FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 8N6YY

Calculation Name: 2YV4-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YV4

Chain ID: A

ChEMBL ID:

UniProt ID: O73972

Base Structure: X-ray

Registration Date: 2025-07-08

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -795931.49691
FMO2-HF: Nuclear repulsion 756268.558734
FMO2-HF: Total energy -39662.938177
FMO2-MP2: Total energy -39779.827513


3D Structure Molmil
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(A:236:ALA)


Summations of interaction energy for fragment #1(A:236:ALA)
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.
-11.451-9.828-0.01-0.956-0.6560.004
Interaction energy analysis for fragmet #1(A:236:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.090 / q_NPA : -0.024
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].
4A238ASN00.032-0.0143.892-3.846-2.395-0.006-0.916-0.5300.004
5A238ASN0-0.1290.0525.3620.9561.012-0.001-0.005-0.0490.000
6A239ALA00.155-0.0526.8940.1650.1650.0000.0000.0000.000
7A239ALA0-0.0640.1019.1910.0750.0750.0000.0000.0000.000
8A240GLU00.047-0.1208.015-0.369-0.3690.0000.0000.0000.000
9A240GLU-1-0.881-0.78211.504-0.589-0.5890.0000.0000.0000.000
10A241VAL00.062-0.0958.5710.1140.1140.0000.0000.0000.000
11A241VAL0-0.0920.0986.7260.0750.0750.0000.0000.0000.000
12A242ILE00.075-0.1079.7370.0220.0220.0000.0000.0000.000
13A242ILE0-0.0850.09113.4440.0040.0040.0000.0000.0000.000
14A243VAL00.089-0.08113.1810.0140.0140.0000.0000.0000.000
15A243VAL0-0.0610.10012.0960.0170.0170.0000.0000.0000.000
16A244VAL00.058-0.10314.432-0.026-0.0260.0000.0000.0000.000
17A244VAL0-0.0910.10817.170-0.004-0.0040.0000.0000.0000.000
18A245GLU00.044-0.11818.1930.0170.0170.0000.0000.0000.000
19A245GLU-1-0.950-0.83518.3710.1190.1190.0000.0000.0000.000
20A246GLY00.007-0.10520.164-0.027-0.0270.0000.0000.0000.000
21A247PRO00.0230.00723.7800.0130.0130.0000.0000.0000.000
22A248ARG00.1800.01624.870-0.016-0.0160.0000.0000.0000.000
23A248ARG10.7641.01724.182-0.100-0.1000.0000.0000.0000.000
24A249GLU00.072-0.09425.912-0.011-0.0110.0000.0000.0000.000
25A249GLU-1-0.906-0.80030.0090.0130.0130.0000.0000.0000.000
26A250LYS00.125-0.08627.532-0.011-0.0110.0000.0000.0000.000
27A250LYS10.7420.99727.198-0.010-0.0100.0000.0000.0000.000
28A251VAL00.072-0.10723.009-0.022-0.0220.0000.0000.0000.000
29A251VAL0-0.0990.11221.1090.0010.0010.0000.0000.0000.000
30A252LYS00.072-0.10723.379-0.018-0.0180.0000.0000.0000.000
31A252LYS10.7250.96324.445-0.012-0.0120.0000.0000.0000.000
32A253GLY00.006-0.08625.227-0.016-0.0160.0000.0000.0000.000
33A254LYS00.1510.03623.700-0.016-0.0160.0000.0000.0000.000
34A254LYS10.7210.99321.9210.0960.0960.0000.0000.0000.000
35A255ILE00.109-0.10021.040-0.027-0.0270.0000.0000.0000.000
36A255ILE0-0.0770.09519.2580.0000.0000.0000.0000.0000.000
37A256THR00.047-0.08821.835-0.029-0.0290.0000.0000.0000.000
38A256THR0-0.0850.03525.8310.0010.0010.0000.0000.0000.000
39A257GLU00.089-0.09124.969-0.012-0.0120.0000.0000.0000.000
40A257GLU-1-0.938-0.79024.979-0.103-0.1030.0000.0000.0000.000
41A258LEU00.045-0.11120.909-0.009-0.0090.0000.0000.0000.000
