# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:40:46 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCON=C1c2ccccc2c3ccccc13
#
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
 7BD  7BD  '3-[(9H-fluoren-9-ylideneamino)oxy]propanoic acid'  ligand  32  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7BD
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
 7BD  C1    C  CR56   0   0.032  -1.8840  -1.1734   0.0172
 7BD  C2    C  CR5    0   0.097  -0.6449  -0.3799   0.0104
 7BD  C3    C  CR5    0   0.042  -1.0490   1.0373   0.0018
 7BD  C4    C  CR5    0   0.082  -2.4560   1.0775   0.0026
 7BD  C5    C  CR56   0   0.105  -2.9723  -0.2930   0.0121
 7BD  C6    C  C1     0  -0.341  -3.1316   2.2845  -0.0044
 7BD  C10   C  CR16   0  -0.346  -4.2701  -0.7762   0.0164
 7BD  C11   C  CR16   0  -0.297  -2.0762  -2.5436   0.0276
 7BD  C12   C  CR16   0  -0.262  -3.3807  -3.0275   0.0324
 7BD  C13   C  CR16   0  -0.249  -4.4651  -2.1538   0.0267
 7BD  C16   C  CH2    0  -0.118   2.7815  -0.7857  -0.0014
 7BD  C17   C  CH2    0  -0.639   3.8757   0.2561  -0.0025
 7BD  C18   C  C      0   0.418   5.2955  -0.3427  -0.0244
 7BD  C7    C  C1     0  -0.295  -0.3165   2.2164  -0.0066
 7BD  C8    C  C1     0  -0.257  -1.0026   3.4280  -0.0138
 7BD  C9    C  C1     0  -0.244  -2.3921   3.4631  -0.0126
 7BD  N14   N  N      0  -0.086   0.4974  -0.9480   0.0119
 7BD  O15   O  O2     0  -0.393   1.5301  -0.0900   0.0061
 7BD  O19   O  OC    -1  -0.623   6.2325   0.4788  -0.0388
 7BD  O20   O  O      0  -0.607   5.3912  -1.5856  -0.0252
 7BD  H6    H  H      0   0.253  -4.2139   2.3198  -0.0032
 7BD  H10   H  HCR6   0   0.252  -5.1184  -0.1030   0.0117
 7BD  H11   H  HCR6   0   0.256  -1.2361  -3.2257   0.0322
 7BD  H12   H  HCR6   0   0.261  -3.5543  -4.0955   0.0409
 7BD  H13   H  HCR6   0   0.262  -5.4717  -2.5514   0.0302
 7BD  H16   H  HCH2   0   0.215   2.8392  -1.4216  -0.8883
 7BD  H16A  H  HCH2   0   0.215   2.8458  -1.4281   0.8804
 7BD  H17   H  HCH2   0   0.237   3.7620   0.9175  -0.8677
 7BD  H17A  H  HCH2   0   0.238   3.7815   0.8987   0.8792
 7BD  H7    H  H      0   0.264   0.7627   2.2143  -0.0078
 7BD  H8    H  H      0   0.262  -0.4430   4.3541  -0.0206
 7BD  H9    H  H      0   0.264  -2.9045   4.4164  -0.0182

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
 7BD  C1   C5    aromatic  1.400  0.020  1.400
 7BD  C2   C1    single    1.471  0.020  1.471
 7BD  C2   C3    single    1.474  0.020  1.474
 7BD  C3   C4    aromatic  1.408  0.020  1.408
 7BD  C4   C6    aromatic  1.383  0.020  1.383
 7BD  C5   C4    aromatic  1.465  0.020  1.465
 7BD  C5   C10   aromatic  1.385  0.020  1.385
 7BD  C6   H6    single    0.930  0.020  1.080
 7BD  C10  H10   single    0.930  0.020  1.080
 7BD  C11  C1    aromatic  1.384  0.020  1.384
 7BD  C11  C12   aromatic  1.391  0.020  1.391
