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

tag_button

FMODB ID: 14MYZ

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1958620.203794
FMO2-HF: Nuclear repulsion 1884317.104268
FMO2-HF: Total energy -74303.099526
FMO2-MP2: Total energy -74519.851016


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.
-1.7620.723-0.017-1.42-1.0480.002
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 : 0.011 / q_NPA : -0.003
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].
3A4SER00.0100.0003.664-2.1940.291-0.017-1.420-1.0480.002
4A5GLY00.0130.0086.314-0.189-0.1890.0000.0000.0000.000
5A6PHE0-0.021-0.0148.0850.0290.0290.0000.0000.0000.000
6A7LYS10.9690.97911.1930.3190.3190.0000.0000.0000.000
7A8ALA00.0450.02713.8320.0070.0070.0000.0000.0000.000
8A9GLU-1-0.728-0.85216.810-0.006-0.0060.0000.0000.0000.000
9A10ARG10.9040.95616.5570.1050.1050.0000.0000.0000.000
10A11LEU00.0430.04017.6000.0010.0010.0000.0000.0000.000
11A12ARG10.8410.88719.321-0.008-0.0080.0000.0000.0000.000
12A13VAL0-0.001-0.00922.0790.0000.0000.0000.0000.0000.000
13A14ASN0-0.034-0.04820.5100.0020.0020.0000.0000.0000.000
14A15LEU00.0280.02622.6560.0020.0020.0000.0000.0000.000
15A16ARG10.8710.94025.0520.0040.0040.0000.0000.0000.000
16A17LEU0-0.028-0.01425.0490.0010.0010.0000.0000.0000.000
17A18VAL00.0290.01225.3420.0000.0000.0000.0000.0000.000
18A19ILE0-0.0080.00728.2290.0010.0010.0000.0000.0000.000
19A20ASN0-0.002-0.01231.1070.0040.0040.0000.0000.0000.000
20A21ARG10.8550.92830.4140.0340.0340.0000.0000.0000.000
21A22LEU00.0240.00930.2050.0000.0000.0000.0000.0000.000
22A23LYS10.8400.91833.7450.0040.0040.0000.0000.0000.000
23A24LEU0-0.054-0.02135.6720.0000.0000.0000.0000.0000.000
24A25LEU0-0.042-0.03633.3010.0000.0000.0000.0000.0000.000
25A26GLH00.0510.00136.2180.0010.0010.0000.0000.0000.000
26A27LYS10.8820.94439.3560.0120.0120.0000.0000.0000.000
27A28LYS10.9680.98139.6790.0240.0240.0000.0000.0000.000
28A29LYS10.7790.87136.2980.0170.0170.0000.0000.0000.000
29A30THR00.0220.00941.7940.0010.0010.0000.0000.0000.000
30A31GLU-1-0.893-0.93544.663-0.012-0.0120.0000.0000.0000.000
31A32LEU0-0.075-0.03942.5580.0000.0000.0000.0000.0000.000
32A33ALA00.0770.03645.1590.0000.0000.0000.0000.0000.000
33A34GLN00.0250.01846.8810.0010.0010.0000.0000.0000.000
34A35LYS10.9370.96249.0500.0140.0140.0000.0000.0000.000
35A36ALA00.0190.01447.4390.0000.0000.0000.0000.0000.000
36A37ARG10.9100.94547.9600.0040.0040.0000.0000.0000.000
37A38LYS10.8540.93752.0190.0090.0090.0000.0000.0000.000
38A39GLU-1-0.815-0.88450.466-0.012-0.0120.0000.0000.0000.000
39A40ILE0-0.014-0.01150.7560.0000.0000.0000.0000.0000.000
40A41ALA00.0220.01254.1000.0000.0000.0000.0000.0000.000
41A42ASP-1-0.822-0.90756.976-0.009-0.0090.0000.0000.0000.000
42A43TYR0-0.128-0.07752.2640.0000.0000.0000.0000.0000.000
43A44LEU00.0220.02156.9760.0000.0000.0000.0000.0000.000
