# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:37:22 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-methoxy-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(NCc2cccnc2)c(cc1[N+]([O-])=O)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
 X69  X69  4-methoxy-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  36  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X69
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
 X69  N01   N  NH1    0  -0.691   1.1879  -0.0717   0.1744
 X69  N02   N  NH2    0  -0.808  -0.8681  -3.6633  -0.3797
 X69  N03   N  N      0  -0.400   5.6653   0.7101   0.9907
 X69  N04   N  N      1   0.330  -4.3874  -0.0868  -0.1078
 X69  C05   C  CR16   0  -0.341  -2.2616  -1.2212   0.0064
 X69  C06   C  CR6    0  -0.143  -0.8879  -1.2924   0.0592
 X69  C07   C  CR6    0   0.458  -0.1496  -0.0691   0.1009
 X69  C08   C  CR16   0  -0.565  -0.8568   1.1437   0.0391
 X69  C09   C  CR6    0   0.465  -2.2377   1.2005  -0.0428
 X69  C10   C  CR6    0   0.152  -2.9606  -0.0205  -0.0515
 X69  C12   C  CH2    0  -0.347   2.0098   1.1162   0.2078
 X69  C13   C  CR6    0  -0.015   3.4562   0.7440   0.0592
 X69  C14   C  CR16   0  -0.096   4.3730   1.0053   1.0691
 X69  C15   C  CR16   0  -0.064   6.1013   0.1257  -0.1174
 X69  C16   C  CR16   0  -0.318   5.2734  -0.1867  -1.1875
 X69  C17   C  CR16   0  -0.169   3.9291   0.1292  -1.0958
 X69  C18   C  CH3    0  -0.449  -2.1881   3.5710  -0.0096
 X69  O19   O  O      0  -0.502   0.9358  -2.7261   0.5712
 X69  O20   O  O     -1  -0.416  -4.9196  -1.1637   0.0931
 X69  O21   O  O      0  -0.399  -5.0208   0.9150  -0.3606
 X69  O22   O  O2     0  -0.433  -2.9020   2.3451  -0.0777
 X69  HN01  H  HNH1   0   0.414   1.6130  -0.9612   0.4034
 X69  H102  H  HNH2   0   0.416  -1.7047  -3.5747  -0.9286
 X69  H202  H  HNH2   0   0.409  -0.4292  -4.5697  -0.3660
 X69  H05   H  HCR6   0   0.293  -2.8426  -2.1322   0.0190
 X69  H08   H  HCR6   0   0.318  -0.2955   2.0644   0.0849
 X69  H112  H  HCH2   0   0.266   1.7286   1.7810  -0.6141
 X69  H212  H  HCH2   0   0.264   1.8613   1.6794   1.1357
 X69  H14   H  HCR6   0   0.264   4.0405   1.4816   1.9867
 X69  H15   H  HCR6   0   0.267   7.1596  -0.1061  -0.1608
 X69  H16   H  HCR6   0   0.275   5.6784  -0.6616  -2.0702
 X69  H17   H  HCR6   0   0.275   3.2551  -0.0935  -1.9143
 X69  H118  H  HCH3   0   0.273  -2.9379   4.3553  -0.0518
 X69  H218  H  HCH3   0   0.243  -1.6298   3.6589   0.9242
 X69  H318  H  HCH3   0   0.241  -1.5046   3.6856  -0.8529
 X69  C11   C  C      0   0.535  -0.1972  -2.6084   0.1036

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
 X69  N01  C07   single    1.340  0.020  1.340
 X69  N01  C12   single    1.445  0.020  1.445
 X69  N01  HN01  single    0.860  0.020  1.020
 X69  N02  C11   single    1.340  0.020  1.340
 X69  N02  H102  single    0.860  0.020  1.020
 X69  N02  H202  single    0.860  0.020  1.020
 X69  N03  C15   aromatic  1.326  0.020  1.326
 X69  N04  O20   single    1.218  0.020  1.218
 X69  C05  C10   aromatic  1.391  0.020  1.391
 X69  C05  H05   single    0.930  0.020  1.080
 X69  C06  C05   aromatic  1.377  0.020  1.377
 X69  C06  C07   aromatic  1.429  0.020  1.429
 X69  C07  C08   aromatic  1.405  0.020  1.405
 X69  C08  C09   aromatic  1.385  0.020  1.385
