# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:02:46 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-(1,3-benzodioxol-5-yl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CO[C@H](C1)CNCc2ccc3OCOc3c2
#
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
 LO5  LO5  1-(1,3-benzodioxol-5-yl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine  ligand  34  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LO5
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
 LO5  C4   C  CR16  0  -0.375  -1.4361   0.2988  -0.3496
 LO5  C5   C  CR6   0   0.069  -1.1083  -1.0687  -0.3537
 LO5  C6   C  CH2   0  -0.316   0.2974  -1.4860  -0.6982
 LO5  C7   C  CH2   0  -0.268   2.6398  -1.0112  -0.3480
 LO5  C8   C  CH1   0   0.050   3.6404  -0.1805   0.4300
 LO5  C10  C  CH2   0  -0.494   5.7925   0.8218   0.2742
 LO5  N    N  NH1   0  -0.589   1.2762  -0.7113   0.0368
 LO5  C    C  CR16  0  -0.331  -2.0793  -2.0145  -0.0614
 LO5  O    O  O2    0  -0.504   3.4795   1.2077   0.1554
 LO5  C1   C  CR16  0  -0.331  -3.4037  -1.6580   0.2330
 LO5  C11  C  CH2   0  -0.156   4.7219   1.7862  -0.2122
 LO5  C12  C  CH2   0   0.069  -4.6000   1.6872   0.5154
 LO5  C2   C  CR56  0   0.284  -3.6992  -0.3195   0.2230
 LO5  C3   C  CR56  0   0.314  -2.7332   0.6346  -0.0629
 LO5  C9   C  CH2   0  -0.498   5.0908  -0.5171   0.0878
 LO5  O1   O  O     0  -0.489  -3.2980   1.8679  -0.0234
 LO5  O2   O  O     0  -0.488  -4.8870   0.2971   0.4490
 LO5  H1   H  HCR6  0   0.262  -0.6859   1.0496  -0.5606
 LO5  H2   H  HCH2  0   0.213   0.3999  -2.5719  -0.5484
 LO5  H3   H  HCH2  0   0.236   0.4707  -1.3134  -1.7661
 LO5  H4   H  HCH2  0   0.221   2.7567  -0.8044  -1.4174
 LO5  H5   H  HCH2  0   0.195   2.9005  -2.0733  -0.2070
 LO5  H6   H  HCH1  0   0.207   3.4722  -0.3428   1.5050
 LO5  H7   H  HCH2  0   0.247   6.7193   0.9065  -0.2927
 LO5  H8   H  HCH2  0   0.235   6.0221   0.9963   1.3277
 LO5  H9   H  HNH1  0   0.339   1.1618  -0.8967   1.0272
 LO5  H11  H  HCR6  0   0.251  -1.8116  -3.0639  -0.0556
 LO5  H12  H  HCR6  0   0.270  -4.1506  -2.4074   0.4576
 LO5  H13  H  HCH2  0   0.221   4.8028   2.7793   0.2365
 LO5  H14  H  HCH2  0   0.198   4.7822   1.9081  -1.3014
 LO5  H15  H  HCH2  0   0.230  -4.6207   2.0219   1.5586
 LO5  H16  H  HCH2  0   0.252   5.4885  -1.3118   0.7181
 LO5  H17  H  HCH2  0   0.233   5.1739  -0.8456  -0.9527
 LO5  H10  H  HCH2  0   0.245  -5.3259   2.2431  -0.0775

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
 LO5  C12  O2   single    1.421  0.020  1.421
 LO5  C12  O1   single    1.421  0.020  1.421
 LO5  O2   C2   single    1.357  0.020  1.357
 LO5  O1   C3   single    1.357  0.020  1.357
 LO5  C2   C3   aromatic  1.387  0.020  1.387
 LO5  C2   C1   aromatic  1.371  0.020  1.371
 LO5  C3   C4   aromatic  1.370  0.020  1.370
 LO5  C10  C11  single    1.521  0.020  1.521
 LO5  C10  C9   single    1.523  0.020  1.523
 LO5  C11  O    single    1.419  0.020  1.419
 LO5  C1   C    aromatic  1.403  0.020  1.403
 LO5  C4   C5   aromatic  1.406  0.020  1.406
 LO5  O    C8   single    1.424  0.020  1.424
 LO5  C9   C8   single    1.528  0.020  1.528
 LO5  C8   C7   single    1.515  0.020  1.515
 LO5  C    C5   aromatic  1.387  0.020  1.387
 LO5  C5   C6   single    1.506  0.020  1.506
 LO5  C7   N    single    1.448  0.020  1.448
 LO5  N    C6   single    1.449  0.020  1.449
 LO5  C4   H1   single    0.930  0.020  1.080
 LO5  C6   H2   single    0.970  0.020  1.090
 LO5  C6   H3   single    0.970  0.020  1.090
 LO5  C7   H4   single    0.970  0.020  1.090
 LO5  C7   H5   single    0.970  0.020  1.090
 LO5  C8   H6   single    0.970  0.020  1.090
 LO5  C10  H7   single    0.970  0.020  1.090
 LO5  C10  H8   single    0.970  0.020  1.090
 LO5  N    H9   single    0.890  0.020  1.040
 LO5  C    H11  single    0.930  0.020  1.080
 LO5  C1   H12  single    0.930  0.020  1.080
 LO5  C11  H13  single    0.970  0.020  1.090
 LO5  C11  H14  single    0.970  0.020  1.090
 LO5  C12  H15  single    0.970  0.020  1.090
 LO5  C9   H16  single    0.970  0.020  1.090
