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: VQM41

Calculation Name: 3LJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LJB

Chain ID: A

ChEMBL ID:

UniProt ID: P20591

Base Structure: X-ray

Registration Date: 2023-09-24

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2659229.437891
FMO2-HF: Nuclear repulsion 2566332.857038
FMO2-HF: Total energy -92896.580853
FMO2-MP2: Total energy -93166.829436


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:366:GLU)


Summations of interaction energy for fragment #1(A:366:GLU)
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.
15.06321.8682.662-3.377-6.0920.02
Interaction energy analysis for fragmet #1(A:366:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.964 / q_NPA : -1.005
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].
3A368GLU-1-0.964-0.9932.36835.46940.1911.674-2.638-3.7590.016
4A369ASN0-0.022-0.0232.287-9.283-7.7470.987-0.634-1.8900.004
5A370GLU-1-0.919-0.9444.06627.72828.2460.002-0.104-0.4160.000
6A371LYS10.8970.9576.025-38.096-38.0960.0000.0000.0000.000
7A372MET00.003-0.0087.089-3.345-3.3450.0000.0000.0000.000
8A373PHE0-0.023-0.0166.470-2.049-2.0490.0000.0000.0000.000
9A374PHE00.0550.04110.079-2.083-2.0830.0000.0000.0000.000
10A375LEU0-0.022-0.01811.648-1.719-1.7190.0000.0000.0000.000
11A376ILE0-0.003-0.01211.407-1.457-1.4570.0000.0000.0000.000
12A377ASP-1-0.888-0.93113.88316.67116.6710.0000.0000.0000.000
13A378LYS10.8250.93216.142-15.696-15.6960.0000.0000.0000.000
14A379VAL0-0.015-0.01017.401-0.947-0.9470.0000.0000.0000.000
15A380ASN0-0.014-0.01217.404-1.050-1.0500.0000.0000.0000.000
16A381ALA0-0.0130.00920.252-0.693-0.6930.0000.0000.0000.000
17A382PHE00.0510.02121.996-0.620-0.6200.0000.0000.0000.000
18A383ASN00.029-0.01522.130-0.818-0.8180.0000.0000.0000.000
19A384GLN00.0280.01824.335-0.599-0.5990.0000.0000.0000.000
20A385ASP-1-0.810-0.89926.10810.30710.3070.0000.0000.0000.000
21A386ILE0-0.076-0.03527.547-0.450-0.4500.0000.0000.0000.000
22A387THR00.012-0.00127.782-0.359-0.3590.0000.0000.0000.000
23A388ALA00.0180.01930.310-0.333-0.3330.0000.0000.0000.000
24A389LEU0-0.041-0.00832.251-0.357-0.3570.0000.0000.0000.000
25A390MET0-0.118-0.03832.030-0.193-0.1930.0000.0000.0000.000
26A391GLN0-0.061-0.02832.632-0.092-0.0920.0000.0000.0000.000
27A392GLY0-0.029-0.00636.136-0.156-0.1560.0000.0000.0000.000
28A393GLU-1-0.931-0.97733.9078.5548.5540.0000.0000.0000.000
29A394GLU-1-0.814-0.89033.4198.3098.3090.0000.0000.0000.000
30A395THR0-0.031-0.01332.271-0.372-0.3720.0000.0000.0000.000
31A396VAL0-0.013-0.01734.9890.1010.1010.0000.0000.0000.000
32A397GLY00.0440.02437.894-0.016-0.0160.0000.0000.0000.000
33A398GLU-1-0.981-0.99739.4906.8506.8500.0000.0000.0000.000
