Manual

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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: LL4Q9

Calculation Name: 7JTL-A-Xray161

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7JTL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-10-05

Reference: Y.Handa, K. Kato, Y. Kawashima, K. Fukuzawa et.al., FMO calculation for SARS Cov-2 related proteins. To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water All crystal waters in PDB.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1036262.658508
FMO2-HF: Nuclear repulsion 985741.581266
FMO2-HF: Total energy -50521.077243
FMO2-MP2: Total energy -50662.184782


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:18:GLN )


Summations of interaction energy for fragment #1(A:18:GLN )
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.
-109.681-102.9288.121-6.556-8.316-0.035
Interaction energy analysis for fragmet #1(A:18:GLN )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.897
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].
3A20CYS 0-0.023-0.0093.3148.55311.7520.035-1.554-1.680-0.003
4A21SER 00.0020.0263.011-4.984-2.8140.435-0.986-1.619-0.004
5A22LEU 0-0.033-0.0173.8162.8552.9890.003-0.059-0.0770.000
6A23GLN 0-0.0020.0026.1551.8461.8460.0000.0000.0000.000
7A24SER 00.0500.0239.0411.1181.1180.0000.0000.0000.000
8A90CYS 0-0.0970.00712.724-0.464-0.4640.0000.0000.0000.000
9A26THR 00.0640.06615.7820.3150.3150.0000.0000.0000.000
10A27GLN 00.018-0.00819.4730.2620.2620.0000.0000.0000.000
11A28HIS 0-0.070-0.01920.5260.6710.6710.0000.0000.0000.000
12A29GLN 00.0030.03121.3260.4280.4280.0000.0000.0000.000
13A30PRO 00.0350.01120.125-0.500-0.5000.0000.0000.0000.000
14A31TYR 0-0.009-0.00910.4010.4280.4280.0000.0000.0000.000
15A32VAL 00.0240.02514.823-0.194-0.1940.0000.0000.0000.000
16A33VAL 0-0.0200.01610.045-0.595-0.5950.0000.0000.0000.000
17A34ASP -1-0.841-0.8867.933-26.233-26.2330.0000.0000.0000.000
18A35ASP -1-0.730-0.8508.233-26.885-26.8850.0000.0000.0000.000
19A36PRO 0-0.013-0.0073.853-1.368-0.8920.016-0.097-0.3940.000
20A102CYS 0-0.079-0.0144.041-7.513-7.123-0.001-0.061-0.3280.000
21A38PRO 00.0060.0045.0340.5060.5060.0000.0000.0000.000
22A39ILE 00.0270.0076.7162.6552.6550.0000.0000.0000.000
23A40HIS 0-0.055-0.04810.198-0.870-0.8700.0000.0000.0000.000
24A41PHE 0-0.016-0.0018.9510.2530.2530.0000.0000.0000.000
25A42TYR 0-0.058-0.01911.4810.2940.2940.0000.0000.0000.000
26A43SER 00.006-0.01810.373-1.774-1.7740.0000.0000.0000.000
27A44LYS 10.8630.96412.12817.60317.6030.0000.0000.0000.000
28A45TRP 00.0120.0099.401-1.909-1.9090.0000.0000.0000.000
29A46TYR 0-0.011-0.01613.3811.0981.0980.0000.0000.0000.000
