Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6G35Z

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 OptH
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 -2297397.892727
FMO2-HF: Nuclear repulsion 2215429.288062
FMO2-HF: Total energy -81968.604666
FMO2-MP2: Total energy -82205.903724


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.
-11.169-8.55714.444-4.934-12.122-0.049
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 : -0.051 / q_NPA : -0.021
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-1-0.917-0.9403.841-1.9760.863-0.034-1.518-1.287-0.004
4E73ASP-1-0.917-0.9326.3051.1931.1930.0000.0000.0000.000
5E74GLY00.014-0.0213.047-0.784-0.1880.326-0.389-0.5320.003
6E75ASP-1-0.880-0.9592.549-7.204-5.0311.202-1.553-1.822-0.020
7E76SER0-0.018-0.0301.949-3.380-4.20010.309-5.283-4.207-0.015
8E77PHE00.031-0.0032.4584.202-0.0560.1835.056-0.981-0.005
9E78LEU00.0310.0054.526-0.150-0.038-0.001-0.020-0.0910.000
10E79HIS0-0.0050.0155.855-0.215-0.2150.0000.0000.0000.000
11E80LEU00.0730.0295.4910.1810.1810.0000.0000.0000.000
12E81ALA0-0.0120.0108.4300.1090.1090.0000.0000.0000.000
13E82ILE0-0.029-0.00710.3880.0570.0570.0000.0000.0000.000
14E83ILE0-0.014-0.0068.9450.0470.0470.0000.0000.0000.000
15E84HIS0-0.098-0.05310.8420.0820.0820.0000.0000.0000.000
16E85GLU-1-0.958-0.96614.505-0.106-0.1060.0000.0000.0000.000
17E86GLU-1-0.894-0.92413.563-0.158-0.1580.0000.0000.0000.000
18E87LYS10.9070.96114.6320.1090.1090.0000.0000.0000.000
19E88ALA0-0.007-0.00216.356-0.005-0.0050.0000.0000.0000.000
20E89LEU00.0220.01611.4120.0010.0010.0000.0000.0000.000
21E90THR00.0560.00111.798-0.018-0.0180.0000.0000.0000.000
22E91MET0-0.039-0.02112.889-0.003-0.0030.0000.0000.0000.000
23E92GLU-1-0.917-0.95014.334-0.136-0.1360.0000.0000.0000.000
24E93VAL00.0150.0078.1300.0030.0030.0000.0000.0000.000
25E94ILE0-0.008-0.01111.3630.0010.0010.0000.0000.0000.000
26E95ARG10.8360.93412.6990.1330.1330.0000.0000.0000.000
27E96GLN0-0.067-0.06311.8360.0010.0010.0000.0000.0000.000
28E97VAL0-0.0470.0138.4800.0050.0050.0000.0000.0000.000
29E98LYS10.9560.95311.2880.1080.1080.0000.0000.0000.000
30E99GLY00.0090.02214.3120.0010.0010.0000.0000.0000.000
31E100ASP-1-0.893-0.9519.188-0.277-0.2770.0000.0000.0000.000
32E101LEU00.0400.01010.265-0.043-0.0430.0000.0000.0000.000
33E102ALA0-0.041-0.0118.663-0.047-0.0470.0000.0000.0000.000
34E103PHE0-0.006-0.0012.089-0.462-0.6031.776-0.382-1.2530.001
35E104LEU00.003-0.0056.687-0.067-0.0670.0000.0000.0000.000
36E105ASN0-0.035-0.0169.3420.0290.0290.0000.0000.0000.000
37E106PHE0-0.0120.0012.672-2.0680.0430.683-0.845-1.949-0.009
