# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 18:43:25 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[[butyl(phenylcarbamoyl)amino]methyl]-N-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN(Cc1ccc(cc1)C(=O)NO)C(=O)Nc2ccccc2
#
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
 N4R  N4R  4-[[butyl(phenylcarbamoyl)amino]methyl]-N-oxidanyl-benzamide  ligand  48  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N4R
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
 N4R  O2    O  O     0  -0.526   1.4552  -1.2455  -1.6982
 N4R  C12   C  C     0   0.745   1.7595  -0.4379  -0.8308
 N4R  N2    N  NH1   0  -0.798   2.8243  -0.6393   0.0151
 N4R  C13   C  CR6   0   0.374   3.6344  -1.7786   0.0509
 N4R  C18   C  CR16  0  -0.344   4.9747  -1.6104   0.4021
 N4R  C17   C  CR16  0  -0.247   5.8182  -2.7042   0.5175
 N4R  C16   C  CR16  0  -0.275   5.3435  -3.9855   0.2730
 N4R  C15   C  CR16  0  -0.251   4.0101  -4.1537  -0.0753
 N4R  C14   C  CR16  0  -0.298   3.1526  -3.0678  -0.1816
 N4R  N     N  NT    0  -0.484   1.0680   0.7170  -0.6285
 N4R  C3    C  CH2   0  -0.352   1.2866   1.6324   0.4783
 N4R  C2    C  CH2   0  -0.419   2.2395   2.7767   0.1453
 N4R  C1    C  CH2   0  -0.424   2.3385   3.7912   1.2764
 N4R  C     C  CH3   0  -0.661   3.2726   4.9466   0.9446
 N4R  C4    C  CH2   0  -0.406   0.0449   1.1098  -1.5780
 N4R  C5    C  CR6   0   0.133  -1.3512   0.9066  -1.0459
 N4R  C10   C  CR16  0  -0.298  -2.1991   1.9912  -0.8506
 N4R  C9    C  CR16  0  -0.250  -3.4816   1.8124  -0.3549
 N4R  C8    C  CR6   0  -0.073  -3.9471   0.5359  -0.0598
 N4R  C7    C  CR16  0  -0.264  -3.0963  -0.5551  -0.2441
 N4R  C6    C  CR16  0  -0.280  -1.8135  -0.3692  -0.7298
 N4R  C11   C  C     0   0.498  -5.3343   0.3999   0.4725
 N4R  O     O  O     0  -0.460  -5.8856   1.2901   1.0934
 N4R  N1    N  NH1   0  -0.384  -5.9073  -0.7998   0.2232
 N4R  O1    O  OH1   0  -0.539  -7.2259  -0.9689   0.5258
 N4R  H2    H  HNH1  0   0.413   3.2033   0.1570   0.5008
 N4R  H18   H  HCR6  0   0.263   5.3591  -0.6143   0.5884
 N4R  H14   H  HCR6  0   0.265   2.1162  -3.2344  -0.4315
 N4R  H17   H  HCR6  0   0.258   6.8531  -2.5482   0.7935
 N4R  H16   H  HCR6  0   0.253   6.0009  -4.8403   0.3587
 N4R  H15   H  HCR6  0   0.256   3.6209  -5.1469  -0.2588
 N4R  H31C  H  HCH2  0   0.264   0.3123   2.0409   0.7607
 N4R  H32C  H  HCH2  0   0.259   1.6267   1.0837   1.3585
 N4R  H41C  H  HCH2  0   0.269   0.1875   2.1638  -1.8294
 N4R  H42C  H  HCH2  0   0.282   0.1799   0.5475  -2.5001
 N4R  H21C  H  HCH2  0   0.220   3.2357   2.3844  -0.0848
 N4R  H22C  H  HCH2  0   0.229   1.8931   3.2766  -0.7645
 N4R  H11C  H  HCH2  0   0.220   1.3406   4.1789   1.5015
 N4R  H12C  H  HCH2  0   0.220   2.6843   3.2918   2.1862
 N4R  HC1   H  HCH3  0   0.229   3.3240   5.6641   1.7637
 N4R  HC2   H  HCH3  0   0.219   4.2862   4.5909   0.7517
 N4R  HC3   H  HCH3  0   0.219   2.9363   5.4824   0.0552
 N4R  H10   H  HCR6  0   0.262  -1.8539   2.9910  -1.0852
