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: R9K98

Calculation Name: 4LEU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LEU

Chain ID: A

ChEMBL ID:

UniProt ID: Q9STF9

Base Structure: X-ray

Registration Date: 2023-06-26

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2012128.822783
FMO2-HF: Nuclear repulsion 1936737.327194
FMO2-HF: Total energy -75391.495589
FMO2-MP2: Total energy -75609.930267


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:71:LYS)


Summations of interaction energy for fragment #1(A:71:LYS)
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.
-93.018-90.252-0.029-0.99-1.7490.002
Interaction energy analysis for fragmet #1(A:71:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.986 / q_NPA : 0.986
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].
3A73ILE00.0190.0143.364-3.048-0.432-0.027-0.982-1.6080.002
4A74GLY00.0530.0386.2483.2333.2330.0000.0000.0000.000
5A75LYS10.9960.9709.53817.75917.7590.0000.0000.0000.000
6A76GLU-1-0.815-0.88313.065-16.999-16.9990.0000.0000.0000.000
7A77ALA00.0610.0298.8090.6400.6400.0000.0000.0000.000
8A78LEU00.0020.0029.5060.3000.3000.0000.0000.0000.000
9A79PHE0-0.020-0.00611.5471.1671.1670.0000.0000.0000.000
10A80VAL00.0310.01113.3651.1211.1210.0000.0000.0000.000
11A81ILE00.0040.0118.5640.7890.7890.0000.0000.0000.000
12A82LEU0-0.011-0.01413.1891.0011.0010.0000.0000.0000.000
13A83GLY0-0.028-0.01115.6701.1221.1220.0000.0000.0000.000
14A84LEU0-0.009-0.01214.0180.9290.9290.0000.0000.0000.000
15A85LYS10.8470.89713.34921.67921.6790.0000.0000.0000.000
16A86ARG10.9020.96717.47014.80814.8080.0000.0000.0000.000
17A87LEU0-0.054-0.03520.6260.7950.7950.0000.0000.0000.000
18A88LYS10.8440.92118.23516.68116.6810.0000.0000.0000.000
19A89GLU-1-0.875-0.94521.171-13.226-13.2260.0000.0000.0000.000
20A90ASP-1-0.841-0.88424.740-10.467-10.4670.0000.0000.0000.000
21A91ASP-1-0.815-0.93625.170-12.696-12.6960.0000.0000.0000.000
22A92GLU-1-0.923-0.93526.349-10.162-10.1620.0000.0000.0000.000
23A93LYS10.7800.84426.20510.38110.3810.0000.0000.0000.000
24A94LEU0-0.0050.00719.465-0.431-0.4310.0000.0000.0000.000
25A95ASP-1-0.779-0.86622.496-12.565-12.5650.0000.0000.0000.000
26A96LYS10.9330.96824.37011.25011.2500.0000.0000.0000.000
27A97PHE0-0.0260.00017.677-0.054-0.0540.0000.0000.0000.000
28A98ILE00.0460.01818.799-0.521-0.5210.0000.0000.0000.000
29A99LYS10.8040.87720.74411.44311.4430.0000.0000.0000.000
30A100THR0-0.093-0.04623.1710.4540.4540.0000.0000.0000.000
31A101HIS0-0.022-0.03718.8070.0620.0620.0000.0000.0000.000
32A102VAL00.0130.01615.400-0.801-0.8010.0000.0000.0000.000
33A103PHE00.0320.00817.010-0.682-0.6820.0000.0000.0000.000
34A104ARG10.8450.91618.09715.73015.7300.0000.0000.0000.000
35A105LEU0-0.049-0.01212.166-0.279-0.2790.0000.0000.0000.000
36A106LEU00.0620.03213.5100.3590.3590.0000.0000.0000.000
37A107LYS10.9620.98811.32920.42420.4240.0000.0000.0000.000
38A108LEU00.006-0.0117.910-1.580-1.5800.0000.0000.0000.000
