# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:55:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-(9H-fluoren-9-yl)propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CCCC1c2ccccc2c3ccccc13
#
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
 56J  56J  3-(9H-fluoren-9-yl)propanal  ligand  31  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_56J
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
 56J  C01   C  CR16  0  -0.260   2.6150   2.7136  -0.0712
 56J  C02   C  CR16  0  -0.257   3.5047   1.7492   0.3947
 56J  C03   C  CR16  0  -0.345   3.1199   0.4176   0.4898
 56J  C04   C  CR56  0   0.108   1.8305   0.0690   0.1097
 56J  C05   C  CR56  0   0.094   0.9369   1.0362  -0.3584
 56J  C06   C  CR16  0  -0.321   1.3220   2.3619  -0.4484
 56J  C07   C  CR15  0  -0.372  -0.4019   0.4173  -0.6792
 56J  C08   C  CR56  0   0.096  -0.1384  -1.0480  -0.4177
 56J  C09   C  CR16  0  -0.328  -0.9586  -2.1460  -0.6190
 56J  C10   C  CR16  0  -0.257  -0.4872  -3.4149  -0.2913
 56J  C11   C  CR16  0  -0.257   0.7944  -3.5857   0.2215
 56J  C12   C  CR16  0  -0.343   1.6328  -2.4924   0.4015
 56J  C13   C  CR56  0   0.101   1.1614  -1.2289   0.0744
 56J  C14   C  CH2   0  -0.433  -1.5011   1.0412   0.1955
 56J  C16   C  C1    0   0.197  -3.9265   1.2517   0.7253
 56J  O17   O  O     0  -0.380  -4.9235   1.8019   0.3276
 56J  C29   C  CH2   0  -0.561  -2.9146   0.5681  -0.1403
 56J  H011  H  HCR6  0   0.256   2.9313   3.7464  -0.1402
 56J  H021  H  HCR6  0   0.257   4.5055   2.0404   0.6861
 56J  H031  H  HCR6  0   0.247   3.8187  -0.3276   0.8506
 56J  H061  H  HCR6  0   0.250   0.6350   3.1196  -0.8069
 56J  H071  H  HCR5  0   0.281  -0.6613   0.5814  -1.7321
 56J  H091  H  HCR6  0   0.253  -1.9489  -2.0393  -1.0431
 56J  H101  H  HCR6  0   0.256  -1.1224  -4.2776  -0.4449
 56J  H111  H  HCR6  0   0.258   1.1463  -4.5787   0.4689
 56J  H121  H  HCR6  0   0.247   2.6375  -2.6336   0.7811
 56J  H142  H  HCH2  0   0.246  -1.2801   0.8419   1.2473
 56J  H143  H  HCH2  0   0.257  -1.4523   2.1255   0.0662
 56J  H1    H  H     0   0.184  -3.6997   1.2126   1.8070
 56J  H292  H  HCH2  0   0.257  -3.1523   0.7286  -1.1930
 56J  H33   H  HCH2  0   0.270  -3.0086  -0.5031   0.0679

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
 56J  C02  C03   aromatic  1.389  0.020  1.389
 56J  C02  C01   aromatic  1.392  0.020  1.392
 56J  C03  C04   aromatic  1.389  0.020  1.389
 56J  C12  C11   aromatic  1.389  0.020  1.389
 56J  C12  C13   aromatic  1.388  0.020  1.388
 56J  C01  C06   aromatic  1.392  0.020  1.392
 56J  C04  C13   aromatic  1.461  0.020  1.461
 56J  C04  C05   aromatic  1.398  0.020  1.398
 56J  C11  C10   aromatic  1.391  0.020  1.391
 56J  C13  C08   aromatic  1.402  0.020  1.402
 56J  C06  C05   aromatic  1.383  0.020  1.383
 56J  C05  C07   single    1.509  0.020  1.509
 56J  C10  C09   aromatic  1.393  0.020  1.393
 56J  C08  C07   single    1.512  0.020  1.512
 56J  C08  C09   aromatic  1.385  0.020  1.385
 56J  C07  C14   single    1.537  0.020  1.537
 56J  C14  C29   single    1.528  0.020  1.528
 56J  C29  C16   single    1.497  0.020  1.497
 56J  O17  C16   double    1.206  0.020  1.206
 56J  C01  H011  single    0.930  0.020  1.080
 56J  C02  H021  single    0.930  0.020  1.080
 56J  C03  H031  single    0.930  0.020  1.080
 56J  C06  H061  single    0.930  0.020  1.080
 56J  C07  H071  single    0.970  0.020  1.090
 56J  C09  H091  single    0.930  0.020  1.080
 56J  C10  H101  single    0.930  0.020  1.080
 56J  C11  H111  single    0.930  0.020  1.080
 56J  C12  H121  single    0.930  0.020  1.080
 56J  C14  H142  single    0.970  0.020  1.090
 56J  C14  H143  single    0.970  0.020  1.090
 56J  C16  H1    single    0.930  0.020  1.080
 56J  C29  H292  single    0.970  0.020  1.090
 56J  C29  H33   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
 56J  H011  C01  C06   119.69  3.000
 56J  H011  C01  C02   119.70  3.000
 56J  C06   C01  C02   120.61  3.000
 56J  H021  C02  C03   119.70  3.000
 56J  H021  C02  C01   119.65  3.000
 56J  C03   C02  C01   120.65  3.000
 56J  H031  C03  C04   121.15  3.000
 56J  H031  C03  C02   120.22  3.000
 56J  C04   C03  C02   118.62  3.000
 56J  C13   C04  C05   108.29  3.000
