# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:20:35 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)Oc2c(Br)cc(Br)cc2CNC(=O)c3ccccc3[N+]([O-])=O
#
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
 FYD  FYD  '2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate'  ligand  48  32  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYD
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
 FYD  C14  C   C      0   0.578   0.1043  -2.0933  -0.7706
 FYD  C16  C   CR16   0  -0.243  -2.1991  -2.2407   0.1499
 FYD  C17  C   CR16   0  -0.270  -3.3672  -2.9312   0.4123
 FYD  C19  C   CR16   0  -0.387  -2.3739  -4.9261  -0.5144
 FYD  C20  C   CR6    0   0.412  -1.1985  -4.2315  -0.8022
 FYD  C22  C   CH3    0  -0.444  -0.1788  -6.1757  -1.7025
 FYD  C29  C   CR16   0  -0.263  -5.2834   2.9692   1.3791
 FYD  C30  C   CR16   0  -0.254  -4.7727   4.0289   2.1127
 FYD  C31  C   CR16   0  -0.219  -3.4767   4.4645   1.8876
 FYD  C32  C   CR16   0  -0.262  -2.6876   3.8441   0.9276
 FYD  O01  O   O      0  -0.469  -2.7125   2.3314  -2.1008
 FYD  C02  C   C      0   0.525  -2.3410   2.2425  -0.9433
 FYD  N03  N   NH1    0  -0.622  -1.1530   1.7508  -0.5743
 FYD  C05  C   CR6    0  -0.011   1.1239   0.9729  -0.8883
 FYD  C06  C   CR16   0  -0.276   2.1910   1.8537  -1.0052
 FYD  C07  C   CR6    0  -0.101   3.3955   1.5699  -0.3813
 FYD  BR1  BR  BR     0  -0.012   4.8341   2.7720  -0.5541
 FYD  C09  C   CR16   0  -0.225   3.5636   0.4216   0.3756
 FYD  C10  C   CR6    0  -0.185   2.4942  -0.4532   0.4943
 FYD  BR2  BR  BR     0   0.013   2.6777  -2.0093   1.5245
 FYD  C12  C   CR6    0   0.428   1.2827  -0.1801  -0.1270
 FYD  O13  O   O2     0  -0.495   0.2166  -1.0149   0.0554
 FYD  C15  C   CR6    0  -0.193  -1.1094  -2.8663  -0.4597
 FYD  C18  C   CR16   0  -0.225  -3.4424  -4.2767   0.0823
 FYD  O23  O   O      0  -0.390   0.9169  -2.3140  -1.6220
 FYD  C24  C   CR6    0  -0.047  -3.1757   2.7769   0.1857
 FYD  C25  C   CR6    0   0.236  -4.4796   2.3565   0.4334
 FYD  N26  N   N      1   0.336  -5.0175   1.2042  -0.2726
 FYD  O27  O   O      0  -0.369  -4.2423   0.3410  -0.6082
 FYD  O28  O   O     -1  -0.368  -6.2086   1.1663  -0.4662
 FYD  H1   H   HCR6   0   0.264  -2.1440  -1.1915   0.4024
 FYD  H2   H   HCR6   0   0.262  -4.2073  -2.4267   0.8677
 FYD  H3   H   HCR6   0   0.292  -2.4683  -5.9763  -0.7517
 FYD  H4   H   HCH3   0   0.236  -0.3294  -6.8065  -0.8236
 FYD  H5   H   HCH3   0   0.236  -0.9632  -6.3873  -2.4327
 FYD  H6   H   HCH3   0   0.266   0.7858  -6.4112  -2.1439
 FYD  H7   H   HCR6   0   0.303  -6.2879   2.6158   1.5630
 FYD  H8   H   HCR6   0   0.285  -5.3903   4.5067   2.8601
 FYD  H9   H   HCR6   0   0.284  -3.0759   5.2945   2.4536
 FYD  H10  H   HCR6   0   0.288  -1.6868   4.2111   0.7411
 FYD  H11  H   HNH1   0   0.421  -0.9330   1.6758   0.4064
 FYD  H12  H   HCH2   0   0.268  -0.5770   0.4076  -2.0799
 FYD  H13  H   HCH2   0   0.283  -0.0340   2.0536  -2.3084
 FYD  H14  H   HCR6   0   0.294   2.0716   2.7552  -1.5916
 FYD  H15  H   HCR6   0   0.309   4.5041   0.2063   0.8640
 FYD  H16  H   HCR6   0   0.273  -4.3453  -4.8365   0.2892
 FYD  O21  O   O2     0  -0.447  -0.1316  -4.8004  -1.3647
