RX  C6   H3   single    0.970  0.020  1.090
 4RX  C5   H4   single    0.970  0.020  1.090
 4RX  C15  H5   single    0.930  0.020  1.080
 4RX  C14  H6   single    0.930  0.020  1.080
 4RX  C16  H7   single    0.930  0.020  1.080
 4RX  C18  H8   single    0.930  0.020  1.080
 4RX  C8   H9   single    0.970  0.020  1.090
 4RX  C8   H10  single    0.970  0.020  1.090
 4RX  C9   H11  single    0.970  0.020  1.090
 4RX  C9   H12  single    0.970  0.020  1.090
 4RX  C21  H13  single    0.970  0.020  1.090
 4RX  C21  H14  single    0.970  0.020  1.090
 4RX  C23  H15  single    0.970  0.020  1.090
 4RX  C23  H16  single    0.970  0.020  1.090
 4RX  C20  H17  single    0.970  0.020  1.090
 4RX  N24  H18  single    0.890  0.020  1.040
 4RX  N24  H19  single    0.890  0.020  1.040
 4RX  N10  H20  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
 4RX  H1   C7   N10  107.09  3.000
 4RX  H1   C7   C8   108.59  3.000
 4RX  N10  C7   C8   111.73  3.000
 4RX  H1   C7   C6   108.45  3.000
 4RX  N10  C7   C6   109.80  3.000
 4RX  C8   C7   C6   111.03  3.000
 4RX  H3   C6   H2   106.91  3.000
 4RX  H3   C6   C5   109.43  3.000
 4RX  H2   C6   C5   110.91  3.000
 4RX  H3   C6   C7   109.87  3.000
 4RX  H2   C6   C7   109.65  3.000
 4RX  C5   C6   C7   110.03  3.000
 4RX  H4   C5   C20  105.90  3.000
 4RX  H4   C5   C4   106.91  3.000
 4RX  C20  C5   C4   108.35  3.000
 4RX  H4   C5   C6   107.12  3.000
 4RX  C20  C5   C6   115.16  3.000
 4RX  C4   C5   C6   112.86  3.000
 4RX  N3   C4   C23  108.28  3.000
 4RX  N3   C4   C9   108.14  3.000
 4RX  C23  C4   C9   109.56  3.000
 4RX  N3   C4   C5   113.79  3.000
 4RX  C23  C4   C5   107.80  3.000
 4RX  C9   C4   C5   109.21  3.000
 4RX  S1   C2   N24  110.73  3.000
 4RX  N24  C2   N3   121.09  3.000
 4RX  S1   C2   N3   127.98  3.000
 4RX  H5   C15  C16  119.38  3.000
 4RX  H5   C15  C14  120.03  3.000
 4RX  C16  C15  C14  120.60  3.000
 4RX  H6   C14  C13  119.95  3.000
 4RX  H6   C14  C15  119.86  3.000
 4RX  C13  C14  C15  120.19  3.000
 4RX  H7   C16  C17  120.62  3.000
 4RX  H7   C16  C15  120.62  3.000
 4RX  C17  C16  C15  118.76  3.000
 4RX  H8   C18  C17  119.29  3.000
 4RX  H8   C18  C13  121.31  3.000
 4RX  C17  C18  C13  119.38  3.000
 4RX  C11  C13  C18  122.13  3.000
 4RX  C18  C13  C14  119.60  3.000
 4RX  C11  C13  C14  118.25  3.000
 4RX  CL1  C17  C18  119.11  3.000
 4RX  CL1  C17  C16  119.42  3.000
 4RX  C18  C17  C16  121.47  3.000
 4RX  O12  C11  N10  123.53  3.000
 4RX  N10  C11  C13  115.96  3.000
 4RX  O12  C11  C13  120.51  3.000
 4RX  H10  C8   H9   107.09  3.000
 4RX  H10  C8   C9   109.84  3.000
 4RX  H9   C8   C9   110.10  3.000
 4RX  H10  C8   C7   109.25  3.000
 4RX  H9   C8   C7   109.50  3.000
 4RX  C9   C8   C7   110.98  3.000
 4RX  H12  C9   H11  106.99  3.000
 4RX  H12  C9   C8   109.30  3.000
 4RX  H11  C9   C8   110.16  3.000
 4RX  H12  C9   C4   109.36  3.000
 4RX  H11  C9   C4   109.33  3.000
 4RX  C8   C9   C4   111.59  3.000
 4RX  H14  C21  H13  107.81  3.000
 4RX  H14  C21  O22  110.99  3.000
 4RX  H13  C21  O22  107.50  3.000
