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: ZN29N

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 OptHSide
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 -2297345.619996
FMO2-HF: Nuclear repulsion 2215375.667274
FMO2-HF: Total energy -81969.952722
FMO2-MP2: Total energy -82207.102426


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.
-14.889-6.6928.16-5.803-10.555-0.047
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 : -0.042 / q_NPA : -0.027
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-1-0.920-0.9423.841-1.8400.888-0.032-1.448-1.248-0.004
4E73ASP-1-0.908-0.9296.3001.2171.2170.0000.0000.0000.000
5E74GLY00.018-0.0173.044-0.882-0.2840.322-0.386-0.5340.003
6E75ASP-1-0.844-0.9272.550-7.184-5.1651.219-1.458-1.781-0.019
7E76SER0-0.035-0.0432.048-4.092-2.7375.309-3.403-3.261-0.014
8E77PHE00.036-0.0022.7561.7110.3140.0722.055-0.730-0.002
9E78LEU00.0280.0074.851-0.0330.044-0.001-0.007-0.0680.000
10E79HIS00.0050.0426.157-0.132-0.1320.0000.0000.0000.000
11E80LEU00.0550.0215.5750.2190.2190.0000.0000.0000.000
12E81ALA0-0.0040.0158.5820.1240.1240.0000.0000.0000.000
13E82ILE0-0.024-0.00210.6950.0670.0670.0000.0000.0000.000
14E83ILE0-0.001-0.0019.0300.0540.0540.0000.0000.0000.000
15E84HIS0-0.105-0.06010.8760.0930.0930.0000.0000.0000.000
16E85GLU-1-0.949-0.96214.654-0.112-0.1120.0000.0000.0000.000
17E86GLU-1-0.904-0.93213.901-0.158-0.1580.0000.0000.0000.000
18E87LYS10.8620.91714.9120.1260.1260.0000.0000.0000.000
19E88ALA0-0.010-0.00416.577-0.007-0.0070.0000.0000.0000.000
20E89LEU00.0230.01711.6680.0000.0000.0000.0000.0000.000
21E90THR00.0460.00411.961-0.025-0.0250.0000.0000.0000.000
22E91MET0-0.039-0.01813.046-0.009-0.0090.0000.0000.0000.000
23E92GLU-1-0.854-0.90414.630-0.151-0.1510.0000.0000.0000.000
24E93VAL00.0140.0098.1860.0010.0010.0000.0000.0000.000
25E94ILE0-0.007-0.01211.442-0.002-0.0020.0000.0000.0000.000
26E95ARG10.7880.88912.8240.1500.1500.0000.0000.0000.000
27E96GLN0-0.072-0.06011.750-0.002-0.0020.0000.0000.0000.000
28E97VAL0-0.0510.0048.5060.0080.0080.0000.0000.0000.000
29E98LYS10.9610.95611.3810.1220.1220.0000.0000.0000.000
30E99GLY00.0070.02114.2980.0010.0010.0000.0000.0000.000
31E100ASP-1-0.874-0.9469.015-0.357-0.3570.0000.0000.0000.000
32E101LEU00.0250.00710.279-0.055-0.0550.0000.0000.0000.000
33E102ALA0-0.039-0.0098.533-0.062-0.0620.0000.0000.0000.000
34E103PHE0-0.004-0.0062.438-0.852-0.3810.654-0.226-0.9000.000
35E104LEU0-0.006-0.0046.704-0.086-0.0860.0000.0000.0000.000
36E105ASN0-0.025-0.0149.4230.0290.0290.0000.0000.0000.000
37E106PHE0-0.0130.0033.098-2.569-0.2230.617-0.930-2.033-0.011
