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: R8418

Calculation Name: 3RV1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RV1

Chain ID: A

ChEMBL ID:

UniProt ID: A7TR32

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:


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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2341776.924498
FMO2-HF: Nuclear repulsion 2253991.436232
FMO2-HF: Total energy -87785.488267
FMO2-MP2: Total energy -88042.750366


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(A:15:SER)


Summations of interaction energy for fragment #1(A:15:SER)
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.
-21.959-17.0845.712-4.115-6.4730.013
Interaction energy analysis for fragmet #1(A:15:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.011
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].
3A17GLU-1-0.807-0.8833.361-2.873-0.6380.074-0.970-1.3400.004
4A18LEU00.0480.0121.915-2.925-2.1733.598-1.627-2.723-0.010
5A19LYS10.8940.9572.253-15.390-13.5022.040-1.518-2.4100.019
6A20VAL00.0140.0165.9440.1410.1410.0000.0000.0000.000
7A21ARG10.7600.8576.3370.1430.1430.0000.0000.0000.000
8A22GLU-1-0.796-0.8767.806-0.323-0.3230.0000.0000.0000.000
9A23PHE0-0.0120.0059.5550.0820.0820.0000.0000.0000.000
10A24TYR00.000-0.04111.5640.0090.0090.0000.0000.0000.000
11A25ARG10.8190.89311.0080.2970.2970.0000.0000.0000.000
12A26LEU0-0.0020.00013.8760.0050.0050.0000.0000.0000.000
13A27HIS00.0140.00715.5150.0050.0050.0000.0000.0000.000
14A28ASN00.014-0.00117.258-0.019-0.0190.0000.0000.0000.000
15A29ALA00.0370.03118.508-0.006-0.0060.0000.0000.0000.000
16A30CYS0-0.046-0.02319.1270.0020.0020.0000.0000.0000.000
17A31VAL0-0.022-0.01321.565-0.002-0.0020.0000.0000.0000.000
18A32LYS10.8730.92523.220-0.024-0.0240.0000.0000.0000.000
19A33LEU0-0.0200.01924.389-0.004-0.0040.0000.0000.0000.000
20A34LYS10.8560.91525.923-0.099-0.0990.0000.0000.0000.000
21A35GLU-1-0.894-0.94027.6800.0310.0310.0000.0000.0000.000
22A36SER0-0.016-0.03228.358-0.004-0.0040.0000.0000.0000.000
23A37ILE0-0.006-0.00830.114-0.003-0.0030.0000.0000.0000.000
24A38LYS10.8680.92032.123-0.050-0.0500.0000.0000.0000.000
25A39LEU0-0.009-0.00632.997-0.002-0.0020.0000.0000.0000.000
26A40ILE0-0.039-0.02432.868-0.003-0.0030.0000.0000.0000.000
27A41TYR0-0.032-0.03233.8040.0000.0000.0000.0000.0000.000
28A42GLU-1-0.840-0.89437.9630.0430.0430.0000.0000.0000.000
29A43ASN00.0060.01939.616-0.002-0.0020.0000.0000.0000.000
30A44PRO00.0470.00641.3400.0000.0000.0000.0000.0000.000
31A45LEU0-0.035-0.00943.325-0.001-0.0010.0000.0000.0000.000
32A46VAL0-0.063-0.04040.532-0.002-0.0020.0000.0000.0000.000
33A47THR00.0060.00243.0170.0000.0000.0000.0000.0000.000
34A48ASP-1-0.902-0.95545.2060.0220.0220.0000.0000.0000.000