 7BD  C11  H11   single    0.930  0.020  1.080
 7BD  C12  C13   aromatic  1.393  0.020  1.393
 7BD  C12  H12   single    0.930  0.020  1.080
 7BD  C13  C10   aromatic  1.391  0.020  1.391
 7BD  C13  H13   single    0.930  0.020  1.080
 7BD  C16  O15   single    1.432  0.020  1.432
 7BD  C16  H16   single    0.970  0.020  1.090
 7BD  C16  H16A  single    0.970  0.020  1.090
 7BD  C17  C16   single    1.511  0.020  1.511
 7BD  C17  H17   single    0.970  0.020  1.090
 7BD  C17  H17A  single    0.970  0.020  1.090
 7BD  C18  C17   single    1.541  0.020  1.541
 7BD  C7   C3    aromatic  1.388  0.020  1.388
 7BD  C7   C8    aromatic  1.392  0.020  1.392
 7BD  C7   H7    single    0.930  0.020  1.080
 7BD  C8   C9    aromatic  1.390  0.020  1.390
 7BD  C8   H8    single    0.930  0.020  1.080
 7BD  C9   C6    aromatic  1.391  0.020  1.391
 7BD  C9   H9    single    0.930  0.020  1.080
 7BD  N14  C2    double    1.276  0.020  1.276
 7BD  O15  N14   single    1.343  0.020  1.343
 7BD  O19  C18   deloc     1.246  0.020  1.246
 7BD  O20  C18   deloc     1.246  0.020  1.246

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
 7BD  C11   C1   C5   120.98  3.000
 7BD  C11   C1   C2   130.62  3.000
 7BD  C5    C1   C2   108.40  3.000
 7BD  N14   C2   C3   132.36  3.000
 7BD  N14   C2   C1   120.92  3.000
 7BD  C3    C2   C1   106.72  3.000
 7BD  C7    C3   C4   120.22  3.000
 7BD  C7    C3   C2   132.23  3.000
 7BD  C4    C3   C2   107.55  3.000
 7BD  C6    C4   C5   130.12  3.000
 7BD  C5    C4   C3   109.01  3.000
 7BD  C6    C4   C3   120.87  3.000
 7BD  C10   C5   C4   131.07  3.000
 7BD  C10   C5   C1   120.61  3.000
 7BD  C4    C5   C1   108.33  3.000
 7BD  H6    C6   C9   120.24  3.000
 7BD  C9    C6   C4   118.66  3.000
 7BD  H6    C6   C4   121.11  3.000
 7BD  H10   C10  C13  120.38  3.000
 7BD  C13   C10  C5   118.48  3.000
 7BD  H10   C10  C5   121.14  3.000
 7BD  H11   C11  C12  120.57  3.000
 7BD  H11   C11  C1   121.09  3.000
 7BD  C12   C11  C1   118.34  3.000
 7BD  H12   C12  C13  119.63  3.000
 7BD  H12   C12  C11  119.58  3.000
 7BD  C13   C12  C11  120.79  3.000
 7BD  H13   C13  C12  119.59  3.000
 7BD  H13   C13  C10  119.61  3.000
 7BD  C12   C13  C10  120.80  3.000
 7BD  H16A  C16  H16  108.04  3.000
 7BD  H16A  C16  O15  109.44  3.000
 7BD  H16   C16  O15  109.45  3.000
 7BD  H16A  C16  C17  111.30  3.000
 7BD  H16   C16  C17  111.25  3.000
 7BD  O15   C16  C17  107.33  3.000
 7BD  H17A  C17  H17  105.84  3.000
 7BD  H17A  C17  C18  108.58  3.000
 7BD  H17   C17  C18  108.61  3.000
 7BD  C18   C17  C16  113.53  3.000
 7BD  H17A  C17  C16  109.99  3.000
 7BD  H17   C17  C16  109.99  3.000
 7BD  O20   C18  O19  126.84  3.000
 7BD  O20   C18  C17  117.27  3.000
 7BD  O19   C18  C17  115.89  3.000
 7BD  H7    C7   C8   119.63  3.000
 7BD  H7    C7   C3   121.74  3.000