42A258LEU0-0.0600.09219.139-0.002-0.0020.0000.0000.0000.000
43A259VAL00.085-0.08720.897-0.041-0.0410.0000.0000.0000.000
44A259VAL0-0.0770.10120.144-0.001-0.0010.0000.0000.0000.000
45A260LYS00.102-0.08821.861-0.027-0.0270.0000.0000.0000.000
46A260LYS10.8441.05126.1980.1150.1150.0000.0000.0000.000
47A261GLU00.117-0.07324.209-0.007-0.0070.0000.0000.0000.000
48A261GLU-1-0.996-0.83522.965-0.242-0.2420.0000.0000.0000.000
49A262LEU00.052-0.10220.052-0.005-0.0050.0000.0000.0000.000
50A262LEU0-0.1040.07017.518-0.014-0.0140.0000.0000.0000.000
51A263LYS00.118-0.07421.419-0.038-0.0380.0000.0000.0000.000
52A263LYS10.7160.97422.1130.2340.2340.0000.0000.0000.000
53A264GLU00.107-0.06823.388-0.014-0.0140.0000.0000.0000.000
54A264GLU-1-1.037-0.87126.598-0.190-0.1900.0000.0000.0000.000
55A265ARG0-0.016-0.11323.3010.0080.0080.0000.0000.0000.000
56A265ARG10.7410.99419.7620.3410.3410.0000.0000.0000.000
57A266GLY00.019-0.10822.945-0.030-0.0300.0000.0000.0000.000
58A267LYS00.028-0.00618.937-0.028-0.0280.0000.0000.0000.000
59A267LYS10.7520.97516.1540.6970.6970.0000.0000.0000.000
60A268LYS00.167-0.05218.3800.0560.0560.0000.0000.0000.000
61A268LYS10.6780.97717.2850.4450.4450.0000.0000.0000.000
62A269VAL00.067-0.11916.589-0.102-0.1020.0000.0000.0000.000
63A269VAL0-0.1090.11116.8630.0070.0070.0000.0000.0000.000
64A270GLY00.011-0.11615.3050.0370.0370.0000.0000.0000.000
65A271VAL00.063-0.01815.564-0.022-0.0220.0000.0000.0000.000
66A271VAL0-0.0940.11317.7050.0040.0040.0000.0000.0000.000
67A272ILE00.110-0.09213.600-0.008-0.0080.0000.0000.0000.000
68A272ILE0-0.1200.11310.7620.0230.0230.0000.0000.0000.000
69A273GLY00.051-0.11515.0650.0380.0380.0000.0000.0000.000
70A274SER00.0350.00818.3870.0150.0150.0000.0000.0000.000
71A274SER0-0.0870.02322.675-0.006-0.0060.0000.0000.0000.000
72A275GLU00.048-0.11921.7410.0070.0070.0000.0000.0000.000
73A275GLU-1-0.919-0.79523.751-0.023-0.0230.0000.0000.0000.000
74A276SER00.081-0.08920.9520.0010.0010.0000.0000.0000.000
75A276SER00.0010.09622.1300.0010.0010.0000.0000.0000.000
76A277TYR00.026-0.07221.759-0.024-0.0240.0000.0000.0000.000
77A277TYR0-0.0700.07220.7710.0040.0040.0000.0000.0000.000
78A278ASN00.131-0.03924.073-0.009-0.0090.0000.0000.0000.000
79A278ASN0-0.1390.04526.240-0.008-0.0080.0000.0000.0000.000
80A279ALA00.185-0.08720.120-0.010-0.0100.0000.0000.0000.000
81A279ALA0-0.1140.08019.2480.0000.0000.0000.0000.0000.000
82A280ASP0-0.016-0.13519.9610.0360.0360.0000.0000.0000.000
83A280ASP-1-0.826-0.79519.465-0.310-0.3100.0000.0000.0000.000
84A281GLU00.009-0.12517.2080.0070.0070.0000.0000.0000.000
85A281GLU-1-0.779-0.74416.423-0.313-0.3130.0000.0000.0000.000
86A282PHE00.047-0.09917.921-0.007-0.0070.0000.0000.0000.000
87A282PHE0-0.0710.09419.0660.0030.0030.0000.0000.0000.000
88A283PHE00.094-0.08215.654-0.009-0.0090.0000.0000.0000.000
89A283PHE0-0.1160.08014.9470.0170.0170.0000.0000.0000.000
90A284PHE00.157-0.07317.0320.0050.0050.0000.0000.0000.000
91A284PHE0-0.1130.10219.7510.0030.0030.0000.0000.0000.000
92A285LEU00.077-0.12215.8010.0360.0360.0000.0000.0000.000
93A285LEU0-0.1100.11414.4660.0030.0030.0000.0000.0000.000
