FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: RY148

Calculation Name: 1NFI-E-Xray372

Preferred Name: NF-kappaB inhibitor alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NFI

Chain ID: E

ChEMBL ID: CHEMBL2898

UniProt ID: P25963

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299448.243665
FMO2-HF: Nuclear repulsion 2217477.504847
FMO2-HF: Total energy -81970.738819
FMO2-MP2: Total energy -82207.71324


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(E:70:LEU)


Summations of interaction energy for fragment #1(E:70:LEU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-17.332-12.77616.402-7.613-13.344-0.069
Interaction energy analysis for fragmet #1(E:70:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.029
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3E72GLU-1-0.956-0.9693.8870.2541.743-0.014-0.709-0.7660.000
4E73ASP-1-0.878-0.9256.3421.4411.4410.0000.0000.0000.000
5E74GLY00.004-0.0032.837-1.051-0.8871.309-0.608-0.8660.006
6E75ASP-1-0.813-0.9172.712-6.583-5.6432.280-0.974-2.246-0.014
7E76SER0-0.039-0.0391.987-8.425-8.75410.014-5.077-4.607-0.044
8E77PHE00.037-0.0043.0231.2440.5910.0211.223-0.590-0.001
9E78LEU00.0250.0175.1310.1440.1440.0000.0000.0000.000
10E79HIS00.0040.0345.829-0.188-0.1880.0000.0000.0000.000
11E80LEU00.0460.0165.4600.2920.2920.0000.0000.0000.000
12E81ALA0-0.0070.0118.3980.1830.1830.0000.0000.0000.000
13E82ILE0-0.012-0.00510.7490.0930.0930.0000.0000.0000.000
14E83ILE0-0.006-0.0088.4380.0800.0800.0000.0000.0000.000
15E84HIS0-0.091-0.04910.8350.1210.1210.0000.0000.0000.000
16E85GLU-1-0.882-0.93314.781-0.140-0.1400.0000.0000.0000.000
17E86GLU-1-0.888-0.93014.014-0.211-0.2110.0000.0000.0000.000
18E87LYS10.8210.91814.9070.1600.1600.0000.0000.0000.000
19E88ALA0-0.020-0.00916.703-0.002-0.0020.0000.0000.0000.000
20E89LEU00.0230.01311.6570.0070.0070.0000.0000.0000.000
21E90THR00.012-0.01211.928-0.028-0.0280.0000.0000.0000.000
22E91MET0-0.014-0.00812.983-0.007-0.0070.0000.0000.0000.000
23E92GLU-1-0.811-0.87014.658-0.157-0.1570.0000.0000.0000.000
24E93VAL0-0.001-0.0098.1940.0110.0110.0000.0000.0000.000
25E94ILE00.001-0.00411.2280.0060.0060.0000.0000.0000.000
26E95ARG10.8080.89712.8070.1650.1650.0000.0000.0000.000
27E96GLN0-0.115-0.07211.9060.0090.0090.0000.0000.0000.000
28E97VAL0-0.0260.0058.3330.0210.0210.0000.0000.0000.000
29E98LYS10.9460.95311.2700.1070.1070.0000.0000.0000.000
30E99GLY00.0140.01814.3550.0170.0170.0000.0000.0000.000
31E100ASP-1-0.866-0.9288.605-0.316-0.3160.0000.0000.0000.000
32E101LEU00.021-0.00110.383-0.051-0.0510.0000.0000.0000.000
33E102ALA0-0.059-0.0188.138-0.050-0.0500.0000.0000.0000.000
34E103PHE0-0.016-0.0202.520-0.989-0.4830.883-0.291-1.098-0.001
