Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3JL7L

Calculation Name: 5C00-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C00

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NFK7

Base Structure: X-ray

Registration Date: 2023-09-23

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2268556.049789
FMO2-HF: Nuclear repulsion 2191064.71187
FMO2-HF: Total energy -77491.337919
FMO2-MP2: Total energy -77718.869235


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:43:LYS)


Summations of interaction energy for fragment #1(A:43: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.
-115.123-111.040.197-1.917-2.363-0.013
Interaction energy analysis for fragmet #1(A:43:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.924 / q_NPA : 0.940
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].
3A45HIS0-0.047-0.0333.017-13.190-9.2140.198-1.915-2.259-0.013
4A46GLN0-0.016-0.0255.3353.8333.940-0.001-0.002-0.1040.000
5A47ALA0-0.0190.0108.7521.0081.0080.0000.0000.0000.000
6A48ASN0-0.001-0.0157.981-2.019-2.0190.0000.0000.0000.000
7A49LYS10.9720.9687.71421.72721.7270.0000.0000.0000.000
8A50TYR0-0.054-0.0439.4640.7960.7960.0000.0000.0000.000
9A51ALA0-0.0440.00812.3440.8190.8190.0000.0000.0000.000
10A52ASP-1-0.864-0.90614.286-14.599-14.5990.0000.0000.0000.000
11A53TYR0-0.069-0.06113.031-0.238-0.2380.0000.0000.0000.000
12A54ASP-1-0.933-0.97319.237-11.057-11.0570.0000.0000.0000.000
13A55LYS10.8860.93920.04612.34112.3410.0000.0000.0000.000
14A56GLU-1-0.912-0.93223.691-9.531-9.5310.0000.0000.0000.000
15A57SER0-0.043-0.01026.556-0.046-0.0460.0000.0000.0000.000
16A58VAL0-0.002-0.00527.8290.1750.1750.0000.0000.0000.000
17A59SER0-0.052-0.03230.1670.0430.0430.0000.0000.0000.000
18A60PHE0-0.056-0.01828.7180.2480.2480.0000.0000.0000.000
19A61THR00.003-0.01030.219-0.306-0.3060.0000.0000.0000.000
20A62GLY00.061-0.00429.6880.0470.0470.0000.0000.0000.000
21A63SER0-0.085-0.03729.7380.1770.1770.0000.0000.0000.000
22A64VAL00.0660.04725.875-0.070-0.0700.0000.0000.0000.000
23A65THR0-0.042-0.03429.3550.1700.1700.0000.0000.0000.000
24A66ASP-1-0.906-0.95332.738-8.143-8.1430.0000.0000.0000.000
25A67SER00.0270.02130.8070.0160.0160.0000.0000.0000.000
26A68ALA00.0040.01930.800-0.201-0.2010.0000.0000.0000.000
27A69ILE0-0.012-0.00625.222-0.049-0.0490.0000.0000.0000.000
28A70VAL0-0.045-0.02629.2970.1320.1320.0000.0000.0000.000
29A71LEU00.0090.02628.427-0.147-0.1470.0000.0000.0000.000
30A72LYS10.8890.92432.3148.6638.6630.0000.0000.0000.000
31A73ALA00.1030.05234.353-0.150-0.1500.0000.0000.0000.000
32A74VAL0-0.002-0.00934.8520.0540.0540.0000.0000.0000.000
33A75ASN0-0.073-0.03237.0240.1180.1180.0000.0000.0000.000
34A76ALA00.0200.02039.1510.1020.1020.0000.0000.0000.000
35A77LYS10.9020.95541.0576.6306.6300.0000.0000.0000.000
36A78LYS10.9100.93243.9086.4196.4190.0000.0000.0000.000
37A79ASP-1-0.962-0.98445.879-6.256-6.2560.0000.0000.0000.000
38A80ALA00.0050.03342.2110.0220.0220.0000.0000.0000.000
39A81LYS10.9130.96643.7156.4226.4220.0000.0000.0000.000
40A82LYS10.9390.96640.6326.6566.6560.0000.0000.0000.000