38E107GLN00.008-0.0217.1360.0380.0380.0000.0000.0000.000
39E108ASN0-0.009-0.0125.367-0.085-0.0850.0000.0000.0000.000
40E109ASN00.0310.0126.3080.2830.2830.0000.0000.0000.000
41E110LEU0-0.062-0.0058.135-0.036-0.0360.0000.0000.0000.000
42E111GLN0-0.030-0.0479.743-0.111-0.1110.0000.0000.0000.000
43E112GLN00.0420.03310.069-0.042-0.0420.0000.0000.0000.000
44E113THR00.030-0.0039.240-0.139-0.1390.0000.0000.0000.000
45E114PRO00.0200.0018.4430.0580.0580.0000.0000.0000.000
46E115LEU00.0570.02110.9960.0620.0620.0000.0000.0000.000
47E116HIS0-0.0170.01413.231-0.008-0.0080.0000.0000.0000.000
48E117LEU00.0230.0189.1900.0330.0330.0000.0000.0000.000
49E118ALA00.0020.01613.7270.0340.0340.0000.0000.0000.000
50E119VAL0-0.028-0.01816.1480.0250.0250.0000.0000.0000.000
51E120ILE0-0.046-0.01414.7630.0200.0200.0000.0000.0000.000
52E121THR0-0.051-0.03615.4880.0150.0150.0000.0000.0000.000
53E122ASN0-0.014-0.02618.4440.0050.0050.0000.0000.0000.000
54E123GLN00.005-0.00816.0910.0110.0110.0000.0000.0000.000
55E124PRO00.016-0.00119.473-0.014-0.0140.0000.0000.0000.000
56E125GLU-1-0.747-0.87320.286-0.150-0.1500.0000.0000.0000.000
57E126ILE00.0400.02114.741-0.007-0.0070.0000.0000.0000.000
58E127ALA00.0110.00716.559-0.022-0.0220.0000.0000.0000.000
59E128GLU-1-0.960-0.99318.112-0.115-0.1150.0000.0000.0000.000
60E129ALA0-0.036-0.01117.2080.0030.0030.0000.0000.0000.000
61E130LEU0-0.015-0.00511.876-0.005-0.0050.0000.0000.0000.000
62E131LEU00.012-0.00915.588-0.002-0.0020.0000.0000.0000.000
63E132GLY0-0.0050.02118.4440.0080.0080.0000.0000.0000.000
64E133ALA0-0.128-0.07714.9530.0090.0090.0000.0000.0000.000
65E134GLY0-0.024-0.02416.026-0.008-0.0080.0000.0000.0000.000
66E135CYS0-0.044-0.00513.5760.0010.0010.0000.0000.0000.000
67E136ASP-1-0.901-0.96014.595-0.134-0.1340.0000.0000.0000.000
68E137PRO0-0.031-0.02816.464-0.009-0.0090.0000.0000.0000.000
69E138GLU-1-0.890-0.94719.083-0.071-0.0710.0000.0000.0000.000
70E139LEU0-0.0230.01612.7630.0170.0170.0000.0000.0000.000
71E140ARG10.7940.87216.5020.0430.0430.0000.0000.0000.000
72E141ASP-1-0.729-0.85714.240-0.054-0.0540.0000.0000.0000.000
73E142PHE0-0.002-0.00813.9730.0260.0260.0000.0000.0000.000
74E143ARG10.7550.86015.6870.0420.0420.0000.0000.0000.000
75E144GLY0-0.026-0.03918.2870.0000.0000.0000.0000.0000.000
76E145ASN00.0220.01018.970-0.002-0.0020.0000.0000.0000.000
77E146THR00.0380.02418.225-0.017-0.0170.0000.0000.0000.000
78E147PRO00.0580.01016.6150.0140.0140.0000.0000.0000.000
79E148LEU00.0650.04319.2840.0090.0090.0000.0000.0000.000
80E149HIS00.0090.02522.0630.0000.0000.0000.0000.0000.000
81E150LEU00.0070.00717.1190.0080.0080.0000.0000.0000.000