35E104LEU0-0.013-0.0096.330-0.135-0.1350.0000.0000.0000.000
36E105ASN00.002-0.0019.4540.0060.0060.0000.0000.0000.000
37E106PHE0-0.0110.0082.736-3.128-0.6891.909-1.177-3.171-0.015
38E107GLN0-0.034-0.0456.6950.0400.0400.0000.0000.0000.000
39E108ASN0-0.013-0.0055.1500.0550.0550.0000.0000.0000.000
40E109ASN00.012-0.0026.1910.2680.2680.0000.0000.0000.000
41E110LEU0-0.053-0.0118.367-0.117-0.1170.0000.0000.0000.000
42E111GLN0-0.032-0.0309.814-0.124-0.1240.0000.0000.0000.000
43E112GLN00.0190.0279.794-0.082-0.0820.0000.0000.0000.000
44E113THR00.0620.0028.941-0.173-0.1730.0000.0000.0000.000
45E114PRO00.006-0.0028.3110.0500.0500.0000.0000.0000.000
46E115LEU00.0480.01810.9200.0670.0670.0000.0000.0000.000
47E116HIS0-0.0080.01612.993-0.006-0.0060.0000.0000.0000.000
48E117LEU00.0240.0248.7240.0340.0340.0000.0000.0000.000
49E118ALA0-0.0010.02513.2760.0340.0340.0000.0000.0000.000
50E119VAL0-0.023-0.00216.0400.0290.0290.0000.0000.0000.000
51E120ILE0-0.057-0.02314.1880.0200.0200.0000.0000.0000.000
52E121THR0-0.031-0.02614.9910.0170.0170.0000.0000.0000.000
53E122ASN0-0.031-0.04317.9170.0080.0080.0000.0000.0000.000
54E123GLN00.006-0.01415.9050.0130.0130.0000.0000.0000.000
55E124PRO00.015-0.00319.353-0.016-0.0160.0000.0000.0000.000
56E125GLU-1-0.790-0.91020.140-0.174-0.1740.0000.0000.0000.000
57E126ILE00.0110.00214.534-0.007-0.0070.0000.0000.0000.000
58E127ALA00.0020.00016.664-0.019-0.0190.0000.0000.0000.000
59E128GLU-1-0.962-0.98318.222-0.125-0.1250.0000.0000.0000.000
60E129ALA0-0.011-0.00217.1360.0030.0030.0000.0000.0000.000
61E130LEU0-0.029-0.01711.906-0.005-0.0050.0000.0000.0000.000
62E131LEU00.009-0.00815.7510.0040.0040.0000.0000.0000.000
63E132GLY0-0.047-0.01518.7120.0120.0120.0000.0000.0000.000
64E133ALA0-0.061-0.03414.8490.0110.0110.0000.0000.0000.000
65E134GLY0-0.012-0.00515.929-0.003-0.0030.0000.0000.0000.000
66E135CYS0-0.058-0.01713.5910.0050.0050.0000.0000.0000.000
67E136ASP-1-0.894-0.95414.741-0.115-0.1150.0000.0000.0000.000
68E137PRO0-0.016-0.01816.479-0.011-0.0110.0000.0000.0000.000
69E138GLU-1-0.850-0.92819.130-0.061-0.0610.0000.0000.0000.000
70E139LEU0-0.0180.01312.7660.0210.0210.0000.0000.0000.000
71E140ARG10.7760.85415.7180.0320.0320.0000.0000.0000.000
72E141ASP-1-0.691-0.84514.143-0.026-0.0260.0000.0000.0000.000
73E142PHE00.000-0.01514.0260.0220.0220.0000.0000.0000.000
74E143ARG10.7260.84915.7060.0330.0330.0000.0000.0000.000
75E144GLY00.009-0.00418.340-0.002-0.0020.0000.0000.0000.000
76E145ASN00.0060.00619.096-0.005-0.0050.0000.0000.0000.000
77E146THR00.0650.01818.198-0.015-0.0150.0000.0000.0000.000
78E147PRO00.0380.00616.4030.0120.0120.0000.0000.0000.000
