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: GNJR1

Calculation Name: 3FRR-A-Xray372

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: 2023-06-19

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1962413.009077
FMO2-HF: Nuclear repulsion 1888109.522031
FMO2-HF: Total energy -74303.487047
FMO2-MP2: Total energy -74520.126305


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-0.751.261-0.009-1.117-0.8850.002
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.001
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].
3A4SER00.012-0.0013.767-0.7211.290-0.009-1.117-0.8850.002
4A5GLY00.0130.0105.878-0.244-0.2440.0000.0000.0000.000
5A6PHE0-0.017-0.0038.253-0.021-0.0210.0000.0000.0000.000
6A7LYS10.9630.97110.9860.2190.2190.0000.0000.0000.000
7A8ALA00.0510.03413.797-0.011-0.0110.0000.0000.0000.000
8A9GLU-1-0.712-0.84016.7920.0440.0440.0000.0000.0000.000
9A10ARG10.8570.92816.7380.0340.0340.0000.0000.0000.000
10A11LEU00.0090.02017.520-0.002-0.0020.0000.0000.0000.000
11A12ARG10.8410.88619.291-0.057-0.0570.0000.0000.0000.000
12A13VAL00.015-0.00222.149-0.003-0.0030.0000.0000.0000.000
13A14ASN00.0260.00219.611-0.007-0.0070.0000.0000.0000.000
14A15LEU00.0270.01822.4220.0000.0000.0000.0000.0000.000
15A16ARG10.8630.92724.942-0.027-0.0270.0000.0000.0000.000
16A17LEU0-0.029-0.01124.949-0.002-0.0020.0000.0000.0000.000
17A18VAL00.0200.00825.157-0.001-0.0010.0000.0000.0000.000
18A19ILE0-0.0110.00428.150-0.001-0.0010.0000.0000.0000.000
19A20ASN00.004-0.00631.0240.0020.0020.0000.0000.0000.000
20A21ARG10.8320.91130.0770.0050.0050.0000.0000.0000.000
21A22LEU00.0080.00329.964-0.001-0.0010.0000.0000.0000.000
22A23LYS10.8380.91033.557-0.019-0.0190.0000.0000.0000.000
23A24LEU0-0.046-0.01435.607-0.001-0.0010.0000.0000.0000.000
24A25LEU0-0.031-0.02033.069-0.001-0.0010.0000.0000.0000.000
25A26GLH00.047-0.00235.818-0.001-0.0010.0000.0000.0000.000
26A27LYS10.8480.92539.152-0.003-0.0030.0000.0000.0000.000
27A28LYS10.9560.97339.3940.0040.0040.0000.0000.0000.000
28A29LYS10.7760.86836.001-0.006-0.0060.0000.0000.0000.000
29A30THR00.0430.01641.5420.0000.0000.0000.0000.0000.000
30A31GLU-1-0.860-0.92044.5140.0020.0020.0000.0000.0000.000
31A32LEU0-0.073-0.03242.168-0.001-0.0010.0000.0000.0000.000
32A33ALA00.0690.03544.8340.0000.0000.0000.0000.0000.000
33A34GLN00.0350.02546.5000.0000.0000.0000.0000.0000.000
34A35LYS10.9230.95848.5790.0010.0010.0000.0000.0000.000
35A36ALA00.0240.01547.0610.0000.0000.0000.0000.0000.000
36A37ARG10.8970.92547.891-0.009-0.0090.0000.0000.0000.000
37A38LYS10.8250.91251.723-0.001-0.0010.0000.0000.0000.000
38A39GLU-1-0.794-0.85450.2980.0000.0000.0000.0000.0000.000
39A40ILE0-0.007-0.00150.5020.0000.0000.0000.0000.0000.000
40A41ALA00.0360.02153.9450.0000.0000.0000.0000.0000.000
41A42ASP-1-0.798-0.88356.8210.0010.0010.0000.0000.0000.000
42A43TYR0-0.143-0.10151.964-0.001-0.0010.0000.0000.0000.000
