Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LNR39

Calculation Name: 5F64-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F64

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACZ7

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 OptH
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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2291044.988998
FMO2-HF: Nuclear repulsion 2210811.688548
FMO2-HF: Total energy -80233.30045
FMO2-MP2: Total energy -80465.034116


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-0.8550.742-0.027-0.796-0.7730
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.024
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].
3A2ASN00.0480.0393.822-0.2211.376-0.027-0.796-0.7730.000
4A3ALA0-0.012-0.0127.0140.0990.0990.0000.0000.0000.000
5A4ILE0-0.018-0.00410.7470.0230.0230.0000.0000.0000.000
6A5ILE0-0.0110.00014.3340.0220.0220.0000.0000.0000.000
7A6ILE0-0.043-0.03016.868-0.003-0.0030.0000.0000.0000.000
8A7ASP-1-0.773-0.90920.4630.0040.0040.0000.0000.0000.000
9A8ASP-1-0.872-0.93523.047-0.031-0.0310.0000.0000.0000.000
10A9HIS00.0210.01625.6640.0070.0070.0000.0000.0000.000
11A10PRO00.011-0.00224.7920.0040.0040.0000.0000.0000.000
12A11LEU0-0.007-0.00724.4800.0060.0060.0000.0000.0000.000
13A12ALA0-0.0120.00023.2420.0120.0120.0000.0000.0000.000
14A13ILE00.0340.03219.7300.0110.0110.0000.0000.0000.000
15A14ALA0-0.031-0.00619.3710.0100.0100.0000.0000.0000.000
16A15ALA00.001-0.01619.2400.0190.0190.0000.0000.0000.000
17A16ILE00.0380.01415.7440.0330.0330.0000.0000.0000.000
18A17ARG10.8430.88715.0040.0150.0150.0000.0000.0000.000
19A18ASN0-0.048-0.02614.2790.0570.0570.0000.0000.0000.000
20A19LEU0-0.017-0.01314.5100.0500.0500.0000.0000.0000.000
21A20LEU00.009-0.00310.8080.0830.0830.0000.0000.0000.000
22A21ILE00.0280.02310.1950.1270.1270.0000.0000.0000.000
23A22LYS10.9040.95210.539-0.206-0.2060.0000.0000.0000.000
24A23ASN0-0.118-0.06910.0970.0610.0610.0000.0000.0000.000
25A24ASP-1-0.909-0.9525.9622.1042.1040.0000.0000.0000.000
26A25ILE0-0.075-0.0175.2040.3190.3190.0000.0000.0000.000
27A26GLU-1-0.953-0.9696.114-0.712-0.7120.0000.0000.0000.000
28A27ILE0-0.028-0.0327.800-0.112-0.1120.0000.0000.0000.000
29A28LEU00.0190.0158.2270.0170.0170.0000.0000.0000.000
30A29ALA0-0.039-0.03111.9610.0460.0460.0000.0000.0000.000
31A30GLU-1-0.784-0.84415.626-0.029-0.0290.0000.0000.0000.000
32A31LEU0-0.045-0.02718.363-0.006-0.0060.0000.0000.0000.000
33A32THR00.015-0.00221.4410.0120.0120.0000.0000.0000.000
34A33GLU-1-0.825-0.88324.753-0.091-0.0910.0000.0000.0000.000
35A34GLY00.0570.02424.669-0.011-0.0110.0000.0000.0000.000
36A35GLY0-0.046-0.03225.924-0.007-0.0070.0000.0000.0000.000
37A36SER0-0.072-0.05623.663-0.011-0.0110.0000.0000.0000.000
38A37ALA00.0150.01121.494-0.018-0.0180.0000.0000.0000.000
39A38VAL00.021-0.00820.468-0.022-0.0220.0000.0000.0000.000
40A39GLN00.0080.00820.609-0.006-0.0060.0000.0000.0000.000
41A40ARG10.9860.98917.6550.1680.1680.0000.0000.0000.000
42A41VAL00.0480.03815.853-0.038-0.0380.0000.0000.0000.000
43A42GLU-1-0.806-0.89315.598-0.264-0.2640.0000.0000.0000.000
44A43THR0-0.121-0.07016.967-0.010-0.0100.0000.0000.0000.000
45A44LEU0-0.026-0.03212.890-0.007-0.0070.0000.0000.0000.000