34A399GLU-1-0.974-0.97742.2916.3156.3150.0000.0000.0000.000
35A400ASP-1-0.920-0.94041.0937.3037.3030.0000.0000.0000.000
36A401ILE0-0.088-0.05943.253-0.085-0.0850.0000.0000.0000.000
37A402ARG10.8800.93337.257-7.758-7.7580.0000.0000.0000.000
38A403LEU00.010-0.01036.937-0.215-0.2150.0000.0000.0000.000
39A404PHE00.0550.02639.664-0.201-0.2010.0000.0000.0000.000
40A405THR00.006-0.00941.372-0.121-0.1210.0000.0000.0000.000
41A406ARG10.9570.97840.197-7.572-7.5720.0000.0000.0000.000
42A407LEU00.0370.02641.415-0.131-0.1310.0000.0000.0000.000
43A408ARG10.9550.99145.018-6.320-6.3200.0000.0000.0000.000
44A409HIS0-0.038-0.02947.459-0.220-0.2200.0000.0000.0000.000
45A410GLU-1-0.838-0.91047.2626.1626.1620.0000.0000.0000.000
46A411PHE00.0540.00545.061-0.144-0.1440.0000.0000.0000.000
47A412HIS0-0.026-0.01050.599-0.079-0.0790.0000.0000.0000.000
48A413LYS10.8800.93250.960-6.223-6.2230.0000.0000.0000.000
49A414TRP00.005-0.00352.591-0.118-0.1180.0000.0000.0000.000
50A415SER0-0.010-0.00154.593-0.107-0.1070.0000.0000.0000.000
51A416THR0-0.029-0.00756.730-0.128-0.1280.0000.0000.0000.000
52A417ILE0-0.023-0.00355.884-0.110-0.1100.0000.0000.0000.000
53A418ILE00.0040.01856.243-0.100-0.1000.0000.0000.0000.000
54A419GLU-1-0.911-0.93960.1394.8314.8310.0000.0000.0000.000
55A420ASN0-0.012-0.02562.527-0.134-0.1340.0000.0000.0000.000
56A421ASN00.0110.00662.482-0.093-0.0930.0000.0000.0000.000
57A422PHE00.0390.02464.209-0.091-0.0910.0000.0000.0000.000
58A423GLN0-0.075-0.04765.920-0.127-0.1270.0000.0000.0000.000
59A424GLU-1-0.959-0.97666.5744.6534.6530.0000.0000.0000.000
60A425GLY00.0410.01468.184-0.081-0.0810.0000.0000.0000.000
61A426HIS00.0280.00269.656-0.041-0.0410.0000.0000.0000.000
62A427LYS10.9300.96971.985-4.287-4.2870.0000.0000.0000.000
63A428ILE0-0.041-0.02770.598-0.098-0.0980.0000.0000.0000.000
64A429LEU00.0050.00773.047-0.072-0.0720.0000.0000.0000.000
65A430SER00.0170.00075.244-0.074-0.0740.0000.0000.0000.000
66A431ARG10.9010.95177.023-4.106-4.1060.0000.0000.0000.000
67A432LYS10.8970.96677.498-4.109-4.1090.0000.0000.0000.000
68A433ILE00.0460.01478.207-0.049-0.0490.0000.0000.0000.000
69A434GLN00.0240.02181.368-0.034-0.0340.0000.0000.0000.000
70A435LYS10.9100.95682.668-3.913-3.9130.0000.0000.0000.000
71A436PHE0-0.051-0.03981.049-0.019-0.0190.0000.0000.0000.000
72A437GLU-1-0.982-0.98584.9923.6883.6880.0000.0000.0000.000
73A438ASN0-0.0490.00087.318-0.059-0.0590.0000.0000.0000.000
74A448PHE00.0520.01580.832-0.007-0.0070.0000.0000.0000.000
75A449VAL00.0210.00781.5710.0400.0400.0000.0000.0000.000
76A450ASN0-0.012-0.01180.8770.0300.0300.0000.0000.0000.000
77A451TYR00.0090.01173.4900.0310.0310.0000.0000.0000.000
78A452ARG11.0050.99675.253-4.134-4.1340.0000.0000.0000.000