43A44LEU00.0250.01956.7290.0000.0000.0000.0000.0000.000
44A45ALA00.0050.01059.4770.0000.0000.0000.0000.0000.000
45A46ALA0-0.0210.00761.4880.0000.0000.0000.0000.0000.000
46A47GLY00.0430.01361.767-0.001-0.0010.0000.0000.0000.000
47A48LYS10.7780.90157.3000.0000.0000.0000.0000.0000.000
48A49ASP-1-0.730-0.88556.7130.0050.0050.0000.0000.0000.000
49A50GLU-1-0.822-0.90354.0660.0060.0060.0000.0000.0000.000
50A51ARG10.8580.92252.7960.0000.0000.0000.0000.0000.000
51A52ALA00.0020.01051.9030.0000.0000.0000.0000.0000.000
52A53ARG10.7830.86451.531-0.006-0.0060.0000.0000.0000.000
53A54ILE00.0020.00547.6350.0000.0000.0000.0000.0000.000
54A55ARG10.8400.89747.3280.0000.0000.0000.0000.0000.000
55A56VAL00.002-0.00747.1580.0000.0000.0000.0000.0000.000
56A57GLU-1-0.787-0.88643.6470.0100.0100.0000.0000.0000.000
57A58HIS0-0.044-0.01240.3470.0010.0010.0000.0000.0000.000
58A59ILE0-0.035-0.01642.6630.0000.0000.0000.0000.0000.000
59A60ILE00.0040.01743.2650.0010.0010.0000.0000.0000.000
60A61ARG10.7990.87838.422-0.010-0.0100.0000.0000.0000.000
61A62GLU-1-0.784-0.89638.7790.0070.0070.0000.0000.0000.000
62A63ASP-1-0.785-0.86440.3910.0120.0120.0000.0000.0000.000
63A64TYR00.0000.00138.9030.0020.0020.0000.0000.0000.000
64A65LEU0-0.0020.00133.7350.0020.0020.0000.0000.0000.000
65A66VAL0-0.013-0.00536.4810.0010.0010.0000.0000.0000.000
66A67GLU-1-0.732-0.85537.9430.0240.0240.0000.0000.0000.000
67A68ALA0-0.012-0.00933.8050.0030.0030.0000.0000.0000.000
68A69MET0-0.069-0.03533.1870.0020.0020.0000.0000.0000.000
69A70GLU-1-0.884-0.93933.6180.0230.0230.0000.0000.0000.000
70A71ILE0-0.017-0.00832.1720.0030.0030.0000.0000.0000.000
71A72LEU00.002-0.00927.9450.0050.0050.0000.0000.0000.000
72A73GLU-1-0.785-0.84629.7280.0240.0240.0000.0000.0000.000
73A74LEU00.0210.01231.3960.0020.0020.0000.0000.0000.000
74A75TYR0-0.034-0.04027.5940.0030.0030.0000.0000.0000.000
75A76CYS0-0.071-0.03926.6810.0060.0060.0000.0000.0000.000
76A77ASP-1-0.801-0.89727.3680.0390.0390.0000.0000.0000.000
77A78LEU00.0130.01928.5550.0030.0030.0000.0000.0000.000
78A79LEU0-0.012-0.01722.2130.0080.0080.0000.0000.0000.000
79A80LEU0-0.061-0.02924.6620.0060.0060.0000.0000.0000.000
80A81ALA00.0130.01526.6460.0030.0030.0000.0000.0000.000
81A82ARG10.8750.92926.471-0.071-0.0710.0000.0000.0000.000
82A83PHE00.0150.01619.5100.0140.0140.0000.0000.0000.000
83A84GLY00.0270.01421.9810.0120.0120.0000.0000.0000.000
84A85LEU00.0270.02121.8110.0180.0180.0000.0000.0000.000
85A86ILE00.0140.02118.0510.0240.0240.0000.0000.0000.000
86A87GLN0-0.038-0.02517.4450.0220.0220.0000.0000.0000.000
87A88SER0-0.057-0.03017.4180.0160.0160.0000.0000.0000.000
88A89MET00.0190.03118.6180.0150.0150.0000.0000.0000.000
89A90LYS10.8470.89514.081-0.341-0.3410.0000.0000.0000.000
90A91GLU-1-0.765-0.86615.4970.3470.3470.0000.0000.0000.000
91A92LEU0-0.0190.00418.159-0.009-0.0090.0000.0000.0000.000