 7BD  C8    C7   C3   118.63  3.000
 7BD  H8    C8   C9   119.70  3.000
 7BD  H8    C8   C7   119.33  3.000
 7BD  C9    C8   C7   120.97  3.000
 7BD  H9    C9   C8   119.70  3.000
 7BD  H9    C9   C6   119.64  3.000
 7BD  C8    C9   C6   120.66  3.000
 7BD  O15   N14  C2   113.83  3.000
 7BD  N14   O15  C16  111.21  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
 7BD  CONST_01  C3   C4   C5   C1      0.00   0.0  0
 7BD  CONST_02  C6   C4   C5   C1    180.00   0.0  0
 7BD  CONST_03  C13  C10  C5   C1      0.00   0.0  0
 7BD  CONST_04  C13  C12  C11  C1      0.00   0.0  0
 7BD  CONST_05  C9   C6   C4   C3      0.00   0.0  0
 7BD  CONST_06  C10  C5   C4   C3    180.00   0.0  0
 7BD  CONST_07  C9   C8   C7   C3      0.00   0.0  0
 7BD  CONST_08  C8   C7   C3   C4      0.00   0.0  0
 7BD  CONST_09  C8   C9   C6   C4      0.00   0.0  0
 7BD  CONST_10  C11  C1   C5   C4    180.00   0.0  0
 7BD  CONST_11  C13  C10  C5   C4    180.00   0.0  0
 7BD  CONST_12  C12  C11  C1   C5      0.00   0.0  0
 7BD  CONST_13  C7   C3   C4   C5    180.00   0.0  0
 7BD  CONST_14  C9   C6   C4   C5    180.00   0.0  0
 7BD  CONST_15  C12  C13  C10  C5      0.00   0.0  0
 7BD  CONST_16  C7   C3   C4   C6      0.00   0.0  0
 7BD  CONST_17  C10  C5   C4   C6      0.00   0.0  0
 7BD  CONST_18  C7   C8   C9   C6      0.00   0.0  0
 7BD  CONST_19  C11  C1   C5   C10     0.00   0.0  0
 7BD  CONST_20  C11  C12  C13  C10     0.00   0.0  0
 7BD  CONST_21  H10  C10  C5   C1    180.00   0.0  0
 7BD  CONST_22  H12  C12  C11  C1    180.00   0.0  0
 7BD  CONST_23  H11  C11  C1   C2      0.00   0.0  0
 7BD  CONST_24  H7   C7   C3   C2      0.00   0.0  0
 7BD  CONST_25  H6   C6   C4   C3    180.00   0.0  0
 7BD  CONST_26  H8   C8   C7   C3    180.00   0.0  0
 7BD  CONST_27  H9   C9   C6   C4    180.00   0.0  0
 7BD  CONST_28  H13  C13  C10  C5    180.00   0.0  0
 7BD  Var_01    N14  C2   C3   C4    179.93  30.0  1
 7BD  Var_02    O19  C18  C17  C16   179.35  30.0  2
 7BD  Var_03    O15  C16  C17  C18  -179.43  30.0  3

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
 7BD  plan-1  C17  0.020
 7BD  plan-1  C18  0.020
 7BD  plan-1  O19  0.020
 7BD  plan-1  O20  0.020
 7BD  plan-2  C1   0.020
 7BD  plan-2  C2   0.020
 7BD  plan-2  C3   0.020
 7BD  plan-2  C4   0.020
 7BD  plan-2  C5   0.020
 7BD  plan-2  C6   0.020
 7BD  plan-2  C10  0.020
 7BD  plan-2  C11  0.020
 7BD  plan-2  C12  0.020
 7BD  plan-2  C13  0.020
 7BD  plan-2  C7   0.020
 7BD  plan-2  C8   0.020
 7BD  plan-2  C9   0.020
 7BD  plan-2  H6   0.020
 7BD  plan-2  H10  0.020
 7BD  plan-2  H11  0.020
 7BD  plan-2  H12  0.020
 7BD  plan-2  H13  0.020
 7BD  plan-2  H7   0.020
 7BD  plan-2  H8   0.020
 7BD  plan-2  H9   0.020
 7BD  plan-3  C1   0.020
 7BD  plan-3  C2   0.020
 7BD  plan-3  C3   0.020
 7BD  plan-3  N14  0.020
 7BD  plan-3  O15  0.020