 4RX  H14  C21  C20  108.02  3.000
 4RX  H13  C21  C20  110.96  3.000
 4RX  O22  C21  C20  111.51  3.000
 4RX  H16  C23  H15  107.91  3.000
 4RX  H16  C23  O22  107.14  3.000
 4RX  H15  C23  O22  110.67  3.000
 4RX  H16  C23  C4   109.95  3.000
 4RX  H15  C23  C4   109.22  3.000
 4RX  O22  C23  C4   111.86  3.000
 4RX  H17  C20  S1   105.33  3.000
 4RX  H17  C20  C21  109.40  3.000
 4RX  S1   C20  C21  110.93  3.000
 4RX  H17  C20  C5   111.17  3.000
 4RX  S1   C20  C5   110.49  3.000
 4RX  C21  C20  C5   109.47  3.000
 4RX  C2   N3   C4   123.23  3.000
 4RX  H19  N24  H18  113.02  3.000
 4RX  H19  N24  C2   114.33  3.000
 4RX  H18  N24  C2   117.44  3.000
 4RX  H20  N10  C11  118.65  3.000
 4RX  H20  N10  C7   116.65  3.000
 4RX  C11  N10  C7   123.54  3.000
 4RX  C23  O22  C21  112.42  3.000
 4RX  C20  S1   C2    99.95  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
 4RX  CONST_01  C18  C13  C14  C15    0.00   0.0  0
 4RX  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 4RX  CONST_03  C17  C16  C15  C14    0.00   0.0  0
 4RX  CONST_04  C17  C18  C13  C14    0.00   0.0  0
 4RX  CONST_05  C13  C14  C15  C16    0.00   0.0  0
 4RX  CONST_06  C13  C18  C17  C16    0.00   0.0  0
 4RX  CONST_07  S1   C2   N3   C4     0.00   0.0  0
 4RX  CONST_08  C11  C13  C14  C15  180.00   0.0  0
 4RX  CONST_09  CL1  C17  C16  C15  180.00   0.0  0
 4RX  CONST_10  CL1  C17  C18  C13  180.00   0.0  0
 4RX  CONST_11  C11  C13  C18  C17  180.00   0.0  0
 4RX  CONST_12  N24  C2   N3   C4   180.00   0.0  0
 4RX  CONST_13  H7   C16  C15  C14  180.00   0.0  0
 4RX  CONST_14  H8   C18  C13  C14  180.00   0.0  0
 4RX  CONST_15  H6   C14  C15  C16  180.00   0.0  0
 4RX  CONST_16  H5   C15  C14  C13  180.00   0.0  0
 4RX  CONST_17  C13  C11  N10  C7   180.00   0.0  0
 4RX  CONST_20  O12  C11  N10  C7     0.00   0.0  0
 4RX  CONST_21  H20  N10  C11  C13    0.00   0.0  0
 4RX  Var_01    C4   C9   C8   C7   -57.10  30.0  1
 4RX  Var_02    C20  C21  O22  C23  -59.17  30.0  3
 4RX  Var_03    N3   C2   S1   C20    6.60  30.0  1
 4RX  Var_04    H15  C23  O22  C21  -61.77  30.0  3
 4RX  Var_05    O12  C11  C13  C14  -26.51  30.0  2

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
 4RX  chir_01  C7   C8   N10  C6  positiv
 4RX  chir_02  C5   C20  C6   C4  negativ
 4RX  chir_03  C4   C5   N3   C9  positiv
 4RX  chir_04  C20  S1   C21  C5  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
 4RX  plan-1  C15  0.020
 4RX  plan-1  C14  0.020
 4RX  plan-1  C16  0.020
 4RX  plan-1  C18  0.020
 4RX  plan-1  C13  0.020
 4RX  plan-1  C17  0.020
 4RX  plan-1  C11  0.020
 4RX  plan-1  CL1  0.020
 4RX  plan-1  H6   0.020
 4RX  plan-1  H7   0.020
 4RX  plan-1  H8   0.020
 4RX  plan-1  H5   0.020
 4RX  plan-2  C7   0.020
 4RX  plan-2  C13  0.020
 4RX  plan-2  C11  0.020
 4RX  plan-2  N10  0.020
 4RX  plan-2  O12  0.020
 4RX  plan-2  H20  0.020
 4RX  plan-3  C4   0.020
 4RX  plan-3  C2   0.020
 4RX  plan-3  N3   0.020
 4RX  plan-3  N24  0.020
 4RX  plan-3  S1   0.020
 4RX  plan-3  H18  0.020
 4RX  plan-3  H19  0.020