 N4R  H6    H  HCR6  0   0.260  -1.1669  -1.2270  -0.8638
 N4R  H9    H  HCR6  0   0.263  -4.1224   2.6711  -0.2047
 N4R  H7    H  HCR6  0   0.264  -3.4180  -1.5574   0.0083
 N4R  H1    H  HNH1  0   0.417  -5.5873  -1.3837  -0.5366
 N4R  HA    H  HOH1  0   0.479  -7.2457  -1.4875   1.3400

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
 N4R  O2   C12   double    1.224  0.020  1.224
 N4R  C12  N2    single    1.375  0.020  1.375
 N4R  C12  N     single    1.361  0.020  1.361
 N4R  N2   C13   single    1.398  0.020  1.398
 N4R  C13  C18   aromatic  1.396  0.020  1.396
 N4R  C13  C14   aromatic  1.396  0.020  1.396
 N4R  C18  C17   aromatic  1.386  0.020  1.386
 N4R  C17  C16   aromatic  1.388  0.020  1.388
 N4R  C16  C15   aromatic  1.388  0.020  1.388
 N4R  C15  C14   aromatic  1.388  0.020  1.388
 N4R  N    C3    single    1.453  0.020  1.453
 N4R  N    C4    single    1.450  0.020  1.450
 N4R  C3   C2    single    1.526  0.020  1.526
 N4R  C2   C1    single    1.523  0.020  1.523
 N4R  C1   C     single    1.522  0.020  1.522
 N4R  C4   C5    single    1.508  0.020  1.508
 N4R  C5   C10   aromatic  1.390  0.020  1.390
 N4R  C5   C6    aromatic  1.393  0.020  1.393
 N4R  C10  C9    aromatic  1.387  0.020  1.387
 N4R  C9   C8    aromatic  1.390  0.020  1.390
 N4R  C8   C7    aromatic  1.396  0.020  1.396
 N4R  C8   C11   single    1.492  0.020  1.492
 N4R  C7   C6    aromatic  1.384  0.020  1.384
 N4R  C11  O     double    1.217  0.020  1.217
 N4R  C11  N1    single    1.353  0.020  1.353
 N4R  N1   O1    single    1.363  0.020  1.363
 N4R  N2   H2    single    0.860  0.020  1.020
 N4R  C18  H18   single    0.930  0.020  1.080
 N4R  C14  H14   single    0.930  0.020  1.080
 N4R  C17  H17   single    0.930  0.020  1.080
 N4R  C16  H16   single    0.930  0.020  1.080
 N4R  C15  H15   single    0.930  0.020  1.080
 N4R  C3   H31C  single    0.970  0.020  1.090
 N4R  C3   H32C  single    0.970  0.020  1.090
 N4R  C4   H41C  single    0.970  0.020  1.090
 N4R  C4   H42C  single    0.970  0.020  1.090
 N4R  C2   H21C  single    0.970  0.020  1.090
 N4R  C2   H22C  single    0.970  0.020  1.090
 N4R  C1   H11C  single    0.970  0.020  1.090
 N4R  C1   H12C  single    0.970  0.020  1.090
 N4R  C    HC1   single    0.970  0.020  1.090
 N4R  C    HC2   single    0.970  0.020  1.090
 N4R  C    HC3   single    0.970  0.020  1.090
 N4R  C10  H10   single    0.930  0.020  1.080
 N4R  C6   H6    single    0.930  0.020  1.080
 N4R  C9   H9    single    0.930  0.020  1.080
 N4R  C7   H7    single    0.930  0.020  1.080
 N4R  N1   H1    single    0.890  0.020  1.040
 N4R  O1   HA    single    0.850  0.020  0.980

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
 N4R  N     C12  N2    115.23  3.000
 N4R  N     C12  O2    122.62  3.000
 N4R  N2    C12  O2    122.15  3.000
 N4R  H2    N2   C13   114.45  3.000
 N4R  H2    N2   C12   118.20  3.000
 N4R  C13   N2   C12   125.72  3.000
 N4R  C14   C13  C18   118.99  3.000
 N4R  C14   C13  N2    123.25  3.000
 N4R  C18   C13  N2    117.68  3.000
