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: GQMQ1

Calculation Name: 3FRR-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FRR

Chain ID: A

ChEMBL ID:

UniProt ID: P53990

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1962513.831923
FMO2-HF: Nuclear repulsion 1888041.02121
FMO2-HF: Total energy -74472.810713
FMO2-MP2: Total energy -74690.00559


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:1:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
1.642.449-0.005-0.379-0.425-0.001
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.002
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].
3A3GLY 00.0170.0233.8511.0161.825-0.005-0.379-0.425-0.001
4A4SER 00.0150.0066.4260.0100.0100.0000.0000.0000.000
5A5GLY 00.0250.01310.0770.0190.0190.0000.0000.0000.000
6A6PHE 0-0.022-0.01513.2120.0550.0550.0000.0000.0000.000
7A7LYS 10.9480.96615.0080.1770.1770.0000.0000.0000.000
8A8ALA 00.0460.02317.5070.0070.0070.0000.0000.0000.000
9A9GLU -1-0.755-0.88619.963-0.025-0.0250.0000.0000.0000.000
10A10ARG 10.8990.95320.4390.0830.0830.0000.0000.0000.000
11A11LEU 00.0460.03821.9520.0010.0010.0000.0000.0000.000
12A12ARG 10.8840.94023.5920.0230.0230.0000.0000.0000.000
13A13VAL 0-0.011-0.01025.8310.0030.0030.0000.0000.0000.000
14A14ASN 0-0.030-0.04625.1460.0040.0040.0000.0000.0000.000
15A15LEU 00.0440.03426.6820.0010.0010.0000.0000.0000.000
16A16ARG 10.9680.99929.5170.0300.0300.0000.0000.0000.000
17A17LEU 0-0.025-0.02029.7670.0020.0020.0000.0000.0000.000
18A18VAL 00.0280.01630.4300.0010.0010.0000.0000.0000.000
19A19ILE 00.0100.01633.2870.0020.0020.0000.0000.0000.000
20A20ASN 0-0.018-0.02235.8120.0040.0040.0000.0000.0000.000
21A21ARG 10.8550.93235.9350.0490.0490.0000.0000.0000.000
22A22LEU 00.0220.00735.5150.0000.0000.0000.0000.0000.000
23A23LYS 10.9931.00738.9830.0260.0260.0000.0000.0000.000
24A24LEU 0-0.065-0.02340.9870.0010.0010.0000.0000.0000.000
25A25LEU 0-0.050-0.04439.1850.0010.0010.0000.0000.0000.000
26A26GLH 00.0450.01341.3800.0010.0010.0000.0000.0000.000
27A27LYS 10.9290.99244.7310.0230.0230.0000.0000.0000.000
28A28LYS 10.9700.98045.0030.0350.0350.0000.0000.0000.000
29A29LYS 10.8080.88642.5080.0400.0400.0000.0000.0000.000
30A30THR 00.0310.01347.7100.0010.0010.0000.0000.0000.000
31A31GLU -1-0.945-0.98250.379-0.023-0.0230.0000.0000.0000.000
32A32LEU 0-0.070-0.04148.8120.0010.0010.0000.0000.0000.000
33A33ALA 00.0750.03751.3400.0000.0000.0000.0000.0000.000
34A34GLN 00.0020.00753.0710.0010.0010.0000.0000.0000.000
35A35LYS 10.9510.96755.3070.0230.0230.0000.0000.0000.000
36A36ALA 00.0270.02153.9800.0000.0000.0000.0000.0000.000
37A37ARG 10.9250.95754.3350.0220.0220.0000.0000.0000.000
38A38LYS 10.9470.99558.4740.0180.0180.0000.0000.0000.000
39A39GLU -1-0.917-0.95857.079-0.025-0.0250.0000.0000.0000.000
40A40ILE 0-0.018-0.01557.5390.0000.0000.0000.0000.0000.000
41A41ALA 00.0170.00560.9000.0010.0010.0000.0000.0000.000
42A42ASP -1-0.885-0.94763.662-0.018-0.0180.0000.0000.0000.000
