# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:38:35 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 6-{[(4-hydroxy-3-iodo-5-nitrophenyl)acetyl]amino}hexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(I)cc(CC(=O)NCCCCCC([O-])=O)cc1[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
 NIP  NIP  6-{[(4-hydroxy-3-iodo-5-nitrophenyl)acetyl]amino}hexanoate  ligand  39  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NIP
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
 NIP  C1    C  CR6    0   0.118  6.0362   3.6743  5.9116
 NIP  C2    C  CR16   0  -0.321  7.3843   3.8116  6.1864
 NIP  C3    C  CR6    0   0.186  7.8495   4.9168  6.8811
 NIP  N3    N  N      1   0.342  9.2802   4.9988  7.1149
 NIP  O3A   O  O     -1  -0.378  9.8701   3.9612  7.3108
 NIP  O3B   O  O      0  -0.368  9.8074   6.0832  7.0774
 NIP  C4    C  CR6    0   0.415  6.9961   5.9271  7.3481
 NIP  O4    O  OH1    0  -0.578  7.5054   6.9342  8.0454
 NIP  C5    C  CR6    0  -0.348  5.6347   5.7624  7.0627
 NIP  I5    I  I      0   0.119  4.2485   7.2067  7.7012
 NIP  C6    C  CR16   0  -0.246  5.1691   4.6661  6.3585
 NIP  C7    C  CH2    0  -0.660  5.5198   2.5275  5.0884
 NIP  C8    C  C      0   0.543  5.5219   2.9464  3.6257
 NIP  O8    O  O      0  -0.490  6.5698   3.0965  3.0145
 NIP  N9    N  NH1    0  -0.613  4.3132   3.1723  3.0959
 NIP  C10   C  CH2    0  -0.307  4.1145   3.7400  1.7772
 NIP  C11   C  CH2    0  -0.428  4.3221   5.2507  1.7270
 NIP  C12   C  CH2    0  -0.416  3.4295   6.0247  2.6887
 NIP  C13   C  CH2    0  -0.400  3.5696   7.5361  2.5487
 NIP  C14   C  CH2    0  -0.582  2.7102   8.2971  3.5449
 NIP  C15   C  C      0   0.411  2.7686   9.8325  3.4619
 NIP  O15   O  O      0  -0.611  3.4338  10.3430  2.5387
 NIP  O16   O  OC    -1  -0.633  2.1265  10.4518  4.3367
 NIP  H2    H  HCR6   0   0.296  8.0826   3.0582  5.8487
 NIP  HO4   H  HOH1   0   0.482  6.8193   7.5055  8.4165
 NIP  H6    H  HCR6   0   0.291  4.1101   4.5715  6.1538
 NIP  H71   H  HCH2   0   0.297  6.1691   1.6581  5.1994
 NIP  H72   H  HCH2   0   0.287  4.5234   2.2396  5.4265
 NIP  HN9   H  HNH1   0   0.405  3.5026   3.0545  3.6807
 NIP  H101  H  HCH2   0   0.248  3.0952   3.4952  1.4761
 NIP  H102  H  HCH2   0   0.251  4.7816   3.2445  1.0708
 NIP  H111  H  HCH2   0   0.224  4.1252   5.5760  0.7006
 NIP  H112  H  HCH2   0   0.222  5.3715   5.4828  1.9280
 NIP  H121  H  HCH2   0   0.206  2.3837   5.7376  2.5271
 NIP  H122  H  HCH2   0   0.205  3.6656   5.7367  3.7188
 NIP  H131  H  HCH2   0   0.201  4.6204   7.8145  2.6785
 NIP  H132  H  HCH2   0   0.202  3.3056   7.8300  1.5290
 NIP  H141  H  HCH2   0   0.216  2.9795   7.9992  4.5650
 NIP  H142  H  HCH2   0   0.216  1.6620   7.9931  3.4310

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
 NIP  C1   C2    aromatic  1.383  0.020  1.383
 NIP  C1   C6    aromatic  1.391  0.020  1.391
 NIP  C1   C7    single    1.503  0.020  1.503
 NIP  C2   C3    aromatic  1.386  0.020  1.386
 NIP  C2   H2    single    0.930  0.020  1.080
 NIP  C3   N3    single    1.452  0.020  1.452
 NIP  C3   C4    aromatic  1.403  0.020  1.403