39A109ASP-1-0.882-0.9467.805-29.570-29.5700.0000.0000.0000.000
40A110MET0-0.0180.0059.294-1.657-1.6570.0000.0000.0000.000
41A111LEU00.0210.0077.064-0.589-0.5890.0000.0000.0000.000
42A112ALA0-0.031-0.0094.920-5.221-5.2210.0000.0000.0000.000
43A113VAL0-0.046-0.0245.907-2.693-2.6930.0000.0000.0000.000
44A114ILE0-0.025-0.0038.3310.3620.3620.0000.0000.0000.000
45A115GLY00.0920.0534.384-0.0320.010-0.001-0.005-0.0360.000
46A116GLU-1-0.811-0.8585.284-42.965-42.857-0.001-0.003-0.1050.000
47A117LEU0-0.056-0.0356.3433.1493.1490.0000.0000.0000.000
48A118GLU-1-0.829-0.9297.506-30.452-30.4520.0000.0000.0000.000
49A119ARG10.7760.8615.01740.36840.3680.0000.0000.0000.000
50A120GLN0-0.124-0.0917.8285.2155.2150.0000.0000.0000.000
51A121GLU-1-0.826-0.91110.862-19.609-19.6090.0000.0000.0000.000
52A122GLU-1-0.791-0.85012.352-16.636-16.6360.0000.0000.0000.000
53A123THR00.0440.00213.9160.1120.1120.0000.0000.0000.000
54A124ALA0-0.0060.00015.1440.1570.1570.0000.0000.0000.000
55A125LEU0-0.009-0.00914.7410.3590.3590.0000.0000.0000.000
56A126ALA00.0250.02511.975-0.120-0.1200.0000.0000.0000.000
57A127ILE00.0330.01413.371-0.058-0.0580.0000.0000.0000.000
58A128LYS10.9120.96116.49914.44914.4490.0000.0000.0000.000
59A129MET0-0.017-0.00411.8780.8710.8710.0000.0000.0000.000
60A130PHE00.0590.02514.2460.1250.1250.0000.0000.0000.000
61A131GLU-1-0.890-0.94315.190-13.380-13.3800.0000.0000.0000.000
62A132VAL0-0.059-0.02816.8330.7030.7030.0000.0000.0000.000
63A133ILE00.017-0.00111.8250.4620.4620.0000.0000.0000.000
64A134GLN0-0.041-0.02416.2211.0561.0560.0000.0000.0000.000
65A135LYS10.7970.90318.81814.74014.7400.0000.0000.0000.000
66A136GLN0-0.058-0.02216.6680.7050.7050.0000.0000.0000.000
67A137GLU-1-0.915-0.96219.591-13.031-13.0310.0000.0000.0000.000
68A138TRP0-0.018-0.02512.860-0.356-0.3560.0000.0000.0000.000
69A139TYR0-0.031-0.01415.425-1.193-1.1930.0000.0000.0000.000
70A140GLN00.0180.00216.2681.3181.3180.0000.0000.0000.000
71A141PRO0-0.051-0.00915.819-1.207-1.2070.0000.0000.0000.000
72A142ASP-1-0.835-0.92611.134-24.618-24.6180.0000.0000.0000.000
73A143VAL00.0370.01814.040-0.501-0.5010.0000.0000.0000.000
74A144PHE00.005-0.0019.144-0.498-0.4980.0000.0000.0000.000
75A145MET0-0.0030.01510.079-1.305-1.3050.0000.0000.0000.000
76A146TYR0-0.032-0.05411.0620.0910.0910.0000.0000.0000.000
77A147LYS10.8310.9129.80927.57227.5720.0000.0000.0000.000
78A148ASP-1-0.946-0.9786.655-39.123-39.1230.0000.0000.0000.000
79A149LEU0-0.0050.0169.6600.7200.7200.0000.0000.0000.000
80A150ILE0-0.048-0.02512.3351.1521.1520.0000.0000.0000.000
81A151VAL0-0.007-0.00411.2121.0311.0310.0000.0000.0000.000
82A152SER0-0.045-0.03010.7311.3531.3530.0000.0000.0000.000
83A153LEU0-0.020-0.02212.5881.0921.0920.0000.0000.0000.000
84A154ALA00.0140.00616.1950.8730.8730.0000.0000.0000.000
85A155LYS10.8670.95710.45326.77026.7700.0000.0000.0000.000
86A156SER0-0.041-0.01315.8440.3240.3240.0000.0000.0000.000
