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: RYGK8

Calculation Name: 3RNV-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RNV

Chain ID: A

ChEMBL ID:

UniProt ID: P89509

Base Structure: X-ray

Registration Date: 2025-07-09

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 OptHSide
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 237
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1076784.095526
FMO2-HF: Nuclear repulsion 1027277.704796
FMO2-HF: Total energy -49506.39073
FMO2-MP2: Total energy -49649.083745


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:336:MET)


Summations of interaction energy for fragment #1(A:336:MET)
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.
-0.6982.694-0.016-1.976-1.40.01
Interaction energy analysis for fragmet #1(A:336:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.125 / q_NPA : 0.019
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].
4A337TYR0-0.1290.0824.247-0.720-0.1300.003-0.248-0.3450.000
5A338ILE00.129-0.0793.826-2.2870.482-0.018-1.712-1.0400.010
6A338ILE0-0.1100.0767.1750.0650.0650.0000.0000.0000.000
7A339ALA00.122-0.1066.8460.2100.2100.0000.0000.0000.000
8A339ALA0-0.0810.1248.5400.0560.0560.0000.0000.0000.000
9A340LYS00.099-0.1019.5080.1060.1060.0000.0000.0000.000
10A340LYS10.8481.05911.9240.6540.6540.0000.0000.0000.000
11A341GLU00.183-0.08612.731-0.037-0.0370.0000.0000.0000.000
12A341GLU-1-1.009-0.84817.171-0.262-0.2620.0000.0000.0000.000
13A342GLY0-0.011-0.10816.243-0.023-0.0230.0000.0000.0000.000
14A343TYR00.0810.01214.1710.0420.0420.0000.0000.0000.000
15A343TYR0-0.1070.08013.4110.0040.0040.0000.0000.0000.000
16A344CYS00.181-0.08111.232-0.194-0.1940.0000.0000.0000.000
17A344CYS0-0.0960.10811.755-0.002-0.0020.0000.0000.0000.000
18A345TYR00.069-0.10411.574-0.057-0.0570.0000.0000.0000.000
19A345TYR0-0.0680.08214.989-0.028-0.0280.0000.0000.0000.000
20A346ILE00.054-0.09910.9570.0840.0840.0000.0000.0000.000
21A346ILE0-0.0640.1009.104-0.015-0.0150.0000.0000.0000.000
22A347ASN00.047-0.1107.939-0.273-0.2730.0000.0000.0000.000
23A347ASN0-0.0480.0807.160-0.501-0.5010.0000.0000.0000.000
24A348ILE00.145-0.0388.723-0.041-0.0410.0000.0000.0000.000
25A348ILE0-0.0870.08412.6160.0200.0200.0000.0000.0000.000
26A349PHE00.089-0.10111.0290.1030.1030.0000.0000.0000.000
27A349PHE0-0.0740.06911.1500.0130.0130.0000.0000.0000.000
28A350LEU00.055-0.1046.4250.3430.3430.0000.0000.0000.000
29A350LEU0-0.0800.0875.127-0.0140.019-0.001-0.016-0.0150.000
30A351ALA00.101-0.0886.612-0.161-0.1610.0000.0000.0000.000
31A351ALA0-0.0390.1308.3570.0320.0320.0000.0000.0000.000
32A352MET00.041-0.1228.0070.2450.2450.0000.0000.0000.000
33A352MET0-0.1110.08011.2670.0130.0130.0000.0000.0000.000
34A353LEU00.022-0.0837.7340.2380.2380.0000.0000.0000.000