92A93ASP-1-0.810-0.91619.6620.1220.1220.0000.0000.0000.000
93A94SER0-0.034-0.02223.357-0.008-0.0080.0000.0000.0000.000
94A95GLY00.0340.02426.081-0.007-0.0070.0000.0000.0000.000
95A96LEU0-0.037-0.03423.116-0.007-0.0070.0000.0000.0000.000
96A97ALA00.0080.01023.057-0.003-0.0030.0000.0000.0000.000
97A98GLU-1-0.767-0.82724.1110.0630.0630.0000.0000.0000.000
98A99SER00.0280.01325.805-0.003-0.0030.0000.0000.0000.000
99A100VAL0-0.009-0.01019.343-0.007-0.0070.0000.0000.0000.000
100A101SER00.0300.00021.7880.0000.0000.0000.0000.0000.000
101A102THR00.0240.00322.766-0.008-0.0080.0000.0000.0000.000
102A103LEU0-0.013-0.00323.240-0.008-0.0080.0000.0000.0000.000
103A104ILE0-0.061-0.03517.915-0.009-0.0090.0000.0000.0000.000
104A105TRP00.002-0.00121.499-0.008-0.0080.0000.0000.0000.000
105A106ALA00.0600.03224.281-0.007-0.0070.0000.0000.0000.000
106A107ALA00.0150.01022.078-0.006-0.0060.0000.0000.0000.000
107A108PRO0-0.067-0.03922.040-0.007-0.0070.0000.0000.0000.000
108A109ARG10.8140.90424.230-0.043-0.0430.0000.0000.0000.000
109A110LEU00.0630.03927.135-0.002-0.0020.0000.0000.0000.000
110A111GLN0-0.035-0.01622.545-0.002-0.0020.0000.0000.0000.000
111A112SER00.0050.00426.321-0.004-0.0040.0000.0000.0000.000
112A113GLU-1-0.856-0.91429.328-0.001-0.0010.0000.0000.0000.000
113A114VAL0-0.0050.00027.473-0.001-0.0010.0000.0000.0000.000
114A115ALA00.0700.04325.0330.0030.0030.0000.0000.0000.000
115A116GLU-1-0.881-0.96223.437-0.009-0.0090.0000.0000.0000.000
116A117LEU00.0330.00622.7280.0040.0040.0000.0000.0000.000
117A118LYS10.8560.92517.0410.0260.0260.0000.0000.0000.000
118A119ILE0-0.0200.00017.9160.0040.0040.0000.0000.0000.000
119A120VAL0-0.003-0.00417.9410.0060.0060.0000.0000.0000.000
120A121ALA00.0530.03018.5950.0160.0160.0000.0000.0000.000
121A122ASP-1-0.840-0.90414.7770.0100.0100.0000.0000.0000.000
122A123GLN0-0.030-0.02012.4040.0310.0310.0000.0000.0000.000
123A124LEU00.0370.02014.3770.0340.0340.0000.0000.0000.000
124A125CYS0-0.058-0.00913.2360.0270.0270.0000.0000.0000.000
125A126ALA0-0.059-0.03110.0940.0420.0420.0000.0000.0000.000
126A127LYS10.7670.89610.097-0.236-0.2360.0000.0000.0000.000
127A128TYR00.012-0.00412.4960.0470.0470.0000.0000.0000.000
128A129SER00.0050.01810.3020.0000.0000.0000.0000.0000.000
129A130LYS10.9770.9678.826-0.105-0.1050.0000.0000.0000.000
130A131GLU-1-0.835-0.91610.6710.1890.1890.0000.0000.0000.000
131A132TYR00.0710.02714.023-0.023-0.0230.0000.0000.0000.000
132A133GLY00.0780.01615.043-0.022-0.0220.0000.0000.0000.000
133A134LYS10.7580.85613.374-0.148-0.1480.0000.0000.0000.000
134A135LEU00.0420.03018.114-0.012-0.0120.0000.0000.0000.000
135A136CYS0-0.0150.01819.633-0.005-0.0050.0000.0000.0000.000
136A137ARG10.8850.93515.802-0.077-0.0770.0000.0000.0000.000
137A138THR0-0.002-0.02322.410-0.008-0.0080.0000.0000.0000.000
138A139ASN00.0580.03124.2950.0030.0030.0000.0000.0000.000
139A140GLN00.0300.03722.8080.0020.0020.0000.0000.0000.000