94A286GLY0-0.015-0.11216.7760.0700.0700.0000.0000.0000.000
95A287SER00.0250.00319.591-0.014-0.0140.0000.0000.0000.000
96A287SER0-0.0800.04723.955-0.010-0.0100.0000.0000.0000.000
97A288SER00.019-0.09421.173-0.022-0.0220.0000.0000.0000.000
98A288SER0-0.0400.04222.3770.0120.0120.0000.0000.0000.000
99A289VAL00.128-0.08818.8280.0140.0140.0000.0000.0000.000
100A289VAL0-0.0490.11818.4500.0000.0000.0000.0000.0000.000
101A290GLU00.101-0.08317.7550.0770.0770.0000.0000.0000.000
102A290GLU-1-0.861-0.77419.9440.3870.3870.0000.0000.0000.000
103A291GLU00.064-0.12117.6940.0690.0690.0000.0000.0000.000
104A291GLU-1-0.819-0.72919.3110.2150.2150.0000.0000.0000.000
105A292VAL00.090-0.07415.5170.0150.0150.0000.0000.0000.000
106A292VAL0-0.0650.10814.2170.0000.0000.0000.0000.0000.000
107A293ALA00.117-0.10313.5230.0970.0970.0000.0000.0000.000
108A293ALA0-0.0840.11814.9170.0000.0000.0000.0000.0000.000
109A294LYS00.068-0.08512.8660.2130.2130.0000.0000.0000.000
110A294LYS10.7410.99116.198-0.401-0.4010.0000.0000.0000.000
111A295ASN00.039-0.14813.1540.0740.0740.0000.0000.0000.000
112A295ASN0-0.1110.09315.013-0.008-0.0080.0000.0000.0000.000
113A296LEU00.151-0.06710.895-0.105-0.1050.0000.0000.0000.000
114A296LEU0-0.0620.1308.9830.0140.0140.0000.0000.0000.000
115A297PHE00.092-0.0937.413-0.163-0.1630.0000.0000.0000.000
116A297PHE0-0.0880.0796.2200.1870.1870.0000.0000.0000.000
117A298LYS00.060-0.0817.898-0.087-0.0870.0000.0000.0000.000
118A298LYS10.8761.06212.041-0.220-0.2200.0000.0000.0000.000
119A299ALA00.091-0.10510.690-0.149-0.1490.0000.0000.0000.000
120A299ALA0-0.0830.09111.6440.0070.0070.0000.0000.0000.000
121A300LEU00.089-0.0937.197-0.166-0.1660.0000.0000.0000.000
122A300LEU0-0.0620.1035.3840.0850.0850.0000.0000.0000.000
123A301ARG00.117-0.0737.727-0.348-0.3480.0000.0000.0000.000
124A301ARG10.8291.0226.397-0.785-0.7850.0000.0000.0000.000
125A302TYR00.076-0.0648.344-0.146-0.1460.0000.0000.0000.000
126A302TYR0-0.1520.03012.8220.0380.0380.0000.0000.0000.000
127A303MET00.091-0.10211.323-0.006-0.0060.0000.0000.0000.000
128A303MET0-0.1220.09310.429-0.010-0.0100.0000.0000.0000.000
129A304ASP00.109-0.0838.5930.1200.1200.0000.0000.0000.000
130A304ASP-1-0.903-0.8106.542-2.597-2.5970.0000.0000.0000.000
131A305LYS00.121-0.0569.999-0.022-0.0220.0000.0000.0000.000
132A305LYS10.8231.03311.6830.3700.3700.0000.0000.0000.000
133A306ALA00.019-0.13212.4300.0470.0470.0000.0000.0000.000
134A306ALA0-0.0840.11914.7610.0150.0150.0000.0000.0000.000
135A307GLY0-0.016-0.10513.4510.0770.0770.0000.0000.0000.000
136A308VAL00.093-0.00313.2690.0570.0570.0000.0000.0000.000
137A308VAL0-0.1510.07412.6770.0170.0170.0000.0000.0000.000
138A309ASP00.087-0.08112.397-0.210-0.2100.0000.0000.0000.000
139A309ASP-1-0.870-0.80115.536-0.697-0.6970.0000.0000.0000.000
140A310VAL00.034-0.11112.663-0.194-0.1940.0000.0000.0000.000
141A310VAL0-0.0770.10613.8070.0170.0170.0000.0000.0000.000
142A311VAL00.147-0.07911.1330.0890.0890.0000.0000.0000.000
143A311VAL0-0.1230.10410.2140.0080.0080.0000.0000.0000.000
144A312ILE00.105-0.09312.1130.0120.0120.0000.0000.0000.000
145A312ILE0-0.0730.11316.1060.0050.0050.0000.0000.0000.000
