# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 17:20:44 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-{[(4-hydroxy-3-nitrophenyl)acetyl]amino}hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNC(=O)Cc1ccc(O)c(c1)[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
 NP  NP  '6-{[(4-hydroxy-3-nitrophenyl)acetyl]amino}hexanoic acid'  ligand  39  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NP
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
 NP  C1'   C  CR6    0   0.091  50.7090  27.0673   -7.1723
 NP  C2'   C  CR16   0  -0.240  50.6318  28.4520   -6.9724
 NP  C3'   C  CR16   0  -0.340  49.5055  29.0430   -6.4492
 NP  C4'   C  CR6    0   0.362  48.3905  28.2805   -6.0855
 NP  O4'   O  OH1    0  -0.602  47.3455  28.9247   -5.5868
 NP  C5'   C  CR6    0   0.191  48.4717  26.8928   -6.2827
 NP  N5'   N  N      1   0.367  47.3691  26.0390   -5.9468
 NP  ON1   O  O     -1  -0.371  47.3942  24.8838   -6.2897
 NP  ON2   O  O      0  -0.425  46.4435  26.5134   -5.3046
 NP  C6'   C  CR16   0  -0.364  49.6169  26.3044   -6.8224
 NP  C1    C  CH2    0  -0.635  51.9554  26.4373   -7.7412
 NP  C2    C  C      0   0.514  52.3583  27.0850   -9.0564
 NP  O2    O  O      0  -0.493  53.2275  27.9472   -9.0889
 NP  N3    N  NH1    0  -0.605  51.6956  26.7019  -10.1601
 NP  C4    C  CH2    0  -0.281  50.7042  25.6511  -10.2909
 NP  C5    C  CH2    0  -0.481  49.8219  25.8934  -11.5062
 NP  C6    C  CH2    0  -0.425  49.0363  27.2037  -11.4723
 NP  C7    C  CH2    0  -0.424  48.1359  27.3948  -10.2531
 NP  C8    C  CH2    0  -0.580  47.1071  26.2871  -10.0841
 NP  C9    C  C      0   0.420  46.0329  26.4997   -8.9985
 NP  O3    O  O      0  -0.621  45.1360  25.6329   -8.9515
 NP  O4    O  OC    -1  -0.601  46.1398  27.4972   -8.2553
 NP  H2'   H  HCR6   0   0.268  51.4752  29.0801   -7.2312
 NP  H3'   H  HCR6   0   0.281  49.4657  30.1151   -6.3066
 NP  HO4'  H  HOH1   0   0.478  46.6556  28.2735   -5.3638
 NP  H6'   H  HCR6   0   0.296  49.6474  25.2320   -6.9602
 NP  H11   H  HCH2   0   0.289  52.7881  26.5773   -7.0502
 NP  H12   H  HCH2   0   0.283  51.8109  25.3616   -7.8528
 NP  HN3   H  HNH1   0   0.388  52.0081  27.1348  -11.0185
 NP  H41   H  HCH2   0   0.246  51.1878  24.6734  -10.3801
 NP  H42   H  HCH2   0   0.248  50.0855  25.6180   -9.3948
 NP  H51   H  HCH2   0   0.237  50.4394  25.8664  -12.4097
 NP  H52   H  HCH2   0   0.241  49.1393  25.0446  -11.5897
 NP  H61   H  HCH2   0   0.218  49.7299  28.0470  -11.5416
 NP  H62   H  HCH2   0   0.218  48.4242  27.2504  -12.3785
 NP  H71   H  HCH2   0   0.212  48.7438  27.4796   -9.3479
 NP  H72   H  HCH2   0   0.212  47.6257  28.3558  -10.3528
 NP  H81   H  HCH2   0   0.210  46.5982  26.1118  -11.0394
 NP  H82   H  HCH2   0   0.218  47.6085  25.3388   -9.8577

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
 NP  C1'  C2'   aromatic  1.401  0.020  1.401
 NP  C1'  C6'   aromatic  1.377  0.020  1.377
 NP  C1'  C1    single    1.508  0.020  1.508
 NP  C2'  C3'   aromatic  1.375  0.020  1.375
 NP  C2'  H2'   single    0.930  0.020  1.080
 NP  C3'  C4'   aromatic  1.399  0.020  1.399