38E107GLN00.028-0.0107.0260.0430.0430.0000.0000.0000.000
39E108ASN00.0290.0405.365-0.035-0.0350.0000.0000.0000.000
40E109ASN00.0490.0156.3070.1010.1010.0000.0000.0000.000
41E110LEU0-0.076-0.0168.136-0.040-0.0400.0000.0000.0000.000
42E111GLN0-0.047-0.0549.742-0.122-0.1220.0000.0000.0000.000
43E112GLN00.0370.02410.070-0.048-0.0480.0000.0000.0000.000
44E113THR00.023-0.0159.238-0.126-0.1260.0000.0000.0000.000
45E114PRO00.0240.0038.1760.0510.0510.0000.0000.0000.000
46E115LEU00.0590.01710.7990.0470.0470.0000.0000.0000.000
47E116HIS0-0.0150.03413.163-0.011-0.0110.0000.0000.0000.000
48E117LEU00.0350.0219.2110.0210.0210.0000.0000.0000.000
49E118ALA00.0050.01013.7270.0270.0270.0000.0000.0000.000
50E119VAL0-0.027-0.01315.9310.0200.0200.0000.0000.0000.000
51E120ILE0-0.060-0.02714.8080.0180.0180.0000.0000.0000.000
52E121THR0-0.054-0.03315.5250.0130.0130.0000.0000.0000.000
53E122ASN0-0.021-0.01518.4450.0020.0020.0000.0000.0000.000
54E123GLN00.0290.01116.0760.0130.0130.0000.0000.0000.000
55E124PRO0-0.002-0.01019.267-0.010-0.0100.0000.0000.0000.000
56E125GLU-1-0.756-0.89819.834-0.133-0.1330.0000.0000.0000.000
57E126ILE00.0170.01614.492-0.006-0.0060.0000.0000.0000.000
58E127ALA00.0050.00316.410-0.017-0.0170.0000.0000.0000.000
59E128GLU-1-0.961-0.99317.888-0.097-0.0970.0000.0000.0000.000
60E129ALA0-0.038-0.01317.0340.0030.0030.0000.0000.0000.000
61E130LEU0-0.035-0.00811.828-0.003-0.0030.0000.0000.0000.000
62E131LEU00.012-0.00415.2770.0000.0000.0000.0000.0000.000
63E132GLY00.0020.02518.1810.0070.0070.0000.0000.0000.000
64E133ALA0-0.132-0.07714.7810.0070.0070.0000.0000.0000.000
65E134GLY0-0.023-0.02615.897-0.006-0.0060.0000.0000.0000.000
66E135CYS0-0.080-0.02013.4230.0060.0060.0000.0000.0000.000
67E136ASP-1-0.863-0.94714.456-0.105-0.1050.0000.0000.0000.000
68E137PRO0-0.035-0.03516.282-0.007-0.0070.0000.0000.0000.000
69E138GLU-1-0.940-0.98718.912-0.053-0.0530.0000.0000.0000.000
70E139LEU0-0.0290.01612.9050.0140.0140.0000.0000.0000.000
71E140ARG10.8570.91716.5030.0250.0250.0000.0000.0000.000
72E141ASP-1-0.715-0.83814.241-0.036-0.0360.0000.0000.0000.000
73E142PHE0-0.012-0.01713.9320.0220.0220.0000.0000.0000.000
74E143ARG10.8600.93615.6860.0200.0200.0000.0000.0000.000
75E144GLY0-0.017-0.04218.285-0.002-0.0020.0000.0000.0000.000
76E145ASN0-0.006-0.00918.973-0.002-0.0020.0000.0000.0000.000
77E146THR00.0370.01818.224-0.013-0.0130.0000.0000.0000.000
78E147PRO00.0690.01416.7430.0110.0110.0000.0000.0000.000
79E148LEU00.0710.03619.3050.0060.0060.0000.0000.0000.000
80E149HIS00.0150.03421.895-0.001-0.0010.0000.0000.0000.000
81E150LEU00.0110.01017.0290.0070.0070.0000.0000.0000.000
