# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:49:43 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: [(3~{S},3~{a}~{S},8~{b}~{S})-3-(hydroxymethyl)-2,3,3~{a},8~{b}-tetrahydro-[1]benzofuro[3,2-b]pyrrol-1-yl]-phenyl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1CN([C@@H]2[C@H]1Oc3ccccc23)C(=O)c4ccccc4
#
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
 LXM  LXM  '[(3~{S},3~{a}~{S},8~{b}~{S})-3-(hydroxymethyl)-2,3,3~{a},8~{b}-tetrahydro-[1]benzofuro[3,2-b]pyrrol-1-yl]-phenyl-methanone'  ligand  39  22  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LXM
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
 LXM  C4   C  CR15  0   0.030  -16.9254  -19.7147  -1.2597
 LXM  C5   C  CR6   0   0.390  -15.6275  -20.5159  -2.9334
 LXM  C6   C  CR16  0  -0.357  -15.1638  -21.3192  -3.9608
 LXM  C7   C  CR16  0  -0.252  -14.1466  -20.8056  -4.7606
 LXM  C8   C  CR16  0  -0.275  -13.6195  -19.5369  -4.5413
 LXM  C10  C  CR6   0   0.043  -15.1051  -19.2532  -2.6949
 LXM  C13  C  CR16  0  -0.273  -13.0882  -16.9444   2.1200
 LXM  C15  C  CR16  0  -0.252  -11.6008  -18.2452   3.4917
 LXM  C17  C  CR16  0  -0.259  -12.5633  -19.2127   1.5115
 LXM  N    N  NR5   0  -0.457  -14.9724  -18.8012  -0.2720
 LXM  C1   C  CR15  0  -0.335  -16.8724  -20.0766   0.2178
 LXM  C11  C  C     0   0.529  -14.0800  -17.8424   0.0315
 LXM  C12  C  CR6   0  -0.051  -13.2483  -18.0273   1.2587
 LXM  C14  C  CR16  0  -0.245  -12.2798  -17.0591   3.2406
 LXM  C16  C  CR16  0  -0.246  -11.7361  -19.3179   2.6209
 LXM  C2   C  CH2   0  -0.315  -15.3892  -19.9322   0.5478
 LXM  C3   C  CR15  0  -0.209  -15.7889  -18.6966  -1.4803
 LXM  C9   C  CR16  0  -0.313  -14.0984  -18.7497  -3.4966
 LXM  O1   O  O2    0  -0.495  -16.6113  -20.8570  -2.0752
 LXM  O2   O  O     0  -0.491  -13.9379  -16.8431  -0.6633
 LXM  H1   H  HCR5  0   0.282  -17.8967  -19.3310  -1.5756
 LXM  H2   H  HCR6  0   0.265  -15.5735  -22.3047  -4.1393
 LXM  H3   H  HCR6  0   0.260  -13.7635  -21.4092  -5.5735
 LXM  H4   H  HCR6  0   0.254  -12.8343  -19.1612  -5.1839
 LXM  H6   H  HCR6  0   0.263  -10.9631  -18.3306   4.3619
 LXM  H7   H  HCR6  0   0.264  -12.6539  -20.0532   0.8352
 LXM  H10  H  HOH1  0   0.459  -19.5734  -18.5832   1.1238
 LXM  H11  H  HCR5  0   0.282  -17.2126  -21.1005   0.3885
 LXM  H12  H  HCR6  0   0.263  -12.1728  -16.2192   3.9144
 LXM  H13  H  HCR6  0   0.263  -11.1972  -20.2384   2.8034
 LXM  H14  H  HCH2  0   0.269  -14.8446  -20.8399   0.2755
 LXM  H15  H  HCH2  0   0.279  -15.2112  -19.7435   1.6056
 LXM  H16  H  HCR5  0   0.296  -16.1517  -17.6771  -1.6111
 LXM  H17  H  HCR6  0   0.258  -13.6899  -17.7647  -3.3144
 LXM  C    C  CH2   0  -0.141  -17.7144  -19.1276   1.0595
 LXM  H5   H  HCR6  0   0.261  -13.6039  -16.0140   1.9196
 LXM  O    O  OH1   0  -0.668  -19.0666  -19.2815   0.7001
 LXM  H8   H  HCH2  0   0.216  -17.5478  -19.3664   2.1179
 LXM  H9   H  HCH2  0   0.206  -17.3747  -18.0932   0.9145

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
 LXM  C7   C8   aromatic  1.391  0.020  1.391
 LXM  C7   C6   aromatic  1.392  0.020  1.392
 LXM  C8   C9   aromatic  1.393  0.020  1.393
 LXM  C6   C5   aromatic  1.384  0.020  1.384
 LXM  C9   C10  aromatic  1.382  0.020  1.382
 LXM  C5   C10  aromatic  1.387  0.020  1.387
 LXM  C5   O1   single    1.349  0.020  1.349
 LXM  C10  C3   single    1.501  0.020  1.501
 LXM  O1   C4   single    1.438  0.020  1.438