 NP  C3'  H3'   single    0.930  0.020  1.080
 NP  C4'  O4'   single    1.325  0.020  1.325
 NP  C4'  C5'   aromatic  1.404  0.020  1.404
 NP  O4'  HO4'  single    0.850  0.020  0.980
 NP  C5'  N5'   single    1.434  0.020  1.434
 NP  C5'  C6'   aromatic  1.396  0.020  1.396
 NP  N5'  ON1   single    1.205  0.020  1.205
 NP  N5'  ON2   double    1.222  0.020  1.222
 NP  C6'  H6'   single    0.930  0.020  1.080
 NP  C1   C2    single    1.520  0.020  1.520
 NP  C1   H11   single    0.970  0.020  1.090
 NP  C1   H12   single    0.970  0.020  1.090
 NP  C2   O2    double    1.225  0.020  1.225
 NP  C2   N3    single    1.343  0.020  1.343
 NP  N3   C4    single    1.451  0.020  1.451
 NP  N3   HN3   single    0.860  0.020  1.020
 NP  C4   C5    single    1.521  0.020  1.521
 NP  C4   H41   single    0.970  0.020  1.090
 NP  C4   H42   single    0.970  0.020  1.090
 NP  C5   C6    single    1.528  0.020  1.528
 NP  C5   H51   single    0.970  0.020  1.090
 NP  C5   H52   single    0.970  0.020  1.090
 NP  C6   C7    single    1.528  0.020  1.528
 NP  C6   H61   single    0.970  0.020  1.090
 NP  C6   H62   single    0.970  0.020  1.090
 NP  C7   C8    single    1.521  0.020  1.521
 NP  C7   H71   single    0.970  0.020  1.090
 NP  C7   H72   single    0.970  0.020  1.090
 NP  C8   C9    single    1.542  0.020  1.542
 NP  C8   H81   single    0.970  0.020  1.090
 NP  C8   H82   single    0.970  0.020  1.090
 NP  C9   O3    deloc     1.248  0.020  1.248
 NP  C9   O4    deloc     1.248  0.020  1.248

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
 NP  C1    C1'  C6'  121.32  3.000
 NP  C1    C1'  C2'  120.81  3.000
 NP  C6'   C1'  C2'  117.87  3.000
 NP  H2'   C2'  C3'  118.65  3.000
 NP  H2'   C2'  C1'  119.75  3.000
 NP  C3'   C2'  C1'  121.60  3.000
 NP  H3'   C3'  C4'  118.45  3.000
 NP  H3'   C3'  C2'  120.39  3.000
 NP  C4'   C3'  C2'  121.16  3.000
 NP  C5'   C4'  O4'  125.38  3.000
 NP  C5'   C4'  C3'  117.14  3.000
 NP  O4'   C4'  C3'  117.48  3.000
 NP  HO4'  O4'  C4'  108.64  3.000
 NP  C6'   C5'  N5'  118.05  3.000
 NP  C6'   C5'  C4'  121.22  3.000
 NP  N5'   C5'  C4'  120.73  3.000
 NP  ON2   N5'  ON1  122.49  3.000
 NP  ON2   N5'  C5'  118.30  3.000
 NP  ON1   N5'  C5'  119.20  3.000
 NP  H6'   C6'  C5'  119.36  3.000
 NP  H6'   C6'  C1'  119.63  3.000
 NP  C5'   C6'  C1'  121.01  3.000
 NP  H12   C1   H11  107.00  3.000
 NP  H12   C1   C2   111.50  3.000
 NP  H11   C1   C2   106.91  3.000
 NP  H12   C1   C1'  109.94  3.000
 NP  H11   C1   C1'  109.77  3.000
 NP  C2    C1   C1'  111.56  3.000
 NP  N3    C2   O2   121.95  3.000
 NP  N3    C2   C1   117.30  3.000
 NP  O2    C2   C1   120.72  3.000
 NP  HN3   N3   C4   116.42  3.000
 NP  HN3   N3   C2   115.03  3.000
 NP  C4    N3   C2   128.16  3.000
 NP  H42   C4   H41  106.91  3.000
 NP  H42   C4   C5   109.42  3.000
 NP  H41   C4   C5   109.48  3.000
 NP  H42   C4   N3   109.63  3.000
 NP  H41   C4   N3   110.64  3.000
 NP  C5    C4   N3   110.67  3.000
 NP  H52   C5   H51  105.68  3.000
 NP  H52   C5   C6   110.29  3.000
 NP  H51   C5   C6   109.24  3.000
 NP  H52   C5   C4   107.44  3.000