30A47ILE 00.0060.01614.233-0.706-0.7060.0000.0000.0000.000
31A48ARG 10.8050.90214.14119.36819.3680.0000.0000.0000.000
32A49VAL 00.0180.00216.3920.1290.1290.0000.0000.0000.000
33A50GLY 00.026-0.01119.493-0.161-0.1610.0000.0000.0000.000
34A51ALA 0-0.0420.00115.001-0.102-0.1020.0000.0000.0000.000
35A52ARG 10.9590.98616.31712.50712.5070.0000.0000.0000.000
36A53LYS 11.0170.99612.47822.25622.2560.0000.0000.0000.000
37A54SER 0-0.034-0.02016.958-0.137-0.1370.0000.0000.0000.000
38A55ALA 0-0.048-0.00719.6290.7900.7900.0000.0000.0000.000
39A56PRO 00.013-0.00119.734-0.670-0.6700.0000.0000.0000.000
40A57LEU 00.0050.01714.503-0.205-0.2050.0000.0000.0000.000
41A58ILE 0-0.039-0.02418.5070.6220.6220.0000.0000.0000.000
42A59GLU -1-0.716-0.80917.733-16.065-16.0650.0000.0000.0000.000
43A60LEU 00.0010.00216.0310.6320.6320.0000.0000.0000.000
44A83CYS 0-0.0050.01019.020-0.101-0.1010.0000.0000.0000.000
45A62VAL 00.0240.01820.8860.1350.1350.0000.0000.0000.000
46A63ASP -1-0.890-0.91123.417-11.628-11.6280.0000.0000.0000.000
47A64GLU -1-0.682-0.87126.326-10.722-10.7220.0000.0000.0000.000
48A65ALA 0-0.170-0.10828.5440.3060.3060.0000.0000.0000.000
49A66GLY 00.0430.03427.527-0.267-0.2670.0000.0000.0000.000
50A67SER 0-0.046-0.01029.0070.3290.3290.0000.0000.0000.000
51A68LYS 10.8900.97032.4298.3138.3130.0000.0000.0000.000
52A69SER 00.029-0.01330.305-0.093-0.0930.0000.0000.0000.000
53A70PRO 0-0.082-0.03332.7060.1300.1300.0000.0000.0000.000
54A71ILE 0-0.025-0.00428.2610.1040.1040.0000.0000.0000.000
55A72GLN 00.0010.00728.8290.0440.0440.0000.0000.0000.000
56A73TYR 0-0.016-0.01724.5950.0270.0270.0000.0000.0000.000
57A74ILE 00.0160.02626.694-0.004-0.0040.0000.0000.0000.000
58A75ASP -1-0.707-0.82023.666-12.338-12.3380.0000.0000.0000.000
59A76ILE 0-0.023-0.01126.0320.2270.2270.0000.0000.0000.000
60A77GLY 0-0.035-0.02226.0640.2690.2690.0000.0000.0000.000
61A78ASN 0-0.030-0.00825.331-0.177-0.1770.0000.0000.0000.000
62A79TYR 0-0.035-0.03915.360-0.262-0.2620.0000.0000.0000.000
63A80THR 00.015-0.00519.817-0.803-0.8030.0000.0000.0000.000
64A81VAL 0-0.0080.01020.3880.5800.5800.0000.0000.0000.000
65A82SER 00.002-0.01020.6520.6430.6430.0000.0000.0000.000
66A84LEU 0-0.0060.03720.186-0.401-0.4010.0000.0000.0000.000
67A85PRO 00.0140.02716.6530.7570.7570.0000.0000.0000.000
68A86PHE 00.0410.02113.5990.5710.5710.0000.0000.0000.000
69A87THR 0-0.031-0.00715.611-0.638-0.6380.0000.0000.0000.000
70A88ILE 00.0120.02214.2460.4980.4980.0000.0000.0000.000
71A89ASN 00.011-0.01917.9800.1020.1020.0000.0000.0000.000
72A91GLN 00.026-0.01117.0890.9330.9330.0000.0000.0000.000
73A92GLU -1-0.688-0.78713.656-19.424-19.4240.0000.0000.0000.000