 NIP  N3   O3A   single    1.210  0.020  1.210
 NIP  N3   O3B   double    1.206  0.020  1.206
 NIP  C4   O4    single    1.327  0.020  1.327
 NIP  C4   C5    aromatic  1.401  0.020  1.401
 NIP  O4   HO4   single    0.850  0.020  0.980
 NIP  C5   I5    single    2.101  0.020  2.101
 NIP  C5   C6    aromatic  1.384  0.020  1.384
 NIP  C6   H6    single    0.930  0.020  1.080
 NIP  C7   C8    single    1.521  0.020  1.521
 NIP  C7   H71   single    0.970  0.020  1.090
 NIP  C7   H72   single    0.970  0.020  1.090
 NIP  C8   O8    double    1.222  0.020  1.222
 NIP  C8   N9    single    1.339  0.020  1.339
 NIP  N9   C10   single    1.449  0.020  1.449
 NIP  N9   HN9   single    0.860  0.020  1.020
 NIP  C10  C11   single    1.526  0.020  1.526
 NIP  C10  H101  single    0.970  0.020  1.090
 NIP  C10  H102  single    0.970  0.020  1.090
 NIP  C11  C12   single    1.523  0.020  1.523
 NIP  C11  H111  single    0.970  0.020  1.090
 NIP  C11  H112  single    0.970  0.020  1.090
 NIP  C12  C13   single    1.524  0.020  1.524
 NIP  C12  H121  single    0.970  0.020  1.090
 NIP  C12  H122  single    0.970  0.020  1.090
 NIP  C13  C14   single    1.520  0.020  1.520
 NIP  C13  H131  single    0.970  0.020  1.090
 NIP  C13  H132  single    0.970  0.020  1.090
 NIP  C14  C15   single    1.539  0.020  1.539
 NIP  C14  H141  single    0.970  0.020  1.090
 NIP  C14  H142  single    0.970  0.020  1.090
 NIP  C15  O15   deloc     1.247  0.020  1.247
 NIP  C15  O16   deloc     1.249  0.020  1.249

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
 NIP  C7    C1   C6    120.38  3.000
 NIP  C7    C1   C2    121.30  3.000
 NIP  C6    C1   C2    118.24  3.000
 NIP  H2    C2   C3    119.70  3.000
 NIP  H2    C2   C1    119.89  3.000
 NIP  C3    C2   C1    120.40  3.000
 NIP  C4    C3   N3    120.35  3.000
 NIP  C4    C3   C2    122.49  3.000
 NIP  N3    C3   C2    117.16  3.000
 NIP  O3B   N3   O3A   124.26  3.000
 NIP  O3B   N3   C3    118.45  3.000
 NIP  O3A   N3   C3    117.27  3.000
 NIP  C5    C4   O4    124.72  3.000
 NIP  C5    C4   C3    116.03  3.000
 NIP  O4    C4   C3    119.22  3.000
 NIP  HO4   O4   C4    112.20  3.000
 NIP  C6    C5   I5    118.50  3.000
 NIP  C6    C5   C4    121.60  3.000
 NIP  I5    C5   C4    119.90  3.000
 NIP  H6    C6   C5    119.64  3.000
 NIP  H6    C6   C1    119.12  3.000
 NIP  C5    C6   C1    121.24  3.000
 NIP  H72   C7   H71   107.57  3.000
 NIP  H72   C7   C8    111.83  3.000
 NIP  H71   C7   C8    108.45  3.000
 NIP  H72   C7   C1    110.20  3.000
 NIP  H71   C7   C1    110.36  3.000
 NIP  C8    C7   C1    108.42  3.000
 NIP  N9    C8   O8    123.73  3.000
 NIP  N9    C8   C7    115.19  3.000
 NIP  O8    C8   C7    121.04  3.000
 NIP  HN9   N9   C10   117.66  3.000
 NIP  HN9   N9   C8    118.51  3.000
 NIP  C10   N9   C8    123.36  3.000
 NIP  H102  C10  H101  106.91  3.000
 NIP  H102  C10  C11   110.20  3.000
 NIP  H101  C10  C11   109.90  3.000
 NIP  H102  C10  N9    109.12  3.000
 NIP  H101  C10  N9    106.94  3.000
 NIP  C11   C10  N9    113.52  3.000
 NIP  H112  C11  H111  106.38  3.000
 NIP  H112  C11  C12   109.78  3.000
