FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 2N8NR

Calculation Name: 3B8P-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: E

ChEMBL ID:

UniProt ID: Q04866

Base Structure: X-ray

Registration Date: 2023-09-23

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

DOI:

Apendix: None


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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1804867.605406
FMO2-HF: Nuclear repulsion 1731133.505616
FMO2-HF: Total energy -73734.09979
FMO2-MP2: Total energy -73953.636888


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:54:GLU)


Summations of interaction energy for fragment #1(E:54:GLU)
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.
-39.719-38.23816.686-8.518-9.6470.015
Interaction energy analysis for fragmet #1(E:54:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.860 / q_NPA : -0.922
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].
3E56TRP0-0.020-0.0042.404-1.5621.2451.245-1.605-2.446-0.006
4E57THR00.012-0.0216.082-2.484-2.4840.0000.0000.0000.000
5E58SER0-0.038-0.0099.826-1.134-1.1340.0000.0000.0000.000
6E59THR0-0.003-0.04012.234-0.079-0.0790.0000.0000.0000.000
7E60ALA0-0.0080.01715.853-0.246-0.2460.0000.0000.0000.000
8E61ILE00.0080.00619.3910.0290.0290.0000.0000.0000.000
9E62ILE00.0240.01822.895-0.266-0.2660.0000.0000.0000.000
10E63THR00.012-0.00125.789-0.098-0.0980.0000.0000.0000.000
11E64GLN00.0240.00529.5320.1440.1440.0000.0000.0000.000
12E65PRO0-0.0120.02732.5610.0130.0130.0000.0000.0000.000
13E66ASP-1-0.794-0.89833.7048.2188.2180.0000.0000.0000.000
14E67ALA00.032-0.00936.318-0.046-0.0460.0000.0000.0000.000
15E68ALA0-0.030-0.01238.757-0.166-0.1660.0000.0000.0000.000
16E69GLN0-0.025-0.02931.551-0.053-0.0530.0000.0000.0000.000
17E70VAL00.0300.02037.0080.0610.0610.0000.0000.0000.000
18E71ALA00.0120.02139.332-0.150-0.1500.0000.0000.0000.000
19E72THR00.006-0.00641.742-0.141-0.1410.0000.0000.0000.000
20E73TYR00.026-0.00340.731-0.191-0.1910.0000.0000.0000.000
21E74THR00.0090.00342.888-0.051-0.0510.0000.0000.0000.000
22E75ASN0-0.017-0.00644.965-0.136-0.1360.0000.0000.0000.000
23E76ALA00.0280.01546.108-0.156-0.1560.0000.0000.0000.000
24E77LEU00.0280.00743.953-0.122-0.1220.0000.0000.0000.000
25E78ASN0-0.056-0.03948.159-0.036-0.0360.0000.0000.0000.000
26E79VAL0-0.029-0.00950.927-0.142-0.1420.0000.0000.0000.000
27E80LEU0-0.029-0.00348.872-0.109-0.1090.0000.0000.0000.000
28E81TYR0-0.036-0.02248.841-0.129-0.1290.0000.0000.0000.000
29E82GLY00.0230.01653.310-0.069-0.0690.0000.0000.0000.000
30E83GLY0-0.035-0.03053.0720.1050.1050.0000.0000.0000.000
31E84ASN0-0.038-0.01953.275-0.034-0.0340.0000.0000.0000.000
32E85ALA00.0040.02348.9070.0910.0910.0000.0000.0000.000
33E86PRO0-0.018-0.00144.811-0.025-0.0250.0000.0000.0000.000
34E87LYS10.8640.90445.615-6.593-6.5930.0000.0000.0000.000
35E88ILE00.0540.01241.9810.1500.1500.0000.0000.0000.000
36E89SER00.0420.01740.7380.1150.1150.0000.0000.0000.000
37E90GLU-1-0.834-0.89440.0867.0097.0090.0000.0000.0000.000
38E91VAL00.0220.01939.9600.1480.1480.0000.0000.0000.000
