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: 5N21Z

Calculation Name: 5LSB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSB

Chain ID: A

ChEMBL ID:

UniProt ID: Q02554

Base Structure: X-ray

Registration Date: 2023-09-26

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 179
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1880463.250945
FMO2-HF: Nuclear repulsion 1808930.602266
FMO2-HF: Total energy -71532.648679
FMO2-MP2: Total energy -71746.362186


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:8:GLY)


Summations of interaction energy for fragment #1(A:8:GLY)
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.
-2.7931.390.463-2.146-2.497-0.004
Interaction energy analysis for fragmet #1(A:8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.022
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].
3A10THR0-0.0190.0122.682-2.8710.5580.045-1.712-1.762-0.002
4A11VAL0-0.011-0.0043.882-1.542-1.3790.001-0.112-0.051-0.001
5A12TYR0-0.015-0.0056.6390.3140.3140.0000.0000.0000.000
6A13VAL00.006-0.0019.325-0.045-0.0450.0000.0000.0000.000
7A14GLY00.0370.00612.7630.0510.0510.0000.0000.0000.000
8A15ASN0-0.065-0.05215.7550.0080.0080.0000.0000.0000.000
9A16ILE0-0.0070.00715.8170.0000.0000.0000.0000.0000.000
10A17ASP-1-0.780-0.87220.264-0.046-0.0460.0000.0000.0000.000
11A18PRO00.0600.01723.3480.0010.0010.0000.0000.0000.000
12A19ARG10.8200.88424.5190.0550.0550.0000.0000.0000.000
13A20ILE0-0.0360.00820.7700.0030.0030.0000.0000.0000.000
14A21THR00.0720.03922.7540.0040.0040.0000.0000.0000.000
15A22LYS10.9360.94816.709-0.094-0.0940.0000.0000.0000.000
16A23GLU-1-0.928-0.95219.656-0.013-0.0130.0000.0000.0000.000
17A24GLN00.0950.04221.583-0.010-0.0100.0000.0000.0000.000
18A25LEU0-0.036-0.00716.304-0.014-0.0140.0000.0000.0000.000
19A26TYR0-0.009-0.01516.440-0.029-0.0290.0000.0000.0000.000
20A27GLU-1-0.911-0.95618.243-0.069-0.0690.0000.0000.0000.000
21A28LEU0-0.0210.00118.193-0.010-0.0100.0000.0000.0000.000
22A29PHE0-0.001-0.03613.304-0.025-0.0250.0000.0000.0000.000
23A30ILE0-0.0140.00115.684-0.030-0.0300.0000.0000.0000.000
24A31GLN0-0.068-0.02817.7500.0030.0030.0000.0000.0000.000
25A32ILE0-0.101-0.03314.151-0.013-0.0130.0000.0000.0000.000
26A33ASN00.0310.00311.9620.0130.0130.0000.0000.0000.000
27A34PRO00.0370.04413.8980.0200.0200.0000.0000.0000.000
28A35VAL00.006-0.01212.296-0.029-0.0290.0000.0000.0000.000
29A36LEU0-0.064-0.00910.0030.0250.0250.0000.0000.0000.000
30A37ARG10.8730.91610.983-0.531-0.5310.0000.0000.0000.000
31A38ILE00.0440.02711.631-0.019-0.0190.0000.0000.0000.000
32A39LYS10.9190.96311.970-0.130-0.1300.0000.0000.0000.000
33A40TYR0-0.008-0.03913.553-0.037-0.0370.0000.0000.0000.000
34A41PRO0-0.071-0.02715.0690.0160.0160.0000.0000.0000.000
35A42LYS10.8720.94318.141-0.024-0.0240.0000.0000.0000.000
36A43ASP-1-0.751-0.87121.9360.0180.0180.0000.0000.0000.000