74A93PRO 0-0.0040.02415.9651.0161.0160.0000.0000.0000.000
75A94LYS 10.9350.95718.85210.67010.6700.0000.0000.0000.000
76A95LEU 0-0.030-0.01120.904-0.025-0.0250.0000.0000.0000.000
77A96GLY 00.017-0.00418.1070.1740.1740.0000.0000.0000.000
78A97SER 0-0.0080.02712.444-0.169-0.1690.0000.0000.0000.000
79A98LEU 00.0490.03911.5030.2600.2600.0000.0000.0000.000
80A99VAL 0-0.074-0.0499.492-1.587-1.5870.0000.0000.0000.000
81A100VAL 00.0520.0357.2711.7391.7390.0000.0000.0000.000
82A101ARG 10.7760.8528.31418.81218.8120.0000.0000.0000.000
83A103SER 0-0.007-0.0388.764-0.900-0.9000.0000.0000.0000.000
84A104PHE 0-0.0140.01011.4800.8290.8290.0000.0000.0000.000
85A105TYR 00.0280.02713.0851.5581.5580.0000.0000.0000.000
86A106GLU -1-0.813-0.89115.856-14.707-14.7070.0000.0000.0000.000
87A107ASP -1-0.885-0.92018.249-15.586-15.5860.0000.0000.0000.000
88A108PHE 0-0.080-0.05112.788-0.039-0.0390.0000.0000.0000.000
89A109LEU 0-0.019-0.00515.879-0.193-0.1930.0000.0000.0000.000
90A110GLU -1-0.880-0.89213.431-19.919-19.9190.0000.0000.0000.000
91A111TYR 0-0.0030.00810.5350.5050.5050.0000.0000.0000.000
92A112HIS 0-0.024-0.0013.4711.4851.7170.005-0.058-0.1800.000
93A113ASP -1-0.767-0.8567.357-24.074-24.0740.0000.0000.0000.000
94A114VAL 0-0.0090.0042.948-6.486-5.1880.459-0.516-1.2410.002
95A115ARG 10.8390.9215.56725.95226.007-0.001-0.003-0.0500.000
96A116VAL 00.0480.0196.022-2.048-2.0480.0000.0000.0000.000
97A117VAL 0-0.066-0.0228.0252.0012.0010.0000.0000.0000.000
98A118LEU 00.0460.0119.416-0.881-0.8810.0000.0000.0000.000
99A119ASP -1-0.762-0.81111.836-18.522-18.5220.0000.0000.0000.000
100A120PHE 0-0.051-0.05113.781-0.061-0.0610.0000.0000.0000.000
101A121ILE -1-0.905-0.92616.321-12.629-12.6290.0000.0000.0000.000
102A201HOH 0-0.007-0.00619.4790.2990.2990.0000.0000.0000.000
103A202HOH 0-0.025-0.03524.4530.0760.0760.0000.0000.0000.000
104A203HOH 0-0.023-0.02417.2270.0390.0390.0000.0000.0000.000
105A204HOH 0-0.048-0.05319.138-0.088-0.0880.0000.0000.0000.000
106A205HOH 00.003-0.00124.211-0.035-0.0350.0000.0000.0000.000
107A206HOH 0-0.031-0.02422.360-0.045-0.0450.0000.0000.0000.000
108A207HOH 0-0.036-0.03712.9870.2200.2200.0000.0000.0000.000
109A208HOH 0-0.051-0.03920.5570.2360.2360.0000.0000.0000.000
110A209HOH 0-0.071-0.06214.4390.3050.3050.0000.0000.0000.000
111A210HOH 00.003-0.00121.451-0.230-0.2300.0000.0000.0000.000
112A211HOH 0-0.023-0.02613.3650.1440.1440.0000.0000.0000.000
113A212HOH 0-0.035-0.03112.0380.3150.3150.0000.0000.0000.000
114A213HOH 0-0.059-0.05119.2770.0380.0380.0000.0000.0000.000
115A214HOH 0-0.001-0.01617.7210.1720.1720.0000.0000.0000.000
116A215HOH 0-0.010-0.01321.1040.0400.0400.0000.0000.0000.000