39E92GLN0-0.042-0.03036.9630.0270.0270.0000.0000.0000.000
40E93ALA00.0270.01135.8090.2940.2940.0000.0000.0000.000
41E94ASN0-0.012-0.00435.8020.2640.2640.0000.0000.0000.000
42E95PHE00.0320.01034.4580.1810.1810.0000.0000.0000.000
43E96ILE00.0220.00928.8930.2440.2440.0000.0000.0000.000
44E97SER0-0.058-0.01230.8640.3220.3220.0000.0000.0000.000
45E98ARG10.8630.91131.744-8.045-8.0450.0000.0000.0000.000
46E99PHE00.0400.02424.5950.3080.3080.0000.0000.0000.000
47E100SER00.016-0.01326.9270.4730.4730.0000.0000.0000.000
48E101SER0-0.048-0.00326.9890.3530.3530.0000.0000.0000.000
49E102ALA00.0900.05127.7440.3090.3090.0000.0000.0000.000
50E103PHE00.024-0.00519.6980.5230.5230.0000.0000.0000.000
51E104SER0-0.090-0.06122.8570.5860.5860.0000.0000.0000.000
52E105ALA00.0300.01623.7960.3700.3700.0000.0000.0000.000
53E106LEU00.0160.00320.7790.3700.3700.0000.0000.0000.000
54E107SER0-0.101-0.06519.0220.5440.5440.0000.0000.0000.000
55E108GLU-1-0.915-0.95919.21114.23614.2360.0000.0000.0000.000
56E109VAL0-0.016-0.00820.9110.2590.2590.0000.0000.0000.000
57E110LEU0-0.019-0.01016.2240.4410.4410.0000.0000.0000.000
58E111ASP-1-0.884-0.93415.21920.84520.8450.0000.0000.0000.000
59E112ASN0-0.030-0.01616.8880.2940.2940.0000.0000.0000.000
60E113GLN0-0.064-0.02514.682-1.426-1.4260.0000.0000.0000.000
61E114LYS10.7880.87212.465-20.867-20.8670.0000.0000.0000.000
62E115GLU-1-0.814-0.90010.83223.92523.9250.0000.0000.0000.000
63E116ARG10.8380.93011.351-19.436-19.4360.0000.0000.0000.000
64E117GLU-1-0.712-0.79510.78422.32322.3230.0000.0000.0000.000
65E118LYS10.9250.97810.730-24.857-24.8570.0000.0000.0000.000
66E119LEU0-0.0020.00713.4490.8220.8220.0000.0000.0000.000
67E120THR0-0.0100.00116.017-0.271-0.2710.0000.0000.0000.000
68E121ILE00.0180.00318.4200.0160.0160.0000.0000.0000.000
69E122GLU-1-0.840-0.89320.57013.94513.9450.0000.0000.0000.000
70E123GLN00.0670.03123.572-0.008-0.0080.0000.0000.0000.000
71E124SER0-0.018-0.02623.9690.1890.1890.0000.0000.0000.000
72E125VAL0-0.0160.00225.2860.2080.2080.0000.0000.0000.000
73E126LYS10.8090.87522.855-13.260-13.2600.0000.0000.0000.000
74E127GLY00.0400.02728.280-0.262-0.2620.0000.0000.0000.000
75E128GLN0-0.097-0.04930.838-0.472-0.4720.0000.0000.0000.000
76E129ALA0-0.020-0.01930.8040.2790.2790.0000.0000.0000.000
77E130LEU00.0120.02730.0760.2220.2220.0000.0000.0000.000
78E131PRO0-0.006-0.00427.133-0.273-0.2730.0000.0000.0000.000
79E132LEU00.0130.00525.1350.0120.0120.0000.0000.0000.000
80E133SER00.0150.02020.436-0.174-0.1740.0000.0000.0000.000
81E134VAL00.0210.01819.2060.0070.0070.0000.0000.0000.000
82E135SER0-0.045-0.02714.6750.8560.8560.0000.0000.0000.000
83E136TYR0-0.003-0.02711.4350.1960.1960.0000.0000.0000.000
84E137VAL0-0.045-0.0036.9960.9550.9550.0000.0000.0000.000
85E138SER00.0510.0387.569-0.300-0.3000.0000.0000.0000.000
86E139THR00.0350.0002.5444.0345.3980.270-0.655-0.978-0.004
87E140THR0-0.072-0.0612.8302.2094.1460.379-1.065-1.251-0.012
88E141ALA00.0660.0325.623-1.752-1.7520.0000.0000.0000.000
89E142GLU-1-0.711-0.8407.93121.14921.1490.0000.0000.0000.000
