# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 14:03:31 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: N-carbamoylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)NC(=O)c1ccccc1
#
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
 YZM  YZM  'N-carbamoylbenzamide     '  ligand  20  12  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YZM
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
 YZM  N1    N  NH2   0  -0.843   3.4794   1.2696   0.3793
 YZM  C1    C  C     0   0.692   2.8072   0.2107  -0.1046
 YZM  O1    O  O     0  -0.485   3.3353  -0.7438  -0.6383
 YZM  N2    N  NH1   0  -0.736   1.4225   0.3309   0.0608
 YZM  C2    C  C     0   0.549   0.4870  -0.6370  -0.2060
 YZM  O2    O  O     0  -0.426   0.7585  -1.7832  -0.4870
 YZM  C3    C  CR6   0  -0.055  -0.9315  -0.1789  -0.1035
 YZM  C4    C  CR16  0  -0.259  -1.9023  -1.1328   0.1990
 YZM  C5    C  CR16  0  -0.242  -3.2366  -0.7699   0.2827
 YZM  C6    C  CR16  0  -0.247  -3.6174   0.5450   0.0436
 YZM  C7    C  CR16  0  -0.239  -2.6582   1.4957  -0.2758
 YZM  C8    C  CR16  0  -0.288  -1.3193   1.1380  -0.3452
 YZM  H11N  H  HNH2  0   0.412   4.4789   1.3013   0.2750
 YZM  H2    H  HNH2  0   0.412   3.0370   2.0548   0.8243
 YZM  H21N  H  HNH1  0   0.425   1.0811   1.1980   0.4473
 YZM  H41   H  HCR6  0   0.265  -1.6121  -2.1592   0.3797
 YZM  H51   H  HCR6  0   0.266  -3.9816  -1.5143   0.5311
 YZM  H61   H  HCR6  0   0.267  -4.6610   0.8255   0.1011
 YZM  H71   H  HCR6  0   0.268  -2.9499   2.5174  -0.4789
 YZM  H81   H  HCR6  0   0.266  -0.5942   1.8943  -0.6190

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
 YZM  N1  C1    single    1.344  0.020  1.344
 YZM  C1  O1    double    1.214  0.020  1.214
 YZM  C1  N2    single    1.400  0.020  1.400
 YZM  N2  C2    single    1.372  0.020  1.372
 YZM  C2  O2    double    1.211  0.020  1.211
 YZM  C2  C3    single    1.494  0.020  1.494
 YZM  C3  C4    aromatic  1.394  0.020  1.394
 YZM  C3  C8    aromatic  1.394  0.020  1.394
 YZM  C4  C5    aromatic  1.385  0.020  1.385
 YZM  C5  C6    aromatic  1.390  0.020  1.390
 YZM  C6  C7    aromatic  1.388  0.020  1.388
 YZM  C7  C8    aromatic  1.388  0.020  1.388
 YZM  N1  H11N  single    0.860  0.020  1.020
 YZM  N1  H2    single    0.860  0.020  1.020
 YZM  N2  H21N  single    0.860  0.020  1.020
 YZM  C4  H41   single    0.930  0.020  1.080
 YZM  C5  H51   single    0.930  0.020  1.080
 YZM  C6  H61   single    0.930  0.020  1.080
 YZM  C7  H71   single    0.930  0.020  1.080
 YZM  C8  H81   single    0.930  0.020  1.080

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
 YZM  H2    N1  H11N  117.31  3.000
 YZM  H2    N1  C1    123.69  3.000
 YZM  H11N  N1  C1    118.98  3.000
 YZM  N2    C1  O1    123.34  3.000
 YZM  N2    C1  N1    112.61  3.000
 YZM  O1    C1  N1    124.05  3.000
 YZM  H21N  N2  C2    116.74  3.000
 YZM  H21N  N2  C1    116.99  3.000
 YZM  C2    N2  C1    126.22  3.000
 YZM  C3    C2  O2    121.26  3.000
 YZM  C3    C2  N2    114.69  3.000
 YZM  O2    C2  N2    124.05  3.000
 YZM  C8    C3  C4    119.35  3.000
 YZM  C8    C3  C2    122.81  3.000
 YZM  C4    C3  C2    117.79  3.000
 YZM  H41   C4  C5    119.79  3.000
 YZM  H41   C4  C3    119.90  3.000
 YZM  C5    C4  C3    120.31  3.000
 YZM  H51   C5  C6    120.12  3.000
 YZM  H51   C5  C4    119.79  3.000
 YZM  C6    C5  C4    120.09  3.000
 YZM  H61   C6  C7    120.08  3.000
 YZM  H61   C6  C5    120.02  3.000
 YZM  C7    C6  C5    119.90  3.000
 YZM  H71   C7  C8    119.62  3.000
 YZM  H71   C7  C6    120.26  3.000
 YZM  C8    C7  C6    120.12  3.000
 YZM  H81   C8  C7    118.60  3.000
 YZM  H81   C8  C3    121.15  3.000
 YZM  C7    C8  C3    120.22  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
 YZM  CONST_01  C6    C5  C4  C3     0.00   0.0  0
 YZM  CONST_02  C6    C7  C8  C3     0.00   0.0  0
 YZM  CONST_03  C7    C8  C3  C4     0.00   0.0  0
 YZM  CONST_04  C7    C6  C5  C4     0.00   0.0  0
 YZM  CONST_05  C8    C3  C4  C5     0.00   0.0  0
 YZM  CONST_06  C8    C7  C6  C5     0.00   0.0  0
 YZM  CONST_07  C5    C4  C3  C2   180.00   0.0  0
 YZM  CONST_08  C7    C8  C3  C2   180.00   0.0  0
 YZM  CONST_09  H51   C5  C4  C3   180.00   0.0  0
 YZM  CONST_10  H71   C7  C8  C3   180.00   0.0  0
 YZM  CONST_11  H81   C8  C3  C4   180.00   0.0  0
 YZM  CONST_12  H61   C6  C5  C4   180.00   0.0  0
 YZM  CONST_13  H41   C4  C5  C6   180.00   0.0  0
 YZM  CONST_14  C3    C2  N2  C1   180.00   0.0  0
 YZM  CONST_15  H21N  N2  C2  C3     0.00   0.0  0
 YZM  CONST_16  O2    C2  N2  C1     0.00   0.0  0
 YZM  CONST_17  C2    N2  C1  O1     0.00   0.0  0
 YZM  CONST_18  C2    N2  C1  N1   180.00   0.0  0
 YZM  CONST_19  H11N  N1  C1  O1     0.00   0.0  0
 YZM  CONST_20  H2    N1  C1  O1   180.00   0.0  0
 YZM  Var_01    C4    C3  C2  N2  -153.65  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
 YZM  plan-1  C2    0.020
 YZM  plan-1  C3    0.020
 YZM  plan-1  C4    0.020
 YZM  plan-1  C5    0.020
 YZM  plan-1  C6    0.020
 YZM  plan-1  C7    0.020
 YZM  plan-1  C8    0.020
 YZM  plan-1  H41   0.020
 YZM  plan-1  H51   0.020
 YZM  plan-1  H61   0.020
 YZM  plan-1  H71   0.020
 YZM  plan-1  H81   0.020
 YZM  plan-2  N1    0.020
 YZM  plan-2  C1    0.020
 YZM  plan-2  O1    0.020
 YZM  plan-2  N2    0.020
 YZM  plan-2  C2    0.020
 YZM  plan-2  O2    0.020
 YZM  plan-2  C3    0.020
 YZM  plan-2  H11N  0.020
 YZM  plan-2  H2    0.020
 YZM  plan-2  H21N  0.020