44A45ALA0-0.0070.00559.6820.0000.0000.0000.0000.0000.000
45A46ALA0-0.063-0.03260.7260.0000.0000.0000.0000.0000.000
46A47GLY00.0620.05961.7140.0000.0000.0000.0000.0000.000
47A48LYS10.8150.89757.6600.0090.0090.0000.0000.0000.000
48A49ASP-1-0.723-0.87957.085-0.004-0.0040.0000.0000.0000.000
49A50GLU-1-0.902-0.94654.122-0.005-0.0050.0000.0000.0000.000
50A51ARG10.8810.93453.2240.0110.0110.0000.0000.0000.000
51A52ALA00.001-0.00152.148-0.001-0.0010.0000.0000.0000.000
52A53ARG10.8350.89951.7380.0030.0030.0000.0000.0000.000
53A54ILE00.0090.01947.6720.0000.0000.0000.0000.0000.000
54A55ARG10.8470.90247.5490.0130.0130.0000.0000.0000.000
55A56VAL00.008-0.00147.447-0.001-0.0010.0000.0000.0000.000
56A57GLU-1-0.811-0.89944.013-0.006-0.0060.0000.0000.0000.000
57A58HIS0-0.043-0.01740.3860.0000.0000.0000.0000.0000.000
58A59ILE0-0.026-0.01242.8630.0000.0000.0000.0000.0000.000
59A60ILE00.0200.02543.3280.0000.0000.0000.0000.0000.000
60A61ARG10.8560.91438.7520.0080.0080.0000.0000.0000.000
61A62GLU-1-0.794-0.89938.893-0.014-0.0140.0000.0000.0000.000
62A63ASP-1-0.801-0.86940.551-0.004-0.0040.0000.0000.0000.000
63A64TYR00.002-0.00138.9410.0020.0020.0000.0000.0000.000
64A65LEU0-0.0150.00033.8810.0010.0010.0000.0000.0000.000
65A66VAL00.010-0.00336.4370.0000.0000.0000.0000.0000.000
66A67GLU-1-0.761-0.86738.1520.0070.0070.0000.0000.0000.000
67A68ALA0-0.010-0.01133.6550.0020.0020.0000.0000.0000.000
68A69MET0-0.074-0.04033.3540.0010.0010.0000.0000.0000.000
69A70GLU-1-0.886-0.93433.9010.0030.0030.0000.0000.0000.000
70A71ILE0-0.018-0.00432.1900.0020.0020.0000.0000.0000.000
71A72LEU0-0.007-0.01728.0600.0030.0030.0000.0000.0000.000
72A73GLU-1-0.791-0.85529.926-0.001-0.0010.0000.0000.0000.000
73A74LEU00.0250.01631.6750.0010.0010.0000.0000.0000.000
74A75TYR0-0.033-0.03827.5710.0020.0020.0000.0000.0000.000
75A76CYS0-0.074-0.04026.7510.0030.0030.0000.0000.0000.000
76A77ASP-1-0.798-0.90227.6420.0120.0120.0000.0000.0000.000
77A78LEU00.0150.01928.3910.0030.0030.0000.0000.0000.000
78A79LEU0-0.016-0.01422.2270.0060.0060.0000.0000.0000.000
79A80LEU0-0.055-0.02825.0560.0040.0040.0000.0000.0000.000
80A81ALA00.0070.01526.9000.0030.0030.0000.0000.0000.000
81A82ARG10.8780.93226.470-0.044-0.0440.0000.0000.0000.000
82A83PHE00.0390.03119.6510.0110.0110.0000.0000.0000.000
83A84GLY00.014-0.00122.0920.0090.0090.0000.0000.0000.000
84A85LEU00.0230.01922.1790.0160.0160.0000.0000.0000.000
85A86ILE0-0.0070.01917.6810.0160.0160.0000.0000.0000.000
86A87GLN0-0.016-0.02017.4980.0200.0200.0000.0000.0000.000
87A88SER0-0.053-0.03017.4150.0240.0240.0000.0000.0000.000
88A89MET00.0210.02218.7620.0190.0190.0000.0000.0000.000
89A90LYS10.8490.90814.105-0.329-0.3290.0000.0000.0000.000
90A91GLU-1-0.772-0.86615.4130.2940.2940.0000.0000.0000.000
91A92LEU0-0.043-0.01917.826-0.015-0.0150.0000.0000.0000.000
92A93ASP-1-0.824-0.92819.5490.0990.0990.0000.0000.0000.000