82E151ALA00.0260.00821.6360.0060.0060.0000.0000.0000.000
83E152CYS0-0.114-0.06023.6940.0070.0070.0000.0000.0000.000
84E153GLU-1-0.871-0.91022.394-0.028-0.0280.0000.0000.0000.000
85E154GLN00.003-0.01120.5020.0030.0030.0000.0000.0000.000
86E155GLY0-0.0110.00325.3350.0020.0020.0000.0000.0000.000
87E156CYM-1-0.835-0.79224.876-0.091-0.0910.0000.0000.0000.000
88E157LEU00.024-0.01326.901-0.003-0.0030.0000.0000.0000.000
89E158ALA0-0.0060.00426.7060.0000.0000.0000.0000.0000.000
90E159SER00.011-0.09722.851-0.008-0.0080.0000.0000.0000.000
91E160VAL0-0.019-0.00424.584-0.004-0.0040.0000.0000.0000.000
92E161GLY00.0160.03126.7700.0000.0000.0000.0000.0000.000
93E162VAL00.0460.03122.2480.0000.0000.0000.0000.0000.000
94E163LEU0-0.030-0.02520.058-0.004-0.0040.0000.0000.0000.000
95E164THR0-0.090-0.05724.0090.0040.0040.0000.0000.0000.000
96E165GLN0-0.064-0.02727.3800.0020.0020.0000.0000.0000.000
97E166SER00.0180.00523.7380.0020.0020.0000.0000.0000.000
98E167CYS00.0130.03322.8870.0020.0020.0000.0000.0000.000
99E168THR0-0.005-0.01625.0010.0050.0050.0000.0000.0000.000
100E169THR0-0.049-0.01325.2040.0030.0030.0000.0000.0000.000
101E170PRO00.0170.00527.9700.0000.0000.0000.0000.0000.000
102E171HIS10.8740.89023.1930.0980.0980.0000.0000.0000.000
103E172LEU00.0620.04726.5000.0000.0000.0000.0000.0000.000
104E173HIS00.0200.00128.0050.0050.0050.0000.0000.0000.000
105E174SER00.009-0.00226.3030.0070.0070.0000.0000.0000.000
106E175ILE00.0490.02923.1960.0050.0050.0000.0000.0000.000
107E176LEU0-0.063-0.03926.0680.0050.0050.0000.0000.0000.000
108E177LYS10.8920.95529.1470.0360.0360.0000.0000.0000.000
109E178ALA0-0.0440.00225.2200.0060.0060.0000.0000.0000.000
110E179THR0-0.0080.00227.181-0.001-0.0010.0000.0000.0000.000
111E180ASN00.0500.02122.6490.0050.0050.0000.0000.0000.000
112E181TYR00.0100.00718.111-0.002-0.0020.0000.0000.0000.000
113E182ASN0-0.036-0.00323.6490.0130.0130.0000.0000.0000.000
114E183GLY0-0.040-0.02526.994-0.001-0.0010.0000.0000.0000.000
115E184HIS0-0.043-0.03227.1300.0010.0010.0000.0000.0000.000
116E185THR00.0630.03127.142-0.005-0.0050.0000.0000.0000.000
117E186CYS00.0280.01626.605-0.001-0.0010.0000.0000.0000.000
118E187LEU00.0510.03328.4310.0010.0010.0000.0000.0000.000
119E188HIS00.0030.01230.6650.0010.0010.0000.0000.0000.000
120E189LEU00.0380.02624.9950.0030.0030.0000.0000.0000.000
121E190ALA0-0.013-0.00429.1810.0010.0010.0000.0000.0000.000
122E191SER0-0.079-0.06431.0730.0020.0020.0000.0000.0000.000
123E192ILE0-0.043-0.00930.4660.0020.0020.0000.0000.0000.000
124E193HIS0-0.0310.00327.6230.0040.0040.0000.0000.0000.000
125E194GLY00.022-0.00932.4340.0000.0000.0000.0000.0000.000