 X69  C08  H08   single    0.930  0.020  1.080
 X69  C09  O22   single    1.324  0.020  1.324
 X69  C10  N04   single    1.429  0.020  1.429
 X69  C10  C09   aromatic  1.419  0.020  1.419
 X69  C11  C06   single    1.487  0.020  1.487
 X69  C12  C13   single    1.501  0.020  1.501
 X69  C12  H112  single    0.970  0.020  1.090
 X69  C12  H212  single    0.970  0.020  1.090
 X69  C13  C17   aromatic  1.391  0.020  1.391
 X69  C14  C13   aromatic  1.389  0.020  1.389
 X69  C14  N03   aromatic  1.328  0.020  1.328
 X69  C14  H14   single    0.930  0.020  1.080
 X69  C15  C16   aromatic  1.389  0.020  1.389
 X69  C15  H15   single    0.930  0.020  1.080
 X69  C16  H16   single    0.930  0.020  1.080
 X69  C17  C16   aromatic  1.384  0.020  1.384
 X69  C17  H17   single    0.930  0.020  1.080
 X69  C18  H118  single    0.970  0.020  1.090
 X69  C18  H218  single    0.970  0.020  1.090
 X69  C18  H318  single    0.970  0.020  1.090
 X69  O19  C11   double    1.231  0.020  1.231
 X69  O21  N04   double    1.212  0.020  1.212
 X69  O22  C18   single    1.420  0.020  1.420

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
 X69  HN01  N01  C12   118.58  3.000
 X69  HN01  N01  C07   115.69  3.000
 X69  C12   N01  C07   124.59  3.000
 X69  H202  N02  H102  116.72  3.000
 X69  H202  N02  C11   119.03  3.000
 X69  H102  N02  C11   122.99  3.000
 X69  C15   N03  C14   117.85  3.000
 X69  O21   N04  O20   122.48  3.000
 X69  O21   N04  C10   119.44  3.000
 X69  O20   N04  C10   118.08  3.000
 X69  H05   C05  C10   117.26  3.000
 X69  H05   C05  C06   119.51  3.000
 X69  C10   C05  C06   123.23  3.000
 X69  C11   C06  C07   121.11  3.000
 X69  C11   C06  C05   120.70  3.000
 X69  C07   C06  C05   118.18  3.000
 X69  C08   C07  C06   118.52  3.000
 X69  C08   C07  N01   120.43  3.000
 X69  C06   C07  N01   121.04  3.000
 X69  H08   C08  C09   119.09  3.000
 X69  H08   C08  C07   118.21  3.000
 X69  C09   C08  C07   122.68  3.000
 X69  O22   C09  C10   119.22  3.000
 X69  C10   C09  C08   118.24  3.000
 X69  O22   C09  C08   122.52  3.000
 X69  C09   C10  C05   119.12  3.000
 X69  C09   C10  N04   123.27  3.000
 X69  C05   C10  N04   117.61  3.000
 X69  H212  C12  H112  106.81  3.000
 X69  H212  C12  C13   109.99  3.000
 X69  H112  C12  C13   108.91  3.000
 X69  H212  C12  N01   111.41  3.000
 X69  H112  C12  N01   109.64  3.000
 X69  C13   C12  N01   110.00  3.000
 X69  C17   C13  C14   117.54  3.000
 X69  C14   C13  C12   121.16  3.000
 X69  C17   C13  C12   121.29  3.000
 X69  H14   C14  C13   119.66  3.000
 X69  H14   C14  N03   116.45  3.000
 X69  C13   C14  N03   123.89  3.000
 X69  H15   C15  C16   120.20  3.000
 X69  H15   C15  N03   116.64  3.000
 X69  C16   C15  N03   123.16  3.000
 X69  H16   C16  C17   121.22  3.000
 X69  C17   C16  C15   118.47  3.000
 X69  H16   C16  C15   120.31  3.000
 X69  H17   C17  C16   120.48  3.000
 X69  H17   C17  C13   120.43  3.000
 X69  C16   C17  C13   119.08  3.000
 X69  H318  C18  H218  109.41  3.000
 X69  H318  C18  H118  109.06  3.000
 X69  H218  C18  H118  109.17  3.000
 X69  H318  C18  O22   111.61  3.000
 X69  H218  C18  O22   111.56  3.000
 X69  H118  C18  O22   105.93  3.000
 X69  C18   O22  C09   119.52  3.000
 X69  O19   C11  C06   121.56  3.000
 X69  O19   C11  N02   121.48  3.000