35A49GLN0-0.033-0.01746.745-0.002-0.0020.0000.0000.0000.000
36A50ASN00.0120.01549.191-0.001-0.0010.0000.0000.0000.000
37A51VAL00.0270.00348.868-0.001-0.0010.0000.0000.0000.000
38A52LEU0-0.046-0.01747.5230.0000.0000.0000.0000.0000.000
39A53ASN0-0.059-0.03251.650-0.001-0.0010.0000.0000.0000.000
40A54LEU00.0440.03147.384-0.001-0.0010.0000.0000.0000.000
41A55GLY0-0.027-0.01851.7180.0010.0010.0000.0000.0000.000
42A56THR0-0.039-0.02553.982-0.001-0.0010.0000.0000.0000.000
43A57ALA0-0.015-0.00255.9220.0000.0000.0000.0000.0000.000
44A58GLU-1-0.932-0.94256.9510.0040.0040.0000.0000.0000.000
45A59ASN0-0.018-0.01854.866-0.001-0.0010.0000.0000.0000.000
46A60THR00.048-0.00155.0240.0000.0000.0000.0000.0000.000
47A61ILE00.0200.02150.772-0.001-0.0010.0000.0000.0000.000
48A62ASP-1-0.763-0.85550.4770.0060.0060.0000.0000.0000.000
49A63TYR0-0.038-0.02950.6460.0000.0000.0000.0000.0000.000
50A64THR0-0.037-0.02847.731-0.001-0.0010.0000.0000.0000.000
51A65ILE0-0.004-0.00945.523-0.001-0.0010.0000.0000.0000.000
52A66LEU00.000-0.00245.8160.0000.0000.0000.0000.0000.000
53A67ASN0-0.079-0.03646.7830.0000.0000.0000.0000.0000.000
54A68THR0-0.0150.00442.385-0.002-0.0020.0000.0000.0000.000
55A69PRO00.0450.00839.1730.0020.0020.0000.0000.0000.000
56A70THR00.0090.01037.8320.0010.0010.0000.0000.0000.000
57A71LEU00.0530.02739.4050.0030.0030.0000.0000.0000.000
58A72ASN0-0.032-0.01941.6380.0030.0030.0000.0000.0000.000
59A73VAL0-0.0070.00334.8190.0020.0020.0000.0000.0000.000
60A74ALA00.0150.00537.3940.0030.0030.0000.0000.0000.000
61A75LYS10.9290.96138.416-0.012-0.0120.0000.0000.0000.000
62A76THR0-0.033-0.01037.2600.0020.0020.0000.0000.0000.000
63A77LEU0-0.045-0.02432.7450.0030.0030.0000.0000.0000.000
64A78LEU0-0.016-0.00336.4110.0040.0040.0000.0000.0000.000
65A79GLY00.0040.00639.0400.0020.0020.0000.0000.0000.000
66A80ASN0-0.025-0.01934.322-0.001-0.0010.0000.0000.0000.000
67A81ARG10.8420.90335.994-0.040-0.0400.0000.0000.0000.000
68A82TYR0-0.032-0.01436.7560.0040.0040.0000.0000.0000.000
69A83SER0-0.080-0.01535.4280.0020.0020.0000.0000.0000.000
70A84LEU0-0.001-0.01728.6720.0050.0050.0000.0000.0000.000
71A85ASP-1-0.722-0.82533.3310.0500.0500.0000.0000.0000.000
72A86LEU00.013-0.01128.3040.0060.0060.0000.0000.0000.000
73A87ILE0-0.013-0.00629.6620.0070.0070.0000.0000.0000.000
74A88ASP-1-0.872-0.93431.2320.0740.0740.0000.0000.0000.000
75A89LEU0-0.036-0.00125.8900.0090.0090.0000.0000.0000.000
76A90PHE0-0.003-0.00623.5480.0110.0110.0000.0000.0000.000
77A91GLN0-0.0020.00027.3480.0080.0080.0000.0000.0000.000
78A92SER0-0.056-0.04229.6120.0090.0090.0000.0000.0000.000
79A93HIS0-0.082-0.04524.1810.0140.0140.0000.0000.0000.000
80A94ASP-1-0.878-0.92325.1160.1690.1690.0000.0000.0000.000
81A95PHE0-0.0060.00420.7680.0140.0140.0000.0000.0000.000