93A94SER0-0.021-0.00523.160-0.011-0.0110.0000.0000.0000.000
94A95GLY00.0330.01725.636-0.007-0.0070.0000.0000.0000.000
95A96LEU0-0.041-0.02223.152-0.009-0.0090.0000.0000.0000.000
96A97ALA00.0170.01323.006-0.005-0.0050.0000.0000.0000.000
97A98GLU-1-0.777-0.84424.0730.0340.0340.0000.0000.0000.000
98A99SER00.0210.01525.741-0.006-0.0060.0000.0000.0000.000
99A100VAL0-0.001-0.00619.309-0.009-0.0090.0000.0000.0000.000
100A101SER00.016-0.01021.867-0.005-0.0050.0000.0000.0000.000
101A102THR00.025-0.00122.861-0.008-0.0080.0000.0000.0000.000
102A103LEU00.0000.00423.223-0.008-0.0080.0000.0000.0000.000
103A104ILE0-0.062-0.03217.898-0.011-0.0110.0000.0000.0000.000
104A105TRP0-0.002-0.00221.515-0.011-0.0110.0000.0000.0000.000
105A106ALA00.0420.01924.185-0.006-0.0060.0000.0000.0000.000
106A107ALA00.0090.00422.048-0.006-0.0060.0000.0000.0000.000
107A108PRO0-0.052-0.03122.092-0.006-0.0060.0000.0000.0000.000
108A109ARG10.8180.90224.410-0.004-0.0040.0000.0000.0000.000
109A110LEU00.0660.03827.348-0.001-0.0010.0000.0000.0000.000
110A111GLN0-0.032-0.00522.545-0.003-0.0030.0000.0000.0000.000
111A112SER0-0.018-0.01126.457-0.004-0.0040.0000.0000.0000.000
112A113GLU-1-0.853-0.91729.124-0.024-0.0240.0000.0000.0000.000
113A114VAL0-0.013-0.00327.6570.0000.0000.0000.0000.0000.000
114A115ALA00.0750.04425.4820.0000.0000.0000.0000.0000.000
115A116GLU-1-0.910-0.97223.515-0.056-0.0560.0000.0000.0000.000
116A117LEU00.0400.01422.9650.0010.0010.0000.0000.0000.000
117A118LYS10.8590.92717.0430.1040.1040.0000.0000.0000.000
118A119ILE0-0.0290.00018.041-0.006-0.0060.0000.0000.0000.000
119A120VAL00.0170.00418.112-0.001-0.0010.0000.0000.0000.000
120A121ALA00.0500.02718.7870.0090.0090.0000.0000.0000.000
121A122ASP-1-0.846-0.91214.742-0.088-0.0880.0000.0000.0000.000
122A123GLN0-0.009-0.00412.9640.0080.0080.0000.0000.0000.000
123A124LEU00.0260.01714.3470.0240.0240.0000.0000.0000.000
124A125CYS0-0.042-0.01113.3870.0300.0300.0000.0000.0000.000
125A126ALA0-0.063-0.02510.2220.0230.0230.0000.0000.0000.000
126A127LYS10.7430.8729.980-0.167-0.1670.0000.0000.0000.000
127A128TYR00.0370.00811.9900.0510.0510.0000.0000.0000.000
128A129SER00.0200.03210.1690.0120.0120.0000.0000.0000.000
129A130LYS11.0000.9718.9110.0620.0620.0000.0000.0000.000
130A131GLU-1-0.846-0.92210.5170.1020.1020.0000.0000.0000.000
131A132TYR00.0570.02313.903-0.015-0.0150.0000.0000.0000.000
132A133GLY00.0670.01214.945-0.016-0.0160.0000.0000.0000.000
133A134LYS10.7580.85412.794-0.063-0.0630.0000.0000.0000.000
134A135LEU00.0250.03017.809-0.007-0.0070.0000.0000.0000.000
135A136CYS00.0100.02519.610-0.001-0.0010.0000.0000.0000.000
136A137ARG10.8840.94015.7100.0010.0010.0000.0000.0000.000
137A138THR00.006-0.01522.209-0.006-0.0060.0000.0000.0000.000
138A139ASN00.0470.01724.2530.0040.0040.0000.0000.0000.000
139A140GLN00.0370.04622.5910.0000.0000.0000.0000.0000.000