90E143GLY0-0.0080.0019.551-1.464-1.4640.0000.0000.0000.000
91E144ALA0-0.001-0.0038.618-0.974-0.9740.0000.0000.0000.000
92E145GLN0-0.065-0.04210.565-0.873-0.8730.0000.0000.0000.000
93E146ARG10.8280.89111.787-20.042-20.0420.0000.0000.0000.000
94E147ARG10.8420.88512.930-18.881-18.8810.0000.0000.0000.000
95E148LEU0-0.0070.00814.598-0.607-0.6070.0000.0000.0000.000
96E149ALA0-0.031-0.02516.233-0.896-0.8960.0000.0000.0000.000
97E150GLU-1-0.914-0.93317.10215.31015.3100.0000.0000.0000.000
98E151TYR00.031-0.01615.077-0.950-0.9500.0000.0000.0000.000
99E152ILE0-0.054-0.02519.746-0.607-0.6070.0000.0000.0000.000
100E153GLN0-0.067-0.03622.350-0.302-0.3020.0000.0000.0000.000
101E154GLN0-0.024-0.01422.805-0.031-0.0310.0000.0000.0000.000
102E155VAL00.0340.01223.573-0.410-0.4100.0000.0000.0000.000
103E156ASP-1-0.821-0.92326.0969.6379.6370.0000.0000.0000.000
104E157GLU-1-0.814-0.89427.9789.8539.8530.0000.0000.0000.000
105E158GLU-1-0.951-0.96226.97810.86110.8610.0000.0000.0000.000
106E159VAL00.0550.01729.918-0.358-0.3580.0000.0000.0000.000
107E160ALA00.0010.00032.028-0.365-0.3650.0000.0000.0000.000
108E161LYS10.7950.87931.043-9.874-9.8740.0000.0000.0000.000
109E162GLU-1-0.911-0.94733.4808.9788.9780.0000.0000.0000.000
110E163LEU0-0.0050.00235.273-0.291-0.2910.0000.0000.0000.000
111E164GLU-1-0.819-0.90237.8977.1667.1660.0000.0000.0000.000
112E165VAL0-0.019-0.00739.099-0.229-0.2290.0000.0000.0000.000
113E166ASP-1-0.753-0.86040.1397.6357.6350.0000.0000.0000.000
114E167LEU0-0.037-0.00942.378-0.221-0.2210.0000.0000.0000.000
115E168LYS10.8190.90741.828-7.524-7.5240.0000.0000.0000.000
116E169ASP-1-0.857-0.90744.9476.7946.7940.0000.0000.0000.000
117E170ASN0-0.031-0.02045.459-0.268-0.2680.0000.0000.0000.000
118E171ILE00.0220.01347.869-0.165-0.1650.0000.0000.0000.000
119E172THR0-0.045-0.02749.487-0.197-0.1970.0000.0000.0000.000
120E173LEU0-0.0020.00550.652-0.140-0.1400.0000.0000.0000.000
121E174GLN00.0290.00652.383-0.171-0.1710.0000.0000.0000.000
122E175THR0-0.046-0.03454.048-0.166-0.1660.0000.0000.0000.000
123E176LYS10.7550.85455.701-5.379-5.3790.0000.0000.0000.000
124E177THR00.0050.00655.862-0.048-0.0480.0000.0000.0000.000
125E178LEU0-0.015-0.02556.780-0.122-0.1220.0000.0000.0000.000
126E179GLN0-0.020-0.00259.700-0.092-0.0920.0000.0000.0000.000
127E180GLU-1-0.765-0.87160.9135.0305.0300.0000.0000.0000.000
128E181SER0-0.006-0.00162.400-0.072-0.0720.0000.0000.0000.000
129E182LEU0-0.049-0.02164.193-0.072-0.0720.0000.0000.0000.000
130E183GLU-1-0.897-0.94965.9954.5614.5610.0000.0000.0000.000
131E184THR0-0.038-0.02366.232-0.081-0.0810.0000.0000.0000.000
132E185GLN0-0.038-0.01568.2220.0100.0100.0000.0000.0000.000
133E186GLU-1-0.842-0.92070.0304.2844.2840.0000.0000.0000.000
134E187VAL0-0.008-0.00271.476-0.084-0.0840.0000.0000.0000.000
135E188VAL0-0.012-0.00971.773-0.014-0.0140.0000.0000.0000.000
136E189ALA0-0.030-0.01474.029-0.068-0.0680.0000.0000.0000.000
137E190GLN0-0.046-0.03075.819-0.143-0.1430.0000.0000.0000.000
138E191GLU-1-0.841-0.91176.4704.0534.0530.0000.0000.0000.000
139E192GLN0-0.0040.00678.295-0.096-0.0960.0000.0000.0000.000