41A83ILE00.0100.01137.6630.0960.0960.0000.0000.0000.000
42A84ASP-1-0.890-0.92336.832-8.022-8.0220.0000.0000.0000.000
43A85PHE00.013-0.00732.9910.1450.1450.0000.0000.0000.000
44A86TYR00.007-0.00433.258-0.185-0.1850.0000.0000.0000.000
45A87GLU-1-0.750-0.88528.734-10.346-10.3460.0000.0000.0000.000
46A88ASP-1-0.691-0.83526.827-11.764-11.7640.0000.0000.0000.000
47A89PHE00.0600.01622.7420.0390.0390.0000.0000.0000.000
48A90SER0-0.033-0.02923.960-0.712-0.7120.0000.0000.0000.000
49A91CYS0-0.0930.01725.4750.2790.2790.0000.0000.0000.000
50A92PRO00.0320.01728.727-0.036-0.0360.0000.0000.0000.000
51A93HIS00.0290.00929.7210.2000.2000.0000.0000.0000.000
52A94CYS0-0.036-0.00829.6460.2460.2460.0000.0000.0000.000
53A95ALA00.0330.01827.5160.0720.0720.0000.0000.0000.000
54A96GLU-1-0.903-0.94929.364-9.323-9.3230.0000.0000.0000.000
55A97LEU0-0.008-0.01032.5050.2070.2070.0000.0000.0000.000
56A98GLY00.0200.01031.1150.2240.2240.0000.0000.0000.000
57A99GLU-1-0.950-0.96830.355-9.952-9.9520.0000.0000.0000.000
58A100VAL0-0.0290.00032.4180.1790.1790.0000.0000.0000.000
59A101THR0-0.059-0.04235.3420.1920.1920.0000.0000.0000.000
60A102ASP-1-0.802-0.91129.818-9.876-9.8760.0000.0000.0000.000
61A103GLY00.0080.02633.1250.0520.0520.0000.0000.0000.000
62A104PRO00.031-0.00434.7250.1160.1160.0000.0000.0000.000
63A105MET0-0.0080.01531.8250.2210.2210.0000.0000.0000.000
64A106THR00.001-0.01631.9250.0470.0470.0000.0000.0000.000
65A107LYS10.8980.95734.1728.5408.5400.0000.0000.0000.000
66A108ALA00.0250.02337.7610.1630.1630.0000.0000.0000.000
67A109ILE0-0.019-0.01033.4680.1530.1530.0000.0000.0000.000
68A110GLU-1-0.840-0.93733.460-8.443-8.4430.0000.0000.0000.000
69A111ASN0-0.031-0.00537.1780.0790.0790.0000.0000.0000.000
70A112GLY0-0.062-0.03139.7890.1880.1880.0000.0000.0000.000
71A113ASP-1-0.858-0.92541.234-6.627-6.6270.0000.0000.0000.000
72A114ILE0-0.055-0.02637.8170.0930.0930.0000.0000.0000.000
73A115VAL0-0.028-0.01436.682-0.119-0.1190.0000.0000.0000.000
74A116VAL00.0260.00733.6490.1020.1020.0000.0000.0000.000
75A117ASN0-0.076-0.04333.695-0.300-0.3000.0000.0000.0000.000
76A118LEU00.0520.02928.4480.0740.0740.0000.0000.0000.000
77A119ARG10.7430.85930.6238.3438.3430.0000.0000.0000.000
78A120ILE00.0050.00125.6890.0520.0520.0000.0000.0000.000
79A121LEU0-0.025-0.01428.9730.0930.0930.0000.0000.0000.000
80A122ASN00.014-0.01425.335-0.016-0.0160.0000.0000.0000.000
81A123PHE00.0800.03627.429-0.154-0.1540.0000.0000.0000.000
82A124LEU0-0.061-0.02527.6530.1090.1090.0000.0000.0000.000
83A125ASP-1-0.796-0.89823.617-13.783-13.7830.0000.0000.0000.000
84A126ARG10.8500.92626.33110.80810.8080.0000.0000.0000.000
85A127ASP-1-0.888-0.94929.535-9.716-9.7160.0000.0000.0000.000
86A128GLY0-0.0320.00725.782-0.039-0.0390.0000.0000.0000.000
87A129ASP-1-0.917-0.95624.082-12.806-12.8060.0000.0000.0000.000
88A130ASP-1-0.797-0.91018.547-17.317-17.3170.0000.0000.0000.000
89A131GLY0-0.0130.00719.609-0.901-0.9010.0000.0000.0000.000
90A132ASN00.011-0.01319.106-1.128-1.1280.0000.0000.0000.000
91A133SER0-0.027-0.03220.306-0.278-0.2780.0000.0000.0000.000
92A134THR0-0.031-0.01220.8250.3560.3560.0000.0000.0000.000
