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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: LZZ29

Calculation Name: 5LKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DRP0

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1794877.282811
FMO2-HF: Nuclear repulsion 1728626.091021
FMO2-HF: Total energy -66251.191791
FMO2-MP2: Total energy -66446.269572


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:277:SER)


Summations of interaction energy for fragment #1(A:277:SER)
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.
-33.205-26.87926.127-13.492-18.959-0.07
Interaction energy analysis for fragmet #1(A:277:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.024
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].
3A279VAL00.0960.0393.888-1.1670.5650.003-0.796-0.9390.003
4A280PHE0-0.030-0.0232.847-3.419-1.6370.392-0.799-1.3750.005
5A281LEU0-0.048-0.0392.947-1.659-0.3670.280-0.576-0.9960.005
6A282GLU-1-0.957-0.9716.1270.9640.9640.0000.0000.0000.000
7A283GLU-1-0.946-0.9628.2150.9080.9080.0000.0000.0000.000
8A284ARG10.7080.8488.375-1.406-1.4060.0000.0000.0000.000
9A285LEU00.0210.00510.021-0.035-0.0350.0000.0000.0000.000
10A286ASP-1-0.853-0.93613.1790.5470.5470.0000.0000.0000.000
11A287GLY0-0.038-0.02014.487-0.053-0.0530.0000.0000.0000.000
12A288ALA0-0.038-0.00713.233-0.053-0.0530.0000.0000.0000.000
13A289THR0-0.064-0.04013.8770.0640.0640.0000.0000.0000.000
14A290GLY00.0240.00715.7140.0350.0350.0000.0000.0000.000
15A291SER0-0.0130.00111.4900.0420.0420.0000.0000.0000.000
16A292SER0-0.066-0.02610.566-0.005-0.0050.0000.0000.0000.000
17A293ILE00.0330.0365.072-0.033-0.0330.0000.0000.0000.000
18A294VAL0-0.011-0.0088.260-0.266-0.2660.0000.0000.0000.000
19A295VAL00.0100.0137.7060.1010.1010.0000.0000.0000.000
20A296THR0-0.038-0.04010.097-0.050-0.0500.0000.0000.0000.000
21A297MET0-0.023-0.01012.527-0.060-0.0600.0000.0000.0000.000
22A298GLU-1-0.811-0.87314.6510.2920.2920.0000.0000.0000.000
23A299GLY00.0370.01616.266-0.028-0.0280.0000.0000.0000.000
24A300THR0-0.102-0.06718.294-0.021-0.0210.0000.0000.0000.000
25A301ARG10.9000.95210.409-0.370-0.3700.0000.0000.0000.000
26A302PRO00.004-0.00210.3120.0640.0640.0000.0000.0000.000
27A303ILE0-0.030-0.0199.4000.0140.0140.0000.0000.0000.000
28A304LEU0-0.0060.0123.981-0.277-0.138-0.001-0.028-0.1100.000
29A305ALA00.0170.0056.9650.3110.3110.0000.0000.0000.000
30A306GLU-1-0.763-0.8648.4011.2541.2540.0000.0000.0000.000
31A307VAL0-0.033-0.0169.925-0.107-0.1070.0000.0000.0000.000
32A308GLN00.025-0.00812.360-0.049-0.0490.0000.0000.0000.000
33A309ALA0-0.046-0.03315.326-0.056-0.0560.0000.0000.0000.000
34A310LEU00.0430.03618.7620.0160.0160.0000.0000.0000.000
35A311VAL0-0.022-0.02221.534-0.021-0.0210.0000.0000.0000.000
36A312THR00.0260.01824.8130.0070.0070.0000.0000.0000.000
