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: 1664Z

Calculation Name: 3LB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LB9

Chain ID: A

ChEMBL ID:

UniProt ID: P09850

Base Structure: X-ray

Registration Date: 2023-09-27

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972053.666193
FMO2-HF: Nuclear repulsion 1902564.332134
FMO2-HF: Total energy -69489.33406
FMO2-MP2: Total energy -69695.735914


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:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-11.276-8.65411.354-5.698-8.281-0.03
Interaction energy analysis for fragmet #1(A:2:ALA)
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 : 0.003
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].
3A4PHE0-0.071-0.0232.787-1.0071.4530.175-1.038-1.5980.001
4A5THR00.0260.0125.8630.2110.2110.0000.0000.0000.000
5A6GLN0-0.025-0.0128.923-0.005-0.0050.0000.0000.0000.000
6A7TYR0-0.041-0.03911.0480.1180.1180.0000.0000.0000.000
7A8TRP00.016-0.00213.2410.0030.0030.0000.0000.0000.000
8A9SER0-0.028-0.01017.2670.0320.0320.0000.0000.0000.000
9A10VAL00.0100.00720.240-0.008-0.0080.0000.0000.0000.000
10A11ARG10.9801.00922.6750.1470.1470.0000.0000.0000.000
11A12GLN0-0.047-0.02726.3250.0030.0030.0000.0000.0000.000
12A13SER0-0.017-0.01428.6830.0060.0060.0000.0000.0000.000
13A14LYS10.9280.97727.8560.1060.1060.0000.0000.0000.000
14A15ARG10.8750.93428.0370.1570.1570.0000.0000.0000.000
15A16PRO0-0.016-0.00630.416-0.002-0.0020.0000.0000.0000.000
16A17THR0-0.027-0.03529.736-0.007-0.0070.0000.0000.0000.000
17A18GLY00.0480.03932.5890.0060.0060.0000.0000.0000.000
18A19SER0-0.0320.00534.9780.0050.0050.0000.0000.0000.000
19A20ASN0-0.003-0.02733.178-0.008-0.0080.0000.0000.0000.000
20A21ALA0-0.0220.00329.7380.0050.0050.0000.0000.0000.000
21A22THR00.003-0.02329.744-0.003-0.0030.0000.0000.0000.000
22A23ILE0-0.025-0.00823.4610.0010.0010.0000.0000.0000.000
23A24THR0-0.016-0.01426.154-0.008-0.0080.0000.0000.0000.000
24A25PHE00.0020.00018.0700.0000.0000.0000.0000.0000.000
25A26THR00.0590.02223.360-0.008-0.0080.0000.0000.0000.000
26A27ASN0-0.011-0.01125.4190.0080.0080.0000.0000.0000.000
27A28HIS00.0050.00621.628-0.004-0.0040.0000.0000.0000.000
28A29VAL00.0040.02020.162-0.008-0.0080.0000.0000.0000.000
29A30ASN00.0170.00021.831-0.002-0.0020.0000.0000.0000.000
30A31ALA00.0200.02024.1170.0080.0080.0000.0000.0000.000
31A32TRP00.008-0.02216.847-0.005-0.0050.0000.0000.0000.000
32A33LYS11.0021.00520.9280.1750.1750.0000.0000.0000.000
33A34SER0-0.087-0.03822.1990.0130.0130.0000.0000.0000.000
34A35HIS10.8670.93221.9490.1530.1530.0000.0000.0000.000
35A36GLY00.0290.01720.647-0.003-0.0030.0000.0000.0000.000
36A37MET0-0.0920.00217.003-0.016-0.0160.0000.0000.0000.000
37A38ASN00.002-0.01016.4920.0090.0090.0000.0000.0000.000
38A39LEU00.0190.00814.315-0.037-0.0370.0000.0000.0000.000