82A96LYS10.8080.88923.603-0.187-0.1870.0000.0000.0000.000
83A97ASP-1-0.807-0.89722.9070.1100.1100.0000.0000.0000.000
84A98SER0-0.037-0.02422.2750.0010.0010.0000.0000.0000.000
85A99ASN0-0.055-0.02121.5610.0070.0070.0000.0000.0000.000
86A100THR00.002-0.01817.0150.0120.0120.0000.0000.0000.000
87A101ASP-1-0.873-0.94216.8540.3380.3380.0000.0000.0000.000
88A102VAL0-0.047-0.02111.7220.0730.0730.0000.0000.0000.000
89A103ASP-1-0.755-0.83814.0030.3060.3060.0000.0000.0000.000
90A104MET0-0.050-0.01413.804-0.022-0.0220.0000.0000.0000.000
91A105PHE0-0.075-0.0429.1840.0880.0880.0000.0000.0000.000
92A106ILE0-0.068-0.02012.0000.0250.0250.0000.0000.0000.000
93A107LYS10.9340.96514.331-0.399-0.3990.0000.0000.0000.000
94A108TYR00.0000.00415.660-0.020-0.0200.0000.0000.0000.000
95A109PRO00.0370.02015.8620.0190.0190.0000.0000.0000.000
96A110VAL00.0630.04810.677-0.007-0.0070.0000.0000.0000.000
97A111VAL00.0180.02213.050-0.016-0.0160.0000.0000.0000.000
98A112TYR0-0.070-0.05311.091-0.020-0.0200.0000.0000.0000.000
99A113ASP-1-0.810-0.9099.974-0.547-0.5470.0000.0000.0000.000
100A114GLU-1-0.904-0.9606.458-1.169-1.1690.0000.0000.0000.000
101A115ASN0-0.072-0.04610.0190.1020.1020.0000.0000.0000.000
102A116LEU00.0050.01312.9000.0600.0600.0000.0000.0000.000
103A117GLU-1-0.757-0.85911.5750.1270.1270.0000.0000.0000.000
104A118ASN0-0.047-0.03710.8650.0920.0920.0000.0000.0000.000
105A119LEU0-0.0040.01514.8070.0240.0240.0000.0000.0000.000
106A120ALA00.0310.00817.5130.0150.0150.0000.0000.0000.000
107A121PHE0-0.053-0.03416.1470.0250.0250.0000.0000.0000.000
108A122MET0-0.048-0.00719.1280.0070.0070.0000.0000.0000.000
109A123HIS00.017-0.00621.602-0.002-0.0020.0000.0000.0000.000
110A124LYS10.8680.93725.2490.0410.0410.0000.0000.0000.000
111A125SER0-0.013-0.00628.2500.0050.0050.0000.0000.0000.000
112A140GLN0-0.002-0.00125.078-0.004-0.0040.0000.0000.0000.000
113A141LEU0-0.039-0.02220.2840.0040.0040.0000.0000.0000.000
114A142SER0-0.020-0.01923.5270.0050.0050.0000.0000.0000.000
115A143ASN00.0170.00822.090-0.011-0.0110.0000.0000.0000.000
116A144GLU-1-0.755-0.87223.438-0.051-0.0510.0000.0000.0000.000
117A145ARG10.9590.97125.2000.0890.0890.0000.0000.0000.000
118A146LEU00.0140.01819.7990.0040.0040.0000.0000.0000.000
119A147GLU-1-0.895-0.95124.037-0.015-0.0150.0000.0000.0000.000
120A148PHE0-0.011-0.00526.3650.0060.0060.0000.0000.0000.000
121A149LEU0-0.0090.00123.9070.0040.0040.0000.0000.0000.000
122A150GLY00.040-0.00325.3150.0050.0050.0000.0000.0000.000
123A151ASP-1-0.904-0.92926.0840.0060.0060.0000.0000.0000.000
124A152SER0-0.036-0.02029.4650.0040.0040.0000.0000.0000.000
125A153TRP00.0280.00126.8150.0050.0050.0000.0000.0000.000
126A154LEU0-0.0010.01327.7850.0070.0070.0000.0000.0000.000
