# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:16:24 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)[C@@H](N=Nc1ccccc1)C(N)=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
 V41  V41  (2R,3Z)-3-amino-3-imino-2-[(E)-phenyldiazenyl]propanamide  ligand  26  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V41
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
 V41  N6   N  N     0  -0.236  -27.4041  -0.9441  -20.8377
 V41  C7   C  CR6   0   0.206  -26.2029  -1.5145  -21.3167
 V41  C8   C  CR16  0  -0.261  -24.9638  -0.8726  -21.3228
 V41  C9   C  CR16  0  -0.244  -23.8538  -1.5380  -21.8111
 V41  C10  C  CR16  0  -0.246  -23.9681  -2.8392  -22.2945
 V41  C11  C  CR16  0  -0.245  -25.2002  -3.4765  -22.2878
 V41  C12  C  CR16  0  -0.273  -26.3164  -2.8139  -21.7975
 V41  N13  N  N     0  -0.184  -27.3235   0.2156  -20.4380
 V41  C14  C  CH1   0  -0.349  -28.5875   0.7373  -19.9589
 V41  C15  C  C     0   0.403  -28.8891   2.0517  -20.6671
 V41  C16  C  C     0   0.539  -28.4598   0.9642  -18.4427
 V41  N17  N  NH2   0  -0.796  -29.5305   1.5382  -17.8841
 V41  N18  N  N     0  -0.638  -30.0305   2.3586  -21.1428
 V41  N19  N  NH2   0  -0.797  -27.8499   2.9220  -20.6729
 V41  O20  O  O     0  -0.455  -27.4666   0.6189  -17.8318
 V41  H1   H  HCR6  0   0.269  -24.8717   0.1365  -20.9447
 V41  H2   H  HCR6  0   0.265  -22.8914  -1.0433  -21.8144
 V41  H3   H  HCR6  0   0.266  -23.0941  -3.3526  -22.6735
 V41  H4   H  HCR6  0   0.264  -25.2932  -4.4873  -22.6619
 V41  H5   H  HCR6  0   0.267  -27.2849  -3.2970  -21.7827
 V41  H6   H  HCH1  0   0.309  -29.4031   0.0283  -20.1422
 V41  H7   H  HNH2  0   0.408  -29.5547   1.7030  -16.8906
 V41  H8   H  HNH2  0   0.408  -30.3435   1.7999  -18.4167
 V41  H9   H  H     0   0.336  -30.6908   1.6004  -21.0205
 V41  H10  H  HNH2  0   0.398  -26.9157   2.5594  -20.5784
 V41  H11  H  HNH2  0   0.388  -27.9381   3.7432  -21.2494

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
 V41  C11  C10  aromatic  1.387  0.020  1.387
 V41  C11  C12  aromatic  1.388  0.020  1.388
 V41  C10  C9   aromatic  1.393  0.020  1.393
 V41  C12  C7   aromatic  1.390  0.020  1.390
 V41  N18  C15  double    1.274  0.020  1.274
 V41  C9   C8   aromatic  1.383  0.020  1.383
 V41  C7   C8   aromatic  1.395  0.020  1.395
 V41  C7   N6   single    1.413  0.020  1.413
 V41  N6   N13  double    1.229  0.020  1.229
 V41  C15  N19  single    1.355  0.020  1.355
 V41  C15  C14  single    1.523  0.020  1.523
 V41  N13  C14  single    1.449  0.020  1.449
 V41  C14  C16  single    1.538  0.020  1.538
 V41  C16  N17  single    1.337  0.020  1.337
 V41  C16  O20  double    1.216  0.020  1.216
 V41  C8   H1   single    0.930  0.020  1.080
 V41  C9   H2   single    0.930  0.020  1.080
 V41  C10  H3   single    0.930  0.020  1.080
 V41  C11  H4   single    0.930  0.020  1.080
 V41  C12  H5   single    0.930  0.020  1.080
 V41  C14  H6   single    0.970  0.020  1.090
 V41  N17  H7   single    0.860  0.020  1.020
 V41  N17  H8   single    0.860  0.020  1.020
 V41  N18  H9   single    0.890  0.020  1.040
 V41  N19  H10  single    0.890  0.020  1.040
 V41  N19  H11  single    0.890  0.020  1.040