43A43TYR 0-0.114-0.06659.6110.0000.0000.0000.0000.0000.000
44A44LEU 00.0070.01563.7820.0000.0000.0000.0000.0000.000
45A45ALA 0-0.0080.00466.6210.0010.0010.0000.0000.0000.000
46A46ALA 0-0.067-0.02767.9230.0000.0000.0000.0000.0000.000
47A47GLY 00.0520.05468.7940.0000.0000.0000.0000.0000.000
48A48LYS 10.8390.90464.8260.0200.0200.0000.0000.0000.000
49A49ASP -1-0.795-0.92364.295-0.019-0.0190.0000.0000.0000.000
50A50GLU -1-0.935-0.96661.557-0.023-0.0230.0000.0000.0000.000
51A51ARG 10.9040.94160.5960.0220.0220.0000.0000.0000.000
52A52ALA 00.0160.00759.401-0.001-0.0010.0000.0000.0000.000
53A53ARG 10.9220.97058.8110.0190.0190.0000.0000.0000.000
54A54ILE 00.0190.02655.015-0.001-0.0010.0000.0000.0000.000
55A55ARG 10.8870.94054.7590.0260.0260.0000.0000.0000.000
56A56VAL 00.0090.00554.471-0.001-0.0010.0000.0000.0000.000
57A57GLU -1-0.859-0.93751.290-0.031-0.0310.0000.0000.0000.000
58A58HIS 0-0.042-0.02147.188-0.001-0.0010.0000.0000.0000.000
59A59ILE 0-0.016-0.00349.602-0.001-0.0010.0000.0000.0000.000
60A60ILE 00.0160.02649.8960.0000.0000.0000.0000.0000.000
61A61ARG 10.9090.94645.6150.0350.0350.0000.0000.0000.000
62A62GLU -1-0.860-0.93045.509-0.038-0.0380.0000.0000.0000.000
63A63ASP -1-0.802-0.90246.731-0.025-0.0250.0000.0000.0000.000
64A64TYR 0-0.017-0.01345.1780.0010.0010.0000.0000.0000.000
65A65LEU 0-0.0040.00140.119-0.001-0.0010.0000.0000.0000.000
66A66VAL 00.007-0.00442.330-0.001-0.0010.0000.0000.0000.000
67A67GLU -1-0.814-0.89043.619-0.026-0.0260.0000.0000.0000.000
68A68ALA 0-0.027-0.02039.5230.0000.0000.0000.0000.0000.000
69A69MET 0-0.085-0.04638.831-0.001-0.0010.0000.0000.0000.000
70A70GLU -1-0.857-0.92139.029-0.026-0.0260.0000.0000.0000.000
71A71ILE 0-0.032-0.00537.2370.0010.0010.0000.0000.0000.000
72A72LEU 0-0.019-0.03033.700-0.001-0.0010.0000.0000.0000.000
73A73GLU -1-0.872-0.94034.769-0.030-0.0300.0000.0000.0000.000
74A74LEU 00.0100.01536.0620.0010.0010.0000.0000.0000.000
75A75TYR 00.0110.00632.2790.0000.0000.0000.0000.0000.000
76A76CYS 0-0.064-0.03631.100-0.003-0.0030.0000.0000.0000.000
77A77ASP -1-0.925-0.96031.547-0.020-0.0200.0000.0000.0000.000
78A78LEU 00.0250.02031.9880.0030.0030.0000.0000.0000.000
79A79LEU 0-0.022-0.01626.5590.0020.0020.0000.0000.0000.000
80A80LEU 0-0.054-0.03128.2760.0020.0020.0000.0000.0000.000
81A81ALA 00.0070.01629.9880.0040.0040.0000.0000.0000.000
82A82ARG 10.8980.94329.1420.0120.0120.0000.0000.0000.000
83A83PHE 00.0280.02422.8750.0000.0000.0000.0000.0000.000
84A84GLY 00.012-0.00524.327-0.001-0.0010.0000.0000.0000.000
85A85LEU 00.0310.01323.6650.0060.0060.0000.0000.0000.000
86A86ILE 0-0.0230.01420.769-0.002-0.0020.0000.0000.0000.000
87A87GLN 0-0.051-0.05319.4850.0010.0010.0000.0000.0000.000
88A88SER 0-0.046-0.01318.7390.0100.0100.0000.0000.0000.000
89A89MET 00.0120.00919.7780.0140.0140.0000.0000.0000.000
90A90LYS 10.9580.97715.587-0.078-0.0780.0000.0000.0000.000
91A91GLU -1-0.923-0.95417.602-0.003-0.0030.0000.0000.0000.000
92A92LEU 0-0.024-0.01020.3780.0000.0000.0000.0000.0000.000