82E151ALA00.0110.00821.6360.0040.0040.0000.0000.0000.000
83E152CYS0-0.111-0.06323.6930.0060.0060.0000.0000.0000.000
84E153GLU-1-0.950-0.98422.794-0.016-0.0160.0000.0000.0000.000
85E154GLN00.002-0.00920.5540.0040.0040.0000.0000.0000.000
86E155GLY0-0.015-0.01125.3360.0020.0020.0000.0000.0000.000
87E156CYM-1-0.850-0.85624.875-0.076-0.0760.0000.0000.0000.000
88E157LEU00.027-0.01626.901-0.002-0.0020.0000.0000.0000.000
89E158ALA0-0.0060.00226.4420.0000.0000.0000.0000.0000.000
90E159SER00.023-0.04822.895-0.007-0.0070.0000.0000.0000.000
91E160VAL0-0.021-0.00224.386-0.003-0.0030.0000.0000.0000.000
92E161GLY00.0140.01826.6630.0000.0000.0000.0000.0000.000
93E162VAL00.0430.02921.9730.0010.0010.0000.0000.0000.000
94E163LEU0-0.036-0.03219.948-0.003-0.0030.0000.0000.0000.000
95E164THR0-0.094-0.04723.6890.0040.0040.0000.0000.0000.000
96E165GLN0-0.064-0.02627.0880.0010.0010.0000.0000.0000.000
97E166SER00.0540.03423.4030.0010.0010.0000.0000.0000.000
98E167CYS00.0070.02322.7590.0030.0030.0000.0000.0000.000
99E168THR0-0.032-0.02324.7890.0050.0050.0000.0000.0000.000
100E169THR0-0.022-0.00525.1090.0030.0030.0000.0000.0000.000
101E170PRO00.0130.00427.8260.0000.0000.0000.0000.0000.000
102E171HIS10.9010.92723.4330.0750.0750.0000.0000.0000.000
103E172LEU00.0770.05426.3460.0010.0010.0000.0000.0000.000
104E173HIS00.0210.00427.8150.0050.0050.0000.0000.0000.000
105E174SER00.022-0.00326.2440.0050.0050.0000.0000.0000.000
106E175ILE00.0490.03022.9030.0050.0050.0000.0000.0000.000
107E176LEU0-0.068-0.03826.0750.0040.0040.0000.0000.0000.000
108E177LYS10.8880.95029.1620.0240.0240.0000.0000.0000.000
109E178ALA0-0.0370.00025.2570.0050.0050.0000.0000.0000.000
110E179THR0-0.029-0.01127.179-0.001-0.0010.0000.0000.0000.000
111E180ASN00.0460.02622.7020.0060.0060.0000.0000.0000.000
112E181TYR00.004-0.00718.477-0.004-0.0040.0000.0000.0000.000
113E182ASN0-0.048-0.01024.0280.0110.0110.0000.0000.0000.000
114E183GLY0-0.048-0.02926.993-0.001-0.0010.0000.0000.0000.000
115E184HIS0-0.020-0.01827.1140.0000.0000.0000.0000.0000.000
116E185THR00.0790.04927.141-0.003-0.0030.0000.0000.0000.000
117E186CYS00.0280.02126.596-0.001-0.0010.0000.0000.0000.000
118E187LEU00.0530.02728.4290.0010.0010.0000.0000.0000.000
119E188HIS0-0.018-0.01530.7010.0020.0020.0000.0000.0000.000
120E189LEU00.0320.02524.9280.0030.0030.0000.0000.0000.000
121E190ALA0-0.012-0.00629.1810.0010.0010.0000.0000.0000.000
122E191SER0-0.087-0.07231.0720.0010.0010.0000.0000.0000.000
123E192ILE0-0.033-0.00230.1780.0020.0020.0000.0000.0000.000
124E193HIS0-0.0210.01227.6980.0040.0040.0000.0000.0000.000
125E194GLY00.016-0.01132.4350.0000.0000.0000.0000.0000.000