37A313PRO00.0210.01428.181-0.005-0.0050.0000.0000.0000.000
38A314THR0-0.035-0.01231.8000.0040.0040.0000.0000.0000.000
39A315MET0-0.026-0.00333.860-0.008-0.0080.0000.0000.0000.000
40A316PHE00.0280.00036.798-0.008-0.0080.0000.0000.0000.000
41A317GLY00.0160.01237.1200.0060.0060.0000.0000.0000.000
42A318ASN00.0150.00235.595-0.003-0.0030.0000.0000.0000.000
43A319ALA00.0120.02731.7810.0060.0060.0000.0000.0000.000
44A320LYS10.7940.87529.951-0.138-0.1380.0000.0000.0000.000
45A321ARG10.8350.90227.477-0.140-0.1400.0000.0000.0000.000
46A322THR00.0050.01025.951-0.013-0.0130.0000.0000.0000.000
47A323THR0-0.040-0.02422.6210.0110.0110.0000.0000.0000.000
48A324THR00.0290.01221.0300.0020.0020.0000.0000.0000.000
49A325GLY0-0.0080.00118.9780.0280.0280.0000.0000.0000.000
50A326LEU00.0220.01817.853-0.010-0.0100.0000.0000.0000.000
51A327ASP-1-0.744-0.86120.7900.1360.1360.0000.0000.0000.000
52A328PHE00.0450.02724.1400.0040.0040.0000.0000.0000.000
53A329ASN0-0.044-0.03026.522-0.010-0.0100.0000.0000.0000.000
54A330ARG10.8360.88821.047-0.133-0.1330.0000.0000.0000.000
55A331ALA00.0150.00922.845-0.005-0.0050.0000.0000.0000.000
56A332SER0-0.005-0.01723.999-0.004-0.0040.0000.0000.0000.000
57A333LEU0-0.024-0.01827.332-0.009-0.0090.0000.0000.0000.000
58A334ILE0-0.0210.00720.955-0.010-0.0100.0000.0000.0000.000
59A335MET0-0.022-0.00724.761-0.002-0.0020.0000.0000.0000.000
60A336ALA00.0280.02326.222-0.007-0.0070.0000.0000.0000.000
61A337VAL0-0.035-0.01725.927-0.011-0.0110.0000.0000.0000.000
62A338LEU0-0.006-0.01021.821-0.011-0.0110.0000.0000.0000.000
63A339GLU-1-0.771-0.85526.1140.0840.0840.0000.0000.0000.000
64A340LYS10.9150.95429.589-0.052-0.0520.0000.0000.0000.000
65A341ARG10.8120.89727.948-0.040-0.0400.0000.0000.0000.000
66A342ALA0-0.028-0.02625.718-0.010-0.0100.0000.0000.0000.000
67A343GLY00.0060.02227.7360.0030.0030.0000.0000.0000.000
68A344LEU0-0.059-0.02723.2470.0040.0040.0000.0000.0000.000
69A345LEU0-0.014-0.00327.9470.0010.0010.0000.0000.0000.000
70A346LEU00.0520.00325.3300.0120.0120.0000.0000.0000.000
71A347GLN0-0.072-0.04829.6010.0060.0060.0000.0000.0000.000
72A348ASN0-0.013-0.00132.8510.0000.0000.0000.0000.0000.000
73A349GLN00.0080.01527.6750.0030.0030.0000.0000.0000.000
74A350ASP-1-0.764-0.86229.1810.1500.1500.0000.0000.0000.000
75A351ALA0-0.012-0.01824.4010.0080.0080.0000.0000.0000.000
76A352TYR0-0.023-0.01323.529-0.011-0.0110.0000.0000.0000.000
77A353LEU00.004-0.00419.6600.0210.0210.0000.0000.0000.000
78A354LYS10.8400.90615.976-0.627-0.6270.0000.0000.0000.000
79A355SER00.0190.00614.6530.0280.0280.0000.0000.0000.000
80A356ALA00.0260.01811.185-0.033-0.0330.0000.0000.0000.000
81A357GLY00.032-0.00213.290-0.014-0.0140.0000.0000.0000.000
82A358GLY0-0.0150.00814.624-0.062-0.0620.0000.0000.0000.000
83A359VAL0-0.024-0.00512.223-0.073-0.0730.0000.0000.0000.000