140A141ILE0-0.072-0.03220.4940.0050.0050.0000.0000.0000.000
141A142GLY00.0260.02323.6730.0050.0050.0000.0000.0000.000
142A143THR0-0.005-0.00324.4890.0000.0000.0000.0000.0000.000
143A144VAL0-0.060-0.03125.378-0.001-0.0010.0000.0000.0000.000
144A145ASN00.022-0.00827.660-0.004-0.0040.0000.0000.0000.000
145A146ASP-1-0.845-0.93431.0300.0280.0280.0000.0000.0000.000
146A147ARG10.9020.94833.725-0.023-0.0230.0000.0000.0000.000
147A148LEU00.0220.00529.781-0.003-0.0030.0000.0000.0000.000
148A149MET0-0.045-0.02330.063-0.003-0.0030.0000.0000.0000.000
149A150HIS0-0.0010.01532.623-0.001-0.0010.0000.0000.0000.000
150A151LYS10.7510.86735.910-0.010-0.0100.0000.0000.0000.000
151A152LEU0-0.046-0.02630.857-0.003-0.0030.0000.0000.0000.000
152A153SER0-0.008-0.00833.545-0.001-0.0010.0000.0000.0000.000
153A154VAL0-0.084-0.04233.077-0.002-0.0020.0000.0000.0000.000
154A155GLU-1-0.921-0.93735.9210.0060.0060.0000.0000.0000.000
155A156ALA0-0.030-0.01338.8520.0000.0000.0000.0000.0000.000
156A157PRO00.0190.00942.2400.0010.0010.0000.0000.0000.000
157A158PRO00.0290.01644.1150.0000.0000.0000.0000.0000.000
158A159LYS10.9810.98246.9950.0000.0000.0000.0000.0000.000
159A160ILE00.0400.02250.1060.0000.0000.0000.0000.0000.000
160A161LEU0-0.027-0.00345.3530.0000.0000.0000.0000.0000.000
161A162VAL00.0250.01148.1370.0000.0000.0000.0000.0000.000
162A163GLU-1-0.743-0.84450.328-0.002-0.0020.0000.0000.0000.000
163A164ARG10.9480.96752.046-0.005-0.0050.0000.0000.0000.000
164A165TYR0-0.039-0.05246.3110.0000.0000.0000.0000.0000.000
165A166LEU0-0.0160.00352.120-0.001-0.0010.0000.0000.0000.000
166A167ILE00.0150.00654.8340.0000.0000.0000.0000.0000.000
167A168GLU-1-0.810-0.89254.2500.0010.0010.0000.0000.0000.000
168A169ILE0-0.040-0.01551.4820.0000.0000.0000.0000.0000.000
169A170ALA00.0350.01155.9910.0000.0000.0000.0000.0000.000
170A171LYS10.8170.89858.691-0.001-0.0010.0000.0000.0000.000
171A172ASN0-0.099-0.06256.8420.0000.0000.0000.0000.0000.000
172A173TYR0-0.063-0.04154.753-0.001-0.0010.0000.0000.0000.000
173A174ASN0-0.068-0.01460.6890.0000.0000.0000.0000.0000.000
174A175VAL0-0.032-0.00260.0040.0000.0000.0000.0000.0000.000
175A176PRO00.005-0.00962.9300.0000.0000.0000.0000.0000.000
176A177TYR0-0.054-0.07656.623-0.001-0.0010.0000.0000.0000.000
177A178GLU-1-0.948-0.95961.914-0.001-0.0010.0000.0000.0000.000
178A179PRO0-0.013-0.01258.5230.0000.0000.0000.0000.0000.000
179A180ASP-1-0.831-0.91756.7220.0000.0000.0000.0000.0000.000
180A181SER0-0.003-0.01258.7960.0010.0010.0000.0000.0000.000
181A182VAL00.0520.02258.1100.0010.0010.0000.0000.0000.000
182A183VAL0-0.013-0.00453.8410.0010.0010.0000.0000.0000.000
183A184MET0-0.065-0.03855.9660.0010.0010.0000.0000.0000.000
184A185ALA0-0.047-0.01558.1200.0010.0010.0000.0000.0000.000
185A186GLU-1-0.962-0.97755.7210.0050.0050.0000.0000.0000.000
186A187ALA0-0.091-0.03154.0370.0010.0010.0000.0000.0000.000