127A155GLY00.0250.01128.9750.0050.0050.0000.0000.0000.000
128A156ALA00.0040.02831.0750.0030.0030.0000.0000.0000.000
129A157LEU00.0340.00926.1010.0040.0040.0000.0000.0000.000
130A158VAL00.0090.00830.5710.0050.0050.0000.0000.0000.000
131A159SER0-0.037-0.05132.6360.0010.0010.0000.0000.0000.000
132A160TYR00.0320.02332.3610.0000.0000.0000.0000.0000.000
133A161ILE0-0.012-0.00429.6350.0030.0030.0000.0000.0000.000
134A162VAL0-0.044-0.02834.1520.0020.0020.0000.0000.0000.000
135A163TYR0-0.0010.00037.6010.0000.0000.0000.0000.0000.000
136A164THR0-0.033-0.02335.7500.0010.0010.0000.0000.0000.000
137A165ARG10.9170.97434.415-0.052-0.0520.0000.0000.0000.000
138A166PHE0-0.057-0.03638.6570.0020.0020.0000.0000.0000.000
139A167PRO00.0630.03141.830-0.002-0.0020.0000.0000.0000.000
140A168SER0-0.021-0.01143.844-0.001-0.0010.0000.0000.0000.000
141A169ALA0-0.052-0.00544.154-0.001-0.0010.0000.0000.0000.000
142A170ASN00.0300.01446.294-0.001-0.0010.0000.0000.0000.000
143A171GLU-1-0.829-0.92245.0130.0120.0120.0000.0000.0000.000
144A172GLY00.0670.04345.0040.0000.0000.0000.0000.0000.000
145A173MET0-0.050-0.03245.4400.0010.0010.0000.0000.0000.000
146A174LEU00.0000.00740.7910.0020.0020.0000.0000.0000.000
147A175SER0-0.001-0.02440.6940.0010.0010.0000.0000.0000.000
148A176GLN0-0.0100.00641.253-0.001-0.0010.0000.0000.0000.000
149A177MET0-0.015-0.00638.2300.0020.0020.0000.0000.0000.000
150A178LYS10.9490.98035.642-0.010-0.0100.0000.0000.0000.000
151A179GLU-1-0.876-0.93036.5040.0160.0160.0000.0000.0000.000
152A180SER0-0.104-0.05337.9020.0010.0010.0000.0000.0000.000
153A181ILE0-0.042-0.02832.3850.0040.0040.0000.0000.0000.000
154A182VAL0-0.008-0.01032.1680.0020.0020.0000.0000.0000.000
155A183ASN00.0160.03433.624-0.002-0.0020.0000.0000.0000.000
156A184ASN00.032-0.02432.9030.0020.0020.0000.0000.0000.000
157A185ASN0-0.033-0.01432.9330.0000.0000.0000.0000.0000.000
158A186ASN00.0340.01331.6590.0070.0070.0000.0000.0000.000
159A187LEU00.0240.01328.4180.0060.0060.0000.0000.0000.000
160A188PHE0-0.046-0.01828.5240.0040.0040.0000.0000.0000.000
161A189ASP-1-0.857-0.93029.1090.0550.0550.0000.0000.0000.000
162A190TRP0-0.057-0.03226.3640.0110.0110.0000.0000.0000.000
163A191SER00.0310.01424.4970.0140.0140.0000.0000.0000.000
164A192THR0-0.045-0.01524.3890.0090.0090.0000.0000.0000.000
165A193LYS10.9400.97725.163-0.089-0.0890.0000.0000.0000.000
166A194LEU0-0.017-0.01121.1680.0180.0180.0000.0000.0000.000
167A195ASN0-0.059-0.04620.4340.0170.0170.0000.0000.0000.000
168A196PHE00.0340.02019.2460.0110.0110.0000.0000.0000.000
169A197THR00.0110.00921.119-0.011-0.0110.0000.0000.0000.000
170A198LYS10.8810.93020.326-0.149-0.1490.0000.0000.0000.000
171A199ARG10.8440.91213.371-0.109-0.1090.0000.0000.0000.000
172A200LEU0-0.0030.00818.523-0.015-0.0150.0000.0000.0000.000