 FYD  C04  C   CH2    0  -0.316  -0.1888   1.2828  -1.5528

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
 FYD  C30  C31  aromatic  1.386  0.020  1.386
 FYD  C30  C29  aromatic  1.386  0.020  1.386
 FYD  C31  C32  aromatic  1.389  0.020  1.389
 FYD  C29  C25  aromatic  1.384  0.020  1.384
 FYD  O27  N26  double    1.208  0.020  1.208
 FYD  C32  C24  aromatic  1.388  0.020  1.388
 FYD  C25  N26  single    1.454  0.020  1.454
 FYD  C25  C24  aromatic  1.392  0.020  1.392
 FYD  N26  O28  single    1.207  0.020  1.207
 FYD  C24  C02  single    1.502  0.020  1.502
 FYD  C02  O01  double    1.219  0.020  1.219
 FYD  C02  N03  single    1.338  0.020  1.338
 FYD  N03  C04  single    1.451  0.020  1.451
 FYD  BR1  C07  single    1.883  0.020  1.883
 FYD  C04  C05  single    1.504  0.020  1.504
 FYD  C06  C05  aromatic  1.389  0.020  1.389
 FYD  C06  C07  aromatic  1.386  0.020  1.386
 FYD  C05  C12  aromatic  1.391  0.020  1.391
 FYD  C07  C09  aromatic  1.385  0.020  1.385
 FYD  C12  C10  aromatic  1.389  0.020  1.389
 FYD  C12  O13  single    1.366  0.020  1.366
 FYD  C09  C10  aromatic  1.387  0.020  1.387
 FYD  C16  C17  aromatic  1.382  0.020  1.382
 FYD  C16  C15  aromatic  1.397  0.020  1.397
 FYD  C17  C18  aromatic  1.387  0.020  1.387
 FYD  C10  BR2  single    1.875  0.020  1.875
 FYD  O13  C14  single    1.363  0.020  1.363
 FYD  O23  C14  double    1.197  0.020  1.197
 FYD  C14  C15  single    1.472  0.020  1.472
 FYD  C15  C20  aromatic  1.410  0.020  1.410
 FYD  C18  C19  aromatic  1.385  0.020  1.385
 FYD  C20  C19  aromatic  1.395  0.020  1.395
 FYD  C20  O21  single    1.334  0.020  1.334
 FYD  O21  C22  single    1.417  0.020  1.417
 FYD  C16  H1   single    0.930  0.020  1.080
 FYD  C17  H2   single    0.930  0.020  1.080
 FYD  C19  H3   single    0.930  0.020  1.080
 FYD  C22  H4   single    0.970  0.020  1.090
 FYD  C22  H5   single    0.970  0.020  1.090
 FYD  C22  H6   single    0.970  0.020  1.090
 FYD  C29  H7   single    0.930  0.020  1.080
 FYD  C30  H8   single    0.930  0.020  1.080
 FYD  C31  H9   single    0.930  0.020  1.080
 FYD  C32  H10  single    0.930  0.020  1.080
 FYD  N03  H11  single    0.860  0.020  1.020
 FYD  C04  H12  single    0.970  0.020  1.090
 FYD  C04  H13  single    0.970  0.020  1.090
 FYD  C06  H14  single    0.930  0.020  1.080
 FYD  C09  H15  single    0.930  0.020  1.080
 FYD  C18  H16  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
 FYD  O23  C14  C15  127.80  3.000
 FYD  C15  C14  O13  110.82  3.000
 FYD  O23  C14  O13  121.38  3.000
 FYD  H1   C16  C15  119.81  3.000
 FYD  H1   C16  C17  118.94  3.000
 FYD  C15  C16  C17  121.23  3.000
 FYD  H2   C17  C18  120.72  3.000
 FYD  H2   C17  C16  120.26  3.000
 FYD  C18  C17  C16  119.02  3.000
 FYD  H3   C19  C18  118.86  3.000
 FYD  H3   C19  C20  120.80  3.000
 FYD  C18  C19  C20  120.34  3.000
 FYD  O21  C20  C15  117.70  3.000
 FYD  O21  C20  C19  123.27  3.000
 FYD  C15  C20  C19  119.01  3.000
 FYD  H6   C22  H5   108.90  3.000
 FYD  H6   C22  H4   108.91  3.000
 FYD  H5   C22  H4   109.09  3.000
 FYD  H6   C22  O21  106.12  3.000
 FYD  H5   C22  O21  111.80  3.000
 FYD  H4   C22  O21  111.91  3.000
