# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:29:58 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(1,3-benzodioxol-5-ylmethyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCc2cc3n(Cc4ccc5OCOc5c4)cnc3cc2C1
#
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
 1JU  1JU  1-(1,3-benzodioxol-5-ylmethyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole  ligand  41  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1JU
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
 1JU  C1   C  CH2   0  -0.431   0.9960   1.8505   1.5460
 1JU  C2   C  CR6   0   0.121   2.0095   1.0088   0.8111
 1JU  C3   C  CH2   0  -0.495  -4.7307  -0.6779  -1.0071
 1JU  C4   C  CR6   0   0.055  -3.4635  -0.0245  -0.5058
 1JU  C5   C  CH2   0  -0.443  -4.7327  -2.1918  -0.8537
 1JU  C6   C  CH2   0  -0.443  -4.3078  -2.5717   0.5562
 1JU  C7   C  CH2   0  -0.496  -2.8741  -2.1271   0.8072
 1JU  C8   C  CR6   0   0.055  -2.6011  -0.7010   0.3872
 1JU  C9   C  CR16  0  -0.352  -1.4592  -0.0764   0.8746
 1JU  C10  C  CR16  0  -0.377  -3.1785   1.2731  -0.9094
 1JU  C11  C  CR56  0   0.360  -1.1927   1.2188   0.4579
 1JU  N12  N  NR5   0  -0.498  -0.1869   2.1068   0.7505
 1JU  C13  C  CR15  0   0.098  -0.4567   3.2355   0.0444
 1JU  C14  C  CR56  0   0.123  -2.0370   1.9040  -0.4276
 1JU  N15  N  N     0  -0.473  -1.5450   3.1685  -0.6663
 1JU  C16  C  CR16  0  -0.304   2.6934   1.5404  -0.2741
 1JU  C17  C  CR16  0  -0.396   2.2489  -0.3101   1.2212
 1JU  O18  O  O     0  -0.485   4.6779  -1.4314  -1.0972
 1JU  C19  C  CR56  0   0.292   3.8482  -0.4964  -0.5753
 1JU  C20  C  CH2   0   0.069   4.6626  -2.5250  -0.1883
 1JU  O21  O  O     0  -0.486   3.5644  -2.3173   0.6910
 1JU  C22  C  CR56  0   0.313   3.1737  -1.0329   0.5083
 1JU  C23  C  CR16  0  -0.329   3.6283   0.7927  -0.9963
 1JU  H1   H  HCH2  0   0.288   0.6945   1.3620   2.4734
 1JU  H2   H  HCH2  0   0.295   1.4191   2.8174   1.8188
 1JU  H4   H  HCH2  0   0.244  -4.8979  -0.4011  -2.0507
 1JU  H5   H  HCH2  0   0.235  -5.7269  -2.5819  -1.0805
 1JU  H6   H  HCH2  0   0.219  -4.0460  -2.6442  -1.5764
 1JU  H7   H  HCH2  0   0.219  -4.9798  -2.0980   1.2791
 1JU  H8   H  HCH2  0   0.235  -4.3896  -3.6492   0.7124
 1JU  H9   H  HCH2  0   0.245  -2.6140  -2.2518   1.8611
 1JU  H10  H  HCH2  0   0.239  -2.1974  -2.7879   0.2543
 1JU  H11  H  HCR6  0   0.251  -0.8080  -0.5994   1.5649
 1JU  H12  H  HCR6  0   0.242  -3.8418   1.7909  -1.5931
 1JU  H13  H  HCR5  0   0.287   0.1982   4.0940   0.1006
 1JU  H14  H  HCR6  0   0.255   2.5078   2.5644  -0.5746
 1JU  H15  H  HCR6  0   0.273   1.7271  -0.7400   2.0670
 1JU  H16  H  HCH2  0   0.247   4.5263  -3.4578  -0.7350
 1JU  H17  H  HCR6  0   0.276   4.1553   1.2160  -1.8404