126E195TYR0-0.0100.02128.4820.0010.0010.0000.0000.0000.000
127E196LEU00.0360.00234.025-0.001-0.0010.0000.0000.0000.000
128E197GLY00.0130.01536.1590.0000.0000.0000.0000.0000.000
129E198ILE00.0370.02429.167-0.001-0.0010.0000.0000.0000.000
130E199VAL0-0.030-0.01033.154-0.001-0.0010.0000.0000.0000.000
131E200GLU-1-0.853-0.93835.097-0.024-0.0240.0000.0000.0000.000
132E201LEU0-0.0230.00531.6880.0000.0000.0000.0000.0000.000
133E202LEU00.030-0.00229.514-0.001-0.0010.0000.0000.0000.000
134E203VAL0-0.0180.00133.5210.0000.0000.0000.0000.0000.000
135E204SER0-0.117-0.04536.6150.0000.0000.0000.0000.0000.000
136E205LEU00.019-0.01130.711-0.001-0.0010.0000.0000.0000.000
137E206GLY0-0.045-0.00734.016-0.002-0.0020.0000.0000.0000.000
138E207ALA0-0.048-0.01432.8300.0010.0010.0000.0000.0000.000
139E208ASP-1-0.851-0.93834.478-0.014-0.0140.0000.0000.0000.000
140E209VAL00.0190.01037.0760.0010.0010.0000.0000.0000.000
141E210ASN0-0.064-0.01738.9350.0020.0020.0000.0000.0000.000
142E211ALA0-0.0050.00334.8750.0020.0020.0000.0000.0000.000
143E212GLN0-0.089-0.06436.9690.0010.0010.0000.0000.0000.000
144E213GLU-1-0.766-0.85532.9480.0070.0070.0000.0000.0000.000
145E214PRO0-0.010-0.01530.8970.0010.0010.0000.0000.0000.000
146E215CYS00.0230.00732.0230.0030.0030.0000.0000.0000.000
147E216ASN0-0.091-0.04734.7580.0000.0000.0000.0000.0000.000
148E217GLY00.1040.04437.115-0.001-0.0010.0000.0000.0000.000
149E218ARG10.8420.93537.328-0.007-0.0070.0000.0000.0000.000
150E219THR00.0510.02337.406-0.001-0.0010.0000.0000.0000.000
151E220ALA00.0780.02036.7550.0010.0010.0000.0000.0000.000
152E221LEU00.0660.02537.8690.0010.0010.0000.0000.0000.000
153E222HIS0-0.0090.01440.1740.0000.0000.0000.0000.0000.000
154E223LEU00.0310.01634.3640.0010.0010.0000.0000.0000.000
155E224ALA00.0490.02438.4290.0000.0000.0000.0000.0000.000
156E225VAL0-0.040-0.01140.3650.0000.0000.0000.0000.0000.000
157E226ASP-1-0.989-0.99138.0630.0060.0060.0000.0000.0000.000
158E227LEU00.0090.01035.4590.0010.0010.0000.0000.0000.000
159E228GLN0-0.070-0.04539.4970.0000.0000.0000.0000.0000.000
160E229ASN00.0620.03738.436-0.001-0.0010.0000.0000.0000.000
161E230PRO00.017-0.01342.128-0.001-0.0010.0000.0000.0000.000
162E231ASP-1-0.858-0.91542.238-0.013-0.0130.0000.0000.0000.000
163E232LEU0-0.0070.00037.404-0.001-0.0010.0000.0000.0000.000
164E233VAL0-0.003-0.00541.0860.0000.0000.0000.0000.0000.000
165E234SER0-0.037-0.03143.9570.0000.0000.0000.0000.0000.000
166E235LEU0-0.0130.00238.8750.0000.0000.0000.0000.0000.000
167E236LEU00.0350.01038.596-0.001-0.0010.0000.0000.0000.000
168E237LEU0-0.023-0.01042.5180.0000.0000.0000.0000.0000.000