 FYD  H7   C29  C25  120.75  3.000
 FYD  H7   C29  C30  120.16  3.000
 FYD  C25  C29  C30  119.08  3.000
 FYD  H8   C30  C31  120.51  3.000
 FYD  H8   C30  C29  119.56  3.000
 FYD  C31  C30  C29  119.93  3.000
 FYD  H9   C31  C32  119.60  3.000
 FYD  H9   C31  C30  120.19  3.000
 FYD  C32  C31  C30  120.21  3.000
 FYD  H10  C32  C24  119.58  3.000
 FYD  H10  C32  C31  119.54  3.000
 FYD  C24  C32  C31  120.86  3.000
 FYD  C24  C02  N03  114.64  3.000
 FYD  N03  C02  O01  124.02  3.000
 FYD  C24  C02  O01  121.22  3.000
 FYD  H11  N03  C04  119.15  3.000
 FYD  H11  N03  C02  119.31  3.000
 FYD  C04  N03  C02  121.51  3.000
 FYD  C12  C05  C06  118.96  3.000
 FYD  C12  C05  C04  120.83  3.000
 FYD  C06  C05  C04  120.19  3.000
 FYD  H14  C06  C07  120.70  3.000
 FYD  H14  C06  C05  119.30  3.000
 FYD  C07  C06  C05  120.01  3.000
 FYD  C09  C07  BR1  119.12  3.000
 FYD  C09  C07  C06  121.40  3.000
 FYD  BR1  C07  C06  119.47  3.000
 FYD  H15  C09  C10  120.43  3.000
 FYD  H15  C09  C07  121.15  3.000
 FYD  C10  C09  C07  118.43  3.000
 FYD  C12  C10  BR2  119.63  3.000
 FYD  BR2  C10  C09  119.67  3.000
 FYD  C12  C10  C09  120.69  3.000
 FYD  O13  C12  C10  120.06  3.000
 FYD  O13  C12  C05  119.37  3.000
 FYD  C10  C12  C05  120.50  3.000
 FYD  C12  O13  C14  117.83  3.000
 FYD  C20  C15  C16  119.36  3.000
 FYD  C20  C15  C14  120.60  3.000
 FYD  C16  C15  C14  120.02  3.000
 FYD  H16  C18  C19  118.90  3.000
 FYD  H16  C18  C17  120.09  3.000
 FYD  C19  C18  C17  121.01  3.000
 FYD  C25  C24  C02  123.14  3.000
 FYD  C02  C24  C32  118.66  3.000
 FYD  C25  C24  C32  117.79  3.000
 FYD  N26  C25  C24  119.95  3.000
 FYD  C24  C25  C29  122.13  3.000
 FYD  N26  C25  C29  117.88  3.000
 FYD  O28  N26  O27  124.48  3.000
 FYD  O28  N26  C25  117.88  3.000
 FYD  O27  N26  C25  117.63  3.000
 FYD  C22  O21  C20  119.21  3.000
 FYD  H13  C04  H12  106.40  3.000
 FYD  H13  C04  C05  109.15  3.000
 FYD  H12  C04  C05  110.99  3.000
 FYD  H13  C04  N03  109.49  3.000
 FYD  H12  C04  N03  110.33  3.000
 FYD  C05  C04  N03  110.39  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
 FYD  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 FYD  CONST_02  C19  C20  C15  C16     0.00   0.0  0
 FYD  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 FYD  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 FYD  CONST_05  C32  C31  C30  C29     0.00   0.0  0
 FYD  CONST_06  C32  C24  C25  C29     0.00   0.0  0
 FYD  CONST_07  C24  C32  C31  C30     0.00   0.0  0
 FYD  CONST_08  C24  C25  C29  C30     0.00   0.0  0
 FYD  CONST_09  C25  C29  C30  C31     0.00   0.0  0
 FYD  CONST_10  C25  C24  C32  C31     0.00   0.0  0
 FYD  CONST_11  C09  C07  C06  C05     0.00   0.0  0
 FYD  CONST_12  C09  C10  C12  C05     0.00   0.0  0
 FYD  CONST_13  C10  C12  C05  C06     0.00   0.0  0
 FYD  CONST_14  C10  C09  C07  C06     0.00   0.0  0
 FYD  CONST_15  C12  C05  C06  C07     0.00   0.0  0
 FYD  CONST_16  C12  C10  C09  C07     0.00   0.0  0
 FYD  CONST_17  C18  C17  C16  C15     0.00   0.0  0
 FYD  CONST_18  C18  C19  C20  C15     0.00   0.0  0
 FYD  CONST_19  C17  C16  C15  C14   180.00   0.0  0
 FYD  CONST_20  C19  C20  C15  C14   180.00   0.0  0