 N4R  H18   C18  C17   119.68  3.000
 N4R  H18   C18  C13   119.64  3.000
 N4R  C17   C18  C13   120.68  3.000
 N4R  H17   C17  C16   120.33  3.000
 N4R  H17   C17  C18   119.30  3.000
 N4R  C16   C17  C18   120.37  3.000
 N4R  H16   C16  C15   120.52  3.000
 N4R  H16   C16  C17   120.51  3.000
 N4R  C15   C16  C17   118.98  3.000
 N4R  H15   C15  C14   118.87  3.000
 N4R  H15   C15  C16   119.93  3.000
 N4R  C14   C15  C16   121.19  3.000
 N4R  H14   C14  C15   119.37  3.000
 N4R  H14   C14  C13   120.85  3.000
 N4R  C15   C14  C13   119.78  3.000
 N4R  C4    N    C3    115.74  3.000
 N4R  C4    N    C12   119.40  3.000
 N4R  C3    N    C12   124.85  3.000
 N4R  H32C  C3   H31C  104.89  3.000
 N4R  H32C  C3   C2    111.00  3.000
 N4R  H31C  C3   C2    109.43  3.000
 N4R  H32C  C3   N     110.15  3.000
 N4R  H31C  C3   N     107.34  3.000
 N4R  C2    C3   N     113.59  3.000
 N4R  H22C  C2   H21C  106.08  3.000
 N4R  H22C  C2   C1    109.50  3.000
 N4R  H21C  C2   C1    109.61  3.000
 N4R  H22C  C2   C3    109.04  3.000
 N4R  H21C  C2   C3    110.20  3.000
 N4R  C1    C2   C3    112.22  3.000
 N4R  H12C  C1   H11C  106.20  3.000
 N4R  H12C  C1   C     109.51  3.000
 N4R  H11C  C1   C     109.61  3.000
 N4R  H12C  C1   C2    109.52  3.000
 N4R  H11C  C1   C2    109.25  3.000
 N4R  C     C1   C2    112.56  3.000
 N4R  HC3   C    HC2   107.59  3.000
 N4R  HC3   C    HC1   107.68  3.000
 N4R  HC2   C    HC1   107.67  3.000
 N4R  HC3   C    C1    111.18  3.000
 N4R  HC2   C    C1    111.16  3.000
 N4R  HC1   C    C1    111.39  3.000
 N4R  H42C  C4   H41C  106.69  3.000
 N4R  H42C  C4   C5    110.13  3.000
 N4R  H41C  C4   C5    109.39  3.000
 N4R  H42C  C4   N     109.10  3.000
 N4R  H41C  C4   N     108.65  3.000
 N4R  C5    C4   N     112.69  3.000
 N4R  C6    C5   C10   118.69  3.000
 N4R  C6    C5   C4    120.71  3.000
 N4R  C10   C5   C4    120.60  3.000
 N4R  H10   C10  C9    119.41  3.000
 N4R  H10   C10  C5    119.67  3.000
 N4R  C9    C10  C5    120.91  3.000
 N4R  H9    C9   C8    120.06  3.000
 N4R  H9    C9   C10   119.68  3.000
 N4R  C8    C9   C10   120.26  3.000
 N4R  C11   C8   C7    122.86  3.000
 N4R  C11   C8   C9    118.07  3.000
 N4R  C7    C8   C9    119.05  3.000
 N4R  H7    C7   C6    118.79  3.000
 N4R  H7    C7   C8    120.79  3.000
 N4R  C6    C7   C8    120.41  3.000
 N4R  H6    C6   C7    119.38  3.000
 N4R  H6    C6   C5    119.95  3.000
 N4R  C7    C6   C5    120.67  3.000
 N4R  N1    C11  O     123.42  3.000
 N4R  N1    C11  C8    114.14  3.000
 N4R  O     C11  C8    122.43  3.000
 N4R  H1    N1   O1    113.68  3.000
 N4R  H1    N1   C11   121.13  3.000
 N4R  O1    N1   C11   118.61  3.000
 N4R  HA    O1   N1    105.88  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
 N4R  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 N4R  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 N4R  CONST_03  C15  C14  C13  C18     0.00   0.0  0
 N4R  CONST_04  C15  C16  C17  C18     0.00   0.0  0