 X69  C06   C11  N02   116.95  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
 X69  CONST_01  C17   C16  C15  N03     0.00   0.0  0
 X69  CONST_02  C17   C13  C14  N03     0.00   0.0  0
 X69  CONST_03  C08   C09  C10  C05     0.00   0.0  0
 X69  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 X69  CONST_05  C09   C10  C05  C06     0.00   0.0  0
 X69  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X69  CONST_07  C10   C05  C06  C07     0.00   0.0  0
 X69  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X69  CONST_09  C15   C16  C17  C13     0.00   0.0  0
 X69  CONST_10  C15   N03  C14  C13     0.00   0.0  0
 X69  CONST_11  C16   C17  C13  C14     0.00   0.0  0
 X69  CONST_12  C16   C15  N03  C14     0.00   0.0  0
 X69  CONST_13  C05   C06  C07  N01   180.00   0.0  0
 X69  CONST_14  C09   C08  C07  N01   180.00   0.0  0
 X69  CONST_15  C12   C13  C14  N03   180.00   0.0  0
 X69  CONST_16  C06   C05  C10  N04   180.00   0.0  0
 X69  CONST_17  C08   C09  C10  N04   180.00   0.0  0
 X69  CONST_18  O22   C09  C10  C05   180.00   0.0  0
 X69  CONST_19  O22   C09  C08  C07   180.00   0.0  0
 X69  CONST_20  C11   C06  C07  C08   180.00   0.0  0
 X69  CONST_21  C11   C06  C05  C10   180.00   0.0  0
 X69  CONST_22  C16   C17  C13  C12   180.00   0.0  0
 X69  CONST_23  H16   C16  C15  N03   180.00   0.0  0
 X69  CONST_24  H08   C08  C07  C06   180.00   0.0  0
 X69  CONST_25  H05   C05  C06  C07   180.00   0.0  0
 X69  CONST_26  H17   C17  C13  C14   180.00   0.0  0
 X69  CONST_27  H15   C15  N03  C14   180.00   0.0  0
 X69  CONST_28  H14   C14  N03  C15   180.00   0.0  0
 X69  CONST_29  O20   N04  C10  C05     0.00   0.0  0
 X69  CONST_30  O21   N04  C10  C05   180.00   0.0  0
 X69  CONST_31  C12   N01  C07  C06   180.00   0.0  0
 X69  CONST_32  C12   N01  C07  C08     0.00   0.0  0
 X69  CONST_33  O20   N04  C10  C09   180.00   0.0  0
 X69  CONST_34  O21   N04  C10  C09     0.00   0.0  0
 X69  CONST_35  HN01  N01  C07  C06     0.00   0.0  0
 X69  CONST_36  H102  N02  C11  C06     0.00   0.0  0
 X69  CONST_37  H202  N02  C11  C06   180.00   0.0  0
 X69  Var_01    C17   C13  C12  N01    62.83  30.0  2
 X69  Var_02    C05   C06  C11  N02    23.29  30.0  2
 X69  Var_03    C13   C12  N01  C07  -170.56  30.0  3
 X69  Var_04    H118  C18  O22  C09  -179.81  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
 X69  plan-1  N03   0.020
 X69  plan-1  C12   0.020
 X69  plan-1  C13   0.020
 X69  plan-1  C14   0.020
 X69  plan-1  C15   0.020
 X69  plan-1  C16   0.020
 X69  plan-1  C17   0.020
 X69  plan-1  H14   0.020
 X69  plan-1  H15   0.020
 X69  plan-1  H16   0.020
 X69  plan-1  H17   0.020
 X69  plan-2  N01   0.020
 X69  plan-2  N04   0.020
 X69  plan-2  C05   0.020
 X69  plan-2  C06   0.020
 X69  plan-2  C07   0.020
 X69  plan-2  C08   0.020
 X69  plan-2  C09   0.020
 X69  plan-2  C10   0.020
 X69  plan-2  O22   0.020
 X69  plan-2  H05   0.020
 X69  plan-2  H08   0.020
 X69  plan-2  C11   0.020
 X69  plan-3  N02   0.020
 X69  plan-3  C06   0.020
 X69  plan-3  O19   0.020
 X69  plan-3  H102  0.020
 X69  plan-3  H202  0.020
 X69  plan-3  C11   0.020
 X69  plan-4  N01   0.020
 X69  plan-4  C07   0.020
 X69  plan-4  C12   0.020
 X69  plan-4  HN01  0.020
 X69  plan-5  N04   0.020
 X69  plan-5  C10   0.020
 X69  plan-5  O20   0.020
 X69  plan-5  O21   0.020