 NP  H51   C5   C4   109.16  3.000
 NP  C6    C5   C4   114.64  3.000
 NP  H62   C6   H61  105.62  3.000
 NP  H62   C6   C7   109.01  3.000
 NP  H61   C6   C7   109.14  3.000
 NP  H62   C6   C5   107.80  3.000
 NP  H61   C6   C5   109.49  3.000
 NP  C7    C6   C5   115.34  3.000
 NP  H72   C7   H71  105.48  3.000
 NP  H72   C7   C8   109.56  3.000
 NP  H71   C7   C8   109.90  3.000
 NP  H72   C7   C6   108.21  3.000
 NP  H71   C7   C6   110.04  3.000
 NP  C8    C7   C6   113.34  3.000
 NP  H82   C8   H81  104.70  3.000
 NP  H82   C8   C9   107.00  3.000
 NP  H81   C8   C9   108.18  3.000
 NP  H82   C8   C7   110.09  3.000
 NP  H81   C8   C7   109.49  3.000
 NP  C9    C8   C7   116.68  3.000
 NP  O4    C9   O3   126.44  3.000
 NP  O4    C9   C8   118.01  3.000
 NP  O3    C9   C8   115.55  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
 NP  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 NP  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 NP  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 NP  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 NP  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 NP  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 NP  CONST_07  N5'  C5'  C6'  C1'   180.00   0.0  0
 NP  CONST_08  O4'  C4'  C3'  C2'   180.00   0.0  0
 NP  CONST_09  C1   C1'  C2'  C3'   180.00   0.0  0
 NP  CONST_10  N5'  C5'  C4'  C3'   180.00   0.0  0
 NP  CONST_11  C6'  C5'  C4'  O4'   180.00   0.0  0
 NP  CONST_12  C1   C1'  C6'  C5'   180.00   0.0  0
 NP  CONST_13  H3'  C3'  C2'  C1'   180.00   0.0  0
 NP  CONST_14  H6'  C6'  C1'  C2'   180.00   0.0  0
 NP  CONST_15  H2'  C2'  C3'  C4'   180.00   0.0  0
 NP  CONST_16  ON1  N5'  C5'  C4'   180.00   0.0  0
 NP  CONST_17  ON2  N5'  C5'  C4'     0.00   0.0  0
 NP  CONST_18  C6'  C5'  N5'  ON1     0.00   0.0  0
 NP  CONST_19  C6'  C5'  N5'  ON2   180.00   0.0  0
 NP  CONST_20  C4   N3   C2   C1      0.00   0.0  0
 NP  CONST_21  C4   N3   C2   O2    180.00   0.0  0
 NP  CONST_22  HN3  N3   C2   C1    180.00   0.0  0
 NP  Var_01    C2   C1   C1'  C2'   -53.85  30.0  2
 NP  Var_02    O2   C2   C1   C1'    98.25  30.0  3
 NP  Var_03    C5   C4   N3   C2    157.39  30.0  3
 NP  Var_04    C6   C5   C4   N3    -60.48  30.0  3
 NP  Var_05    C7   C6   C5   C4    -56.43  30.0  3
 NP  Var_06    C8   C7   C6   C5    -57.67  30.0  3
 NP  Var_07    C9   C8   C7   C6   -171.72  30.0  3
 NP  Var_08    O3   C9   C8   C7    174.31  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
 NP  plan-1  C1'  0.020
 NP  plan-1  C2'  0.020
 NP  plan-1  C3'  0.020
 NP  plan-1  C4'  0.020
 NP  plan-1  O4'  0.020
 NP  plan-1  C5'  0.020
 NP  plan-1  N5'  0.020
 NP  plan-1  C6'  0.020
 NP  plan-1  C1   0.020
 NP  plan-1  H2'  0.020
 NP  plan-1  H3'  0.020
 NP  plan-1  H6'  0.020
 NP  plan-2  C1   0.020
 NP  plan-2  C2   0.020
 NP  plan-2  O2   0.020
 NP  plan-2  N3   0.020
 NP  plan-2  C4   0.020
 NP  plan-2  HN3  0.020
 NP  plan-3  C5'  0.020
 NP  plan-3  N5'  0.020
 NP  plan-3  ON1  0.020
 NP  plan-3  ON2  0.020
 NP  plan-4  C8   0.020
 NP  plan-4  C9   0.020
 NP  plan-4  O3   0.020
 NP  plan-4  O4   0.020