146A313ALA00.074-0.10112.944-0.002-0.0020.0000.0000.0000.000
147A313ALA0-0.0810.09612.0810.0250.0250.0000.0000.0000.000
148A314GLU00.113-0.10714.233-0.001-0.0010.0000.0000.0000.000
149A314GLU-1-0.893-0.71918.1740.0490.0490.0000.0000.0000.000
150A315GLY0-0.012-0.12317.3190.0520.0520.0000.0000.0000.000
151A316VAL00.071-0.00617.887-0.001-0.0010.0000.0000.0000.000
152A316VAL0-0.1090.09920.926-0.001-0.0010.0000.0000.0000.000
153A317GLU00.118-0.12021.4060.0390.0390.0000.0000.0000.000
154A317GLU-1-0.947-0.81723.6520.0860.0860.0000.0000.0000.000
155A318GLU00.056-0.10523.7500.0240.0240.0000.0000.0000.000
156A318GLU-1-0.883-0.79525.9960.0870.0870.0000.0000.0000.000
157A319ARG00.016-0.09924.524-0.006-0.0060.0000.0000.0000.000
158A319ARG10.8451.02723.836-0.163-0.1630.0000.0000.0000.000
159A320GLY00.043-0.08722.0360.0250.0250.0000.0000.0000.000
160A321LEU00.002-0.02218.8860.0530.0530.0000.0000.0000.000
161A321LEU0-0.0470.11618.783-0.005-0.0050.0000.0000.0000.000
162A322GLY00.091-0.06217.0160.0420.0420.0000.0000.0000.000
163A323LEU00.1530.01716.0600.0430.0430.0000.0000.0000.000
164A323LEU0-0.0980.10917.416-0.008-0.0080.0000.0000.0000.000
165A324ALA00.054-0.10915.9240.0830.0830.0000.0000.0000.000
166A324ALA0-0.0900.08916.631-0.009-0.0090.0000.0000.0000.000
167A325VAL00.041-0.11012.7790.1620.1620.0000.0000.0000.000
168A325VAL0-0.0780.10411.820-0.004-0.0040.0000.0000.0000.000
169A326MET00.112-0.10211.4390.1870.1870.0000.0000.0000.000
170A326MET0-0.0670.11314.130-0.021-0.0210.0000.0000.0000.000
171A327ASN00.088-0.08111.5170.1570.1570.0000.0000.0000.000
172A327ASN0-0.1340.06114.643-0.021-0.0210.0000.0000.0000.000
173A328ARG00.062-0.09910.8170.1970.1970.0000.0000.0000.000
174A328ARG10.7321.0129.333-1.576-1.5760.0000.0000.0000.000
175A329LEU00.091-0.1137.2320.6810.6810.0000.0000.0000.000
176A329LEU0-0.0810.1225.953-0.018-0.0180.0000.0000.0000.000
177A330ARG00.038-0.0697.0130.2690.2690.0000.0000.0000.000
178A330ARG10.7650.9685.829-4.293-4.2930.0000.0000.0000.000
179A331LYS00.176-0.0189.381-0.277-0.2770.0000.0000.0000.000
180A331LYS10.9131.06111.426-0.626-0.6260.0000.0000.0000.000
181A332ALA00.074-0.1068.0770.4040.4040.0000.0000.0000.000
182A332ALA0-0.0800.1098.2340.0120.0120.0000.0000.0000.000
183A333SER00.007-0.0864.1970.9121.025-0.001-0.007-0.1050.000
184A333SER0-0.0580.0444.0290.0120.0630.000-0.025-0.0250.000
185A334GLY00.032-0.0825.073-1.423-1.471-0.002-0.0030.0530.000
186A335TYR00.0150.0057.065-0.228-0.2280.0000.0000.0000.000
187A335TYR0-0.0870.0717.851-0.008-0.0080.0000.0000.0000.000
188A336LYS00.145-0.0609.6940.0670.0670.0000.0000.0000.000
189A336LYS10.7270.98413.6440.4550.4550.0000.0000.0000.000
190A337ILE00.050-0.12513.4480.0300.0300.0000.0000.0000.000
191A337ILE0-0.0550.11914.4110.0040.0040.0000.0000.0000.000
192A338VAL00.030-0.12716.074-0.019-0.0190.0000.0000.0000.000
193A338VAL0-0.0600.12017.533-0.005-0.0050.0000.0000.0000.000
194A339LYS00.182-0.06419.3270.0170.0170.0000.0000.0000.000
195A339LYS10.8651.07622.654-0.020-0.0200.0000.0000.0000.000
196A340ALA0-0.136-0.18822.269-0.024-0.0240.0000.0000.0000.000
197A340ALA00.0520.05623.3750.0040.0040.0000.0000.0000.000