 1JU  H18  H  HCH2  0   0.234   5.5971  -2.5462   0.3824
 1JU  H3   H  HCH2  0   0.238  -5.5804  -0.2682  -0.4500

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
 1JU  C20  O21  single    1.422  0.020  1.422
 1JU  C20  O18  single    1.422  0.020  1.422
 1JU  O21  C22  single    1.355  0.020  1.355
 1JU  O18  C19  single    1.355  0.020  1.355
 1JU  C22  C19  aromatic  1.385  0.020  1.385
 1JU  C22  C17  aromatic  1.373  0.020  1.373
 1JU  C19  C23  aromatic  1.374  0.020  1.374
 1JU  C17  C2   aromatic  1.402  0.020  1.402
 1JU  C23  C16  aromatic  1.398  0.020  1.398
 1JU  C2   C16  aromatic  1.389  0.020  1.389
 1JU  C2   C1   single    1.509  0.020  1.509
 1JU  C1   N12  single    1.448  0.020  1.448
 1JU  C7   C8   single    1.512  0.020  1.512
 1JU  C7   C6   single    1.522  0.020  1.522
 1JU  C9   C8   aromatic  1.390  0.020  1.390
 1JU  C9   C11  aromatic  1.386  0.020  1.386
 1JU  N12  C11  aromatic  1.373  0.020  1.373
 1JU  N12  C13  aromatic  1.358  0.020  1.358
 1JU  C8   C4   aromatic  1.414  0.020  1.414
 1JU  C11  C14  aromatic  1.402  0.020  1.402
 1JU  C6   C5   single    1.521  0.020  1.521
 1JU  C13  N15  aromatic  1.301  0.020  1.301
 1JU  C5   C3   single    1.522  0.020  1.522
 1JU  C14  N15  aromatic  1.378  0.020  1.378
 1JU  C14  C10  aromatic  1.390  0.020  1.390
 1JU  C4   C10  aromatic  1.389  0.020  1.389
 1JU  C4   C3   single    1.511  0.020  1.511
 1JU  C1   H1   single    0.970  0.020  1.090
 1JU  C1   H2   single    0.970  0.020  1.090
 1JU  C3   H3   single    0.970  0.020  1.090
 1JU  C3   H4   single    0.970  0.020  1.090
 1JU  C5   H5   single    0.970  0.020  1.090
 1JU  C5   H6   single    0.970  0.020  1.090
 1JU  C6   H7   single    0.970  0.020  1.090
 1JU  C6   H8   single    0.970  0.020  1.090
 1JU  C7   H9   single    0.970  0.020  1.090
 1JU  C7   H10  single    0.970  0.020  1.090
 1JU  C9   H11  single    0.930  0.020  1.080
 1JU  C10  H12  single    0.930  0.020  1.080
 1JU  C13  H13  single    0.930  0.020  1.080
 1JU  C16  H14  single    0.930  0.020  1.080
 1JU  C17  H15  single    0.930  0.020  1.080
 1JU  C20  H16  single    0.970  0.020  1.090
 1JU  C23  H17  single    0.930  0.020  1.080
 1JU  C20  H18  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
 1JU  H2   C1   H1   106.97  3.000
 1JU  H2   C1   N12  107.31  3.000
 1JU  H1   C1   N12  108.70  3.000
 1JU  H2   C1   C2   110.85  3.000
 1JU  H1   C1   C2   110.49  3.000
 1JU  N12  C1   C2   112.32  3.000
 1JU  C17  C2   C16  120.32  3.000
 1JU  C16  C2   C1   119.87  3.000
 1JU  C17  C2   C1   119.81  3.000
 1JU  H4   C3   H3   105.80  3.000
 1JU  H4   C3   C5   110.38  3.000
 1JU  H3   C3   C5   108.65  3.000
 1JU  H4   C3   C4   109.61  3.000