117A216HOH 0-0.051-0.03522.2270.1530.1530.0000.0000.0000.000
118A217HOH 00.003-0.00816.551-0.348-0.3480.0000.0000.0000.000
119A218HOH 0-0.078-0.05314.7160.3880.3880.0000.0000.0000.000
120A219HOH 00.0070.00512.6310.4440.4440.0000.0000.0000.000
121A220HOH 00.003-0.00913.9230.0510.0510.0000.0000.0000.000
122A221HOH 0-0.020-0.02512.526-0.427-0.4270.0000.0000.0000.000
123A222HOH 0-0.004-0.00424.1620.0660.0660.0000.0000.0000.000
124A223HOH 0-0.038-0.04420.228-0.186-0.1860.0000.0000.0000.000
125A224HOH 0-0.016-0.01711.373-0.002-0.0020.0000.0000.0000.000
126A225HOH 0-0.051-0.04411.505-0.484-0.4840.0000.0000.0000.000
127A226HOH 0-0.040-0.02525.3150.1390.1390.0000.0000.0000.000
128A227HOH 00.001-0.00625.4050.0110.0110.0000.0000.0000.000
129A228HOH 00.020-0.00619.830-0.195-0.1950.0000.0000.0000.000
130A229HOH 0-0.005-0.00816.4330.0150.0150.0000.0000.0000.000
131A230HOH 0-0.009-0.01724.1850.1330.1330.0000.0000.0000.000
132A231HOH 0-0.034-0.04411.318-0.678-0.6780.0000.0000.0000.000
133A232HOH 0-0.038-0.03322.949-0.047-0.0470.0000.0000.0000.000
134A233HOH 0-0.003-0.01418.779-0.160-0.1600.0000.0000.0000.000
135A234HOH 00.0340.02925.662-0.036-0.0360.0000.0000.0000.000
136A235HOH 0-0.057-0.04427.1010.1430.1430.0000.0000.0000.000
137A236HOH 0-0.0030.00322.406-0.040-0.0400.0000.0000.0000.000
138A237HOH 0-0.013-0.00814.6020.4010.4010.0000.0000.0000.000
139A238HOH 00.0190.00428.157-0.063-0.0630.0000.0000.0000.000
140A239HOH 0-0.033-0.01824.7440.1820.1820.0000.0000.0000.000
141A240HOH 0-0.026-0.02825.315-0.019-0.0190.0000.0000.0000.000
142A241HOH 0-0.049-0.04020.2690.1610.1610.0000.0000.0000.000
143A242HOH 0-0.026-0.02221.5350.1810.1810.0000.0000.0000.000
144A243HOH 00.0070.00513.005-0.381-0.3810.0000.0000.0000.000
145A244HOH 00.0420.02621.782-0.257-0.2570.0000.0000.0000.000
146A245HOH 00.0370.0246.8901.3621.3620.0000.0000.0000.000
147A246HOH 0-0.046-0.0472.031-16.050-18.3687.122-2.639-2.165-0.028
148A247HOH 0-0.090-0.06417.538-0.040-0.0400.0000.0000.0000.000
149A248HOH 0-0.087-0.0656.5662.3652.3650.0000.0000.0000.000
150A249HOH 0-0.007-0.01513.256-0.286-0.2860.0000.0000.0000.000
151A250HOH 00.002-0.00824.392-0.212-0.2120.0000.0000.0000.000
152A251HOH 00.0120.00625.523-0.082-0.0820.0000.0000.0000.000
153A252HOH 00.016-0.01212.8490.4290.4290.0000.0000.0000.000
154A253HOH 0-0.021-0.02519.329-0.089-0.0890.0000.0000.0000.000
155A254HOH 0-0.003-0.0073.5410.1200.2780.001-0.082-0.0770.000
156A255HOH 0-0.014-0.01019.805-0.132-0.1320.0000.0000.0000.000
157A256HOH 0-0.014-0.01814.7260.4290.4290.0000.0000.0000.000
158A257HOH 0-0.019-0.00722.213-0.230-0.2300.0000.0000.0000.000
159A258HOH 0-0.003-0.00316.488-0.162-0.1620.0000.0000.0000.000