140E193LYS10.7410.86079.895-4.047-4.0470.0000.0000.0000.000
141E194ASP-1-0.820-0.92481.6493.8193.8190.0000.0000.0000.000
142E195LEU0-0.038-0.01182.161-0.054-0.0540.0000.0000.0000.000
143E196ARG10.8880.93581.228-3.948-3.9480.0000.0000.0000.000
144E197ILE0-0.007-0.00685.031-0.045-0.0450.0000.0000.0000.000
145E198LYS10.8180.88387.186-3.669-3.6690.0000.0000.0000.000
146E199GLN0-0.036-0.01187.706-0.001-0.0010.0000.0000.0000.000
147E200ILE0-0.095-0.04090.170-0.035-0.0350.0000.0000.0000.000
148E201GLU-1-0.849-0.90191.2443.5253.5250.0000.0000.0000.000
149E202GLU-1-0.987-0.98092.9593.3243.3240.0000.0000.0000.000
150E253ALA00.0520.02766.494-0.023-0.0230.0000.0000.0000.000
151E254TYR00.036-0.00166.4310.0390.0390.0000.0000.0000.000
152E255TYR00.0520.03566.5780.0420.0420.0000.0000.0000.000
153E256GLN00.0260.00160.278-0.036-0.0360.0000.0000.0000.000
154E257THR00.0420.03861.9850.1000.1000.0000.0000.0000.000
155E258LYS10.9180.96861.717-4.709-4.7090.0000.0000.0000.000
156E259GLN0-0.040-0.02062.194-0.003-0.0030.0000.0000.0000.000
157E260THR00.0700.02256.9660.0650.0650.0000.0000.0000.000
158E261LEU00.0020.00457.4130.0980.0980.0000.0000.0000.000
159E262LEU0-0.080-0.02657.8680.0470.0470.0000.0000.0000.000
160E263ASP-1-0.886-0.96055.6735.4965.4960.0000.0000.0000.000
161E264ILE0-0.006-0.01252.9170.1220.1220.0000.0000.0000.000
162E265LYS10.9080.96552.990-5.247-5.2470.0000.0000.0000.000
163E266ASN0-0.059-0.03253.7550.0490.0490.0000.0000.0000.000
164E267LEU0-0.0080.01949.0190.0720.0720.0000.0000.0000.000
165E268LYS10.8200.90042.823-6.953-6.9530.0000.0000.0000.000
166E269VAL00.0070.00542.3370.0220.0220.0000.0000.0000.000
167E270THR0-0.061-0.03941.251-0.019-0.0190.0000.0000.0000.000
168E271ALA00.0220.00037.3900.0610.0610.0000.0000.0000.000
169E272ASP-1-0.832-0.89835.7947.8787.8780.0000.0000.0000.000
170E273THR0-0.042-0.02635.8110.1130.1130.0000.0000.0000.000
171E274VAL0-0.0300.00735.4530.0110.0110.0000.0000.0000.000
172E275HIS0-0.046-0.02131.4370.3900.3900.0000.0000.0000.000
173E276VAL0-0.003-0.01630.913-0.242-0.2420.0000.0000.0000.000
174E277TYR0-0.026-0.01625.4330.2920.2920.0000.0000.0000.000
175E278ARG10.9140.96629.561-9.370-9.3700.0000.0000.0000.000
176E279TYR00.001-0.01122.0930.3900.3900.0000.0000.0000.000
177E280VAL0-0.033-0.01725.756-0.425-0.4250.0000.0000.0000.000
178E281MET0-0.029-0.01520.6850.1510.1510.0000.0000.0000.000
179E282LYS10.9470.98021.014-12.026-12.0260.0000.0000.0000.000
180E283PRO00.0000.01316.1050.0960.0960.0000.0000.0000.000
181E284THR00.0480.02314.7840.1580.1580.0000.0000.0000.000
182E285LEU00.0210.03611.3600.8640.8640.0000.0000.0000.000
183E286PRO0-0.046-0.0168.466-0.543-0.5430.0000.0000.0000.000
184E287VAL00.014-0.0039.1461.8801.8800.0000.0000.0000.000
185E288ARG10.8270.9038.711-26.687-26.6870.0000.0000.0000.000
186E289ARG10.9230.9601.929-84.269-88.89614.792-5.193-4.9720.037
187E290ASP-1-0.757-0.8595.88927.20327.2030.0000.0000.0000.000
188E291SER0-0.021-0.0125.8155.0185.0180.0000.0000.0000.000
189E292PRO00.0120.0166.347-3.640-3.6400.0000.0000.0000.000