46A45LYS10.8500.95211.5980.3490.3490.0000.0000.0000.000
47A46PRO00.0190.0279.509-0.130-0.1300.0000.0000.0000.000
48A47ASP-1-0.792-0.8976.003-2.369-2.3690.0000.0000.0000.000
49A48ILE0-0.030-0.0128.8360.2360.2360.0000.0000.0000.000
50A49VAL0-0.012-0.00411.663-0.006-0.0060.0000.0000.0000.000
51A50ILE0-0.005-0.00613.8470.0380.0380.0000.0000.0000.000
52A51ILE0-0.0020.00117.224-0.002-0.0020.0000.0000.0000.000
53A52ASP-1-0.758-0.88020.889-0.002-0.0020.0000.0000.0000.000
54A53VAL0-0.062-0.05023.974-0.010-0.0100.0000.0000.0000.000
55A54ASP-1-0.856-0.90326.870-0.021-0.0210.0000.0000.0000.000
56A55ILE0-0.0250.01424.6550.0010.0010.0000.0000.0000.000
57A56PRO00.0260.00627.625-0.002-0.0020.0000.0000.0000.000
58A57GLY0-0.017-0.00329.137-0.008-0.0080.0000.0000.0000.000
59A58VAL0-0.064-0.03127.8250.0020.0020.0000.0000.0000.000
60A59ASN00.1010.03328.035-0.002-0.0020.0000.0000.0000.000
61A60GLY00.1150.06725.413-0.009-0.0090.0000.0000.0000.000
62A61ILE00.0340.00225.053-0.010-0.0100.0000.0000.0000.000
63A62GLN0-0.066-0.01327.1140.0030.0030.0000.0000.0000.000
64A63VAL00.0370.01122.318-0.008-0.0080.0000.0000.0000.000
65A64LEU0-0.0200.01221.584-0.014-0.0140.0000.0000.0000.000
66A65GLU-1-0.816-0.93623.701-0.084-0.0840.0000.0000.0000.000
67A66THR0-0.112-0.04525.067-0.003-0.0030.0000.0000.0000.000
68A67LEU00.0220.00719.187-0.005-0.0050.0000.0000.0000.000
69A68ARG10.7880.91017.1230.1900.1900.0000.0000.0000.000
70A69LYS10.9921.00423.1220.1100.1100.0000.0000.0000.000
71A70ARG10.6750.82323.5770.1720.1720.0000.0000.0000.000
72A71GLN0-0.029-0.02421.735-0.015-0.0150.0000.0000.0000.000
73A72TYR00.000-0.00313.1600.0130.0130.0000.0000.0000.000
74A73SER0-0.012-0.01215.2300.0200.0200.0000.0000.0000.000
75A74GLY00.0490.03513.013-0.020-0.0200.0000.0000.0000.000
76A75ILE0-0.001-0.00210.1730.1010.1010.0000.0000.0000.000
77A76ILE0-0.016-0.01313.934-0.014-0.0140.0000.0000.0000.000
78A77ILE0-0.020-0.01414.7260.0290.0290.0000.0000.0000.000
79A78ILE0-0.0020.00518.327-0.002-0.0020.0000.0000.0000.000
80A79VAL0-0.002-0.00420.2940.0200.0200.0000.0000.0000.000
81A80SER00.017-0.01523.109-0.008-0.0080.0000.0000.0000.000
82A81ALA00.0340.02926.5280.0100.0100.0000.0000.0000.000
83A82LYS10.8990.96028.5020.0070.0070.0000.0000.0000.000
84A83ASN00.0150.00029.6390.0040.0040.0000.0000.0000.000
85A84ASP-1-0.763-0.85430.037-0.003-0.0030.0000.0000.0000.000
86A85HIS00.002-0.01130.5760.0000.0000.0000.0000.0000.000
87A86PHE00.004-0.01430.7630.0000.0000.0000.0000.0000.000
88A87TYR0-0.0110.01029.640-0.006-0.0060.0000.0000.0000.000
89A88GLY00.0600.02427.029-0.006-0.0060.0000.0000.0000.000
90A89LYS10.9510.98227.1470.0140.0140.0000.0000.0000.000
91A90HIS0-0.0070.00428.848-0.008-0.0080.0000.0000.0000.000
92A91CYS0-0.026-0.00424.579-0.008-0.0080.0000.0000.0000.000
93A92ALA0-0.006-0.00124.401-0.011-0.0110.0000.0000.0000.000
94A93ASP-1-0.923-0.95925.483-0.042-0.0420.0000.0000.0000.000
95A94ALA0-0.054-0.02326.650-0.005-0.0050.0000.0000.0000.000
96A95GLY00.0270.01023.374-0.012-0.0120.0000.0000.0000.000
97A96ALA0-0.033-0.01520.526-0.020-0.0200.0000.0000.0000.000
98A97ASN00.0420.01816.192-0.014-0.0140.0000.0000.0000.000
99A98GLY00.0470.01018.6720.0250.0250.0000.0000.0000.000