39A40GLY0-0.006-0.00412.6880.0370.0370.0000.0000.0000.000
40A41SER0-0.019-0.02013.6200.0070.0070.0000.0000.0000.000
41A42ASN0-0.023-0.00512.9560.0180.0180.0000.0000.0000.000
42A43TRP00.0690.03413.505-0.086-0.0860.0000.0000.0000.000
43A44ALA0-0.052-0.01911.9980.0210.0210.0000.0000.0000.000
44A45TYR00.1090.04912.1050.0240.0240.0000.0000.0000.000
45A46GLN00.004-0.00915.438-0.020-0.0200.0000.0000.0000.000
46A47VAL00.0070.01517.2260.0420.0420.0000.0000.0000.000
47A48MET0-0.0150.02519.419-0.024-0.0240.0000.0000.0000.000
48A49ALA0-0.016-0.01518.0600.0170.0170.0000.0000.0000.000
49A50THR0-0.038-0.02020.1520.0240.0240.0000.0000.0000.000
50A51GLU-1-0.870-0.93414.101-0.542-0.5420.0000.0000.0000.000
51A52GLY00.0020.01717.3790.0400.0400.0000.0000.0000.000
52A53TYR0-0.015-0.04613.790-0.036-0.0360.0000.0000.0000.000
53A54GLN0-0.0140.00517.2970.0120.0120.0000.0000.0000.000
54A55SER0-0.055-0.02519.6320.0110.0110.0000.0000.0000.000
55A56SER00.0230.02422.593-0.002-0.0020.0000.0000.0000.000
56A57GLY0-0.019-0.00725.2960.0020.0020.0000.0000.0000.000
57A58SER0-0.023-0.00527.165-0.001-0.0010.0000.0000.0000.000
58A59SER0-0.007-0.00124.9740.0030.0030.0000.0000.0000.000
59A60ASN00.006-0.00428.054-0.001-0.0010.0000.0000.0000.000
60A61VAL00.0410.02825.2800.0060.0060.0000.0000.0000.000
61A62THR00.0210.00728.2440.0000.0000.0000.0000.0000.000
62A63VAL0-0.026-0.01524.9680.0010.0010.0000.0000.0000.000
63A64TRP00.0080.00528.3240.0000.0000.0000.0000.0000.000
64A65GLY00.039-0.00329.887-0.006-0.0060.0000.0000.0000.000
65A66ALA00.003-0.00330.9620.0030.0030.0000.0000.0000.000
66A67SER0-0.038-0.06228.139-0.001-0.0010.0000.0000.0000.000
67A68THR0-0.0630.04026.019-0.011-0.0110.0000.0000.0000.000
68A69ASP-1-0.826-0.90824.094-0.201-0.2010.0000.0000.0000.000
69A70TYR0-0.0190.00716.1600.0060.0060.0000.0000.0000.000
70A71TRP00.026-0.00721.7070.0020.0020.0000.0000.0000.000
71A72GLN0-0.012-0.00413.8540.0090.0090.0000.0000.0000.000
72A73ASN0-0.013-0.01918.3640.0090.0090.0000.0000.0000.000
73A74TRP00.0250.01810.315-0.005-0.0050.0000.0000.0000.000
74A75THR00.026-0.01515.1830.0200.0200.0000.0000.0000.000
75A76ASP-1-0.896-0.93311.719-0.279-0.2790.0000.0000.0000.000
76A77GLY0-0.016-0.00213.6280.0540.0540.0000.0000.0000.000
77A78GLY00.0110.01216.9390.0350.0350.0000.0000.0000.000
78A79GLY00.001-0.00917.9310.0200.0200.0000.0000.0000.000
79A80ILE0-0.040-0.01121.035-0.011-0.0110.0000.0000.0000.000
80A81VAL00.033-0.00919.493-0.005-0.0050.0000.0000.0000.000
81A82ASN0-0.0330.00222.922-0.005-0.0050.0000.0000.0000.000
82A83ALA00.0270.01822.913-0.002-0.0020.0000.0000.0000.000
83A84VAL00.0170.01524.9810.0020.0020.0000.0000.0000.000
84A85ASN00.011-0.01026.106-0.006-0.0060.0000.0000.0000.000
85A86GLY00.0410.01827.5440.0100.0100.0000.0000.0000.000
86A87SER00.0120.00430.251-0.002-0.0020.0000.0000.0000.000
87A88GLY00.0120.00031.8740.0010.0010.0000.0000.0000.000