160A259HOH 0-0.004-0.02326.3990.1480.1480.0000.0000.0000.000
161A260HOH 00.0020.00520.847-0.119-0.1190.0000.0000.0000.000
162A261HOH 0-0.018-0.0043.103-0.3680.0340.030-0.174-0.2570.000
163A262HOH 00.0040.00118.632-0.203-0.2030.0000.0000.0000.000
164A263HOH 00.0100.00612.1170.6660.6660.0000.0000.0000.000
165A264HOH 00.0610.04818.938-0.447-0.4470.0000.0000.0000.000
166A265HOH 0-0.0030.00025.503-0.159-0.1590.0000.0000.0000.000
167A266HOH 00.0330.01416.610-0.438-0.4380.0000.0000.0000.000
168A267HOH 00.0230.01718.811-0.184-0.1840.0000.0000.0000.000
169A268HOH 0-0.013-0.01225.795-0.040-0.0400.0000.0000.0000.000
170A269HOH 00.008-0.00115.048-0.054-0.0540.0000.0000.0000.000
171A270HOH 0-0.004-0.01014.4510.4630.4630.0000.0000.0000.000
172A271HOH 0-0.028-0.03117.1420.1570.1570.0000.0000.0000.000
173A272HOH 0-0.033-0.02010.999-0.182-0.1820.0000.0000.0000.000
174A273HOH 0-0.006-0.00724.2820.0080.0080.0000.0000.0000.000
175A274HOH 0-0.045-0.02622.8600.0120.0120.0000.0000.0000.000
176A275HOH 00.007-0.0069.5820.3620.3620.0000.0000.0000.000
177A276HOH 0-0.043-0.0395.675-0.269-0.2690.0000.0000.0000.000
178A277HOH 0-0.017-0.02216.3900.0470.0470.0000.0000.0000.000
179A278HOH 0-0.038-0.02323.2520.2180.2180.0000.0000.0000.000
180A279HOH 0-0.0010.00120.7650.0220.0220.0000.0000.0000.000
181A280HOH 00.0300.01829.399-0.081-0.0810.0000.0000.0000.000
182A281HOH 00.0290.0153.587-6.062-5.5050.017-0.327-0.248-0.002
183A282HOH 0-0.035-0.02523.5370.0850.0850.0000.0000.0000.000
184A283HOH 00.003-0.00718.6970.0310.0310.0000.0000.0000.000
185A284HOH 00.0290.02519.2060.0810.0810.0000.0000.0000.000
186A285HOH 00.0160.01113.796-0.692-0.6920.0000.0000.0000.000
187A286HOH 00.0340.02122.442-0.192-0.1920.0000.0000.0000.000
188A287HOH 00.0350.02228.006-0.053-0.0530.0000.0000.0000.000
189A288HOH 0-0.054-0.0359.4800.6140.6140.0000.0000.0000.000
190A289HOH 0-0.0090.0037.3230.9450.9450.0000.0000.0000.000
191A290HOH 0-0.032-0.02714.9570.2330.2330.0000.0000.0000.000
192A291HOH 00.0020.01024.4660.0420.0420.0000.0000.0000.000
193A292HOH 0-0.002-0.00419.8170.0910.0910.0000.0000.0000.000
194A293HOH 0-0.012-0.02119.217-0.106-0.1060.0000.0000.0000.000
195A294HOH 00.0330.02620.174-0.106-0.1060.0000.0000.0000.000
196A295HOH 0-0.029-0.02314.0940.3990.3990.0000.0000.0000.000
197A296HOH 00.0070.00324.234-0.205-0.2050.0000.0000.0000.000
198A297HOH 0-0.021-0.01617.712-0.384-0.3840.0000.0000.0000.000
199A298HOH 00.0270.02531.685-0.008-0.0080.0000.0000.0000.000
200A299HOH 00.001-0.00225.2320.0930.0930.0000.0000.0000.000
201A300HOH 00.005-0.00230.760-0.136-0.1360.0000.0000.0000.000
202A301HOH 0-0.001-0.00326.173-0.102-0.1020.0000.0000.0000.000