100A99PHE0-0.049-0.02220.204-0.015-0.0150.0000.0000.0000.000
101A100VAL00.0300.00220.1450.0130.0130.0000.0000.0000.000
102A101SER0-0.019-0.00523.105-0.006-0.0060.0000.0000.0000.000
103A102LYS10.8280.87422.7620.0040.0040.0000.0000.0000.000
104A103LYS10.9070.97224.923-0.025-0.0250.0000.0000.0000.000
105A104GLU-1-0.922-0.96426.2780.0690.0690.0000.0000.0000.000
106A105GLY0-0.0020.01924.1980.0120.0120.0000.0000.0000.000
107A106MET00.006-0.01718.612-0.007-0.0070.0000.0000.0000.000
108A107ASN00.001-0.00418.776-0.004-0.0040.0000.0000.0000.000
109A108ASN00.0740.03618.9740.0290.0290.0000.0000.0000.000
110A109ILE0-0.013-0.00615.567-0.013-0.0130.0000.0000.0000.000
111A110ILE00.0390.01211.592-0.033-0.0330.0000.0000.0000.000
112A111ALA00.0230.02914.0390.0380.0380.0000.0000.0000.000
113A112ALA0-0.008-0.00516.058-0.007-0.0070.0000.0000.0000.000
114A113ILE00.0110.00810.537-0.039-0.0390.0000.0000.0000.000
115A114GLU-1-0.932-0.97210.9010.7720.7720.0000.0000.0000.000
116A115ALA0-0.035-0.01212.473-0.025-0.0250.0000.0000.0000.000
117A116ALA00.0230.00912.902-0.028-0.0280.0000.0000.0000.000
118A117LYS10.8920.9446.161-1.608-1.6080.0000.0000.0000.000
119A118ASN0-0.084-0.02910.590-0.017-0.0170.0000.0000.0000.000
120A119GLY0-0.0080.00213.179-0.020-0.0200.0000.0000.0000.000
121A120TYR0-0.057-0.02715.374-0.010-0.0100.0000.0000.0000.000
122A121CYS0-0.033-0.01316.734-0.006-0.0060.0000.0000.0000.000
123A122TYR0-0.024-0.00918.8540.0190.0190.0000.0000.0000.000
124A123PHE00.0160.00120.777-0.008-0.0080.0000.0000.0000.000
125A124PRO0-0.0130.00024.2090.0080.0080.0000.0000.0000.000
126A125PHE00.0550.03627.320-0.007-0.0070.0000.0000.0000.000
127A126SER0-0.016-0.01929.7320.0030.0030.0000.0000.0000.000
128A127LEU00.0640.03233.319-0.003-0.0030.0000.0000.0000.000
129A128ASN00.0400.01035.797-0.001-0.0010.0000.0000.0000.000
130A129ARG10.8320.91332.476-0.004-0.0040.0000.0000.0000.000
131A130PHE0-0.047-0.03333.173-0.003-0.0030.0000.0000.0000.000
132A131VAL00.0310.02438.8210.0000.0000.0000.0000.0000.000
133A132GLY00.0090.00841.1560.0010.0010.0000.0000.0000.000
134A133SER0-0.019-0.03244.082-0.002-0.0020.0000.0000.0000.000
135A134LEU00.0010.01342.096-0.001-0.0010.0000.0000.0000.000
136A135THR00.0360.03440.852-0.002-0.0020.0000.0000.0000.000
137A136SER00.0550.02341.547-0.001-0.0010.0000.0000.0000.000
138A137ASP-1-0.818-0.91742.9530.0010.0010.0000.0000.0000.000
139A138GLN0-0.044-0.02336.1550.0000.0000.0000.0000.0000.000
140A139GLN00.003-0.00238.190-0.001-0.0010.0000.0000.0000.000
141A140LYS10.9320.98039.8050.0000.0000.0000.0000.0000.000
142A141LEU0-0.0080.00137.223-0.003-0.0030.0000.0000.0000.000
143A142ASP-1-0.844-0.92035.246-0.009-0.0090.0000.0000.0000.000
144A143SER0-0.050-0.01736.499-0.004-0.0040.0000.0000.0000.000
145A144LEU0-0.057-0.01937.538-0.002-0.0020.0000.0000.0000.000
146A145SER00.0270.00536.971-0.003-0.0030.0000.0000.0000.000
147A146LYS10.9250.93130.9700.0670.0670.0000.0000.0000.000
148A147GLN00.0160.00434.9810.0010.0010.0000.0000.0000.000
149A148GLU-1-0.814-0.89837.766-0.022-0.0220.0000.0000.0000.000
150A149ILE00.0700.04333.6580.0030.0030.0000.0000.0000.000
151A150SER0-0.0060.00134.7620.0030.0030.0000.0000.0000.000