79E148LEU00.0540.03419.0580.0070.0070.0000.0000.0000.000
80E149HIS00.0030.01921.860-0.001-0.0010.0000.0000.0000.000
81E150LEU00.0040.00516.6980.0080.0080.0000.0000.0000.000
82E151ALA00.0150.01421.2460.0050.0050.0000.0000.0000.000
83E152CYS0-0.102-0.05223.4970.0080.0080.0000.0000.0000.000
84E153GLU-1-0.852-0.89421.804-0.026-0.0260.0000.0000.0000.000
85E154GLN0-0.017-0.02219.8130.0040.0040.0000.0000.0000.000
86E155GLY00.0050.01424.6090.0010.0010.0000.0000.0000.000
87E156CYM-1-0.815-0.76624.159-0.109-0.1090.0000.0000.0000.000
88E157LEU00.012-0.01326.127-0.003-0.0030.0000.0000.0000.000
89E158ALA0-0.0080.00126.4790.0000.0000.0000.0000.0000.000
90E159SER00.026-0.09522.426-0.010-0.0100.0000.0000.0000.000
91E160VAL0-0.036-0.02124.266-0.003-0.0030.0000.0000.0000.000
92E161GLY00.0170.03426.6790.0020.0020.0000.0000.0000.000
93E162VAL00.0300.02721.9560.0020.0020.0000.0000.0000.000
94E163LEU0-0.035-0.01719.830-0.004-0.0040.0000.0000.0000.000
95E164THR0-0.069-0.05723.9320.0080.0080.0000.0000.0000.000
96E165GLN0-0.019-0.01227.3560.0030.0030.0000.0000.0000.000
97E166SER00.0070.00323.8070.0050.0050.0000.0000.0000.000
98E167CYS0-0.020-0.00222.8210.0000.0000.0000.0000.0000.000
99E168THR00.024-0.00324.9260.0050.0050.0000.0000.0000.000
100E169THR0-0.087-0.03225.5370.0050.0050.0000.0000.0000.000
101E170PRO00.038-0.00228.171-0.001-0.0010.0000.0000.0000.000
102E171HIS10.8690.91222.6050.0920.0920.0000.0000.0000.000
103E172LEU00.0590.04726.1340.0010.0010.0000.0000.0000.000
104E173HIS00.013-0.00627.8930.0070.0070.0000.0000.0000.000
105E174SER0-0.023-0.00825.9790.0070.0070.0000.0000.0000.000
106E175ILE00.0310.01523.0980.0060.0060.0000.0000.0000.000
107E176LEU0-0.021-0.01125.8840.0040.0040.0000.0000.0000.000
108E177LYS10.8860.95129.2370.0300.0300.0000.0000.0000.000
109E178ALA0-0.0180.00725.0440.0060.0060.0000.0000.0000.000
110E179THR00.0010.01026.904-0.004-0.0040.0000.0000.0000.000
111E180ASN00.0190.01122.5940.0070.0070.0000.0000.0000.000
112E181TYR00.003-0.00917.612-0.003-0.0030.0000.0000.0000.000
113E182ASN0-0.040-0.00423.2440.0130.0130.0000.0000.0000.000
114E183GLY0-0.023-0.00326.590-0.001-0.0010.0000.0000.0000.000
115E184HIS0-0.037-0.03927.199-0.001-0.0010.0000.0000.0000.000
116E185THR00.0460.01326.931-0.004-0.0040.0000.0000.0000.000
117E186CYS00.0130.01226.298-0.001-0.0010.0000.0000.0000.000
118E187LEU00.0470.02727.9950.0000.0000.0000.0000.0000.000
119E188HIS0-0.0030.01330.4880.0010.0010.0000.0000.0000.000
120E189LEU00.0130.00624.6850.0030.0030.0000.0000.0000.000
121E190ALA00.0200.01728.8580.0000.0000.0000.0000.0000.000
122E191SER0-0.063-0.04830.8290.0010.0010.0000.0000.0000.000
123E192ILE0-0.047-0.02430.0250.0030.0030.0000.0000.0000.000