126E195TYR0-0.0060.01228.2660.0010.0010.0000.0000.0000.000
127E196LEU00.0340.00734.025-0.002-0.0020.0000.0000.0000.000
128E197GLY00.0040.00936.1600.0000.0000.0000.0000.0000.000
129E198ILE00.0400.02129.209-0.001-0.0010.0000.0000.0000.000
130E199VAL0-0.027-0.00833.155-0.001-0.0010.0000.0000.0000.000
131E200GLU-1-0.774-0.88535.098-0.029-0.0290.0000.0000.0000.000
132E201LEU0-0.0270.00131.8900.0000.0000.0000.0000.0000.000
133E202LEU00.042-0.00229.428-0.001-0.0010.0000.0000.0000.000
134E203VAL0-0.0100.00333.5010.0000.0000.0000.0000.0000.000
135E204SER0-0.120-0.04436.7290.0000.0000.0000.0000.0000.000
136E205LEU00.014-0.01030.978-0.001-0.0010.0000.0000.0000.000
137E206GLY0-0.043-0.00734.254-0.002-0.0020.0000.0000.0000.000
138E207ALA0-0.044-0.01132.7950.0010.0010.0000.0000.0000.000
139E208ASP-1-0.834-0.92534.466-0.020-0.0200.0000.0000.0000.000
140E209VAL00.0180.00737.0650.0010.0010.0000.0000.0000.000
141E210ASN0-0.095-0.04638.9370.0030.0030.0000.0000.0000.000
142E211ALA0-0.005-0.00234.8910.0020.0020.0000.0000.0000.000
143E212GLN0-0.083-0.06436.9710.0000.0000.0000.0000.0000.000
144E213GLU-1-0.784-0.89132.9300.0010.0010.0000.0000.0000.000
145E214PRO00.003-0.00530.8250.0020.0020.0000.0000.0000.000
146E215CYS0-0.0030.01532.1960.0030.0030.0000.0000.0000.000
147E216ASN0-0.056-0.02634.7590.0010.0010.0000.0000.0000.000
148E217GLY00.0980.05037.1130.0000.0000.0000.0000.0000.000
149E218ARG10.7810.88937.275-0.003-0.0030.0000.0000.0000.000
150E219THR00.0550.01837.407-0.002-0.0020.0000.0000.0000.000
151E220ALA00.0640.01336.6410.0010.0010.0000.0000.0000.000
152E221LEU00.0630.02537.8700.0010.0010.0000.0000.0000.000
153E222HIS0-0.0110.01740.2300.0000.0000.0000.0000.0000.000
154E223LEU00.0280.01534.3220.0010.0010.0000.0000.0000.000
155E224ALA00.0440.02438.4290.0010.0010.0000.0000.0000.000
156E225VAL0-0.020-0.00240.3650.0010.0010.0000.0000.0000.000
157E226ASP-1-0.865-0.90338.7820.0030.0030.0000.0000.0000.000
158E227LEU0-0.024-0.00435.3850.0020.0020.0000.0000.0000.000
159E228GLN0-0.071-0.05339.4970.0000.0000.0000.0000.0000.000
160E229ASN00.0450.02738.233-0.001-0.0010.0000.0000.0000.000
161E230PRO00.0250.00342.127-0.001-0.0010.0000.0000.0000.000
162E231ASP-1-0.862-0.91842.287-0.016-0.0160.0000.0000.0000.000
163E232LEU00.0180.00737.395-0.001-0.0010.0000.0000.0000.000
164E233VAL0-0.013-0.01141.087-0.001-0.0010.0000.0000.0000.000
165E234SER0-0.025-0.02343.9570.0000.0000.0000.0000.0000.000
166E235LEU0-0.0130.00038.9480.0000.0000.0000.0000.0000.000
167E236LEU00.0450.01838.514-0.001-0.0010.0000.0000.0000.000
168E237LEU0-0.019-0.00742.5190.0000.0000.0000.0000.0000.000