88A89GLY00.0640.03028.281-0.008-0.0080.0000.0000.0000.000
89A90ASN0-0.076-0.04828.096-0.006-0.0060.0000.0000.0000.000
90A91TYR0-0.003-0.01323.409-0.006-0.0060.0000.0000.0000.000
91A92SER00.0110.01728.0370.0040.0040.0000.0000.0000.000
92A93VAL00.0030.00023.091-0.008-0.0080.0000.0000.0000.000
93A94ASN0-0.013-0.01226.1100.0010.0010.0000.0000.0000.000
94A95TRP0-0.0080.02722.437-0.001-0.0010.0000.0000.0000.000
95A96SER0-0.008-0.03424.0550.0100.0100.0000.0000.0000.000
96A97ASN00.024-0.00623.528-0.006-0.0060.0000.0000.0000.000
97A98THR00.0010.02118.8330.0090.0090.0000.0000.0000.000
98A99GLY00.0170.01816.0620.0200.0200.0000.0000.0000.000
99A100ASN0-0.084-0.02512.057-0.087-0.0870.0000.0000.0000.000
100A101PHE00.0150.00114.3530.0040.0040.0000.0000.0000.000
101A102VAL00.0250.02313.4090.0060.0060.0000.0000.0000.000
102A103VAL00.0070.00916.4550.0080.0080.0000.0000.0000.000
103A104GLY00.0230.00819.7480.0100.0100.0000.0000.0000.000
104A105LYS10.8310.94520.9030.1560.1560.0000.0000.0000.000
105A106GLY0-0.002-0.02521.5950.0000.0000.0000.0000.0000.000
106A107TRP0-0.022-0.02720.7370.0190.0190.0000.0000.0000.000
107A108THR00.0290.00219.303-0.040-0.0400.0000.0000.0000.000
108A109THR0-0.0110.00018.087-0.024-0.0240.0000.0000.0000.000
109A110GLY0-0.036-0.01817.7040.0230.0230.0000.0000.0000.000
110A111SER00.004-0.00418.8190.0150.0150.0000.0000.0000.000
111A112PRO00.0220.00020.247-0.006-0.0060.0000.0000.0000.000
112A113PHE00.019-0.00721.7070.0090.0090.0000.0000.0000.000
113A114ARG10.8550.96322.1970.2360.2360.0000.0000.0000.000
114A115THR0-0.006-0.01724.8730.0050.0050.0000.0000.0000.000
115A116ILE0-0.0100.00222.8130.0010.0010.0000.0000.0000.000
116A117ASN00.0530.04027.2450.0050.0050.0000.0000.0000.000
117A118TYR0-0.016-0.03227.065-0.002-0.0020.0000.0000.0000.000
118A119ASN00.0230.02229.5000.0090.0090.0000.0000.0000.000
119A120ALA0-0.011-0.00628.630-0.002-0.0020.0000.0000.0000.000
120A121GLY00.0120.02230.3290.0070.0070.0000.0000.0000.000
121A122VAL0-0.002-0.01030.8300.0080.0080.0000.0000.0000.000
122A123TRP0-0.046-0.01323.045-0.012-0.0120.0000.0000.0000.000
123A124ALA0-0.008-0.00129.3160.0060.0060.0000.0000.0000.000
124A125PRO0-0.046-0.01225.1490.0020.0020.0000.0000.0000.000
125A126ASN0-0.001-0.01026.6720.0080.0080.0000.0000.0000.000
126A127GLY00.1090.02724.2120.0070.0070.0000.0000.0000.000
127A128ASN0-0.0170.01117.8470.0080.0080.0000.0000.0000.000
128A129GLY00.0790.03620.470-0.008-0.0080.0000.0000.0000.000
129A130TYR0-0.025-0.02715.9490.0380.0380.0000.0000.0000.000
130A131LEU00.0140.01820.860-0.009-0.0090.0000.0000.0000.000
131A132THR00.011-0.02217.5430.0130.0130.0000.0000.0000.000
132A133LEU00.0110.00718.871-0.003-0.0030.0000.0000.0000.000
133A134TYR0-0.120-0.05510.4330.0090.0090.0000.0000.0000.000
134A135GLY00.0540.01914.0430.0540.0540.0000.0000.0000.000
135A136TRP00.0260.0125.290-0.088-0.0880.0000.0000.0000.000