 1JU  H3   C3   C4   108.66  3.000
 1JU  C5   C3   C4   113.44  3.000
 1JU  C10  C4   C8   120.37  3.000
 1JU  C10  C4   C3   118.67  3.000
 1JU  C8   C4   C3   120.94  3.000
 1JU  H6   C5   H5   106.64  3.000
 1JU  H6   C5   C6   109.48  3.000
 1JU  H5   C5   C6   110.96  3.000
 1JU  H6   C5   C3   110.10  3.000
 1JU  H5   C5   C3   109.62  3.000
 1JU  C6   C5   C3   109.98  3.000
 1JU  H8   C6   H7   106.66  3.000
 1JU  H8   C6   C7   109.59  3.000
 1JU  H7   C6   C7   110.05  3.000
 1JU  H8   C6   C5   110.99  3.000
 1JU  H7   C6   C5   109.43  3.000
 1JU  C7   C6   C5   110.06  3.000
 1JU  H10  C7   H9   105.72  3.000
 1JU  H10  C7   C8   108.50  3.000
 1JU  H9   C7   C8   109.43  3.000
 1JU  H10  C7   C6   108.82  3.000
 1JU  H9   C7   C6   110.49  3.000
 1JU  C8   C7   C6   113.58  3.000
 1JU  C9   C8   C7   118.36  3.000
 1JU  C9   C8   C4   120.51  3.000
 1JU  C7   C8   C4   121.11  3.000
 1JU  H11  C9   C11  121.80  3.000
 1JU  H11  C9   C8   120.01  3.000
 1JU  C11  C9   C8   118.19  3.000
 1JU  H12  C10  C14  120.27  3.000
 1JU  H12  C10  C4   120.27  3.000
 1JU  C14  C10  C4   119.46  3.000
 1JU  C14  C11  N12  105.04  3.000
 1JU  C14  C11  C9   122.04  3.000
 1JU  N12  C11  C9   132.91  3.000
 1JU  C13  N12  C11  106.32  3.000
 1JU  C13  N12  C1   126.50  3.000
 1JU  C11  N12  C1   126.92  3.000
 1JU  H13  C13  N15  125.15  3.000
 1JU  H13  C13  N12  120.82  3.000
 1JU  N15  C13  N12  114.03  3.000
 1JU  N15  C14  C11  110.05  3.000
 1JU  N15  C14  C10  130.52  3.000
 1JU  C11  C14  C10  119.43  3.000
 1JU  C14  N15  C13  104.55  3.000
 1JU  H14  C16  C23  118.49  3.000
 1JU  H14  C16  C2   119.63  3.000
 1JU  C23  C16  C2   121.89  3.000
 1JU  H15  C17  C22  121.40  3.000
 1JU  H15  C17  C2   121.32  3.000
 1JU  C22  C17  C2   117.28  3.000
 1JU  C20  O18  C19  106.14  3.000
 1JU  C23  C19  C22  121.70  3.000
 1JU  C23  C19  O18  128.88  3.000
 1JU  C22  C19  O18  109.42  3.000
 1JU  H18  C20  H16  110.58  3.000
 1JU  H18  C20  O21  109.85  3.000
 1JU  H16  C20  O21  109.79  3.000
 1JU  H18  C20  O18  109.80  3.000
 1JU  H16  C20  O18  109.81  3.000
 1JU  O21  C20  O18  106.93  3.000
 1JU  C22  O21  C20  106.13  3.000
 1JU  O21  C22  C19  109.41  3.000
 1JU  C19  C22  C17  122.03  3.000
 1JU  O21  C22  C17  128.55  3.000
 1JU  H17  C23  C19  121.90  3.000
 1JU  H17  C23  C16  121.31  3.000
 1JU  C19  C23  C16  116.79  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
 1JU  CONST_01  C19  C22  C17  C2      0.00   0.0  0
 1JU  CONST_02  C19  C23  C16  C2      0.00   0.0  0
 1JU  CONST_03  C11  C9   C8   C4      0.00   0.0  0
 1JU  CONST_04  C11  C14  C10  C4      0.00   0.0  0
 1JU  CONST_05  N15  C14  C10  C4    180.00   0.0  0