37A44LYS10.9010.92322.360-0.056-0.0560.0000.0000.0000.000
38A45VAL00.0110.01526.6290.0010.0010.0000.0000.0000.000
39A46LEU00.0140.00327.462-0.001-0.0010.0000.0000.0000.000
40A47GLN0-0.036-0.01027.323-0.001-0.0010.0000.0000.0000.000
41A48ALA00.0280.03726.212-0.002-0.0020.0000.0000.0000.000
42A49TYR0-0.047-0.03420.6390.0060.0060.0000.0000.0000.000
43A50GLN0-0.034-0.03219.4050.0050.0050.0000.0000.0000.000
44A51GLY00.0590.05019.980-0.006-0.0060.0000.0000.0000.000
45A52TYR0-0.080-0.03813.535-0.018-0.0180.0000.0000.0000.000
46A53ALA0-0.007-0.01313.7390.0380.0380.0000.0000.0000.000
47A54PHE0-0.013-0.0037.775-0.036-0.0360.0000.0000.0000.000
48A55ILE00.0070.0079.1650.1180.1180.0000.0000.0000.000
49A56GLU-1-0.799-0.8776.8640.8930.8930.0000.0000.0000.000
50A57PHE00.0460.0067.308-0.025-0.0250.0000.0000.0000.000
51A58TYR00.0620.0138.0720.2940.2940.0000.0000.0000.000
52A59ASN0-0.033-0.0166.3780.0600.0600.0000.0000.0000.000
53A60GLN00.002-0.0082.809-0.929-0.6070.421-0.290-0.452-0.001
54A61GLY00.0510.0284.750-0.145-0.097-0.001-0.007-0.0400.000
55A62ASP-1-0.825-0.9138.440-0.371-0.3710.0000.0000.0000.000
56A63ALA00.0020.0045.1920.0670.102-0.001-0.010-0.0230.000
57A64GLN0-0.052-0.0384.3910.4290.514-0.001-0.005-0.0790.000
58A65TYR0-0.032-0.0117.8530.1790.1790.0000.0000.0000.000
59A66ALA00.0520.01610.1110.0960.0960.0000.0000.0000.000
60A67ILE0-0.063-0.0306.7470.0910.0910.0000.0000.0000.000
61A68LYS10.9080.95010.8990.5860.5860.0000.0000.0000.000
62A69ILE00.0180.02813.5580.0520.0520.0000.0000.0000.000
63A70MET00.0280.01114.2310.0560.0560.0000.0000.0000.000
64A71ASN0-0.049-0.01014.0010.0370.0370.0000.0000.0000.000
65A72ASN0-0.060-0.03415.9910.0260.0260.0000.0000.0000.000
66A73THR00.0520.02918.9570.0180.0180.0000.0000.0000.000
67A74VAL00.0500.02719.9060.0190.0190.0000.0000.0000.000
68A75ARG10.8040.88221.4730.0980.0980.0000.0000.0000.000
69A76LEU00.0330.02120.2530.0070.0070.0000.0000.0000.000
70A77TYR00.005-0.02224.2930.0020.0020.0000.0000.0000.000
71A78ASP-1-0.878-0.94027.567-0.076-0.0760.0000.0000.0000.000
72A79ARG10.7520.87623.2530.0830.0830.0000.0000.0000.000
73A80LEU00.0000.00421.156-0.006-0.0060.0000.0000.0000.000
74A81ILE00.0420.04016.432-0.002-0.0020.0000.0000.0000.000
75A82LYS10.7860.89115.3660.1810.1810.0000.0000.0000.000
76A83VAL00.0320.01610.4330.0090.0090.0000.0000.0000.000
77A84ARG10.9440.97210.0060.3390.3390.0000.0000.0000.000
78A85GLN00.0760.0494.812-0.201-0.2010.0000.0000.0000.000
79A86VAL00.0150.0144.2910.2860.387-0.001-0.010-0.0900.000
80A106PRO0-0.018-0.03319.916-0.004-0.0040.0000.0000.0000.000
81A107ILE0-0.0350.00622.9140.0050.0050.0000.0000.0000.000
82A108ALA00.0700.04425.474-0.001-0.0010.0000.0000.0000.000
83A109LYS10.7910.91127.9300.0870.0870.0000.0000.0000.000
84A110LEU00.0390.02130.1550.0010.0010.0000.0000.0000.000
85A111PHE0-0.027-0.02733.790-0.003-0.0030.0000.0000.0000.000
