# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 20:54:00 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-(phenylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Cc2ccccc2)cc1
#
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
 9JH  9JH  4-(phenylmethyl)benzamide  ligand  29  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9JH
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
 9JH  O15   O  O     0  -0.483   4.7371  -0.9677   0.1164
 9JH  C14   C  C     0   0.484   3.9589  -0.0648   0.3942
 9JH  N16   N  NH2   0  -0.812   4.2942   0.9627   1.1907
 9JH  C3    C  CR16  0  -0.321  -3.0978   1.2002  -0.3956
 9JH  C4    C  CR6   0   0.151  -2.4478  -0.0118  -0.6071
 9JH  C5    C  CR16  0  -0.293  -2.7117  -1.0717   0.2582
 9JH  C7    C  CH2   0  -0.619  -1.4484  -0.1744  -1.7261
 9JH  C6    C  CR16  0  -0.240  -3.6034  -0.9235   1.3105
 9JH  C1    C  CR16  0  -0.271  -4.2450   0.2926   1.5158
 9JH  C2    C  CR16  0  -0.239  -3.9907   1.3538   0.6587
 9JH  C10   C  CR16  0  -0.251   2.0108  -1.2542  -0.5744
 9JH  C11   C  CR6   0  -0.056   2.5670  -0.0513  -0.1505
 9JH  C9    C  CR16  0  -0.312   0.7230  -1.2937  -1.0859
 9JH  C8    C  CR6   0   0.156  -0.0348  -0.1329  -1.2048
 9JH  C13   C  CR16  0  -0.278   0.5339   1.0733  -0.8018
 9JH  C12   C  CR16  0  -0.266   1.8153   1.1165  -0.2791
 9JH  H1    H  HCR6  0   0.255  -4.9409   0.4086   2.3365
 9JH  H2    H  HCR6  0   0.254  -4.4886   2.3036   0.8069
 9JH  H6    H  HCR6  0   0.255  -3.8002  -1.7585   1.9709
 9JH  H5    H  HCR6  0   0.247  -2.2155  -2.0236   0.1067
 9JH  H71C  H  HCH2  0   0.272  -1.6190  -1.1223  -2.2402
 9JH  H72C  H  HCH2  0   0.274  -1.5923   0.6166  -2.4650
 9JH  H9    H  HCR6  0   0.254   0.3055  -2.2430  -1.3992
 9JH  H13   H  HCR6  0   0.254  -0.0292   1.9939  -0.9009
 9JH  H10   H  HCR6  0   0.260   2.5826  -2.1693  -0.4950
 9JH  H12   H  HCR6  0   0.259   2.2262   2.0777   0.0029
 9JH  H161  H  HNH2  0   0.405   5.2056   0.9808   1.6186
 9JH  H162  H  HNH2  0   0.412   3.6138   1.6094   1.5495
 9JH  H3    H  HCR6  0   0.248  -2.9088   2.0331  -1.0629

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
 9JH  C1   C2    aromatic  1.388  0.020  1.388
 9JH  C1   C6    aromatic  1.390  0.020  1.390
 9JH  C2   C3    aromatic  1.390  0.020  1.390
 9JH  C3   C4    aromatic  1.391  0.020  1.391
 9JH  C4   C5    aromatic  1.393  0.020  1.393
 9JH  C4   C7    single    1.509  0.020  1.509
 9JH  C5   C6    aromatic  1.387  0.020  1.387
 9JH  C7   C8    single    1.507  0.020  1.507
 9JH  C8   C9    aromatic  1.391  0.020  1.391
 9JH  C8   C13   aromatic  1.393  0.020  1.393
 9JH  C9   C10   aromatic  1.386  0.020  1.386
 9JH  C10  C11   aromatic  1.391  0.020  1.391
 9JH  C11  C12   aromatic  1.395  0.020  1.395
 9JH  C11  C14   single    1.495  0.020  1.495
 9JH  C12  C13   aromatic  1.385  0.020  1.385
 9JH  C14  O15   double    1.224  0.020  1.224
 9JH  C14  N16   single    1.343  0.020  1.343
 9JH  C1   H1    single    0.930  0.020  1.080
 9JH  C2   H2    single    0.930  0.020  1.080
 9JH  C6   H6    single    0.930  0.020  1.080
 9JH  C3   H3    single    0.930  0.020  1.080
 9JH  C5   H5    single    0.930  0.020  1.080
 9JH  C7   H71C  single    0.970  0.020  1.090
 9JH  C7   H72C  single    0.970  0.020  1.090
 9JH  C9   H9    single    0.930  0.020  1.080
 9JH  C13  H13   single    0.930  0.020  1.080
 9JH  C10  H10   single    0.930  0.020  1.080
 9JH  C12  H12   single    0.930  0.020  1.080
 9JH  N16  H161  single    0.860  0.020  1.020
 9JH  N16  H162  single    0.860  0.020  1.020

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
 9JH  C11   C14  N16   116.22  3.000
 9JH  N16   C14  O15   122.71  3.000
 9JH  C11   C14  O15   121.07  3.000
 9JH  H162  N16  H161  116.71  3.000
 9JH  H162  N16  C14   122.36  3.000
 9JH  H161  N16  C14   119.46  3.000
 9JH  H3    C3   C2    119.60  3.000
 9JH  H3    C3   C4    119.63  3.000
 9JH  C2    C3   C4    120.77  3.000
 9JH  C7    C4   C5    120.26  3.000
