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: QY4YY

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 OptAll
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 -2015583.248122
FMO2-HF: Nuclear repulsion 1940191.201418
FMO2-HF: Total energy -75392.046704
FMO2-MP2: Total energy -75610.413355


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.
-92.113-89.2340-1.128-1.7480.002
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 : 0.998 / q_NPA : 0.995
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].
3A73ILE00.0010.0053.669-6.254-3.8530.004-1.103-1.3010.002
4A74GLY00.0560.0426.0323.3933.3930.0000.0000.0000.000
5A75LYS10.9740.9649.49318.14618.1460.0000.0000.0000.000
6A76GLU-1-0.789-0.85812.884-17.248-17.2480.0000.0000.0000.000
7A77ALA00.0530.0258.4740.4830.4830.0000.0000.0000.000
8A78LEU0-0.010-0.0049.0410.2450.2450.0000.0000.0000.000
9A79PHE0-0.019-0.00911.0701.2211.2210.0000.0000.0000.000
10A80VAL00.0280.01312.8391.1391.1390.0000.0000.0000.000
11A81ILE0-0.0050.0087.8320.9170.9170.0000.0000.0000.000
12A82LEU0-0.015-0.01712.3201.1451.1450.0000.0000.0000.000
13A83GLY0-0.042-0.02615.3181.2241.2240.0000.0000.0000.000
14A84LEU00.002-0.00913.4631.0101.0100.0000.0000.0000.000
15A85LYS10.8410.90212.89822.36522.3650.0000.0000.0000.000
16A86ARG10.8910.96017.01315.13815.1380.0000.0000.0000.000
17A87LEU0-0.048-0.02919.9270.8990.8990.0000.0000.0000.000
18A88LYS10.8450.92617.89616.89816.8980.0000.0000.0000.000
19A89GLU-1-0.875-0.93620.553-13.771-13.7710.0000.0000.0000.000
20A90ASP-1-0.842-0.90423.969-10.667-10.6670.0000.0000.0000.000
21A91ASP-1-0.780-0.90624.513-13.045-13.0450.0000.0000.0000.000
22A92GLU-1-0.896-0.91625.522-10.430-10.4300.0000.0000.0000.000
23A93LYS10.7880.84625.67210.64010.6400.0000.0000.0000.000
24A94LEU0-0.0050.01118.826-0.488-0.4880.0000.0000.0000.000
25A95ASP-1-0.802-0.87621.680-12.780-12.7800.0000.0000.0000.000
26A96LYS10.9230.95923.68111.37911.3790.0000.0000.0000.000
27A97PHE0-0.0150.01016.907-0.056-0.0560.0000.0000.0000.000
28A98ILE00.0380.00118.246-0.542-0.5420.0000.0000.0000.000
29A99LYS10.8200.88420.25911.62011.6200.0000.0000.0000.000
30A100THR0-0.092-0.04222.9110.5760.5760.0000.0000.0000.000
31A101HIS0-0.024-0.02518.9580.0820.0820.0000.0000.0000.000
32A102VAL00.0090.01014.842-0.685-0.6850.0000.0000.0000.000
33A103PHE00.027-0.00616.621-0.828-0.8280.0000.0000.0000.000
34A104ARG10.8210.89717.91916.36616.3660.0000.0000.0000.000
35A105LEU0-0.044-0.01011.876-0.220-0.2200.0000.0000.0000.000
36A106LEU00.0530.02512.9110.3060.3060.0000.0000.0000.000
37A107LYS10.8880.95311.27119.78019.7800.0000.0000.0000.000
38A108LEU00.0220.0027.914-1.740-1.7400.0000.0000.0000.000
39A109ASP-1-0.853-0.9327.362-30.467-30.4670.0000.0000.0000.000
40A110MET0-0.017-0.0018.869-2.113-2.1130.0000.0000.0000.000
41A111LEU00.0360.0156.590-0.568-0.5680.0000.0000.0000.000