 NIP  H111  C11  C12   109.61  3.000
 NIP  H112  C11  C10   109.55  3.000
 NIP  H111  C11  C10   107.50  3.000
 NIP  C12   C11  C10   113.74  3.000
 NIP  H122  C12  H121  105.98  3.000
 NIP  H122  C12  C13   109.11  3.000
 NIP  H121  C12  C13   109.50  3.000
 NIP  H122  C12  C11   109.50  3.000
 NIP  H121  C12  C11   109.44  3.000
 NIP  C13   C12  C11   113.07  3.000
 NIP  H132  C13  H131  105.90  3.000
 NIP  H132  C13  C14   109.88  3.000
 NIP  H131  C13  C14   109.73  3.000
 NIP  H132  C13  C12   109.27  3.000
 NIP  H131  C13  C12   109.24  3.000
 NIP  C14   C13  C12   112.60  3.000
 NIP  H142  C14  H141  104.83  3.000
 NIP  H142  C14  C15   107.89  3.000
 NIP  H141  C14  C15   108.18  3.000
 NIP  H142  C14  C13   109.48  3.000
 NIP  H141  C14  C13   109.56  3.000
 NIP  C15   C14  C13   116.28  3.000
 NIP  O16   C15  O15   126.12  3.000
 NIP  O16   C15  C14   115.93  3.000
 NIP  O15   C15  C14   117.94  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
 NIP  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 NIP  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 NIP  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 NIP  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 NIP  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 NIP  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 NIP  CONST_07  N3   C3   C2   C1    180.00   0.0  0
 NIP  CONST_08  I5   C5   C6   C1    180.00   0.0  0
 NIP  CONST_09  O4   C4   C3   C2    180.00   0.0  0
 NIP  CONST_10  C7   C1   C2   C3    180.00   0.0  0
 NIP  CONST_11  I5   C5   C4   C3    180.00   0.0  0
 NIP  CONST_12  C5   C4   C3   N3    180.00   0.0  0
 NIP  CONST_13  C6   C5   C4   O4    180.00   0.0  0
 NIP  CONST_14  C7   C1   C6   C5    180.00   0.0  0
 NIP  CONST_15  H6   C6   C1   C2    180.00   0.0  0
 NIP  CONST_16  H2   C2   C3   C4    180.00   0.0  0
 NIP  CONST_21  C10  N9   C8   C7    180.00   0.0  0
 NIP  CONST_22  C10  N9   C8   O8      0.00   0.0  0
 NIP  CONST_23  HN9  N9   C8   C7      0.00   0.0  0
 NIP  Var_01    C8   C7   C1   C2    -89.88  30.0  2
 NIP  Var_02    O8   C8   C7   C1     70.06  30.0  3
 NIP  Var_03    C11  C10  N9   C8    -77.77  30.0  3
 NIP  Var_04    C12  C11  C10  N9    -57.11  30.0  3
 NIP  Var_05    C13  C12  C11  C10  -175.46  30.0  3
 NIP  Var_06    C14  C13  C12  C11  -178.05  30.0  3
 NIP  Var_07    C15  C14  C13  C12  -178.99  30.0  3
 NIP  Var_08    O15  C15  C14  C13     4.80  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
 NIP  plan-1  C1   0.020
 NIP  plan-1  C2   0.020
 NIP  plan-1  C3   0.020
 NIP  plan-1  N3   0.020
 NIP  plan-1  C4   0.020
 NIP  plan-1  O4   0.020
 NIP  plan-1  C5   0.020
 NIP  plan-1  I5   0.020
 NIP  plan-1  C6   0.020
 NIP  plan-1  C7   0.020
 NIP  plan-1  H2   0.020
 NIP  plan-1  H6   0.020
 NIP  plan-2  C7   0.020
 NIP  plan-2  C8   0.020
 NIP  plan-2  O8   0.020
 NIP  plan-2  N9   0.020
 NIP  plan-2  C10  0.020
 NIP  plan-2  HN9  0.020
 NIP  plan-3  C3   0.020
 NIP  plan-3  N3   0.020
 NIP  plan-3  O3A  0.020
 NIP  plan-3  O3B  0.020
 NIP  plan-4  C14  0.020
 NIP  plan-4  C15  0.020
 NIP  plan-4  O15  0.020
 NIP  plan-4  O16  0.020