173A201GLN0-0.0170.02421.197-0.024-0.0240.0000.0000.0000.000
174A202GLY00.0400.00421.4800.0150.0150.0000.0000.0000.000
175A203ASN0-0.049-0.01222.9760.0030.0030.0000.0000.0000.000
176A204ILE0-0.0050.00125.6330.0000.0000.0000.0000.0000.000
177A205ALA00.0240.02228.0870.0040.0040.0000.0000.0000.000
178A217LYS10.8180.87631.2980.0080.0080.0000.0000.0000.000
179A218ARG10.9740.98826.596-0.002-0.0020.0000.0000.0000.000
180A219TYR0-0.036-0.04725.056-0.004-0.0040.0000.0000.0000.000
181A220ALA00.0290.01925.8790.0040.0040.0000.0000.0000.000
182A221ASP-1-0.680-0.81527.061-0.005-0.0050.0000.0000.0000.000
183A222CYS0-0.053-0.01422.003-0.006-0.0060.0000.0000.0000.000
184A223VAL0-0.022-0.00522.2120.0010.0010.0000.0000.0000.000
185A224GLN0-0.032-0.03223.3830.0010.0010.0000.0000.0000.000
186A225ALA00.0210.01522.060-0.006-0.0060.0000.0000.0000.000
187A226TYR0-0.051-0.04615.305-0.010-0.0100.0000.0000.0000.000
188A227ILE00.0010.00219.633-0.005-0.0050.0000.0000.0000.000
189A228GLY00.0650.02821.956-0.005-0.0050.0000.0000.0000.000
190A229ALA0-0.028-0.01317.029-0.011-0.0110.0000.0000.0000.000
191A230LEU0-0.057-0.02816.752-0.011-0.0110.0000.0000.0000.000
192A231VAL0-0.011-0.01118.926-0.003-0.0030.0000.0000.0000.000
193A232ILE0-0.035-0.02018.899-0.003-0.0030.0000.0000.0000.000
194A233ASP-1-0.798-0.91214.746-0.186-0.1860.0000.0000.0000.000
195A234ARG10.7940.90215.714-0.008-0.0080.0000.0000.0000.000
196A235PHE0-0.063-0.00120.3440.0100.0100.0000.0000.0000.000
197A236GLY00.0570.02123.118-0.011-0.0110.0000.0000.0000.000
198A237THR0-0.010-0.03124.7060.0000.0000.0000.0000.0000.000
199A238GLU-1-0.934-0.94327.4080.0180.0180.0000.0000.0000.000
200A239PHE00.0270.00628.6560.0020.0020.0000.0000.0000.000
201A240LEU0-0.027-0.00429.033-0.002-0.0020.0000.0000.0000.000
202A241ASP-1-0.838-0.91331.357-0.011-0.0110.0000.0000.0000.000
203A242ILE0-0.003-0.01434.770-0.001-0.0010.0000.0000.0000.000
204A243LYS10.8020.89430.0530.0470.0470.0000.0000.0000.000
205A244GLU-1-0.899-0.96732.492-0.038-0.0380.0000.0000.0000.000
206A245TRP00.0060.02135.3170.0000.0000.0000.0000.0000.000
207A246LEU0-0.011-0.01635.9270.0000.0000.0000.0000.0000.000
208A247GLU-1-0.851-0.89832.984-0.048-0.0480.0000.0000.0000.000
209A248GLU-1-0.917-0.96037.105-0.024-0.0240.0000.0000.0000.000
210A249LEU0-0.057-0.02840.1590.0000.0000.0000.0000.0000.000
211A250SER0-0.104-0.05838.6980.0010.0010.0000.0000.0000.000
212A251GLU-1-0.877-0.92939.042-0.042-0.0420.0000.0000.0000.000
213A252LYS10.9320.95041.0970.0260.0260.0000.0000.0000.000
214A253LYS10.8880.93341.2200.0210.0210.0000.0000.0000.000
215A254LEU00.0360.02535.811-0.001-0.0010.0000.0000.0000.000
216A255ALA00.0160.02938.990-0.003-0.0030.0000.0000.0000.000
217A256LYS10.8390.93041.0060.0260.0260.0000.0000.0000.000