152A151VAL00.0150.01236.4770.0020.0020.0000.0000.0000.000
153A152MET0-0.020-0.00738.1520.0020.0020.0000.0000.0000.000
154A153ARG10.7060.80131.5660.0160.0160.0000.0000.0000.000
155A154TYR00.0110.00335.4360.0030.0030.0000.0000.0000.000
156A155ILE0-0.024-0.00939.7450.0020.0020.0000.0000.0000.000
157A156LEU0-0.065-0.04139.3040.0020.0020.0000.0000.0000.000
158A157ASP-1-0.912-0.96037.3220.0010.0010.0000.0000.0000.000
159A158GLY0-0.070-0.01740.3250.0010.0010.0000.0000.0000.000
160A159LYS10.8780.95438.1240.0090.0090.0000.0000.0000.000
161A160ASP-1-0.834-0.90943.677-0.010-0.0100.0000.0000.0000.000
162A161ASN0-0.058-0.07845.6590.0000.0000.0000.0000.0000.000
163A162ASN00.0290.02546.436-0.003-0.0030.0000.0000.0000.000
164A163ASP-1-0.755-0.86742.841-0.013-0.0130.0000.0000.0000.000
165A164ILE0-0.050-0.02741.117-0.002-0.0020.0000.0000.0000.000
166A165ALA0-0.072-0.02941.586-0.003-0.0030.0000.0000.0000.000
167A166GLU-1-0.885-0.94041.276-0.023-0.0230.0000.0000.0000.000
168A167LYS10.9280.97334.8230.0220.0220.0000.0000.0000.000
169A168MET0-0.111-0.06037.640-0.002-0.0020.0000.0000.0000.000
170A169PHE0-0.024-0.00135.415-0.003-0.0030.0000.0000.0000.000
171A170ILE0-0.057-0.02340.340-0.001-0.0010.0000.0000.0000.000
172A171SER00.0510.01543.4570.0030.0030.0000.0000.0000.000
173A172ASN00.065-0.01046.8850.0010.0010.0000.0000.0000.000
174A173LYS10.9740.98348.8980.0190.0190.0000.0000.0000.000
175A174THR00.0380.04644.8190.0010.0010.0000.0000.0000.000
176A175VAL00.0540.04243.7580.0000.0000.0000.0000.0000.000
177A176SER0-0.004-0.01445.8370.0010.0010.0000.0000.0000.000
178A177THR0-0.062-0.03446.7650.0010.0010.0000.0000.0000.000
179A178TYR0-0.020-0.01641.2320.0000.0000.0000.0000.0000.000
180A179LYS10.9660.97344.9930.0120.0120.0000.0000.0000.000
181A180SER00.0180.00946.5930.0020.0020.0000.0000.0000.000
182A181ARG10.9560.99242.8830.0280.0280.0000.0000.0000.000
183A182LEU0-0.0290.00141.8740.0010.0010.0000.0000.0000.000
184A183MET0-0.037-0.01844.6550.0010.0010.0000.0000.0000.000
185A184GLU-1-0.929-0.94347.632-0.013-0.0130.0000.0000.0000.000
186A185LYS10.8290.91341.1080.0240.0240.0000.0000.0000.000
187A186LEU0-0.072-0.04341.8440.0010.0010.0000.0000.0000.000
188A187GLU-1-0.948-0.96045.785-0.003-0.0030.0000.0000.0000.000
189A188CYS0-0.096-0.04347.8760.0020.0020.0000.0000.0000.000
190A189LYS10.9440.97350.2810.0030.0030.0000.0000.0000.000
191A190SER0-0.0040.00152.7630.0000.0000.0000.0000.0000.000
192A191LEU00.0760.01349.1260.0000.0000.0000.0000.0000.000
193A192MET00.0270.01350.0390.0010.0010.0000.0000.0000.000
194A193ASP-1-0.811-0.89850.8090.0000.0000.0000.0000.0000.000
195A194LEU00.019-0.00244.3470.0010.0010.0000.0000.0000.000
196A195TYR00.0100.00446.2220.0010.0010.0000.0000.0000.000
197A196THR00.006-0.00446.6980.0020.0020.0000.0000.0000.000
198A197PHE0-0.0010.00541.8670.0020.0020.0000.0000.0000.000
199A198ALA00.006-0.01542.3010.0010.0010.0000.0000.0000.000
200A199GLN0-0.0160.00142.2420.0020.0020.0000.0000.0000.000
201A200ARG10.8450.93143.550-0.003-0.0030.0000.0000.0000.000
202A201ASN0-0.069-0.05440.0330.0020.0020.0000.0000.0000.000
203A202LYS10.9040.97138.031-0.022-0.0220.0000.0000.0000.000
204A203ILE0-0.0080.00636.7240.0010.0010.0000.0000.0000.000