169E238LYS10.8170.91743.6980.0200.0200.0000.0000.0000.000
170E239CYS0-0.076-0.04041.599-0.001-0.0010.0000.0000.0000.000
171E240GLY00.0100.01743.5070.0000.0000.0000.0000.0000.000
172E241ALA0-0.060-0.02542.7090.0010.0010.0000.0000.0000.000
173E242ASP-1-0.853-0.94744.284-0.006-0.0060.0000.0000.0000.000
174E243VAL0-0.027-0.01845.9170.0010.0010.0000.0000.0000.000
175E244ASN00.0370.01447.9140.0020.0020.0000.0000.0000.000
176E245ARG10.9420.99141.7420.0070.0070.0000.0000.0000.000
177E246VAL0-0.012-0.01745.6910.0000.0000.0000.0000.0000.000
178E247THR0-0.034-0.01641.9590.0000.0000.0000.0000.0000.000
179E248TYR0-0.008-0.02136.597-0.001-0.0010.0000.0000.0000.000
180E249GLN0-0.105-0.05742.5240.0000.0000.0000.0000.0000.000
181E250GLY00.0190.01745.5760.0000.0000.0000.0000.0000.000
182E251TYR0-0.0240.00445.745-0.001-0.0010.0000.0000.0000.000
183E252SER00.0490.03246.041-0.001-0.0010.0000.0000.0000.000
184E253PRO00.027-0.01344.2460.0010.0010.0000.0000.0000.000
185E254TYR00.0340.03946.0620.0000.0000.0000.0000.0000.000
186E255GLN0-0.0120.01049.1010.0000.0000.0000.0000.0000.000
187E256LEU0-0.024-0.00142.6670.0010.0010.0000.0000.0000.000
188E257THR0-0.048-0.04746.5600.0000.0000.0000.0000.0000.000
189E258TRP0-0.037-0.02248.5940.0000.0000.0000.0000.0000.000
190E259GLY00.0170.01449.1690.0010.0010.0000.0000.0000.000
191E260ARG10.7990.89842.097-0.004-0.0040.0000.0000.0000.000
192E261PRO0-0.004-0.00546.5550.0000.0000.0000.0000.0000.000
193E262SER0-0.025-0.01047.549-0.001-0.0010.0000.0000.0000.000
194E263THR00.0930.04249.4510.0000.0000.0000.0000.0000.000
195E264ARG10.9810.99748.8440.0060.0060.0000.0000.0000.000
196E265ILE00.0130.00744.9930.0000.0000.0000.0000.0000.000
197E266GLN0-0.022-0.00949.1560.0000.0000.0000.0000.0000.000
198E267GLN0-0.050-0.03451.8850.0000.0000.0000.0000.0000.000
199E268GLN0-0.069-0.05247.4100.0000.0000.0000.0000.0000.000
200E269LEU00.0570.02546.8690.0000.0000.0000.0000.0000.000
201E270GLY00.0140.04751.3150.0000.0000.0000.0000.0000.000
202E271GLN0-0.108-0.05552.6210.0000.0000.0000.0000.0000.000
203E272LEU00.009-0.00550.596-0.001-0.0010.0000.0000.0000.000
204E273THR0-0.046-0.04253.4470.0010.0010.0000.0000.0000.000
205E274LEU00.065-0.00555.4640.0000.0000.0000.0000.0000.000
206E275GLU-1-0.996-0.99055.3400.0010.0010.0000.0000.0000.000
207E276ASN0-0.0070.01751.4950.0010.0010.0000.0000.0000.000
208E277LEU00.0020.02352.4200.0000.0000.0000.0000.0000.000
209E278GLN00.012-0.00553.8090.0000.0000.0000.0000.0000.000
210E279MET00.0060.03149.8550.0000.0000.0000.0000.0000.000
211E280LEU00.0310.01252.8170.0000.0000.0000.0000.0000.000
212E281PRO0-0.020-0.00355.7630.0000.0000.0000.0000.0000.000