140A141ILE0-0.073-0.03320.3830.0060.0060.0000.0000.0000.000
141A142GLY00.0230.02323.5110.0040.0040.0000.0000.0000.000
142A143THR0-0.047-0.03224.6470.0010.0010.0000.0000.0000.000
143A144VAL0-0.049-0.03425.377-0.001-0.0010.0000.0000.0000.000
144A145ASN00.024-0.00527.644-0.006-0.0060.0000.0000.0000.000
145A146ASP-1-0.848-0.93631.1880.0500.0500.0000.0000.0000.000
146A147ARG10.9130.95533.842-0.041-0.0410.0000.0000.0000.000
147A148LEU00.0190.01429.697-0.003-0.0030.0000.0000.0000.000
148A149MET0-0.046-0.02530.266-0.002-0.0020.0000.0000.0000.000
149A150HIS0-0.023-0.00732.801-0.001-0.0010.0000.0000.0000.000
150A151LYS10.7460.86336.104-0.028-0.0280.0000.0000.0000.000
151A152LEU0-0.030-0.01630.672-0.002-0.0020.0000.0000.0000.000
152A153SER0-0.044-0.03833.0260.0000.0000.0000.0000.0000.000
153A154VAL0-0.048-0.03532.805-0.002-0.0020.0000.0000.0000.000
154A155GLU-1-0.873-0.89335.7560.0230.0230.0000.0000.0000.000
155A156ALA00.0200.02138.943-0.001-0.0010.0000.0000.0000.000
156A157PRO0-0.013-0.00942.5240.0010.0010.0000.0000.0000.000
157A158PRO00.0470.02543.917-0.001-0.0010.0000.0000.0000.000
158A159LYS10.8790.92846.923-0.010-0.0100.0000.0000.0000.000
159A160ILE00.0460.01550.150-0.001-0.0010.0000.0000.0000.000
160A161LEU0-0.031-0.01645.5500.0000.0000.0000.0000.0000.000
161A162VAL00.0150.01248.075-0.001-0.0010.0000.0000.0000.000
162A163GLU-1-0.719-0.83250.3800.0080.0080.0000.0000.0000.000
163A164ARG10.9660.97452.324-0.015-0.0150.0000.0000.0000.000
164A165TYR0-0.058-0.06346.3140.0000.0000.0000.0000.0000.000
165A166LEU0-0.0100.00852.022-0.001-0.0010.0000.0000.0000.000
166A167ILE00.0250.01254.813-0.001-0.0010.0000.0000.0000.000
167A168GLU-1-0.810-0.89154.1950.0100.0100.0000.0000.0000.000
168A169ILE0-0.039-0.01451.2440.0000.0000.0000.0000.0000.000
169A170ALA00.0180.00655.745-0.001-0.0010.0000.0000.0000.000
170A171LYS10.8180.89258.851-0.011-0.0110.0000.0000.0000.000
171A172ASN0-0.093-0.05056.7800.0000.0000.0000.0000.0000.000
172A173TYR0-0.055-0.05154.318-0.001-0.0010.0000.0000.0000.000
173A174ASN0-0.065-0.01660.2810.0000.0000.0000.0000.0000.000
174A175VAL0-0.043-0.00259.7460.0000.0000.0000.0000.0000.000
175A176PRO00.013-0.01262.6850.0000.0000.0000.0000.0000.000
176A177TYR0-0.044-0.05956.5030.0000.0000.0000.0000.0000.000
177A178GLU-1-0.932-0.95561.5430.0060.0060.0000.0000.0000.000
178A179PRO0-0.039-0.01258.4480.0000.0000.0000.0000.0000.000
179A180ASP-1-0.782-0.89356.6740.0090.0090.0000.0000.0000.000
180A181SER00.001-0.01558.7180.0010.0010.0000.0000.0000.000
181A182VAL0-0.0100.01758.2070.0000.0000.0000.0000.0000.000
182A183VAL00.0220.01253.6750.0010.0010.0000.0000.0000.000
183A184MET0-0.059-0.04956.0070.0010.0010.0000.0000.0000.000
184A185ALA0-0.053-0.00958.1610.0000.0000.0000.0000.0000.000
185A186GLU-1-0.944-0.97155.5780.0130.0130.0000.0000.0000.000
186A187ALA0-0.107-0.04054.0610.0010.0010.0000.0000.0000.000