79A453THR00.0010.00074.8040.0570.0570.0000.0000.0000.000
80A454PHE00.010-0.00175.3180.0290.0290.0000.0000.0000.000
81A455GLU-1-0.860-0.94270.4084.5584.5580.0000.0000.0000.000
82A456THR0-0.026-0.01270.4830.0850.0850.0000.0000.0000.000
83A457ILE0-0.034-0.01669.9200.0480.0480.0000.0000.0000.000
84A458VAL00.0160.01567.0860.0480.0480.0000.0000.0000.000
85A459LYS10.8940.96165.980-4.682-4.6820.0000.0000.0000.000
86A460GLN0-0.001-0.02665.0050.0280.0280.0000.0000.0000.000
87A461GLN0-0.0250.00865.2340.0570.0570.0000.0000.0000.000
88A462ILE00.0480.02960.5580.0730.0730.0000.0000.0000.000
89A463LYS10.8530.90358.979-5.268-5.2680.0000.0000.0000.000
90A464ALA0-0.031-0.00960.3510.0740.0740.0000.0000.0000.000
91A465LEU0-0.003-0.00457.8370.0510.0510.0000.0000.0000.000
92A466GLU-1-0.793-0.87055.1755.7225.7220.0000.0000.0000.000
93A467GLU-1-0.810-0.91954.4835.9025.9020.0000.0000.0000.000
94A468PRO00.0280.02753.7890.1080.1080.0000.0000.0000.000
95A469ALA0-0.0140.00452.3870.1100.1100.0000.0000.0000.000
96A470VAL0-0.018-0.01349.2590.1550.1550.0000.0000.0000.000
97A471ASP-1-0.902-0.95149.1926.1016.1010.0000.0000.0000.000
98A472MET0-0.051-0.02048.4510.1260.1260.0000.0000.0000.000
99A473LEU0-0.031-0.00943.8180.1550.1550.0000.0000.0000.000
100A474HIS10.8790.90044.768-6.576-6.5760.0000.0000.0000.000
101A475THR00.0040.01844.6530.1100.1100.0000.0000.0000.000
102A476VAL00.006-0.01842.3950.1270.1270.0000.0000.0000.000
103A477THR0-0.052-0.01240.3090.2610.2610.0000.0000.0000.000
104A478ASP-1-0.787-0.87239.6227.5247.5240.0000.0000.0000.000
105A479MET0-0.103-0.04540.0560.1720.1720.0000.0000.0000.000
106A480VAL0-0.0100.00735.9260.1560.1560.0000.0000.0000.000
107A481ARG10.9440.98335.468-8.113-8.1130.0000.0000.0000.000
108A482LEU0-0.077-0.02634.9760.2440.2440.0000.0000.0000.000
109A483ALA00.0320.02735.3210.1670.1670.0000.0000.0000.000
110A484PHE00.026-0.01031.2930.2560.2560.0000.0000.0000.000
111A485THR0-0.064-0.04430.5920.4210.4210.0000.0000.0000.000
112A486ASP-1-0.845-0.93131.1048.9708.9700.0000.0000.0000.000
113A487VAL0-0.019-0.00127.4750.2180.2180.0000.0000.0000.000
114A488SER0-0.015-0.03126.7360.5290.5290.0000.0000.0000.000
115A489ILE0-0.037-0.01426.7890.3620.3620.0000.0000.0000.000
116A490LYS10.9230.96127.125-10.437-10.4370.0000.0000.0000.000
117A491ASN0-0.087-0.04823.3610.5810.5810.0000.0000.0000.000
118A492PHE0-0.035-0.03320.5660.7210.7210.0000.0000.0000.000
119A493GLU-1-0.935-0.96623.84510.38010.3800.0000.0000.0000.000
120A494GLU-1-0.927-0.94722.79811.96811.9680.0000.0000.0000.000
121A495PHE0-0.014-0.01117.4520.4440.4440.0000.0000.0000.000
122A496PHE00.0310.00821.651-0.140-0.1400.0000.0000.0000.000
123A497ASN0-0.038-0.01820.143-1.150-1.1500.0000.0000.0000.000