84A360LYS10.9540.98615.650-0.291-0.2910.0000.0000.0000.000
85A361LEU0-0.013-0.00813.4050.0010.0010.0000.0000.0000.000
86A362ASP-1-0.862-0.93417.4750.1260.1260.0000.0000.0000.000
87A363GLU-1-0.724-0.80916.0510.0100.0100.0000.0000.0000.000
88A364PRO00.036-0.00519.4980.0160.0160.0000.0000.0000.000
89A365ALA0-0.0180.00016.1050.0010.0010.0000.0000.0000.000
90A366ILE00.0510.02615.087-0.005-0.0050.0000.0000.0000.000
91A367ASP-1-0.803-0.88616.4920.1370.1370.0000.0000.0000.000
92A368LEU0-0.013-0.01216.2410.0170.0170.0000.0000.0000.000
93A369ALA00.0470.02712.9240.0130.0130.0000.0000.0000.000
94A370VAL00.0260.02414.6770.0550.0550.0000.0000.0000.000
95A371ALA0-0.017-0.01117.4300.0100.0100.0000.0000.0000.000
96A372VAL0-0.010-0.01014.103-0.001-0.0010.0000.0000.0000.000
97A373ALA00.0080.01914.7430.0200.0200.0000.0000.0000.000
98A374ILE00.022-0.00516.0930.0000.0000.0000.0000.0000.000
99A375ALA0-0.037-0.02719.175-0.008-0.0080.0000.0000.0000.000
100A376SER0-0.020-0.02115.8720.0080.0080.0000.0000.0000.000
101A377SER00.0640.03117.897-0.006-0.0060.0000.0000.0000.000
102A378TYR0-0.052-0.03420.175-0.021-0.0210.0000.0000.0000.000
103A379LYS10.8860.94921.341-0.148-0.1480.0000.0000.0000.000
104A380ASP-1-0.838-0.89320.7520.2760.2760.0000.0000.0000.000
105A381LYS10.8330.90818.292-0.220-0.2200.0000.0000.0000.000
106A382PRO00.0580.06213.471-0.005-0.0050.0000.0000.0000.000
107A383THR0-0.020-0.03410.892-0.004-0.0040.0000.0000.0000.000
108A384ASN00.0200.0007.5940.5170.5170.0000.0000.0000.000
109A385PRO00.0430.0245.531-0.164-0.1640.0000.0000.0000.000
110A386GLN00.0070.0133.203-1.2750.2610.079-0.712-0.9030.005
111A387GLU-1-0.806-0.8774.232-2.534-2.398-0.001-0.018-0.1180.000
112A388CYS0-0.048-0.0036.5850.1940.1940.0000.0000.0000.000
113A389PHE00.011-0.0058.457-0.186-0.1860.0000.0000.0000.000
114A390VAL00.013-0.00411.8860.0390.0390.0000.0000.0000.000
115A391GLY0-0.014-0.02714.474-0.035-0.0350.0000.0000.0000.000
116A392GLU-1-0.800-0.85718.2710.0310.0310.0000.0000.0000.000
117A393LEU0-0.031-0.02021.463-0.016-0.0160.0000.0000.0000.000
118A394GLY00.0200.01323.4870.0070.0070.0000.0000.0000.000
119A395LEU00.0500.01927.2770.0060.0060.0000.0000.0000.000
120A396THR0-0.048-0.05030.0790.0050.0050.0000.0000.0000.000
121A397GLY0-0.023-0.00126.670-0.002-0.0020.0000.0000.0000.000
122A398GLU-1-0.784-0.86325.608-0.006-0.0060.0000.0000.0000.000
123A399ILE0-0.013-0.00719.7190.0120.0120.0000.0000.0000.000
124A400ARG10.7460.85222.667-0.010-0.0100.0000.0000.0000.000
125A401ARG10.9220.94821.5920.1060.1060.0000.0000.0000.000
126A402VAL00.0440.04017.0080.0190.0190.0000.0000.0000.000
127A403ASN00.0250.01019.334-0.035-0.0350.0000.0000.0000.000
128A404ARG10.9340.93217.2360.1280.1280.0000.0000.0000.000
129A405ILE00.0420.02515.150-0.031-0.0310.0000.0000.0000.000
130A406GLU-1-0.765-0.89114.776-0.570-0.5700.0000.0000.0000.000