86A112ILE00.0060.00435.9700.0030.0030.0000.0000.0000.000
87A113LYS10.9480.97638.8800.0390.0390.0000.0000.0000.000
88A114ASN0-0.025-0.03341.7990.0020.0020.0000.0000.0000.000
89A115LEU0-0.002-0.00539.3270.0020.0020.0000.0000.0000.000
90A116ALA00.0440.02843.9580.0000.0000.0000.0000.0000.000
91A117ASP-1-0.841-0.93044.884-0.034-0.0340.0000.0000.0000.000
92A118SER0-0.033-0.02645.0550.0000.0000.0000.0000.0000.000
93A119ILE0-0.068-0.01740.9750.0000.0000.0000.0000.0000.000
94A120ASP-1-0.811-0.90138.969-0.041-0.0410.0000.0000.0000.000
95A121SER00.0670.02134.475-0.002-0.0020.0000.0000.0000.000
96A122ASP-1-0.825-0.91336.397-0.033-0.0330.0000.0000.0000.000
97A123GLN0-0.004-0.01537.9050.0020.0020.0000.0000.0000.000
98A124LEU00.0150.02036.5530.0010.0010.0000.0000.0000.000
99A125VAL00.0190.01433.4110.0000.0000.0000.0000.0000.000
100A126LYS10.8290.89336.0320.0310.0310.0000.0000.0000.000
101A127ILE0-0.075-0.03739.2320.0020.0020.0000.0000.0000.000
102A128PHE00.037-0.00635.6450.0010.0010.0000.0000.0000.000
103A129ASN00.0320.00934.281-0.002-0.0020.0000.0000.0000.000
104A130LYS10.8620.95536.3110.0260.0260.0000.0000.0000.000
105A131PHE0-0.003-0.00137.4090.0020.0020.0000.0000.0000.000
106A132GLY00.0150.00634.0110.0010.0010.0000.0000.0000.000
107A133LYS10.8210.91126.6170.0490.0490.0000.0000.0000.000
108A134LEU00.0340.02229.711-0.003-0.0030.0000.0000.0000.000
109A135ILE0-0.0040.00022.130-0.001-0.0010.0000.0000.0000.000
110A136ARG10.8580.92719.6380.1040.1040.0000.0000.0000.000
111A137GLU-1-0.868-0.92626.526-0.073-0.0730.0000.0000.0000.000
112A138PRO0-0.048-0.03529.349-0.004-0.0040.0000.0000.0000.000
113A139GLU-1-0.863-0.90629.517-0.089-0.0890.0000.0000.0000.000
114A140ILE00.005-0.00532.0360.0020.0020.0000.0000.0000.000
115A141PHE0-0.017-0.01434.371-0.002-0.0020.0000.0000.0000.000
116A142TYR00.0470.02036.7820.0020.0020.0000.0000.0000.000
117A143LEU00.0290.02537.937-0.002-0.0020.0000.0000.0000.000
118A144SER0-0.021-0.02441.4100.0030.0030.0000.0000.0000.000
119A145ASN00.0050.00643.6640.0040.0040.0000.0000.0000.000
120A146GLY00.0820.03442.965-0.002-0.0020.0000.0000.0000.000
121A147LYS10.8640.93444.2050.0360.0360.0000.0000.0000.000
122A148LEU00.0310.02343.3940.0010.0010.0000.0000.0000.000
123A149LYS10.8650.94541.1520.0360.0360.0000.0000.0000.000
124A150CYS0-0.069-0.02338.4790.0020.0020.0000.0000.0000.000
125A151ALA00.0470.01335.680-0.001-0.0010.0000.0000.0000.000
126A152TYR0-0.036-0.01331.0060.0000.0000.0000.0000.0000.000
127A153VAL00.0330.01732.055-0.001-0.0010.0000.0000.0000.000
128A154TYR0-0.022-0.02126.356-0.004-0.0040.0000.0000.0000.000
129A155PHE00.0460.01729.2340.0010.0010.0000.0000.0000.000
130A156GLU-1-0.871-0.94525.421-0.056-0.0560.0000.0000.0000.000
131A157ASP-1-0.731-0.85127.053-0.034-0.0340.0000.0000.0000.000
132A158PHE00.026-0.01127.516-0.002-0.0020.0000.0000.0000.000