124E193HIS0-0.0310.00227.4670.0040.0040.0000.0000.0000.000
125E194GLY00.008-0.00532.4780.0010.0010.0000.0000.0000.000
126E195TYR0-0.0220.00627.6370.0000.0000.0000.0000.0000.000
127E196LEU00.013-0.00733.571-0.002-0.0020.0000.0000.0000.000
128E197GLY00.0140.00635.9730.0000.0000.0000.0000.0000.000
129E198ILE00.0190.01228.874-0.001-0.0010.0000.0000.0000.000
130E199VAL0-0.017-0.00732.8320.0000.0000.0000.0000.0000.000
131E200GLU-1-0.785-0.88334.834-0.030-0.0300.0000.0000.0000.000
132E201LEU0-0.0090.01231.5830.0000.0000.0000.0000.0000.000
133E202LEU00.0460.01229.088-0.001-0.0010.0000.0000.0000.000
134E203VAL0-0.0060.00233.0670.0010.0010.0000.0000.0000.000
135E204SER0-0.106-0.05636.1230.0000.0000.0000.0000.0000.000
136E205LEU0-0.002-0.00530.823-0.001-0.0010.0000.0000.0000.000
137E206GLY0-0.032-0.00533.683-0.002-0.0020.0000.0000.0000.000
138E207ALA0-0.050-0.02132.7200.0020.0020.0000.0000.0000.000
139E208ASP-1-0.830-0.91434.397-0.017-0.0170.0000.0000.0000.000
140E209VAL00.0430.01436.7290.0010.0010.0000.0000.0000.000
141E210ASN0-0.102-0.06238.8000.0030.0030.0000.0000.0000.000
142E211ALA00.0120.01034.5980.0020.0020.0000.0000.0000.000
143E212GLN0-0.083-0.04836.5890.0000.0000.0000.0000.0000.000
144E213GLU-1-0.753-0.88332.9240.0060.0060.0000.0000.0000.000
145E214PRO00.0040.00130.3430.0020.0020.0000.0000.0000.000
146E215CYS0-0.0260.00832.1880.0030.0030.0000.0000.0000.000
147E216ASN0-0.064-0.04334.8000.0000.0000.0000.0000.0000.000
148E217GLY00.0950.05537.111-0.001-0.0010.0000.0000.0000.000
149E218ARG10.7560.86537.011-0.006-0.0060.0000.0000.0000.000
150E219THR00.0380.00437.099-0.002-0.0020.0000.0000.0000.000
151E220ALA00.0640.02136.6210.0010.0010.0000.0000.0000.000
152E221LEU00.0440.01937.7660.0000.0000.0000.0000.0000.000
153E222HIS0-0.0190.00840.0380.0000.0000.0000.0000.0000.000
154E223LEU00.0150.00834.0400.0020.0020.0000.0000.0000.000
155E224ALA00.0220.01738.1320.0010.0010.0000.0000.0000.000
156E225VAL0-0.0050.00439.9370.0000.0000.0000.0000.0000.000
157E226ASP-1-0.832-0.86338.9240.0040.0040.0000.0000.0000.000
158E227LEU0-0.0090.00134.9500.0010.0010.0000.0000.0000.000
159E228GLN0-0.063-0.04539.076-0.001-0.0010.0000.0000.0000.000
160E229ASN00.0500.02937.754-0.001-0.0010.0000.0000.0000.000
161E230PRO00.0190.00741.658-0.001-0.0010.0000.0000.0000.000
162E231ASP-1-0.860-0.92342.223-0.018-0.0180.0000.0000.0000.000
163E232LEU00.0250.01737.074-0.001-0.0010.0000.0000.0000.000
164E233VAL0-0.001-0.00540.8450.0000.0000.0000.0000.0000.000
165E234SER0-0.045-0.03643.7060.0000.0000.0000.0000.0000.000
166E235LEU0-0.0240.00038.6350.0000.0000.0000.0000.0000.000
167E236LEU00.0310.00538.320-0.001-0.0010.0000.0000.0000.000