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
 V41  N13  N6   C7   115.80  3.000
 V41  C12  C7   C8   120.06  3.000
 V41  C8   C7   N6   124.79  3.000
 V41  C12  C7   N6   115.15  3.000
 V41  H1   C8   C9   120.26  3.000
 V41  H1   C8   C7   120.21  3.000
 V41  C9   C8   C7   119.53  3.000
 V41  H2   C9   C10  119.94  3.000
 V41  H2   C9   C8   119.66  3.000
 V41  C10  C9   C8   120.40  3.000
 V41  H3   C10  C11  120.07  3.000
 V41  H3   C10  C9   119.90  3.000
 V41  C11  C10  C9   120.03  3.000
 V41  H4   C11  C12  119.95  3.000
 V41  H4   C11  C10  120.26  3.000
 V41  C12  C11  C10  119.79  3.000
 V41  H5   C12  C11  120.76  3.000
 V41  H5   C12  C7   119.05  3.000
 V41  C11  C12  C7   120.19  3.000
 V41  C14  N13  N6   112.96  3.000
 V41  H6   C14  C16  108.79  3.000
 V41  H6   C14  C15  109.45  3.000
 V41  C16  C14  C15  110.33  3.000
 V41  H6   C14  N13  111.16  3.000
 V41  C16  C14  N13  107.86  3.000
 V41  C15  C14  N13  109.25  3.000
 V41  N19  C15  N18  122.04  3.000
 V41  N19  C15  C14  113.84  3.000
 V41  N18  C15  C14  123.98  3.000
 V41  O20  C16  N17  124.48  3.000
 V41  O20  C16  C14  121.40  3.000
 V41  N17  C16  C14  114.11  3.000
 V41  H8   N17  H7   117.38  3.000
 V41  H8   N17  C16  122.50  3.000
 V41  H7   N17  C16  120.10  3.000
 V41  H9   N18  C15  111.01  3.000
 V41  H11  N19  H10  115.38  3.000
 V41  H11  N19  C15  117.31  3.000
 V41  H10  N19  C15  118.68  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
 V41  CONST_01  C10  C11  C12  C7     0.00  0.0  0
 V41  CONST_02  C10  C9   C8   C7     0.00  0.0  0
 V41  CONST_03  C11  C10  C9   C8     0.00  0.0  0
 V41  CONST_04  C11  C12  C7   C8     0.00  0.0  0
 V41  CONST_05  C12  C11  C10  C9     0.00  0.0  0
 V41  CONST_06  C12  C7   C8   C9     0.00  0.0  0
 V41  CONST_07  C11  C12  C7   N6   180.00  0.0  0
 V41  CONST_08  C9   C8   C7   N6   180.00  0.0  0
 V41  CONST_09  H4   C11  C12  C7   180.00  0.0  0
 V41  CONST_10  H2   C9   C8   C7   180.00  0.0  0
 V41  CONST_11  H3   C10  C9   C8   180.00  0.0  0
 V41  CONST_12  H5   C12  C7   C8   180.00  0.0  0
 V41  CONST_13  H1   C8   C9   C10  180.00  0.0  0
 V41  CONST_14  N13  N6   C7   C8     0.00  0.0  0
 V41  CONST_15  N13  N6   C7   C12  180.00  0.0  0
 V41  CONST_16  H7   N17  C16  C14  180.00  0.0  0
 V41  CONST_17  H8   N17  C16  C14    0.00  0.0  0
 V41  CONST_18  H9   N18  C15  C14    0.00  0.0  0
 V41  CONST_20  H11  N19  C15  C14  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 V41  chir_01  C14  C15  N13  C16  negativ

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
 V41  plan-1  N6   0.020
 V41  plan-1  C7   0.020
 V41  plan-1  C8   0.020
 V41  plan-1  C9   0.020
 V41  plan-1  C10  0.020
 V41  plan-1  C11  0.020
 V41  plan-1  C12  0.020
 V41  plan-1  N13  0.020
 V41  plan-1  C14  0.020
 V41  plan-1  H1   0.020
 V41  plan-1  H2   0.020
 V41  plan-1  H3   0.020
 V41  plan-1  H4   0.020
 V41  plan-1  H5   0.020
 V41  plan-2  C14  0.020
 V41  plan-2  C16  0.020
 V41  plan-2  N17  0.020
 V41  plan-2  O20  0.020
 V41  plan-2  H7   0.020
 V41  plan-2  H8   0.020
 V41  plan-3  C14  0.020
 V41  plan-3  C15  0.020
 V41  plan-3  N18  0.020
 V41  plan-3  N19  0.020
 V41  plan-3  H9   0.020
 V41  plan-3  H10  0.020
 V41  plan-3  H11  0.020