 FYD  CONST_21  O21  C20  C15  C16   180.00   0.0  0
 FYD  CONST_22  C02  C24  C25  C29   180.00   0.0  0
 FYD  CONST_23  N26  C25  C29  C30   180.00   0.0  0
 FYD  CONST_24  C02  C24  C32  C31   180.00   0.0  0
 FYD  CONST_25  N26  C25  C24  C32   180.00   0.0  0
 FYD  CONST_26  C07  C06  C05  C04   180.00   0.0  0
 FYD  CONST_27  C10  C12  C05  C04   180.00   0.0  0
 FYD  CONST_28  BR1  C07  C06  C05   180.00   0.0  0
 FYD  CONST_29  BR2  C10  C12  C05   180.00   0.0  0
 FYD  CONST_30  O13  C12  C05  C06   180.00   0.0  0
 FYD  CONST_31  BR2  C10  C09  C07   180.00   0.0  0
 FYD  CONST_32  C10  C09  C07  BR1   180.00   0.0  0
 FYD  CONST_33  O13  C12  C10  C09   180.00   0.0  0
 FYD  CONST_34  O21  C20  C19  C18   180.00   0.0  0
 FYD  CONST_35  H16  C18  C17  C16   180.00   0.0  0
 FYD  CONST_36  H3   C19  C18  C17   180.00   0.0  0
 FYD  CONST_37  H2   C17  C18  C19   180.00   0.0  0
 FYD  CONST_38  H1   C16  C15  C20   180.00   0.0  0
 FYD  CONST_39  H9   C31  C30  C29   180.00   0.0  0
 FYD  CONST_40  H10  C32  C31  C30   180.00   0.0  0
 FYD  CONST_41  H7   C29  C30  C31   180.00   0.0  0
 FYD  CONST_42  H8   C30  C31  C32   180.00   0.0  0
 FYD  CONST_43  H15  C09  C07  C06   180.00   0.0  0
 FYD  CONST_44  H14  C06  C07  C09   180.00   0.0  0
 FYD  CONST_49  C24  C02  N03  C04   180.00   0.0  0
 FYD  CONST_50  H11  N03  C02  C24     0.00   0.0  0
 FYD  CONST_51  C04  N03  C02  O01     0.00   0.0  0
 FYD  Var_01    C05  C12  O13  C14    96.40  30.0  1
 FYD  Var_02    O13  C14  C15  C16    25.18  30.0  1
 FYD  Var_03    C15  C20  O21  C22   179.02  30.0  2
 FYD  Var_04    O01  C02  C24  C32  -114.40  30.0  2
 FYD  Var_05    C06  C05  C04  N03  -103.38  30.0  2
 FYD  Var_06    C15  C14  O13  C12  -178.72  30.0  3
 FYD  Var_07    C05  C04  N03  C02   171.79  30.0  3
 FYD  Var_08    H4   C22  O21  C20   -61.58  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
 FYD  plan-1  C14  0.020
 FYD  plan-1  C16  0.020
 FYD  plan-1  C17  0.020
 FYD  plan-1  C19  0.020
 FYD  plan-1  C20  0.020
 FYD  plan-1  C15  0.020
 FYD  plan-1  C18  0.020
 FYD  plan-1  H1   0.020
 FYD  plan-1  H2   0.020
 FYD  plan-1  H3   0.020
 FYD  plan-1  H16  0.020
 FYD  plan-1  O21  0.020
 FYD  plan-2  C29  0.020
 FYD  plan-2  C30  0.020
 FYD  plan-2  C31  0.020
 FYD  plan-2  C32  0.020
 FYD  plan-2  C02  0.020
 FYD  plan-2  C24  0.020
 FYD  plan-2  C25  0.020
 FYD  plan-2  N26  0.020
 FYD  plan-2  H7   0.020
 FYD  plan-2  H8   0.020
 FYD  plan-2  H9   0.020
 FYD  plan-2  H10  0.020
 FYD  plan-3  C05  0.020
 FYD  plan-3  C06  0.020
 FYD  plan-3  C07  0.020
 FYD  plan-3  BR1  0.020
 FYD  plan-3  C09  0.020
 FYD  plan-3  C10  0.020
 FYD  plan-3  BR2  0.020
 FYD  plan-3  C12  0.020
 FYD  plan-3  O13  0.020
 FYD  plan-3  H14  0.020
 FYD  plan-3  H15  0.020
 FYD  plan-3  C04  0.020
 FYD  plan-4  O01  0.020
 FYD  plan-4  C02  0.020
 FYD  plan-4  N03  0.020
 FYD  plan-4  C24  0.020
 FYD  plan-4  H11  0.020
 FYD  plan-4  C04  0.020
 FYD  plan-5  C25  0.020
 FYD  plan-5  N26  0.020
 FYD  plan-5  O27  0.020
 FYD  plan-5  O28  0.020
 FYD  plan-6  C14  0.020
 FYD  plan-6  O13  0.020
 FYD  plan-6  C15  0.020
 FYD  plan-6  O23  0.020