42A112ALA0-0.038-0.0174.471-6.479-6.379-0.001-0.007-0.0920.000
43A113VAL0-0.045-0.0265.410-3.053-3.0530.0000.0000.0000.000
44A114ILE0-0.0050.0137.904-0.245-0.2450.0000.0000.0000.000
45A115GLY00.0960.0554.1980.7960.850-0.001-0.007-0.0450.000
46A116GLU-1-0.817-0.8574.840-47.444-47.254-0.001-0.007-0.1810.000
47A117LEU0-0.049-0.0365.6414.2734.2730.0000.0000.0000.000
48A118GLU-1-0.830-0.9327.288-30.134-30.1340.0000.0000.0000.000
49A119ARG10.7660.8554.50642.15942.293-0.001-0.004-0.1290.000
50A120GLN0-0.104-0.0817.3315.5435.5430.0000.0000.0000.000
51A121GLU-1-0.816-0.90110.444-19.469-19.4690.0000.0000.0000.000
52A122GLU-1-0.769-0.83412.137-17.026-17.0260.0000.0000.0000.000
53A123THR00.029-0.01013.3800.4920.4920.0000.0000.0000.000
54A124ALA0-0.024-0.00714.7490.3170.3170.0000.0000.0000.000
55A125LEU0-0.013-0.01114.1270.4830.4830.0000.0000.0000.000
56A126ALA00.0100.01111.727-0.160-0.1600.0000.0000.0000.000
57A127ILE00.0440.02812.9620.0090.0090.0000.0000.0000.000
58A128LYS10.8940.94616.28914.66914.6690.0000.0000.0000.000
59A129MET0-0.026-0.00911.1440.8550.8550.0000.0000.0000.000
60A130PHE00.0760.02913.8730.0220.0220.0000.0000.0000.000
61A131GLU-1-0.912-0.93314.844-13.434-13.4340.0000.0000.0000.000
62A132VAL0-0.047-0.02216.0170.7130.7130.0000.0000.0000.000
63A133ILE00.0080.00011.2200.5200.5200.0000.0000.0000.000
64A134GLN0-0.027-0.03215.6141.0861.0860.0000.0000.0000.000
65A135LYS10.8010.90018.36615.09215.0920.0000.0000.0000.000
66A136GLN0-0.061-0.02116.4080.6860.6860.0000.0000.0000.000
67A137GLU-1-0.915-0.96519.460-13.237-13.2370.0000.0000.0000.000
68A138TRP00.012-0.00712.406-0.353-0.3530.0000.0000.0000.000
69A139TYR0-0.002-0.00815.310-1.470-1.4700.0000.0000.0000.000
70A140GLN0-0.002-0.01116.2261.4271.4270.0000.0000.0000.000
71A141PRO0-0.048-0.00315.623-1.255-1.2550.0000.0000.0000.000
72A142ASP-1-0.779-0.90511.031-24.542-24.5420.0000.0000.0000.000
73A143VAL00.0360.02914.051-0.334-0.3340.0000.0000.0000.000
74A144PHE0-0.013-0.0078.883-0.296-0.2960.0000.0000.0000.000
75A145MET0-0.029-0.0149.859-1.078-1.0780.0000.0000.0000.000
76A146TYR0-0.039-0.05110.7780.2760.2760.0000.0000.0000.000
77A147LYS10.8360.9199.69527.86627.8660.0000.0000.0000.000
78A148ASP-1-0.914-0.9606.559-38.128-38.1280.0000.0000.0000.000
79A149LEU00.0160.0219.4000.8950.8950.0000.0000.0000.000
80A150ILE0-0.038-0.01711.8181.2811.2810.0000.0000.0000.000
81A151VAL0-0.027-0.02511.0801.0521.0520.0000.0000.0000.000
82A152SER0-0.062-0.04110.1641.1101.1100.0000.0000.0000.000
83A153LEU0-0.032-0.02612.0561.2541.2540.0000.0000.0000.000
84A154ALA00.0080.01015.6570.9420.9420.0000.0000.0000.000
85A155LYS10.9080.98010.32926.77626.7760.0000.0000.0000.000
86A156SER0-0.039-0.02715.1440.6130.6130.0000.0000.0000.000
87A157LYS10.7700.86817.36714.91114.9110.0000.0000.0000.000
88A158ARG10.7940.89018.20816.26416.2640.0000.0000.0000.000
89A159MET00.0400.02520.054-0.541-0.5410.0000.0000.0000.000