169E238LYS10.7460.86843.3830.0260.0260.0000.0000.0000.000
170E239CYS0-0.084-0.04741.752-0.001-0.0010.0000.0000.0000.000
171E240GLY00.0080.01343.490-0.001-0.0010.0000.0000.0000.000
172E241ALA0-0.060-0.02442.6700.0010.0010.0000.0000.0000.000
173E242ASP-1-0.793-0.90644.285-0.009-0.0090.0000.0000.0000.000
174E243VAL0-0.032-0.02145.9190.0010.0010.0000.0000.0000.000
175E244ASN00.0060.00347.9150.0020.0020.0000.0000.0000.000
176E245ARG10.9180.98341.8840.0130.0130.0000.0000.0000.000
177E246VAL0-0.028-0.03245.6920.0000.0000.0000.0000.0000.000
178E247THR0-0.023-0.01041.9540.0000.0000.0000.0000.0000.000
179E248TYR0-0.014-0.03536.512-0.001-0.0010.0000.0000.0000.000
180E249GLN0-0.100-0.04843.0670.0000.0000.0000.0000.0000.000
181E250GLY00.0150.01645.5770.0000.0000.0000.0000.0000.000
182E251TYR0-0.0220.00445.8290.0000.0000.0000.0000.0000.000
183E252SER00.0710.04246.041-0.001-0.0010.0000.0000.0000.000
184E253PRO00.036-0.00544.3620.0010.0010.0000.0000.0000.000
185E254TYR00.0490.03146.0620.0000.0000.0000.0000.0000.000
186E255GLN0-0.0010.01649.1810.0000.0000.0000.0000.0000.000
187E256LEU0-0.033-0.00842.7050.0010.0010.0000.0000.0000.000
188E257THR0-0.047-0.04046.5590.0000.0000.0000.0000.0000.000
189E258TRP0-0.036-0.02248.5940.0000.0000.0000.0000.0000.000
190E259GLY00.0110.01149.1690.0010.0010.0000.0000.0000.000
191E260ARG10.7640.87241.471-0.001-0.0010.0000.0000.0000.000
192E261PRO00.006-0.00346.5520.0000.0000.0000.0000.0000.000
193E262SER0-0.026-0.01047.4260.0000.0000.0000.0000.0000.000
194E263THR00.0870.03849.4500.0000.0000.0000.0000.0000.000
195E264ARG10.9540.98548.6890.0100.0100.0000.0000.0000.000
196E265ILE00.0340.01844.9710.0000.0000.0000.0000.0000.000
197E266GLN0-0.003-0.00749.1560.0000.0000.0000.0000.0000.000
198E267GLN0-0.066-0.03751.8850.0000.0000.0000.0000.0000.000
199E268GLN0-0.083-0.06147.0660.0010.0010.0000.0000.0000.000
200E269LEU00.0590.02846.916-0.001-0.0010.0000.0000.0000.000
201E270GLY00.0020.04451.3150.0000.0000.0000.0000.0000.000
202E271GLN0-0.129-0.07652.5720.0000.0000.0000.0000.0000.000
203E272LEU0-0.014-0.00750.046-0.001-0.0010.0000.0000.0000.000
204E273THR00.017-0.00253.4700.0010.0010.0000.0000.0000.000
205E274LEU00.0610.01055.4650.0000.0000.0000.0000.0000.000
206E275GLU-1-1.004-0.99055.356-0.002-0.0020.0000.0000.0000.000
207E276ASN0-0.031-0.02151.7650.0010.0010.0000.0000.0000.000
208E277LEU00.0150.03552.4210.0000.0000.0000.0000.0000.000
209E278GLN00.010-0.00753.8090.0000.0000.0000.0000.0000.000
210E279MET00.0060.02649.4080.0000.0000.0000.0000.0000.000
211E280LEU00.0270.01253.0400.0000.0000.0000.0000.0000.000
212E281PRO0-0.017-0.00455.7630.0000.0000.0000.0000.0000.000