93A93ASP -1-0.852-0.93222.974-0.003-0.0030.0000.0000.0000.000
94A94SER 00.0600.01026.187-0.004-0.0040.0000.0000.0000.000
95A95GLY 0-0.0230.00029.050-0.003-0.0030.0000.0000.0000.000
96A96LEU 0-0.046-0.02626.330-0.002-0.0020.0000.0000.0000.000
97A97ALA 00.0230.01727.466-0.006-0.0060.0000.0000.0000.000
98A98GLU -1-0.814-0.88028.485-0.035-0.0350.0000.0000.0000.000
99A99SER 00.0200.00730.131-0.004-0.0040.0000.0000.0000.000
100A100VAL 0-0.012-0.00924.035-0.006-0.0060.0000.0000.0000.000
101A101SER 00.0450.01827.301-0.011-0.0110.0000.0000.0000.000
102A102THR 00.0180.01128.277-0.004-0.0040.0000.0000.0000.000
103A103LEU 0-0.007-0.00228.410-0.003-0.0030.0000.0000.0000.000
104A104ILE 0-0.057-0.03223.596-0.007-0.0070.0000.0000.0000.000
105A105TRP 0-0.026-0.00927.427-0.006-0.0060.0000.0000.0000.000
106A106ALA 00.0480.01430.465-0.001-0.0010.0000.0000.0000.000
107A107ALA 0-0.0070.00328.4240.0000.0000.0000.0000.0000.000
108A108PRO 0-0.048-0.03028.8120.0000.0000.0000.0000.0000.000
109A109ARG 10.8440.92831.3840.0690.0690.0000.0000.0000.000
110A110LEU 00.0650.03933.9580.0030.0030.0000.0000.0000.000
111A111GLN 0-0.038-0.01129.566-0.002-0.0020.0000.0000.0000.000
112A112SER 0-0.053-0.02632.9980.0000.0000.0000.0000.0000.000
113A113GLU -1-0.819-0.89035.825-0.043-0.0430.0000.0000.0000.000
114A114VAL 0-0.006-0.00933.2470.0030.0030.0000.0000.0000.000
115A115ALA 00.0740.04031.379-0.004-0.0040.0000.0000.0000.000
116A116GLU -1-0.916-0.97529.112-0.072-0.0720.0000.0000.0000.000
117A117LEU 00.0440.01828.455-0.003-0.0030.0000.0000.0000.000
118A118LYS 10.8980.94724.1840.1350.1350.0000.0000.0000.000
119A119ILE 0-0.050-0.00923.468-0.012-0.0120.0000.0000.0000.000
120A120VAL 00.0060.00123.560-0.008-0.0080.0000.0000.0000.000
121A121ALA 00.0400.02423.888-0.004-0.0040.0000.0000.0000.000
122A122ASP -1-0.847-0.91920.838-0.164-0.1640.0000.0000.0000.000
123A123GLN 0-0.0080.00418.115-0.017-0.0170.0000.0000.0000.000
124A124LEU 00.0160.01119.124-0.005-0.0050.0000.0000.0000.000
125A125CYS 0-0.041-0.01319.7110.0030.0030.0000.0000.0000.000
126A126ALA 0-0.064-0.02215.346-0.021-0.0210.0000.0000.0000.000
127A127LYS 10.7830.90014.9010.0220.0220.0000.0000.0000.000
128A128TYR 00.0510.01816.1510.0060.0060.0000.0000.0000.000
129A129SER 00.0160.02415.9220.0060.0060.0000.0000.0000.000
130A130LYS 10.9960.96916.5920.2830.2830.0000.0000.0000.000
131A131GLU -1-0.934-0.97216.312-0.211-0.2110.0000.0000.0000.000
132A132TYR 00.0470.00019.7820.0160.0160.0000.0000.0000.000
133A133GLY 00.0680.01121.0080.0100.0100.0000.0000.0000.000
134A134LYS 10.8500.90820.1190.1860.1860.0000.0000.0000.000
135A135LEU 00.0310.03624.3900.0080.0080.0000.0000.0000.000
136A136CYS 0-0.0190.01225.1130.0110.0110.0000.0000.0000.000
137A137ARG 10.9230.95922.8150.1340.1340.0000.0000.0000.000
138A138THR 0-0.012-0.03028.9010.0050.0050.0000.0000.0000.000
139A139ASN 00.0490.01630.5730.0040.0040.0000.0000.0000.000
140A140GLN 00.0360.04728.957-0.001-0.0010.0000.0000.0000.000