35A353LEU0-0.0800.0876.002-0.056-0.0560.0000.0000.0000.000
36A354VAL00.026-0.1108.7360.0340.0340.0000.0000.0000.000
37A354VAL0-0.0560.1167.2530.0360.0360.0000.0000.0000.000
38A355ASN00.075-0.0749.6380.1080.1080.0000.0000.0000.000
39A355ASN0-0.1620.02913.2140.0310.0310.0000.0000.0000.000
40A356VAL00.084-0.07712.1310.0270.0270.0000.0000.0000.000
41A356VAL0-0.1040.08611.489-0.012-0.0120.0000.0000.0000.000
42A357LYS00.162-0.07712.9740.0290.0290.0000.0000.0000.000
43A357LYS10.7951.04216.9650.1570.1570.0000.0000.0000.000
44A358GLU00.125-0.12513.130-0.098-0.0980.0000.0000.0000.000
45A358GLU-1-0.961-0.80312.4080.0780.0780.0000.0000.0000.000
46A359SER0-0.033-0.10214.177-0.068-0.0680.0000.0000.0000.000
47A359SER0-0.0210.06718.6580.0040.0040.0000.0000.0000.000
48A360GLN0-0.024-0.14715.539-0.003-0.0030.0000.0000.0000.000
49A360GLN0-0.0060.12415.8700.0220.0220.0000.0000.0000.000
50A361ALA00.170-0.05211.570-0.050-0.0500.0000.0000.0000.000
51A361ALA0-0.0360.13310.5490.0010.0010.0000.0000.0000.000
52A362LYS00.041-0.10412.039-0.194-0.1940.0000.0000.0000.000
53A362LYS10.8961.05813.0250.5080.5080.0000.0000.0000.000
54A363GLU00.067-0.14413.609-0.101-0.1010.0000.0000.0000.000
55A363GLU-1-0.932-0.77316.876-0.353-0.3530.0000.0000.0000.000
56A364PHE00.171-0.05913.3990.0000.0000.0000.0000.0000.000
57A364PHE0-0.0820.10311.2090.0210.0210.0000.0000.0000.000
58A365THR00.036-0.10510.8290.0090.0090.0000.0000.0000.000
59A365THR0-0.0750.0569.252-0.144-0.1440.0000.0000.0000.000
60A366LYS00.042-0.09211.835-0.109-0.1090.0000.0000.0000.000
61A366LYS10.8601.05814.7230.5290.5290.0000.0000.0000.000
62A367VAL00.067-0.06114.9350.0200.0200.0000.0000.0000.000
63A367VAL0-0.0510.10816.2320.0100.0100.0000.0000.0000.000
64A368VAL00.095-0.08012.9070.1070.1070.0000.0000.0000.000
65A368VAL0-0.0780.09311.418-0.026-0.0260.0000.0000.0000.000
66A369ARG00.084-0.09313.0940.0570.0570.0000.0000.0000.000
67A369ARG10.6980.97211.3751.0051.0050.0000.0000.0000.000
68A370ASP00.040-0.09913.9450.0230.0230.0000.0000.0000.000
69A370ASP-1-0.890-0.81816.573-0.715-0.7150.0000.0000.0000.000
70A371LYS00.094-0.04917.5340.0540.0540.0000.0000.0000.000
71A371LYS10.6880.94319.3390.3740.3740.0000.0000.0000.000
72A372LEU00.126-0.08917.5060.0470.0470.0000.0000.0000.000
73A372LEU0-0.1080.08215.979-0.003-0.0030.0000.0000.0000.000
74A373VAL00.073-0.09715.7720.0660.0660.0000.0000.0000.000
75A373VAL0-0.0990.08913.611-0.021-0.0210.0000.0000.0000.000
76A374GLY0-0.018-0.11916.9780.0370.0370.0000.0000.0000.000
77A375GLU00.0850.01620.2270.0340.0340.0000.0000.0000.000
78A375GLU-1-0.886-0.78921.645-0.368-0.3680.0000.0000.0000.000
79A376LEU00.054-0.09619.5010.0480.0480.0000.0000.0000.000
80A376LEU0-0.1270.07517.571-0.008-0.0080.0000.0000.0000.000