133A159GLU-1-0.913-0.93731.853-0.023-0.0230.0000.0000.0000.000
134A160LYS10.7770.87733.1290.0280.0280.0000.0000.0000.000
135A161ALA0-0.001-0.00532.7270.0010.0010.0000.0000.0000.000
136A162ASP-1-0.794-0.87234.765-0.035-0.0350.0000.0000.0000.000
137A163LEU0-0.057-0.01837.6490.0020.0020.0000.0000.0000.000
138A164ALA00.0070.00937.3810.0010.0010.0000.0000.0000.000
139A165ILE00.0090.01236.7620.0010.0010.0000.0000.0000.000
140A166LYS10.9260.96640.4440.0220.0220.0000.0000.0000.000
141A167SER0-0.058-0.04042.7860.0020.0020.0000.0000.0000.000
142A168LEU0-0.036-0.01840.4550.0010.0010.0000.0000.0000.000
143A169ASN00.0320.02342.901-0.001-0.0010.0000.0000.0000.000
144A170ASN0-0.017-0.01144.4200.0020.0020.0000.0000.0000.000
145A171GLN00.0480.03246.8590.0020.0020.0000.0000.0000.000
146A172LEU0-0.049-0.01048.031-0.001-0.0010.0000.0000.0000.000
147A173VAL00.0350.00844.5530.0010.0010.0000.0000.0000.000
148A174ALA00.0310.00647.731-0.001-0.0010.0000.0000.0000.000
149A175ASN0-0.007-0.01849.5080.0000.0000.0000.0000.0000.000
150A176ASN0-0.0120.01748.2150.0000.0000.0000.0000.0000.000
151A177ARG10.8720.93848.8770.0230.0230.0000.0000.0000.000
152A178ILE00.0220.02542.693-0.001-0.0010.0000.0000.0000.000
153A179THR0-0.023-0.02142.2850.0010.0010.0000.0000.0000.000
154A180VAL0-0.034-0.02438.480-0.002-0.0020.0000.0000.0000.000
155A181ASP-1-0.872-0.93138.541-0.041-0.0410.0000.0000.0000.000
156A182TYR0-0.020-0.04832.723-0.005-0.0050.0000.0000.0000.000
157A183ALA0-0.019-0.00231.4940.0000.0000.0000.0000.0000.000
158A184PHE00.0950.06432.763-0.001-0.0010.0000.0000.0000.000
159A185LYS11.0181.12427.2610.0750.0750.0000.0000.0000.000
160A186DGL0-1.351-0.45627.415-0.007-0.0070.0000.0000.0000.000
161A187ASN-1-0.163-0.83333.044-0.071-0.0710.0000.0000.0000.000
162A188GLY00.5120.17832.601-0.003-0.0030.0000.0000.0000.000
163A189LYS10.8340.90225.7950.0910.0910.0000.0000.0000.000
164A190GLY00.1020.04530.5650.0030.0030.0000.0000.0000.000
165A191ASN0-0.037-0.01528.5680.0040.0040.0000.0000.0000.000
166A192ALA00.1010.04331.246-0.001-0.0010.0000.0000.0000.000
167A193LYS10.8830.94227.3330.0580.0580.0000.0000.0000.000
168A194TYR0-0.060-0.02325.063-0.006-0.0060.0000.0000.0000.000
169A195GLY00.1040.06828.0260.0040.0040.0000.0000.0000.000
170A196ASP-1-0.810-0.90422.685-0.068-0.0680.0000.0000.0000.000
171A197ASP-1-0.864-0.94323.433-0.057-0.0570.0000.0000.0000.000
172A198VAL00.0570.02425.4440.0020.0020.0000.0000.0000.000
173A199ASP-1-0.797-0.89722.638-0.014-0.0140.0000.0000.0000.000
174A200ARG10.8020.89420.1140.0650.0650.0000.0000.0000.000
175A201LEU0-0.026-0.00121.9670.0010.0010.0000.0000.0000.000
176A202LEU0-0.0280.00424.9140.0040.0040.0000.0000.0000.000
177A203ASN0-0.070-0.05419.9360.0170.0170.0000.0000.0000.000
178A204LYS10.8820.96120.089-0.002-0.0020.0000.0000.0000.000
179A205GLU-1-0.917-0.95017.374-0.066-0.0660.0000.0000.0000.000