 LXM  C3   C4   single    1.542  0.020  1.542
 LXM  C3   N    single    1.462  0.020  1.462
 LXM  C4   C1   single    1.522  0.020  1.522
 LXM  O2   C11  double    1.225  0.020  1.225
 LXM  N    C11  single    1.345  0.020  1.345
 LXM  N    C2   single    1.458  0.020  1.458
 LXM  C11  C12  single    1.494  0.020  1.494
 LXM  C1   C2   single    1.526  0.020  1.526
 LXM  C1   C    single    1.523  0.020  1.523
 LXM  O    C    single    1.408  0.020  1.408
 LXM  C12  C17  aromatic  1.392  0.020  1.392
 LXM  C12  C13  aromatic  1.393  0.020  1.393
 LXM  C17  C16  aromatic  1.388  0.020  1.388
 LXM  C13  C14  aromatic  1.387  0.020  1.387
 LXM  C16  C15  aromatic  1.388  0.020  1.388
 LXM  C14  C15  aromatic  1.390  0.020  1.390
 LXM  C4   H1   single    0.970  0.020  1.090
 LXM  C6   H2   single    0.930  0.020  1.080
 LXM  C7   H3   single    0.930  0.020  1.080
 LXM  C8   H4   single    0.930  0.020  1.080
 LXM  C13  H5   single    0.930  0.020  1.080
 LXM  C15  H6   single    0.930  0.020  1.080
 LXM  C17  H7   single    0.930  0.020  1.080
 LXM  C    H8   single    0.970  0.020  1.090
 LXM  C    H9   single    0.970  0.020  1.090
 LXM  O    H10  single    0.850  0.020  0.980
 LXM  C1   H11  single    0.970  0.020  1.090
 LXM  C14  H12  single    0.930  0.020  1.080
 LXM  C16  H13  single    0.930  0.020  1.080
 LXM  C2   H14  single    0.970  0.020  1.090
 LXM  C2   H15  single    0.970  0.020  1.090
 LXM  C3   H16  single    0.970  0.020  1.090
 LXM  C9   H17  single    0.930  0.020  1.080

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
 LXM  H1   C4   O1   108.03  3.000
 LXM  H1   C4   C3   112.49  3.000
 LXM  O1   C4   C3   106.40  3.000
 LXM  H1   C4   C1   113.31  3.000
 LXM  C3   C4   C1   105.68  3.000
 LXM  O1   C4   C1   110.73  3.000
 LXM  O1   C5   C10  113.29  3.000
 LXM  O1   C5   C6   124.72  3.000
 LXM  C10  C5   C6   121.99  3.000
 LXM  H2   C6   C7   121.19  3.000
 LXM  H2   C6   C5   121.61  3.000
 LXM  C7   C6   C5   117.20  3.000
 LXM  H3   C7   C8   119.52  3.000
 LXM  H3   C7   C6   118.97  3.000
 LXM  C8   C7   C6   121.51  3.000
 LXM  H4   C8   C9   119.91  3.000
 LXM  H4   C8   C7   119.87  3.000
 LXM  C9   C8   C7   120.22  3.000
 LXM  C9   C10  C3   131.78  3.000
 LXM  C3   C10  C5   107.76  3.000
 LXM  C9   C10  C5   120.42  3.000
 LXM  H5   C13  C14  119.90  3.000
 LXM  H5   C13  C12  119.93  3.000
 LXM  C14  C13  C12  120.16  3.000
 LXM  H6   C15  C16  120.05  3.000
 LXM  H6   C15  C14  120.04  3.000
 LXM  C16  C15  C14  119.90  3.000
 LXM  H7   C17  C16  119.36  3.000
 LXM  H7   C17  C12  120.43  3.000
 LXM  C16  C17  C12  120.20  3.000
 LXM  C3   N    C2   111.14  3.000
 LXM  C2   N    C11  128.03  3.000
 LXM  C3   N    C11  120.41  3.000
 LXM  H11  C1   C2   110.95  3.000
 LXM  H11  C1   C    109.00  3.000
 LXM  C2   C1   C    111.03  3.000
 LXM  H11  C1   C4   111.33  3.000
 LXM  C    C1   C4   111.67  3.000
 LXM  C2   C1   C4   102.78  3.000
 LXM  O2   C11  C12  120.14  3.000
 LXM  C12  C11  N    117.82  3.000
 LXM  O2   C11  N    122.04  3.000
 LXM  C11  C12  C17  121.90  3.000
 LXM  C17  C12  C13  119.55  3.000
 LXM  C11  C12  C13  118.41  3.000
 LXM  H12  C14  C15  120.11  3.000
 LXM  H12  C14  C13  119.78  3.000
 LXM  C15  C14  C13  120.11  3.000
 LXM  H13  C16  C17  119.74  3.000
 LXM  H13  C16  C15  120.20  3.000
 LXM  C17  C16  C15  120.06  3.000
 LXM  H15  C2   H14  107.72  3.000