90A160ASP-1-0.860-0.92421.889-12.011-12.0110.0000.0000.0000.000
91A161GLU-1-0.798-0.89319.957-14.164-14.1640.0000.0000.0000.000
92A162ALA0-0.0030.00218.196-0.424-0.4240.0000.0000.0000.000
93A163MET0-0.0030.00119.104-0.386-0.3860.0000.0000.0000.000
94A164ALA0-0.022-0.00222.3280.2010.2010.0000.0000.0000.000
95A165LEU0-0.035-0.02916.9110.1310.1310.0000.0000.0000.000
96A166TRP00.0160.00518.129-0.549-0.5490.0000.0000.0000.000
97A167GLU-1-0.810-0.90320.401-11.418-11.4180.0000.0000.0000.000
98A168LYS10.7560.88619.55315.58815.5880.0000.0000.0000.000
99A169MET0-0.0110.00517.526-0.115-0.1150.0000.0000.0000.000
100A170LYS10.8020.87120.17712.21412.2140.0000.0000.0000.000
101A171LYS10.8280.90723.36812.11612.1160.0000.0000.0000.000
102A172GLU-1-0.799-0.86419.827-14.986-14.9860.0000.0000.0000.000
103A173ASN0-0.091-0.05022.2550.0490.0490.0000.0000.0000.000
104A174LEU0-0.0180.01316.914-0.163-0.1630.0000.0000.0000.000
105A175PHE00.0210.00019.4680.4420.4420.0000.0000.0000.000
106A176PRO0-0.025-0.01917.312-0.886-0.8860.0000.0000.0000.000
107A177ASP-1-0.745-0.84415.215-19.096-19.0960.0000.0000.0000.000
108A178SER0-0.016-0.03818.033-0.057-0.0570.0000.0000.0000.000
109A179GLN0-0.036-0.01212.858-0.678-0.6780.0000.0000.0000.000
110A180THR00.017-0.02314.423-0.769-0.7690.0000.0000.0000.000
111A181TYR00.0330.00115.4900.0430.0430.0000.0000.0000.000
112A182THR0-0.030-0.03617.8960.5620.5620.0000.0000.0000.000
113A183GLU-1-0.863-0.91511.358-24.133-24.1330.0000.0000.0000.000
114A184VAL00.0240.01415.574-0.032-0.0320.0000.0000.0000.000
115A185ILE0-0.0110.00517.2820.5840.5840.0000.0000.0000.000
116A186ARG10.8610.92014.84418.63518.6350.0000.0000.0000.000
117A187GLY0-0.0060.00117.4520.2110.2110.0000.0000.0000.000
118A188PHE00.0680.02818.1110.4120.4120.0000.0000.0000.000
119A189LEU0-0.028-0.01421.5140.6570.6570.0000.0000.0000.000
120A190ARG10.8430.92918.97514.56714.5670.0000.0000.0000.000
121A191ASP-1-0.785-0.89720.309-14.836-14.8360.0000.0000.0000.000
122A192GLY0-0.056-0.00922.9720.4500.4500.0000.0000.0000.000
123A193CYS0-0.026-0.01324.1870.5340.5340.0000.0000.0000.000
124A194PRO00.004-0.00425.712-0.262-0.2620.0000.0000.0000.000
125A195ALA00.0310.00827.9570.0270.0270.0000.0000.0000.000
126A196ASP-1-0.796-0.89023.880-11.978-11.9780.0000.0000.0000.000
127A197ALA0-0.015-0.01223.572-0.253-0.2530.0000.0000.0000.000
128A198MET00.002-0.00524.591-0.108-0.1080.0000.0000.0000.000
129A199ASN0-0.047-0.02326.3960.2710.2710.0000.0000.0000.000
130A200VAL00.0180.00920.5330.0120.0120.0000.0000.0000.000
131A201TYR0-0.027-0.05123.834-0.273-0.2730.0000.0000.0000.000
132A202GLU-1-0.798-0.91325.843-9.687-9.6870.0000.0000.0000.000
133A203ASP-1-0.821-0.86924.680-11.619-11.6190.0000.0000.0000.000
134A204MET0-0.0080.00823.580-0.212-0.2120.0000.0000.0000.000
135A205LEU0-0.067-0.03425.1490.1130.1130.0000.0000.0000.000