124A498LEU00.0620.05317.929-0.215-0.2150.0000.0000.0000.000
125A499HIS00.0650.05721.494-0.191-0.1910.0000.0000.0000.000
126A500ARG10.8340.90924.217-12.607-12.6070.0000.0000.0000.000
127A501THR0-0.022-0.02821.997-0.269-0.2690.0000.0000.0000.000
128A502ALA00.0360.02324.329-0.258-0.2580.0000.0000.0000.000
129A503LYS10.9820.98225.782-9.988-9.9880.0000.0000.0000.000
130A504SER0-0.085-0.04527.351-0.247-0.2470.0000.0000.0000.000
131A505LYS10.9110.95423.054-13.010-13.0100.0000.0000.0000.000
132A506ILE0-0.0010.00228.801-0.273-0.2730.0000.0000.0000.000
133A507GLU-1-0.891-0.93731.2008.3558.3550.0000.0000.0000.000
134A508ASP-1-0.916-0.94631.0759.5969.5960.0000.0000.0000.000
135A509ILE0-0.060-0.04229.151-0.234-0.2340.0000.0000.0000.000
136A510ARG10.7980.87633.568-7.907-7.9070.0000.0000.0000.000
137A511ALA00.0020.00036.575-0.251-0.2510.0000.0000.0000.000
138A512GLU-1-0.944-0.97835.6438.1928.1920.0000.0000.0000.000
139A513GLN00.025-0.00635.103-0.334-0.3340.0000.0000.0000.000
140A514GLU-1-0.731-0.82838.7067.1447.1440.0000.0000.0000.000
141A515ARG10.8970.95939.190-8.004-8.0040.0000.0000.0000.000
142A516GLU-1-0.954-0.97040.9107.1557.1550.0000.0000.0000.000
143A517GLY00.0300.00042.601-0.163-0.1630.0000.0000.0000.000
144A518GLU-1-0.863-0.94844.2966.3456.3450.0000.0000.0000.000
145A519LYS10.9290.97345.251-7.131-7.1310.0000.0000.0000.000
146A520LEU00.0190.00245.791-0.171-0.1710.0000.0000.0000.000
147A521ILE00.0060.01147.619-0.156-0.1560.0000.0000.0000.000
148A522ARG10.7600.86150.280-6.160-6.1600.0000.0000.0000.000
149A523LEU0-0.011-0.00550.476-0.138-0.1380.0000.0000.0000.000
150A524HIS0-0.030-0.02452.101-0.040-0.0400.0000.0000.0000.000
151A525PHE00.013-0.00253.831-0.123-0.1230.0000.0000.0000.000
152A526GLN0-0.066-0.02955.538-0.019-0.0190.0000.0000.0000.000
153A527MET0-0.039-0.01153.104-0.094-0.0940.0000.0000.0000.000
154A528GLU-1-0.710-0.83857.6255.2995.2990.0000.0000.0000.000
155A529GLN0-0.119-0.02760.103-0.192-0.1920.0000.0000.0000.000
156A530ILE0-0.039-0.01960.757-0.084-0.0840.0000.0000.0000.000
157A531VAL0-0.028-0.00863.7820.0320.0320.0000.0000.0000.000
158A532TYR0-0.0040.00862.842-0.009-0.0090.0000.0000.0000.000
159A573SER00.0620.02783.403-0.036-0.0360.0000.0000.0000.000
160A574MET0-0.037-0.02980.5360.0360.0360.0000.0000.0000.000
161A575GLU-1-0.865-0.95979.7654.0754.0750.0000.0000.0000.000
162A576GLU-1-0.907-0.94878.6034.0154.0150.0000.0000.0000.000
163A577ILE0-0.039-0.01876.9320.0560.0560.0000.0000.0000.000
164A578PHE0-0.009-0.00875.1750.0700.0700.0000.0000.0000.000
165A579GLN00.0110.00074.2770.0990.0990.0000.0000.0000.000
166A580HIS00.0180.02571.9800.0530.0530.0000.0000.0000.000
167A581LEU00.001-0.00671.2200.0760.0760.0000.0000.0000.000