87A157LYS10.7830.88318.02114.49514.4950.0000.0000.0000.000
88A158ARG10.7900.89319.05415.87415.8740.0000.0000.0000.000
89A159MET00.0190.00020.347-0.662-0.6620.0000.0000.0000.000
90A160ASP-1-0.859-0.92022.431-11.889-11.8890.0000.0000.0000.000
91A161GLU-1-0.815-0.90020.515-13.808-13.8080.0000.0000.0000.000
92A162ALA00.0130.01018.579-0.354-0.3540.0000.0000.0000.000
93A163MET0-0.007-0.00719.548-0.385-0.3850.0000.0000.0000.000
94A164ALA0-0.0190.00222.5070.1220.1220.0000.0000.0000.000
95A165LEU0-0.026-0.02317.3040.1510.1510.0000.0000.0000.000
96A166TRP00.0070.00217.953-0.533-0.5330.0000.0000.0000.000
97A167GLU-1-0.821-0.91020.502-11.490-11.4900.0000.0000.0000.000
98A168LYS10.7780.88920.10815.07615.0760.0000.0000.0000.000
99A169MET0-0.0010.00417.872-0.255-0.2550.0000.0000.0000.000
100A170LYS10.7780.86420.54612.20212.2020.0000.0000.0000.000
101A171LYS10.8500.93023.53012.06712.0670.0000.0000.0000.000
102A172GLU-1-0.825-0.87320.279-14.635-14.6350.0000.0000.0000.000
103A173ASN0-0.099-0.04422.8940.1040.1040.0000.0000.0000.000
104A174LEU0-0.0020.00617.354-0.265-0.2650.0000.0000.0000.000
105A175PHE00.019-0.00619.4830.4510.4510.0000.0000.0000.000
106A176PRO0-0.024-0.00917.442-0.819-0.8190.0000.0000.0000.000
107A177ASP-1-0.755-0.84415.009-19.472-19.4720.0000.0000.0000.000
108A178SER0-0.004-0.03918.261-0.042-0.0420.0000.0000.0000.000
109A179GLN0-0.028-0.02412.567-0.604-0.6040.0000.0000.0000.000
110A180THR00.021-0.01314.455-0.949-0.9490.0000.0000.0000.000
111A181TYR00.0420.01115.499-0.049-0.0490.0000.0000.0000.000
112A182THR0-0.032-0.02417.7310.5230.5230.0000.0000.0000.000
113A183GLU-1-0.925-0.95111.137-25.565-25.5650.0000.0000.0000.000
114A184VAL00.0400.02415.7420.0470.0470.0000.0000.0000.000
115A185ILE00.0000.01617.3330.5780.5780.0000.0000.0000.000
116A186ARG10.9300.95715.37218.07918.0790.0000.0000.0000.000
117A187GLY00.0010.00117.4560.3140.3140.0000.0000.0000.000
118A188PHE00.0510.01618.1820.3270.3270.0000.0000.0000.000
119A189LEU0-0.036-0.01821.5290.5760.5760.0000.0000.0000.000
120A190ARG10.8510.93319.32114.50014.5000.0000.0000.0000.000
121A191ASP-1-0.738-0.87721.046-14.391-14.3910.0000.0000.0000.000
122A192GLY0-0.089-0.02423.1350.4340.4340.0000.0000.0000.000
123A193CYS0-0.017-0.00724.5230.5310.5310.0000.0000.0000.000
124A194PRO00.0190.00325.887-0.255-0.2550.0000.0000.0000.000
125A195ALA00.0210.01228.069-0.011-0.0110.0000.0000.0000.000
126A196ASP-1-0.787-0.89724.048-12.057-12.0570.0000.0000.0000.000
127A197ALA0-0.006-0.00523.681-0.254-0.2540.0000.0000.0000.000
128A198MET0-0.014-0.01524.718-0.154-0.1540.0000.0000.0000.000
129A199ASN0-0.032-0.01926.4500.2270.2270.0000.0000.0000.000
130A200VAL00.0180.01520.613-0.008-0.0080.0000.0000.0000.000
131A201TYR0-0.034-0.06123.985-0.230-0.2300.0000.0000.0000.000
132A202GLU-1-0.798-0.91625.858-9.717-9.7170.0000.0000.0000.000
133A203ASP-1-0.850-0.89624.532-11.698-11.6980.0000.0000.0000.000
134A204MET0-0.029-0.01723.195-0.220-0.2200.0000.0000.0000.000