136A206LYS10.7710.86127.86511.11511.1150.0000.0000.0000.000
137A207SER0-0.036-0.01923.668-0.147-0.1470.0000.0000.0000.000
138A208PRO0-0.049-0.02324.7310.3900.3900.0000.0000.0000.000
139A209ASP-1-0.882-0.91023.176-12.968-12.9680.0000.0000.0000.000
140A210PRO0-0.009-0.00226.0980.1680.1680.0000.0000.0000.000
141A211PRO0-0.008-0.00925.757-0.383-0.3830.0000.0000.0000.000
142A212GLU-1-0.830-0.88521.330-14.325-14.3250.0000.0000.0000.000
143A213GLU-1-0.697-0.83825.213-10.502-10.5020.0000.0000.0000.000
144A214LEU0-0.029-0.00619.5950.0710.0710.0000.0000.0000.000
145A215PRO00.0540.01322.012-0.015-0.0150.0000.0000.0000.000
146A216PHE00.0510.02723.3630.1780.1780.0000.0000.0000.000
147A217ARG10.7930.88025.33411.04911.0490.0000.0000.0000.000
148A218VAL0-0.073-0.03220.9020.0940.0940.0000.0000.0000.000
149A219LEU00.0170.01024.2430.1820.1820.0000.0000.0000.000
150A220LEU00.0070.00926.7660.3200.3200.0000.0000.0000.000
151A221LYS10.9570.99625.00812.23912.2390.0000.0000.0000.000
152A222GLY0-0.036-0.02326.5190.1220.1220.0000.0000.0000.000
153A223LEU00.006-0.01427.3720.1830.1830.0000.0000.0000.000
154A224LEU0-0.0140.00830.5540.3770.3770.0000.0000.0000.000
155A225PRO0-0.040-0.02531.2230.2980.2980.0000.0000.0000.000
156A226HIS0-0.0080.00530.7330.3450.3450.0000.0000.0000.000
157A227PRO00.0570.02034.401-0.070-0.0700.0000.0000.0000.000
158A228LEU00.001-0.00136.7070.0510.0510.0000.0000.0000.000
159A229LEU00.0200.01531.4560.0170.0170.0000.0000.0000.000
160A230ARG10.8260.90532.2949.2459.2450.0000.0000.0000.000
161A231ASN00.019-0.00933.735-0.146-0.1460.0000.0000.0000.000
162A232LYS10.7890.89533.1399.4899.4890.0000.0000.0000.000
163A233VAL00.0190.00929.5150.0010.0010.0000.0000.0000.000
164A234LYS10.7530.85732.6818.1388.1380.0000.0000.0000.000
165A235LYS10.8550.91935.0758.2298.2290.0000.0000.0000.000
166A236ASP-1-0.799-0.85933.212-9.176-9.1760.0000.0000.0000.000
167A237PHE00.033-0.00430.1980.0090.0090.0000.0000.0000.000
168A238GLU-1-0.865-0.92933.896-7.944-7.9440.0000.0000.0000.000
169A239GLU-1-0.886-0.93837.111-8.017-8.0170.0000.0000.0000.000
170A240LEU0-0.040-0.01431.8850.0510.0510.0000.0000.0000.000
171A241PHE0-0.043-0.01729.857-0.106-0.1060.0000.0000.0000.000
172A242PRO00.0060.01235.3310.0420.0420.0000.0000.0000.000
173A243GLU-1-0.941-0.96837.931-8.090-8.0900.0000.0000.0000.000
174A244LYS10.8430.89330.10810.18210.1820.0000.0000.0000.000
175A245HIS0-0.064-0.04635.4860.0080.0080.0000.0000.0000.000
176A246ALA00.0000.00936.4170.0420.0420.0000.0000.0000.000
177A247TYR0-0.071-0.03534.1480.0200.0200.0000.0000.0000.000
178A248ASP-1-0.858-0.90430.903-10.290-10.2900.0000.0000.0000.000
179A249PRO00.0670.05032.985-0.254-0.2540.0000.0000.0000.000
180A250PRO0-0.026-0.01429.615-0.160-0.1600.0000.0000.0000.000
181A251GLU-1-0.892-0.94330.406-8.762-8.7620.0000.0000.0000.000
182A252GLU-1-0.964-0.96932.095-8.911-8.9110.0000.0000.0000.000