168A582MET0-0.0050.00769.5980.0800.0800.0000.0000.0000.000
169A583ALA0-0.0200.00968.8460.0700.0700.0000.0000.0000.000
170A584TYR00.005-0.03163.8330.0450.0450.0000.0000.0000.000
171A585HIS00.0170.01064.7260.0440.0440.0000.0000.0000.000
172A586GLN00.0050.00564.1290.1360.1360.0000.0000.0000.000
173A587GLU-1-0.944-0.97061.9195.0805.0800.0000.0000.0000.000
174A588ALA00.0310.00060.5320.1040.1040.0000.0000.0000.000
175A589SER0-0.032-0.01859.4080.0930.0930.0000.0000.0000.000
176A590LYS10.9100.95458.630-5.017-5.0170.0000.0000.0000.000
177A591ARG10.8870.92656.083-5.203-5.2030.0000.0000.0000.000
178A592ILE00.0140.02354.6800.1370.1370.0000.0000.0000.000
179A593SER0-0.013-0.02254.0190.1450.1450.0000.0000.0000.000
180A594SER0-0.023-0.00852.3600.1350.1350.0000.0000.0000.000
181A595HIS00.002-0.01549.5270.2090.2090.0000.0000.0000.000
182A596ILE00.0240.01549.2400.1320.1320.0000.0000.0000.000
183A597PRO00.0190.00547.7160.1490.1490.0000.0000.0000.000
184A598LEU0-0.0120.01344.7710.1780.1780.0000.0000.0000.000
185A599ILE0-0.0040.00244.4590.2000.2000.0000.0000.0000.000
186A600ILE00.0300.00443.5470.2020.2020.0000.0000.0000.000
187A601GLN00.0100.01241.4930.1430.1430.0000.0000.0000.000
188A602PHE0-0.024-0.00439.0010.2450.2450.0000.0000.0000.000
189A603PHE00.0290.02438.7190.2260.2260.0000.0000.0000.000
190A604MET0-0.019-0.01237.9020.2380.2380.0000.0000.0000.000
191A605LEU00.0110.01535.8850.0560.0560.0000.0000.0000.000
192A606GLN0-0.022-0.01835.3070.4310.4310.0000.0000.0000.000
193A607THR00.0170.00034.1380.3160.3160.0000.0000.0000.000
194A608TYR0-0.083-0.06832.8480.2970.2970.0000.0000.0000.000
195A609GLY00.0530.01231.5630.3130.3130.0000.0000.0000.000
196A610GLN00.0190.01129.6840.3420.3420.0000.0000.0000.000
197A611GLN0-0.067-0.04428.5910.4500.4500.0000.0000.0000.000
198A612LEU00.0130.02127.2420.4540.4540.0000.0000.0000.000
199A613GLN0-0.030-0.03325.2490.3780.3780.0000.0000.0000.000
200A614LYS10.9270.95523.716-10.156-10.1560.0000.0000.0000.000
201A615ALA00.0000.00523.4620.5240.5240.0000.0000.0000.000
202A616MET00.0020.01321.3310.4350.4350.0000.0000.0000.000
203A617LEU00.0270.01718.9230.7600.7600.0000.0000.0000.000
204A618GLN0-0.001-0.00418.4620.5540.5540.0000.0000.0000.000
205A619LEU0-0.058-0.02817.8300.4000.4000.0000.0000.0000.000
206A620LEU00.0190.01313.2810.8950.8950.0000.0000.0000.000
207A621GLN0-0.0540.01613.8921.0361.0360.0000.0000.0000.000
208A622ASP-1-0.875-0.94714.48821.27821.2780.0000.0000.0000.000
209A623LYS10.9710.9764.853-48.320-48.291-0.001-0.001-0.0270.000
210A624ASP-1-0.906-0.93810.80328.27628.2760.0000.0000.0000.000
211A625THR0-0.063-0.02812.220-1.289-1.2890.0000.0000.0000.000
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