 9JH  C7    C4   C3    121.05  3.000
 9JH  C5    C4   C3    118.66  3.000
 9JH  H5    C5   C6    119.61  3.000
 9JH  H5    C5   C4    119.63  3.000
 9JH  C6    C5   C4    120.76  3.000
 9JH  H72C  C7   H71C  106.85  3.000
 9JH  H72C  C7   C8    109.74  3.000
 9JH  H71C  C7   C8    109.47  3.000
 9JH  H72C  C7   C4    109.66  3.000
 9JH  H71C  C7   C4    109.82  3.000
 9JH  C8    C7   C4    111.20  3.000
 9JH  H6    C6   C1    120.05  3.000
 9JH  H6    C6   C5    119.81  3.000
 9JH  C1    C6   C5    120.15  3.000
 9JH  H1    C1   C2    120.29  3.000
 9JH  H1    C1   C6    120.17  3.000
 9JH  C2    C1   C6    119.55  3.000
 9JH  H2    C2   C1    120.14  3.000
 9JH  H2    C2   C3    119.75  3.000
 9JH  C1    C2   C3    120.11  3.000
 9JH  H10   C10  C9    119.60  3.000
 9JH  H10   C10  C11   119.84  3.000
 9JH  C9    C10  C11   120.56  3.000
 9JH  C12   C11  C10   118.71  3.000
 9JH  C12   C11  C14   122.89  3.000
 9JH  C10   C11  C14   118.39  3.000
 9JH  H9    C9   C8    119.76  3.000
 9JH  H9    C9   C10   119.32  3.000
 9JH  C8    C9   C10   120.91  3.000
 9JH  C13   C8   C9    118.38  3.000
 9JH  C13   C8   C7    120.45  3.000
 9JH  C9    C8   C7    121.16  3.000
 9JH  H13   C13  C12   119.27  3.000
 9JH  H13   C13  C8    119.80  3.000
 9JH  C12   C13  C8    120.93  3.000
 9JH  H12   C12  C13   118.51  3.000
 9JH  H12   C12  C11   120.98  3.000
 9JH  C13   C12  C11   120.50  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
 9JH  CONST_01  C6    C1   C2   C3     0.00   0.0  0
 9JH  CONST_02  C6    C5   C4   C3     0.00   0.0  0
 9JH  CONST_03  C1    C2   C3   C4     0.00   0.0  0
 9JH  CONST_04  C1    C6   C5   C4     0.00   0.0  0
 9JH  CONST_05  C2    C3   C4   C5     0.00   0.0  0
 9JH  CONST_06  C2    C1   C6   C5     0.00   0.0  0
 9JH  CONST_07  C13   C8   C9   C10    0.00   0.0  0
 9JH  CONST_08  C13   C12  C11  C10    0.00   0.0  0
 9JH  CONST_09  C8    C9   C10  C11    0.00   0.0  0
 9JH  CONST_10  C8    C13  C12  C11    0.00   0.0  0
 9JH  CONST_11  C12   C13  C8   C9     0.00   0.0  0
 9JH  CONST_12  C12   C11  C10  C9     0.00   0.0  0
 9JH  CONST_13  C9    C10  C11  C14  180.00   0.0  0
 9JH  CONST_14  C13   C12  C11  C14  180.00   0.0  0
 9JH  CONST_15  C2    C3   C4   C7   180.00   0.0  0
 9JH  CONST_16  C6    C5   C4   C7   180.00   0.0  0
 9JH  CONST_17  C10   C9   C8   C7   180.00   0.0  0
 9JH  CONST_18  C12   C13  C8   C7   180.00   0.0  0
 9JH  CONST_19  H1    C1   C2   C3   180.00   0.0  0
 9JH  CONST_20  H5    C5   C4   C3   180.00   0.0  0
 9JH  CONST_21  H2    C2   C3   C4   180.00   0.0  0
 9JH  CONST_22  H6    C6   C5   C4   180.00   0.0  0
 9JH  CONST_23  H3    C3   C4   C5   180.00   0.0  0
 9JH  CONST_24  H12   C12  C11  C10  180.00   0.0  0
 9JH  CONST_25  H9    C9   C10  C11  180.00   0.0  0
 9JH  CONST_26  H13   C13  C12  C11  180.00   0.0  0
 9JH  CONST_27  H10   C10  C9   C8   180.00   0.0  0
 9JH  CONST_28  H161  N16  C14  C11  180.00   0.0  0
 9JH  CONST_29  H162  N16  C14  C11    0.00   0.0  0
 9JH  Var_01    C8    C7   C4   C3   102.65  30.0  2
 9JH  Var_02    C9    C8   C7   C4   104.52  30.0  2
 9JH  Var_03    C10   C11  C14  O15   22.13  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
 9JH  plan-1  C3    0.020
 9JH  plan-1  C4    0.020
 9JH  plan-1  C5    0.020
 9JH  plan-1  C7    0.020
 9JH  plan-1  C6    0.020
 9JH  plan-1  C1    0.020
 9JH  plan-1  C2    0.020
 9JH  plan-1  H1    0.020
 9JH  plan-1  H2    0.020
 9JH  plan-1  H6    0.020
 9JH  plan-1  H5    0.020
 9JH  plan-1  H3    0.020
 9JH  plan-2  C14   0.020
 9JH  plan-2  C7    0.020
 9JH  plan-2  C10   0.020
 9JH  plan-2  C11   0.020
 9JH  plan-2  C9    0.020
 9JH  plan-2  C8    0.020
 9JH  plan-2  C13   0.020
 9JH  plan-2  C12   0.020
 9JH  plan-2  H9    0.020
 9JH  plan-2  H13   0.020
 9JH  plan-2  H10   0.020
 9JH  plan-2  H12   0.020
 9JH  plan-3  O15   0.020
 9JH  plan-3  C14   0.020
 9JH  plan-3  N16   0.020
 9JH  plan-3  C11   0.020
 9JH  plan-3  H161  0.020
 9JH  plan-3  H162  0.020