 56J  C05   C04  C03   120.77  3.000
 56J  C13   C04  C03   130.92  3.000
 56J  C07   C05  C06   128.75  3.000
 56J  C07   C05  C04   110.77  3.000
 56J  C06   C05  C04   120.47  3.000
 56J  H061  C06  C05   121.00  3.000
 56J  H061  C06  C01   120.12  3.000
 56J  C05   C06  C01   118.88  3.000
 56J  H071  C07  C14   108.44  3.000
 56J  H071  C07  C08   110.63  3.000
 56J  C14   C07  C08   114.82  3.000
 56J  H071  C07  C05   110.63  3.000
 56J  C14   C07  C05   110.30  3.000
 56J  C08   C07  C05   101.90  3.000
 56J  C13   C08  C09   119.85  3.000
 56J  C09   C08  C07   129.80  3.000
 56J  C13   C08  C07   110.33  3.000
 56J  H091  C09  C10   119.45  3.000
 56J  H091  C09  C08   121.36  3.000
 56J  C10   C09  C08   119.18  3.000
 56J  H101  C10  C11   119.69  3.000
 56J  H101  C10  C09   119.62  3.000
 56J  C11   C10  C09   120.70  3.000
 56J  H111  C11  C12   119.75  3.000
 56J  H111  C11  C10   119.77  3.000
 56J  C12   C11  C10   120.48  3.000
 56J  H121  C12  C13   121.08  3.000
 56J  H121  C12  C11   120.17  3.000
 56J  C13   C12  C11   118.74  3.000
 56J  C12   C13  C08   121.02  3.000
 56J  C08   C13  C04   108.58  3.000
 56J  C12   C13  C04   130.37  3.000
 56J  H143  C14  H142  106.59  3.000
 56J  H143  C14  C29   108.81  3.000
 56J  H142  C14  C29   110.00  3.000
 56J  H143  C14  C07   107.67  3.000
 56J  H142  C14  C07   109.21  3.000
 56J  C29   C14  C07   114.26  3.000
 56J  H1    C16  C29   114.26  3.000
 56J  H1    C16  O17   120.54  3.000
 56J  C29   C16  O17   125.20  3.000
 56J  H33   C29  H292  107.97  3.000
 56J  H33   C29  C16   106.18  3.000
 56J  H292  C29  C16   110.09  3.000
 56J  H33   C29  C14   109.91  3.000
 56J  H292  C29  C14   111.60  3.000
 56J  C16   C29  C14   110.91  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
 56J  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 56J  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 56J  CONST_03  C13   C04  C03  C02   180.00   0.0  0
 56J  CONST_04  C05   C04  C03  C02     0.00   0.0  0
 56J  CONST_05  C05   C06  C01  C02     0.00   0.0  0
 56J  CONST_06  C06   C01  C02  C03     0.00   0.0  0
 56J  CONST_07  C12   C13  C04  C03     0.00   0.0  0
 56J  CONST_08  C08   C13  C04  C03   180.00   0.0  0
 56J  CONST_09  C06   C05  C04  C03     0.00   0.0  0
 56J  CONST_10  C11   C12  C13  C04   180.00   0.0  0
 56J  CONST_11  C09   C08  C13  C04   180.00   0.0  0
 56J  CONST_12  C12   C13  C04  C05   180.00   0.0  0
 56J  CONST_13  C08   C13  C04  C05     0.00   0.0  0
 56J  CONST_14  C13   C04  C05  C06   180.00   0.0  0
 56J  CONST_15  C11   C12  C13  C08     0.00   0.0  0
 56J  CONST_16  C11   C10  C09  C08     0.00   0.0  0
 56J  CONST_17  C12   C11  C10  C09     0.00   0.0  0
 56J  CONST_18  C12   C13  C08  C09     0.00   0.0  0
 56J  CONST_19  C13   C12  C11  C10     0.00   0.0  0
 56J  CONST_20  C13   C08  C09  C10     0.00   0.0  0
 56J  CONST_21  H031  C03  C02  C01   180.00   0.0  0
 56J  CONST_22  H061  C06  C01  C02   180.00   0.0  0
 56J  CONST_23  H011  C01  C02  C03   180.00   0.0  0
 56J  CONST_24  H021  C02  C03  C04   180.00   0.0  0
 56J  CONST_25  H121  C12  C13  C04     0.00   0.0  0
 56J  CONST_26  H091  C09  C08  C07     0.00   0.0  0
 56J  CONST_27  H101  C10  C09  C08   180.00   0.0  0
 56J  CONST_28  H111  C11  C10  C09   180.00   0.0  0
 56J  Var_01    C16   C29  C14  C07  -178.26  30.0  3
 56J  Var_02    O17   C16  C29  C14   129.95  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
 56J  chir_01  C07  C05  C08  C14  negativ

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
 56J  plan-1  C16   0.020
 56J  plan-1  O17   0.020
 56J  plan-1  C29   0.020
 56J  plan-1  H1    0.020
 56J  plan-2  C01   0.020
 56J  plan-2  C02   0.020
 56J  plan-2  C03   0.020
 56J  plan-2  C04   0.020
 56J  plan-2  C05   0.020
 56J  plan-2  C06   0.020
 56J  plan-2  C07   0.020
 56J  plan-2  C08   0.020
 56J  plan-2  C09   0.020
 56J  plan-2  C10   0.020
 56J  plan-2  C11   0.020
 56J  plan-2  C12   0.020
 56J  plan-2  C13   0.020
 56J  plan-2  H011  0.020
 56J  plan-2  H021  0.020
 56J  plan-2  H031  0.020
 56J  plan-2  H061  0.020
 56J  plan-2  H091  0.020
 56J  plan-2  H101  0.020
 56J  plan-2  H111  0.020
 56J  plan-2  H121  0.020