 1JU  CONST_06  N12  C11  C9   C8    180.00   0.0  0
 1JU  CONST_07  C14  C11  C9   C8      0.00   0.0  0
 1JU  CONST_08  C14  C10  C4   C8      0.00   0.0  0
 1JU  CONST_09  C10  C4   C8   C9      0.00   0.0  0
 1JU  CONST_10  C13  N12  C11  C9    180.00   0.0  0
 1JU  CONST_11  N15  C14  C11  C9    180.00   0.0  0
 1JU  CONST_12  C10  C14  C11  C9      0.00   0.0  0
 1JU  CONST_13  N12  C11  C14  C10   180.00   0.0  0
 1JU  CONST_14  C13  N15  C14  C10   180.00   0.0  0
 1JU  CONST_15  N15  C13  N12  C11     0.00   0.0  0
 1JU  CONST_16  C13  N15  C14  C11     0.00   0.0  0
 1JU  CONST_17  N15  C14  C11  N12     0.00   0.0  0
 1JU  CONST_18  C14  N15  C13  N12     0.00   0.0  0
 1JU  CONST_19  C14  C11  N12  C13     0.00   0.0  0
 1JU  CONST_20  C22  C19  C23  C16     0.00   0.0  0
 1JU  CONST_21  C22  C17  C2   C16     0.00   0.0  0
 1JU  CONST_22  C23  C19  C22  C17     0.00   0.0  0
 1JU  CONST_23  C23  C16  C2   C17     0.00   0.0  0
 1JU  CONST_24  C22  C17  C2   C1    180.00   0.0  0
 1JU  CONST_25  C23  C16  C2   C1    180.00   0.0  0
 1JU  CONST_26  C9   C11  N12  C1      0.00   0.0  0
 1JU  CONST_27  C14  C11  N12  C1    180.00   0.0  0
 1JU  CONST_28  N15  C13  N12  C1    180.00   0.0  0
 1JU  CONST_29  H17  C23  C16  C2    180.00   0.0  0
 1JU  CONST_30  H12  C10  C4   C3      0.00   0.0  0
 1JU  CONST_31  H11  C9   C8   C4    180.00   0.0  0
 1JU  CONST_32  H13  C13  N12  C11   180.00   0.0  0
 1JU  CONST_33  H15  C17  C2   C16   180.00   0.0  0
 1JU  CONST_34  H14  C16  C2   C17   180.00   0.0  0
 1JU  Var_01    C7   C6   C5   C3    -63.60  30.0  1
 1JU  Var_02    C6   C7   C8   C4    -18.13  30.0  1
 1JU  Var_03    C6   C5   C3   C4     48.65  30.0  1
 1JU  Var_04    C8   C7   C6   C5     47.64  30.0  1
 1JU  Var_05    C8   C4   C3   C5    -19.14  30.0  1
 1JU  Var_06    O21  C20  O18  C19    13.67  30.0  1
 1JU  Var_07    C22  C19  O18  C20    -8.57  30.0  1
 1JU  Var_08    C11  N12  C1   C2     74.26  30.0  2
 1JU  Var_09    C17  C2   C1   N12  -110.26  30.0  2

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
 1JU  plan-1  C1   0.020
 1JU  plan-1  C2   0.020
 1JU  plan-1  C16  0.020
 1JU  plan-1  C17  0.020
 1JU  plan-1  O18  0.020
 1JU  plan-1  C19  0.020
 1JU  plan-1  O21  0.020
 1JU  plan-1  C22  0.020
 1JU  plan-1  C23  0.020
 1JU  plan-1  H14  0.020
 1JU  plan-1  H15  0.020
 1JU  plan-1  H17  0.020
 1JU  plan-2  C1   0.020
 1JU  plan-2  C3   0.020
 1JU  plan-2  C4   0.020
 1JU  plan-2  C7   0.020
 1JU  plan-2  C8   0.020
 1JU  plan-2  C9   0.020
 1JU  plan-2  C10  0.020
 1JU  plan-2  C11  0.020
 1JU  plan-2  N12  0.020
 1JU  plan-2  C13  0.020
 1JU  plan-2  C14  0.020
 1JU  plan-2  N15  0.020
 1JU  plan-2  H11  0.020
 1JU  plan-2  H12  0.020
 1JU  plan-2  H13  0.020