81A377GLY00.032-0.07619.9910.0380.0380.0000.0000.0000.000
82A378LYS00.1010.02918.829-0.064-0.0640.0000.0000.0000.000
83A378LYS10.8001.03218.8470.3540.3540.0000.0000.0000.000
84A379TRP0-0.047-0.09319.0940.0260.0260.0000.0000.0000.000
85A379TRP0-0.0980.05618.722-0.006-0.0060.0000.0000.0000.000
86A380PRO00.115-0.05518.5740.0390.0390.0000.0000.0000.000
87A381THR00.016-0.00721.233-0.003-0.0030.0000.0000.0000.000
88A381THR0-0.0410.04424.8350.0060.0060.0000.0000.0000.000
89A382LEU00.137-0.06920.917-0.039-0.0390.0000.0000.0000.000
90A382LEU0-0.0910.08919.8420.0030.0030.0000.0000.0000.000
91A383LEU00.048-0.12921.758-0.023-0.0230.0000.0000.0000.000
92A383LEU0-0.0510.13325.6680.0040.0040.0000.0000.0000.000
93A384ASP00.089-0.09623.1510.0030.0030.0000.0000.0000.000
94A384ASP-1-0.860-0.77822.588-0.258-0.2580.0000.0000.0000.000
95A385VAL00.114-0.07818.669-0.021-0.0210.0000.0000.0000.000
96A385VAL0-0.1050.09816.687-0.008-0.0080.0000.0000.0000.000
97A386ALA00.163-0.07418.895-0.044-0.0440.0000.0000.0000.000
98A386ALA0-0.0910.09721.0290.0080.0080.0000.0000.0000.000
99A387THR0-0.037-0.14520.5870.0030.0030.0000.0000.0000.000
100A387THR0-0.0600.07623.4590.0110.0110.0000.0000.0000.000
101A388ALA00.078-0.09319.1310.0280.0280.0000.0000.0000.000
102A388ALA0-0.0410.11918.471-0.012-0.0120.0000.0000.0000.000
103A389CYS00.027-0.13417.359-0.032-0.0320.0000.0000.0000.000
104A389CYS0-0.1280.06416.928-0.013-0.0130.0000.0000.0000.000
105A390TYR00.110-0.06918.270-0.001-0.0010.0000.0000.0000.000
106A390TYR0-0.1160.08522.8420.0100.0100.0000.0000.0000.000
107A391PHE00.110-0.05821.4760.0270.0270.0000.0000.0000.000
108A391PHE0-0.1000.06419.800-0.001-0.0010.0000.0000.0000.000
109A392LEU00.063-0.12117.2120.0280.0280.0000.0000.0000.000
110A392LEU0-0.0800.10214.671-0.011-0.0110.0000.0000.0000.000
111A393LYS00.104-0.05418.6620.0000.0000.0000.0000.0000.000
112A393LYS10.8051.01219.7470.1620.1620.0000.0000.0000.000
113A394VAL00.004-0.11220.0270.0190.0190.0000.0000.0000.000
114A394VAL0-0.0720.10723.4380.0040.0040.0000.0000.0000.000
115A395PHE00.062-0.09821.1580.0300.0300.0000.0000.0000.000
116A395PHE0-0.0990.07820.271-0.001-0.0010.0000.0000.0000.000
117A396TYR00.010-0.10017.3800.0240.0240.0000.0000.0000.000
118A396TYR0-0.1520.02016.752-0.033-0.0330.0000.0000.0000.000
119A397PRO00.094-0.08418.112-0.012-0.0120.0000.0000.0000.000
120A398ASP00.079-0.01518.0830.0070.0070.0000.0000.0000.000
121A398ASP-1-0.935-0.82717.222-0.126-0.1260.0000.0000.0000.000
122A399VAL00.102-0.10314.9540.0420.0420.0000.0000.0000.000
123A399VAL0-0.0710.12213.852-0.011-0.0110.0000.0000.0000.000
124A400ALA00.055-0.09915.768-0.024-0.0240.0000.0000.0000.000
125A400ALA0-0.0750.09320.0300.0040.0040.0000.0000.0000.000
126A401ASN00.043-0.09517.703-0.004-0.0040.0000.0000.0000.000