141A141ILE 0-0.072-0.03425.6650.0030.0030.0000.0000.0000.000
142A142GLY 00.0330.02429.2560.0040.0040.0000.0000.0000.000
143A143THR 0-0.013-0.00429.6380.0020.0020.0000.0000.0000.000
144A144VAL 0-0.042-0.02431.0760.0000.0000.0000.0000.0000.000
145A145ASN 00.027-0.00633.2400.0020.0020.0000.0000.0000.000
146A146ASP -1-0.849-0.93536.465-0.035-0.0350.0000.0000.0000.000
147A147ARG 10.8970.94539.3900.0240.0240.0000.0000.0000.000
148A148LEU 00.0240.01035.437-0.001-0.0010.0000.0000.0000.000
149A149MET 0-0.036-0.02636.144-0.003-0.0030.0000.0000.0000.000
150A150HIS 0-0.0040.00838.761-0.001-0.0010.0000.0000.0000.000
151A151LYS 10.8040.90341.8370.0280.0280.0000.0000.0000.000
152A152LEU 0-0.038-0.02137.079-0.001-0.0010.0000.0000.0000.000
153A153SER 0-0.0040.01340.319-0.003-0.0030.0000.0000.0000.000
154A154VAL 0-0.062-0.03740.3100.0010.0010.0000.0000.0000.000
155A155GLU -1-0.975-0.97543.044-0.036-0.0360.0000.0000.0000.000
156A156ALA 0-0.022-0.01045.9640.0010.0010.0000.0000.0000.000
157A157PRO 00.0110.00749.4040.0010.0010.0000.0000.0000.000
158A158PRO 00.0370.01850.8420.0010.0010.0000.0000.0000.000
159A159LYS 11.0541.01353.8320.0230.0230.0000.0000.0000.000
160A160ILE 00.0440.02856.5690.0000.0000.0000.0000.0000.000
161A161LEU 0-0.033-0.00751.9470.0010.0010.0000.0000.0000.000
162A162VAL 00.0190.00855.1500.0000.0000.0000.0000.0000.000
163A163GLU -1-0.751-0.87057.153-0.019-0.0190.0000.0000.0000.000
164A164ARG 10.9500.96857.9450.0190.0190.0000.0000.0000.000
165A165TYR 0-0.022-0.01552.4820.0000.0000.0000.0000.0000.000
166A166LEU 0-0.030-0.00558.6220.0000.0000.0000.0000.0000.000
167A167ILE 00.0070.00661.5130.0010.0010.0000.0000.0000.000
168A168GLU -1-0.883-0.95360.078-0.016-0.0160.0000.0000.0000.000
169A169ILE 0-0.072-0.03758.0360.0000.0000.0000.0000.0000.000
170A170ALA 00.0390.00962.3830.0000.0000.0000.0000.0000.000
171A171LYS 10.9000.95865.4160.0160.0160.0000.0000.0000.000
172A172ASN 0-0.039-0.02061.7650.0010.0010.0000.0000.0000.000
173A173TYR 0-0.085-0.04860.8390.0000.0000.0000.0000.0000.000
174A174ASN 0-0.060-0.00966.9700.0000.0000.0000.0000.0000.000
175A175VAL 0-0.036-0.00666.6610.0000.0000.0000.0000.0000.000
176A176PRO 00.006-0.00869.5440.0000.0000.0000.0000.0000.000
177A177TYR 0-0.039-0.06763.630-0.001-0.0010.0000.0000.0000.000
178A178GLU -1-0.953-0.96468.739-0.014-0.0140.0000.0000.0000.000
179A179PRO 0-0.017-0.01765.1870.0000.0000.0000.0000.0000.000
180A180ASP -1-0.884-0.94063.991-0.018-0.0180.0000.0000.0000.000
181A181SER 00.002-0.01265.6810.0000.0000.0000.0000.0000.000
182A182VAL 00.0560.02865.0350.0000.0000.0000.0000.0000.000
183A183VAL 0-0.029-0.00260.7040.0000.0000.0000.0000.0000.000
184A184MET 0-0.069-0.04362.6680.0000.0000.0000.0000.0000.000
185A185ALA 0-0.038-0.01264.7650.0000.0000.0000.0000.0000.000
186A186GLU -1-0.964-0.98362.420-0.018-0.0180.0000.0000.0000.000
187A187ALA 0-0.078-0.02660.504-0.001-0.0010.0000.0000.0000.000
188A188NME 0-0.021-0.00459.6750.0010.0010.0000.0000.0000.000