136A137THR0-0.009-0.00410.2650.1250.1250.0000.0000.0000.000
137A138ARG10.9180.9548.9530.4180.4180.0000.0000.0000.000
138A139SER0-0.0050.0299.5770.0510.0510.0000.0000.0000.000
139A140PRO00.0700.0429.5800.0490.0490.0000.0000.0000.000
140A141LEU00.004-0.0233.093-0.1960.1620.124-0.103-0.3790.000
141A142ILE0-0.037-0.0137.316-0.123-0.1230.0000.0000.0000.000
142A143GLU-1-0.738-0.8358.063-1.250-1.2500.0000.0000.0000.000
143A144TYR0-0.033-0.0209.8260.0980.0980.0000.0000.0000.000
144A145TYR00.014-0.00411.7240.0580.0580.0000.0000.0000.000
145A146VAL0-0.046-0.03016.2830.0340.0340.0000.0000.0000.000
146A147VAL00.0150.01619.0430.0090.0090.0000.0000.0000.000
147A148ASP-1-0.722-0.83821.584-0.168-0.1680.0000.0000.0000.000
148A149SER00.002-0.01624.3990.0210.0210.0000.0000.0000.000
149A150TRP00.0480.00923.061-0.024-0.0240.0000.0000.0000.000
150A151GLY00.0370.02623.9380.0140.0140.0000.0000.0000.000
151A152THR0-0.081-0.06624.4620.0070.0070.0000.0000.0000.000
152A153TYR00.0150.01318.3310.0020.0020.0000.0000.0000.000
153A154ARG10.7760.89122.3970.1300.1300.0000.0000.0000.000
154A155PRO00.0340.00817.8060.0110.0110.0000.0000.0000.000
155A156THR0-0.045-0.00919.3640.0090.0090.0000.0000.0000.000
156A157GLY00.0560.01017.531-0.034-0.0340.0000.0000.0000.000
157A158THR0-0.044-0.01017.1740.0400.0400.0000.0000.0000.000
158A159TYR00.0260.00919.495-0.023-0.0230.0000.0000.0000.000
159A160LYS10.9290.95318.4850.1870.1870.0000.0000.0000.000
160A161GLY00.0090.01122.8350.0100.0100.0000.0000.0000.000
161A162THR0-0.0070.00025.076-0.008-0.0080.0000.0000.0000.000
162A163VAL0-0.024-0.01624.7260.0050.0050.0000.0000.0000.000
163A164LYS10.9240.97127.7260.1090.1090.0000.0000.0000.000
164A165SER00.006-0.01327.8170.0000.0000.0000.0000.0000.000
165A166ASP-1-0.758-0.87428.721-0.152-0.1520.0000.0000.0000.000
166A167GLY00.0040.00331.8010.0010.0010.0000.0000.0000.000
167A168GLY0-0.039-0.02430.6680.0040.0040.0000.0000.0000.000
168A169THR0-0.0100.00229.433-0.005-0.0050.0000.0000.0000.000
169A170TYR0-0.102-0.05924.0870.0030.0030.0000.0000.0000.000
170A171ASP-1-0.784-0.88924.376-0.122-0.1220.0000.0000.0000.000
171A172ILE0-0.037-0.01820.230-0.018-0.0180.0000.0000.0000.000
172A173TYR00.0260.00518.2790.0260.0260.0000.0000.0000.000
173A174THR00.0090.00514.862-0.018-0.0180.0000.0000.0000.000
174A175THR00.0010.00511.8290.0790.0790.0000.0000.0000.000
175A176THR00.0240.0068.795-0.122-0.1220.0000.0000.0000.000
176A177ARG10.9500.9946.3471.3051.3050.0000.0000.0000.000
177A178TYR00.021-0.0025.279-0.933-0.924-0.001-0.0160.0080.000
178A179ASN00.0060.0022.676-0.3100.5172.122-1.497-1.4530.011
179A180ALA0-0.045-0.0182.439-1.672-1.8591.4520.328-1.5930.000
180A181PRO00.0110.0052.070-8.192-9.3217.480-3.275-3.076-0.041
181A182SER0-0.001-0.0113.871-0.478-0.1940.002-0.097-0.190-0.001
182A183ILE00.0220.0236.6710.1480.1480.0000.0000.0000.000