 LO5  C9   H17  single    0.970  0.020  1.090
 LO5  C12  H10  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
 LO5  H1   C4   C3   121.81  3.000
 LO5  H1   C4   C5   120.83  3.000
 LO5  C3   C4   C5   117.36  3.000
 LO5  C    C5   C6   120.84  3.000
 LO5  C6   C5   C4   119.18  3.000
 LO5  C    C5   C4   119.97  3.000
 LO5  H3   C6   H2   105.86  3.000
 LO5  H3   C6   N    107.66  3.000
 LO5  H2   C6   N    113.30  3.000
 LO5  H3   C6   C5   109.08  3.000
 LO5  H2   C6   C5   109.21  3.000
 LO5  N    C6   C5   111.49  3.000
 LO5  H5   C7   H4   106.35  3.000
 LO5  H5   C7   N    112.83  3.000
 LO5  H4   C7   N    108.71  3.000
 LO5  H5   C7   C8   107.83  3.000
 LO5  H4   C7   C8   109.10  3.000
 LO5  N    C7   C8   111.83  3.000
 LO5  H6   C8   C9   109.36  3.000
 LO5  H6   C8   O    108.35  3.000
 LO5  C9   C8   O    106.19  3.000
 LO5  H6   C8   C7   108.65  3.000
 LO5  C9   C8   C7   113.03  3.000
 LO5  O    C8   C7   111.14  3.000
 LO5  H8   C10  H7   108.09  3.000
 LO5  H8   C10  C9   110.81  3.000
 LO5  H7   C10  C9   113.35  3.000
 LO5  H8   C10  C11  110.81  3.000
 LO5  H7   C10  C11  112.52  3.000
 LO5  C9   C10  C11  101.19  3.000
 LO5  H9   N    C7   109.14  3.000
 LO5  H9   N    C6   108.76  3.000
 LO5  C7   N    C6   112.99  3.000
 LO5  H11  C    C1   118.59  3.000
 LO5  H11  C    C5   119.27  3.000
 LO5  C1   C    C5   122.14  3.000
 LO5  C11  O    C8   110.39  3.000
 LO5  H12  C1   C2   121.95  3.000
 LO5  H12  C1   C    121.30  3.000
 LO5  C2   C1   C    116.75  3.000
 LO5  H14  C11  H13  107.61  3.000
 LO5  H14  C11  O    110.51  3.000
 LO5  H13  C11  O    109.20  3.000
 LO5  H14  C11  C10  110.44  3.000
 LO5  H13  C11  C10  113.13  3.000
 LO5  O    C11  C10  105.96  3.000
 LO5  H10  C12  H15  110.46  3.000
 LO5  H10  C12  O2   109.82  3.000
 LO5  H15  C12  O2   109.84  3.000
 LO5  H10  C12  O1   109.84  3.000
 LO5  H15  C12  O1   109.85  3.000
 LO5  O2   C12  O1   106.97  3.000
 LO5  O2   C2   C3   109.34  3.000
 LO5  C3   C2   C1   121.53  3.000
 LO5  O2   C2   C1   129.12  3.000
 LO5  O1   C3   C2   109.22  3.000
 LO5  C2   C3   C4   122.25  3.000
 LO5  O1   C3   C4   128.52  3.000
 LO5  H17  C9   H16  107.66  3.000
 LO5  H17  C9   C10  110.20  3.000
 LO5  H16  C9   C10  113.72  3.000
 LO5  H17  C9   C8   110.56  3.000
 LO5  H16  C9   C8   112.19  3.000
 LO5  C10  C9   C8   102.49  3.000
 LO5  C3   O1   C12  106.07  3.000
 LO5  C2   O2   C12  105.98  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
 LO5  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 LO5  CONST_02  C1   C    C5   C4      0.00   0.0  0
 LO5  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 LO5  CONST_04  C2   C1   C    C5      0.00   0.0  0
 LO5  CONST_05  C3   C2   C1   C       0.00   0.0  0
 LO5  CONST_06  C3   C4   C5   C       0.00   0.0  0
 LO5  CONST_07  C3   C4   C5   C6    180.00   0.0  0
 LO5  CONST_08  C1   C    C5   C6    180.00   0.0  0
 LO5  CONST_09  H11  C    C5   C4    180.00   0.0  0
 LO5  CONST_10  H12  C1   C    C5    180.00   0.0  0
 LO5  CONST_11  H1   C4   C5   C     180.00   0.0  0
 LO5  Var_01    C10  C11  O    C8    -18.40  30.0  1
 LO5  Var_02    C11  C10  C9   C8    -35.65  30.0  1
 LO5  Var_03    C9   C10  C11  O      33.84  30.0  1
 LO5  Var_04    C3   C2   O2   C12    -9.38  30.0  1
 LO5  Var_05    C2   C3   O1   C12     9.53  30.0  1
 LO5  Var_06    O1   C12  O2   C2     15.07  30.0  1
 LO5  Var_07    O2   C12  O1   C3    -15.14  30.0  1
 LO5  Var_08    N    C6   C5   C4     48.08  30.0  2
 LO5  Var_09    C7   N    C6   C5   -175.35  30.0  1
 LO5  Var_10    C8   C7   N    C6    179.63  30.0  1

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
 LO5  chir_01  C8  O  C9  C7  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
 LO5  plan-1  C4   0.020
 LO5  plan-1  C5   0.020
 LO5  plan-1  C6   0.020
 LO5  plan-1  C    0.020
 LO5  plan-1  C1   0.020
 LO5  plan-1  C2   0.020
 LO5  plan-1  C3   0.020
 LO5  plan-1  O1   0.020
 LO5  plan-1  O2   0.020
 LO5  plan-1  H1   0.020
 LO5  plan-1  H11  0.020
 LO5  plan-1  H12  0.020