127A401ASN0-0.0930.06117.690-0.010-0.0100.0000.0000.0000.000
128A402ALA00.114-0.08813.1070.0800.0800.0000.0000.0000.000
129A402ALA0-0.0580.13312.056-0.022-0.0220.0000.0000.0000.000
130A403GLU00.069-0.12112.979-0.063-0.0630.0000.0000.0000.000
131A403GLU-1-0.975-0.83012.0420.2050.2050.0000.0000.0000.000
132A404LEU00.012-0.12911.319-0.076-0.0760.0000.0000.0000.000
133A404LEU0-0.1020.09012.727-0.016-0.0160.0000.0000.0000.000
134A405PRO00.024-0.0888.4900.0750.0750.0000.0000.0000.000
135A406ARG00.1600.05710.922-0.024-0.0240.0000.0000.0000.000
136A406ARG10.6820.94713.512-0.145-0.1450.0000.0000.0000.000
137A407MET00.049-0.11413.826-0.042-0.0420.0000.0000.0000.000
138A407MET0-0.1090.09915.112-0.010-0.0100.0000.0000.0000.000
139A408LEU00.126-0.10416.4470.0270.0270.0000.0000.0000.000
140A408LEU0-0.1330.09817.3070.0030.0030.0000.0000.0000.000
141A409VAL00.106-0.11918.859-0.033-0.0330.0000.0000.0000.000
142A409VAL0-0.0900.11321.510-0.001-0.0010.0000.0000.0000.000
143A410ASP00.139-0.08522.2030.0260.0260.0000.0000.0000.000
144A410ASP-1-0.892-0.75823.542-0.080-0.0800.0000.0000.0000.000
145A411HIS00.061-0.12324.602-0.016-0.0160.0000.0000.0000.000
146A411HIS0-0.0630.11326.533-0.007-0.0070.0000.0000.0000.000
147A412LYS00.106-0.08827.946-0.002-0.0020.0000.0000.0000.000
148A412LYS10.8661.07628.5330.0620.0620.0000.0000.0000.000
149A413THR0-0.038-0.13726.2470.0030.0030.0000.0000.0000.000
150A413THR0-0.0610.03725.136-0.006-0.0060.0000.0000.0000.000
151A414LYS00.081-0.04126.628-0.011-0.0110.0000.0000.0000.000
152A414LYS10.7941.03327.6340.0900.0900.0000.0000.0000.000
153A415ILE00.059-0.11122.598-0.014-0.0140.0000.0000.0000.000
154A415ILE0-0.0770.09520.483-0.001-0.0010.0000.0000.0000.000
155A416ILE00.084-0.10120.0430.0330.0330.0000.0000.0000.000
156A416ILE0-0.0720.10418.0470.0010.0010.0000.0000.0000.000
157A417HIS00.093-0.10216.785-0.057-0.0570.0000.0000.0000.000
158A417HIS0-0.0940.08716.334-0.018-0.0180.0000.0000.0000.000
159A418VAL00.114-0.10613.0260.0850.0850.0000.0000.0000.000
160A418VAL0-0.0960.11711.029-0.012-0.0120.0000.0000.0000.000
161A419VAL00.046-0.11211.204-0.095-0.0950.0000.0000.0000.000
162A419VAL0-0.1280.07412.6030.0180.0180.0000.0000.0000.000
163A420ASP00.132-0.1027.7040.0250.0250.0000.0000.0000.000
164A420ASP-1-0.921-0.7826.8790.1610.1610.0000.0000.0000.000
165A421SER00.096-0.0568.3690.2350.2350.0000.0000.0000.000
166A421SER0-0.0870.03810.8620.0160.0160.0000.0000.0000.000
167A422TYR00.100-0.06311.111-0.058-0.0580.0000.0000.0000.000
168A422TYR0-0.0580.11013.5530.0120.0120.0000.0000.0000.000
169A423GLY00.031-0.09814.157-0.047-0.0470.0000.0000.0000.000
170A424SER00.0200.04417.433-0.019-0.0190.0000.0000.0000.000
171A424SER0-0.0280.04117.743-0.014-0.0140.0000.0000.0000.000