131A407GLN00.0050.02513.837-0.068-0.0680.0000.0000.0000.000
132A408ARG10.7140.82211.1760.0100.0100.0000.0000.0000.000
133A409ILE00.0370.0139.859-0.152-0.1520.0000.0000.0000.000
134A410ASN0-0.013-0.0229.692-0.334-0.3340.0000.0000.0000.000
135A411GLU-1-0.811-0.8836.966-0.820-0.8200.0000.0000.0000.000
136A412ALA00.0100.0015.465-0.509-0.5090.0000.0000.0000.000
137A413ALA00.003-0.0024.881-1.644-1.510-0.001-0.005-0.1270.000
138A414LYS10.8120.8926.3570.1300.1300.0000.0000.0000.000
139A415LEU0-0.048-0.0242.778-0.3290.4060.273-0.323-0.6850.000
140A416GLY00.0380.0282.096-7.672-8.4188.188-3.399-4.042-0.041
141A417PHE0-0.041-0.0221.964-14.589-15.01216.890-6.963-9.504-0.047
142A418THR00.0130.0033.4351.3741.3830.0250.127-0.1600.000
143A419LYS10.8110.8975.8130.6740.6740.0000.0000.0000.000
144A420ILE00.0240.0047.9800.0510.0510.0000.0000.0000.000
145A421TYR0-0.048-0.02110.319-0.004-0.0040.0000.0000.0000.000
146A422VAL00.0320.01113.6200.0380.0380.0000.0000.0000.000
147A423PRO00.0400.01816.0810.0140.0140.0000.0000.0000.000
148A424LYS10.9910.98819.9090.1240.1240.0000.0000.0000.000
149A425ASN0-0.052-0.03021.414-0.022-0.0220.0000.0000.0000.000
150A426SER0-0.008-0.01820.0210.0250.0250.0000.0000.0000.000
151A427LEU00.0290.01817.132-0.020-0.0200.0000.0000.0000.000
152A428THR0-0.076-0.03921.092-0.004-0.0040.0000.0000.0000.000
153A429GLY00.0230.01724.3670.0170.0170.0000.0000.0000.000
154A430ILE0-0.059-0.01418.4760.0020.0020.0000.0000.0000.000
155A431THR0-0.009-0.00719.5020.0140.0140.0000.0000.0000.000
156A432LEU0-0.0030.00316.117-0.042-0.0420.0000.0000.0000.000
157A433PRO00.0430.03512.2830.0640.0640.0000.0000.0000.000
158A434LYS10.8420.88914.0650.6420.6420.0000.0000.0000.000
159A435GLU-1-0.871-0.9269.543-1.155-1.1550.0000.0000.0000.000
160A436ILE0-0.0050.0116.714-0.348-0.3480.0000.0000.0000.000
161A437GLN00.001-0.0059.3930.3400.3400.0000.0000.0000.000
162A438VAL00.0160.00211.5620.0590.0590.0000.0000.0000.000
163A439ILE0-0.042-0.01313.5800.0860.0860.0000.0000.0000.000
164A440GLY00.0100.00115.6780.0360.0360.0000.0000.0000.000
165A441VAL0-0.077-0.03117.9380.0220.0220.0000.0000.0000.000
166A442THR0-0.063-0.06020.475-0.002-0.0020.0000.0000.0000.000
167A443THR00.0240.01523.5830.0150.0150.0000.0000.0000.000
168A444ILE00.0730.03420.510-0.005-0.0050.0000.0000.0000.000
169A445GLN00.0320.00322.1780.0060.0060.0000.0000.0000.000
170A446GLU-1-0.812-0.87121.905-0.099-0.0990.0000.0000.0000.000
171A447VAL00.0410.01717.105-0.012-0.0120.0000.0000.0000.000
172A448LEU0-0.001-0.00618.9590.0110.0110.0000.0000.0000.000
173A449LYS10.9180.95720.6680.0120.0120.0000.0000.0000.000
174A450LYS10.8270.91017.4070.1170.1170.0000.0000.0000.000
175A451VAL0-0.0200.00914.314-0.012-0.0120.0000.0000.0000.000
176A452PHE0-0.0220.00216.4730.0210.0210.0000.0000.0000.000