135A205LEU0-0.057-0.02524.9930.0740.0740.0000.0000.0000.000
136A206LYS10.7880.88628.19311.02611.0260.0000.0000.0000.000
137A207SER0-0.0250.01123.955-0.114-0.1140.0000.0000.0000.000
138A208PRO0-0.042-0.02124.7970.3600.3600.0000.0000.0000.000
139A209ASP-1-0.913-0.95123.412-13.023-13.0230.0000.0000.0000.000
140A210PRO0-0.0020.00026.1620.1330.1330.0000.0000.0000.000
141A211PRO0-0.0060.00025.585-0.423-0.4230.0000.0000.0000.000
142A212GLU-1-0.816-0.88221.236-14.413-14.4130.0000.0000.0000.000
143A213GLU-1-0.706-0.85125.141-10.633-10.6330.0000.0000.0000.000
144A214LEU0-0.030-0.01119.3040.0400.0400.0000.0000.0000.000
145A215PRO00.0530.01321.6520.0600.0600.0000.0000.0000.000
146A216PHE00.0570.02523.1930.1450.1450.0000.0000.0000.000
147A217ARG10.8040.90425.15611.31111.3110.0000.0000.0000.000
148A218VAL0-0.081-0.03920.8450.0410.0410.0000.0000.0000.000
149A219LEU00.0170.01424.1900.2220.2220.0000.0000.0000.000
150A220LEU00.0220.01226.5380.3010.3010.0000.0000.0000.000
151A221LYS10.9621.00024.51412.46312.4630.0000.0000.0000.000
152A222GLY0-0.052-0.03326.3330.1000.1000.0000.0000.0000.000
153A223LEU00.0220.00227.2090.1730.1730.0000.0000.0000.000
154A224LEU0-0.0300.00230.4270.3820.3820.0000.0000.0000.000
155A225PRO0-0.039-0.02631.3580.2890.2890.0000.0000.0000.000
156A226HIS0-0.0080.00531.1240.3630.3630.0000.0000.0000.000
157A227PRO00.0760.02534.750-0.093-0.0930.0000.0000.0000.000
158A228LEU00.0060.00536.9220.0580.0580.0000.0000.0000.000
159A229LEU00.0060.00731.5540.0110.0110.0000.0000.0000.000
160A230ARG10.8660.94132.2249.3009.3000.0000.0000.0000.000
161A231ASN0-0.003-0.02233.620-0.159-0.1590.0000.0000.0000.000
162A232LYS10.8160.91133.2939.4419.4410.0000.0000.0000.000
163A233VAL00.006-0.00129.497-0.016-0.0160.0000.0000.0000.000
164A234LYS10.7530.86132.6948.2228.2220.0000.0000.0000.000
165A235LYS10.8800.93834.6518.2408.2400.0000.0000.0000.000
166A236ASP-1-0.773-0.85832.851-9.222-9.2220.0000.0000.0000.000
167A237PHE00.0320.00529.637-0.028-0.0280.0000.0000.0000.000
168A238GLU-1-0.858-0.93433.431-8.052-8.0520.0000.0000.0000.000
169A239GLU-1-0.945-0.96336.643-8.062-8.0620.0000.0000.0000.000
170A240LEU0-0.039-0.00531.5840.0550.0550.0000.0000.0000.000
171A241PHE0-0.067-0.03429.570-0.111-0.1110.0000.0000.0000.000
172A242PRO00.0470.04035.0180.0370.0370.0000.0000.0000.000
173A243GLU-1-0.941-0.97137.476-8.025-8.0250.0000.0000.0000.000
174A244LYS10.8460.90429.69810.35110.3510.0000.0000.0000.000
175A245HIS0-0.066-0.04534.821-0.004-0.0040.0000.0000.0000.000
176A246ALA0-0.047-0.00235.9350.0340.0340.0000.0000.0000.000
177A247TYR0-0.041-0.02733.740-0.039-0.0390.0000.0000.0000.000
178A248ASP-1-0.884-0.94930.738-10.411-10.4110.0000.0000.0000.000
179A249PRO00.0610.04732.974-0.176-0.1760.0000.0000.0000.000
180A250PRO0-0.025-0.01129.279-0.216-0.2160.0000.0000.0000.000
181A251GLU-1-0.915-0.95830.370-8.729-8.7290.0000.0000.0000.000
182A252GLU-1-0.949-0.97331.833-9.139-9.1390.0000.0000.0000.000