168E237LEU0-0.013-0.00342.3800.0000.0000.0000.0000.0000.000
169E238LYS10.7650.87143.0080.0270.0270.0000.0000.0000.000
170E239CYS0-0.075-0.03841.418-0.002-0.0020.0000.0000.0000.000
171E240GLY0-0.0090.00343.6400.0000.0000.0000.0000.0000.000
172E241ALA0-0.044-0.02442.4780.0010.0010.0000.0000.0000.000
173E242ASP-1-0.799-0.89744.202-0.007-0.0070.0000.0000.0000.000
174E243VAL0-0.009-0.01245.7830.0010.0010.0000.0000.0000.000
175E244ASN0-0.016-0.00447.7620.0020.0020.0000.0000.0000.000
176E245ARG10.8690.94641.9310.0100.0100.0000.0000.0000.000
177E246VAL0-0.022-0.01945.2660.0000.0000.0000.0000.0000.000
178E247THR00.0170.00841.4830.0000.0000.0000.0000.0000.000
179E248TYR0-0.055-0.05236.205-0.001-0.0010.0000.0000.0000.000
180E249GLN0-0.047-0.01342.8550.0000.0000.0000.0000.0000.000
181E250GLY0-0.0060.00945.5640.0000.0000.0000.0000.0000.000
182E251TYR0-0.032-0.01045.7980.0000.0000.0000.0000.0000.000
183E252SER00.0890.03645.699-0.001-0.0010.0000.0000.0000.000
184E253PRO00.004-0.01344.0460.0010.0010.0000.0000.0000.000
185E254TYR00.0490.03245.8140.0000.0000.0000.0000.0000.000
186E255GLN00.0060.01848.9570.0000.0000.0000.0000.0000.000
187E256LEU0-0.014-0.00542.4030.0010.0010.0000.0000.0000.000
188E257THR0-0.051-0.03946.2750.0000.0000.0000.0000.0000.000
189E258TRP0-0.053-0.03348.5340.0000.0000.0000.0000.0000.000
190E259GLY00.0130.01049.4300.0010.0010.0000.0000.0000.000
191E260ARG10.7820.87241.367-0.001-0.0010.0000.0000.0000.000
192E261PRO00.0130.01046.4700.0000.0000.0000.0000.0000.000
193E262SER00.0030.00646.846-0.001-0.0010.0000.0000.0000.000
194E263THR00.0520.01048.9300.0000.0000.0000.0000.0000.000
195E264ARG10.9510.98748.1100.0120.0120.0000.0000.0000.000
196E265ILE00.0400.02544.5490.0000.0000.0000.0000.0000.000
197E266GLN0-0.011-0.01148.7950.0000.0000.0000.0000.0000.000
198E267GLN0-0.046-0.03751.6770.0000.0000.0000.0000.0000.000
199E268GLN0-0.075-0.05346.5990.0000.0000.0000.0000.0000.000
200E269LEU00.0330.02446.525-0.001-0.0010.0000.0000.0000.000
201E270GLY0-0.0030.02150.9530.0010.0010.0000.0000.0000.000
202E271GLN0-0.109-0.06852.035-0.001-0.0010.0000.0000.0000.000
203E272LEU0-0.033-0.00750.125-0.001-0.0010.0000.0000.0000.000
204E273THR00.012-0.00653.0130.0010.0010.0000.0000.0000.000
205E274LEU00.0390.01055.2080.0000.0000.0000.0000.0000.000
206E275GLU-1-0.936-0.96855.095-0.001-0.0010.0000.0000.0000.000
207E276ASN0-0.032-0.02051.3920.0010.0010.0000.0000.0000.000
208E277LEU00.0120.03952.1340.0000.0000.0000.0000.0000.000
209E278GLN00.013-0.00353.7630.0000.0000.0000.0000.0000.000
210E279MET00.0180.02949.3650.0000.0000.0000.0000.0000.000
211E280LEU00.0090.00053.0640.0000.0000.0000.0000.0000.000
212E281PRO0-0.018-0.00155.5970.0010.0010.0000.0000.0000.000