 N4R  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 N4R  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 N4R  CONST_07  C8   C9   C10  C5      0.00   0.0  0
 N4R  CONST_08  C8   C7   C6   C5      0.00   0.0  0
 N4R  CONST_09  C7   C6   C5   C10     0.00   0.0  0
 N4R  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 N4R  CONST_11  C6   C5   C10  C9      0.00   0.0  0
 N4R  CONST_12  C6   C7   C8   C9      0.00   0.0  0
 N4R  CONST_13  C17  C18  C13  N2    180.00   0.0  0
 N4R  CONST_14  C15  C14  C13  N2    180.00   0.0  0
 N4R  CONST_15  C9   C10  C5   C4    180.00   0.0  0
 N4R  CONST_16  C7   C6   C5   C4    180.00   0.0  0
 N4R  CONST_17  C11  C8   C9   C10   180.00   0.0  0
 N4R  CONST_18  C11  C8   C7   C6    180.00   0.0  0
 N4R  CONST_19  H17  C17  C18  C13   180.00   0.0  0
 N4R  CONST_20  H15  C15  C14  C13   180.00   0.0  0
 N4R  CONST_21  H14  C14  C13  C18   180.00   0.0  0
 N4R  CONST_22  H16  C16  C17  C18   180.00   0.0  0
 N4R  CONST_23  H18  C18  C17  C16   180.00   0.0  0
 N4R  CONST_24  H9   C9   C10  C5    180.00   0.0  0
 N4R  CONST_25  H7   C7   C6   C5    180.00   0.0  0
 N4R  CONST_26  H6   C6   C5   C10   180.00   0.0  0
 N4R  CONST_27  H10  C10  C9   C8    180.00   0.0  0
 N4R  CONST_31  C13  N2   C12  O2      0.00   0.0  0
 N4R  CONST_32  O1   N1   C11  C8    180.00   0.0  0
 N4R  CONST_33  N    C12  N2   C13   180.00   0.0  0
 N4R  CONST_35  C3   N    C12  O2    180.00   0.0  0
 N4R  CONST_36  C4   N    C12  O2      0.00   0.0  0
 N4R  CONST_37  O1   N1   C11  O       0.00   0.0  0
 N4R  CONST_38  C3   N    C12  N2      0.00   0.0  0
 N4R  CONST_39  C4   N    C12  N2    180.00   0.0  0
 N4R  Var_01    C10  C5   C4   N     116.41  30.0  2
 N4R  Var_02    O    C11  C8   C9    -26.93  30.0  2
 N4R  Var_03    C5   C4   N    C12   105.81  30.0  3
 N4R  Var_04    C2   C3   N    C12    94.42  30.0  3
 N4R  Var_05    C1   C2   C3   N     174.30  30.0  3
 N4R  Var_06    C    C1   C2   C3   -179.20  30.0  3
 N4R  Var_07    HC1  C    C1   C2    179.62  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
 N4R  plan-1  N2   0.020
 N4R  plan-1  C13  0.020
 N4R  plan-1  C18  0.020
 N4R  plan-1  C17  0.020
 N4R  plan-1  C16  0.020
 N4R  plan-1  C15  0.020
 N4R  plan-1  C14  0.020
 N4R  plan-1  H18  0.020
 N4R  plan-1  H14  0.020
 N4R  plan-1  H17  0.020
 N4R  plan-1  H16  0.020
 N4R  plan-1  H15  0.020
 N4R  plan-2  C4   0.020
 N4R  plan-2  C5   0.020
 N4R  plan-2  C10  0.020
 N4R  plan-2  C9   0.020
 N4R  plan-2  C8   0.020
 N4R  plan-2  C7   0.020
 N4R  plan-2  C6   0.020
 N4R  plan-2  C11  0.020
 N4R  plan-2  H10  0.020
 N4R  plan-2  H6   0.020
 N4R  plan-2  H9   0.020
 N4R  plan-2  H7   0.020
 N4R  plan-3  O2   0.020
 N4R  plan-3  C12  0.020
 N4R  plan-3  N2   0.020
 N4R  plan-3  C13  0.020
 N4R  plan-3  N    0.020
 N4R  plan-3  C3   0.020
 N4R  plan-3  C4   0.020
 N4R  plan-3  H2   0.020
 N4R  plan-4  C8   0.020
 N4R  plan-4  C11  0.020
 N4R  plan-4  O    0.020
 N4R  plan-4  N1   0.020
 N4R  plan-4  O1   0.020
 N4R  plan-4  H1   0.020