 LXM  H15  C2   C1   112.65  3.000
 LXM  H14  C2   C1   110.60  3.000
 LXM  H15  C2   N    111.41  3.000
 LXM  H14  C2   N    111.21  3.000
 LXM  C1   C2   N    103.28  3.000
 LXM  H16  C3   N    110.61  3.000
 LXM  H16  C3   C10  113.66  3.000
 LXM  N    C3   C10  112.82  3.000
 LXM  H16  C3   C4   112.92  3.000
 LXM  N    C3   C4   104.25  3.000
 LXM  C10  C3   C4   101.93  3.000
 LXM  H17  C9   C10  120.61  3.000
 LXM  H17  C9   C8   120.73  3.000
 LXM  C10  C9   C8   118.66  3.000
 LXM  C5   O1   C4   108.61  3.000
 LXM  H9   C    H8   106.57  3.000
 LXM  H9   C    C1   110.05  3.000
 LXM  H8   C    C1   108.27  3.000
 LXM  H9   C    O    111.49  3.000
 LXM  H8   C    O    111.61  3.000
 LXM  C1   C    O    108.78  3.000
 LXM  H10  O    C    108.33  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
 LXM  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 LXM  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 LXM  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 LXM  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 LXM  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 LXM  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 LXM  CONST_07  C16  C17  C12  C13     0.00   0.0  0
 LXM  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 LXM  CONST_09  C12  C17  C16  C15     0.00   0.0  0
 LXM  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 LXM  CONST_11  C14  C13  C12  C17     0.00   0.0  0
 LXM  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 LXM  CONST_13  C16  C17  C12  C11   180.00   0.0  0
 LXM  CONST_14  C14  C13  C12  C11   180.00   0.0  0
 LXM  CONST_15  C3   N    C11  C12   180.00   0.0  0
 LXM  CONST_16  C2   N    C11  C12     0.00   0.0  0
 LXM  CONST_17  H3   C7   C6   C5    180.00   0.0  0
 LXM  CONST_18  H17  C9   C10  C5    180.00   0.0  0
 LXM  CONST_19  H4   C8   C7   C6    180.00   0.0  0
 LXM  CONST_20  H2   C6   C7   C8    180.00   0.0  0
 LXM  CONST_21  H7   C17  C12  C13   180.00   0.0  0
 LXM  CONST_22  H6   C15  C14  C13   180.00   0.0  0
 LXM  CONST_23  H5   C13  C14  C15   180.00   0.0  0
 LXM  CONST_24  H13  C16  C17  C12   180.00   0.0  0
 LXM  CONST_25  H12  C14  C13  C12   180.00   0.0  0
 LXM  CONST_26  O2   C11  N    C2    180.00   0.0  0
 LXM  CONST_27  O2   C11  N    C3      0.00   0.0  0
 LXM  Var_01    C6   C5   O1   C4   -173.05  30.0  1
 LXM  Var_02    C3   N    C2   C1    -28.55  30.0  1
 LXM  Var_03    N    C11  C12  C13  -134.81  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
 LXM  chir_01  C4  O1  C3  C1   positiv
 LXM  chir_02  C1  C4  C2  C    negativ
 LXM  chir_03  C3  N   C4  C10  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
 LXM  plan-1  C13  0.020
 LXM  plan-1  C15  0.020
 LXM  plan-1  C17  0.020
 LXM  plan-1  C11  0.020
 LXM  plan-1  C12  0.020
 LXM  plan-1  C14  0.020
 LXM  plan-1  C16  0.020
 LXM  plan-1  H6   0.020
 LXM  plan-1  H7   0.020
 LXM  plan-1  H12  0.020
 LXM  plan-1  H13  0.020
 LXM  plan-1  H5   0.020
 LXM  plan-2  C5   0.020
 LXM  plan-2  C6   0.020
 LXM  plan-2  C7   0.020
 LXM  plan-2  C8   0.020
 LXM  plan-2  C10  0.020
 LXM  plan-2  C3   0.020
 LXM  plan-2  C9   0.020
 LXM  plan-2  O1   0.020
 LXM  plan-2  H2   0.020
 LXM  plan-2  H3   0.020
 LXM  plan-2  H4   0.020
 LXM  plan-2  H17  0.020
 LXM  plan-3  N    0.020
 LXM  plan-3  C11  0.020
 LXM  plan-3  C12  0.020
 LXM  plan-3  C2   0.020
 LXM  plan-3  C3   0.020
 LXM  plan-3  O2   0.020