172A425LEU00.097-0.09719.1620.0230.0230.0000.0000.0000.000
173A425LEU0-0.0740.13921.421-0.003-0.0030.0000.0000.0000.000
174A426SER00.074-0.07719.052-0.009-0.0090.0000.0000.0000.000
175A426SER00.0040.11019.8030.0010.0010.0000.0000.0000.000
176A427THR0-0.069-0.10220.372-0.009-0.0090.0000.0000.0000.000
177A427THR0-0.0390.05522.943-0.006-0.0060.0000.0000.0000.000
178A428GLY00.090-0.07223.3820.0010.0010.0000.0000.0000.000
179A429TYR00.1010.01725.212-0.006-0.0060.0000.0000.0000.000
180A429TYR0-0.0340.11028.2410.0010.0010.0000.0000.0000.000
181A430HIS00.047-0.07523.984-0.014-0.0140.0000.0000.0000.000
182A430HIS0-0.1270.06223.2020.0100.0100.0000.0000.0000.000
183A431VAL00.155-0.10120.517-0.014-0.0140.0000.0000.0000.000
184A431VAL0-0.1110.10518.8260.0030.0030.0000.0000.0000.000
185A432LEU00.132-0.07020.2620.0160.0160.0000.0000.0000.000
186A432LEU0-0.0740.10319.790-0.002-0.0020.0000.0000.0000.000
187A433LYS0-0.028-0.08719.474-0.008-0.0080.0000.0000.0000.000
188A433LYS10.8471.04021.755-0.023-0.0230.0000.0000.0000.000
189A434THR00.050-0.09519.7980.0220.0220.0000.0000.0000.000
190A434THR0-0.0660.06918.303-0.006-0.0060.0000.0000.0000.000
191A435ASN00.212-0.04816.706-0.037-0.0370.0000.0000.0000.000
192A435ASN0-0.1200.07117.251-0.003-0.0030.0000.0000.0000.000
193A436THR00.083-0.03915.5000.0050.0050.0000.0000.0000.000
194A436THR0-0.0640.05216.3920.0030.0030.0000.0000.0000.000
195A437VAL00.127-0.10916.2190.0030.0030.0000.0000.0000.000
196A437VAL0-0.0760.13614.675-0.006-0.0060.0000.0000.0000.000
197A438GLU00.176-0.07517.286-0.007-0.0070.0000.0000.0000.000
198A438GLU-1-0.914-0.78420.721-0.120-0.1200.0000.0000.0000.000
199A439GLN0-0.013-0.14820.2070.0050.0050.0000.0000.0000.000
200A439GLN0-0.0490.11220.135-0.001-0.0010.0000.0000.0000.000
201A440LEU00.143-0.08519.4080.0250.0250.0000.0000.0000.000
202A440LEU0-0.0840.12117.509-0.002-0.0020.0000.0000.0000.000
203A441ILE00.087-0.08620.7820.0010.0010.0000.0000.0000.000
204A441ILE0-0.0930.09620.0470.0030.0030.0000.0000.0000.000
205A442LYS00.072-0.11922.8340.0020.0020.0000.0000.0000.000
206A442LYS10.7060.97023.9360.0920.0920.0000.0000.0000.000
207A443PHE00.052-0.07724.4250.0090.0090.0000.0000.0000.000
208A443PHE0-0.0910.06923.7120.0030.0030.0000.0000.0000.000
209A444THR00.005-0.08424.7220.0140.0140.0000.0000.0000.000
210A444THR0-0.0100.07223.7910.0020.0020.0000.0000.0000.000
211A445ARG00.060-0.05825.921-0.002-0.0020.0000.0000.0000.000
212A445ARG10.8681.05126.9560.1060.1060.0000.0000.0000.000
213A446CYS00.110-0.09828.3330.0050.0050.0000.0000.0000.000
214A446CYS0-0.1430.09530.1420.0030.0030.0000.0000.0000.000
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216A447ASN0-0.0940.06935.2210.0000.0000.0000.0000.0000.000
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