93A135LYS10.8290.93315.03618.29218.2920.0000.0000.0000.000
94A136ALA00.0150.01817.794-0.285-0.2850.0000.0000.0000.000
95A137GLY00.011-0.00319.3170.2020.2020.0000.0000.0000.000
96A138ALA0-0.010-0.01119.2000.3340.3340.0000.0000.0000.000
97A139ALA0-0.0020.00615.8170.0250.0250.0000.0000.0000.000
98A140ALA00.0330.00817.3440.2090.2090.0000.0000.0000.000
99A141LEU0-0.018-0.00920.1530.4480.4480.0000.0000.0000.000
100A142ALA00.006-0.00217.2300.4180.4180.0000.0000.0000.000
101A143VAL0-0.013-0.00117.0280.1880.1880.0000.0000.0000.000
102A144ALA00.0050.01419.4100.4240.4240.0000.0000.0000.000
103A145GLN0-0.042-0.01521.6050.5710.5710.0000.0000.0000.000
104A146SER0-0.098-0.06319.7750.2580.2580.0000.0000.0000.000
105A147GLY0-0.018-0.00421.8780.2070.2070.0000.0000.0000.000
106A148ASP-1-0.843-0.87120.257-11.976-11.9760.0000.0000.0000.000
107A149TRP00.0330.00022.721-0.384-0.3840.0000.0000.0000.000
108A150GLU-1-0.812-0.90524.221-10.508-10.5080.0000.0000.0000.000
109A151THR0-0.083-0.07117.961-0.250-0.2500.0000.0000.0000.000
110A152TYR0-0.015-0.01220.886-0.382-0.3820.0000.0000.0000.000
111A153TRP0-0.041-0.02622.267-0.253-0.2530.0000.0000.0000.000
112A154ASN00.006-0.01221.856-0.019-0.0190.0000.0000.0000.000
113A155TYR0-0.055-0.03814.524-0.187-0.1870.0000.0000.0000.000
114A156ARG10.7670.85620.16510.21910.2190.0000.0000.0000.000
115A157ALA00.0670.03123.038-0.065-0.0650.0000.0000.0000.000
116A158LEU0-0.026-0.00317.572-0.026-0.0260.0000.0000.0000.000
117A159LEU0-0.040-0.02317.327-0.293-0.2930.0000.0000.0000.000
118A160MET0-0.037-0.01121.051-0.087-0.0870.0000.0000.0000.000
119A161LYS10.9690.99023.33612.31212.3120.0000.0000.0000.000
120A162GLU-1-0.857-0.94219.418-14.266-14.2660.0000.0000.0000.000
121A163GLN00.0330.05020.666-0.389-0.3890.0000.0000.0000.000
122A164LYS10.8430.88021.68211.93911.9390.0000.0000.0000.000
123A165ASN0-0.058-0.02818.451-0.153-0.1530.0000.0000.0000.000
124A166ILE00.0050.02716.690-1.004-1.0040.0000.0000.0000.000
125A167TYR0-0.018-0.00117.243-0.838-0.8380.0000.0000.0000.000
126A168GLY0-0.028-0.02218.2430.1910.1910.0000.0000.0000.000
127A169LYS10.8120.91214.78716.22416.2240.0000.0000.0000.000
128A170TRP00.0260.02212.436-1.826-1.8260.0000.0000.0000.000
129A171GLY0-0.002-0.00811.3531.4491.4490.0000.0000.0000.000
130A172ASP-1-0.764-0.89311.521-20.517-20.5170.0000.0000.0000.000
131A173ASN0-0.009-0.0136.2261.4431.4430.0000.0000.0000.000
132A174ASP-1-0.779-0.8668.261-32.705-32.7050.0000.0000.0000.000
133A175PHE00.0470.01510.0401.1351.1350.0000.0000.0000.000
134A176ALA00.0020.0148.8171.2181.2180.0000.0000.0000.000
135A177ASP-1-0.719-0.8456.216-35.705-35.7050.0000.0000.0000.000
136A178VAL0-0.015-0.0028.9631.3971.3970.0000.0000.0000.000
137A179ALA00.0310.02012.6751.2381.2380.0000.0000.0000.000
138A180LYS10.9070.9619.20118.87818.8780.0000.0000.0000.000
139A181SER0-0.065-0.03511.2320.7940.7940.0000.0000.0000.000
140A182LEU00.0050.01513.2220.8170.8170.0000.0000.0000.000
141A183GLY0-0.039-0.02315.2550.9940.9940.0000.0000.0000.000
142A184ALA00.0040.02314.0640.4820.4820.0000.0000.0000.000
143A185SER00.0320.00514.156-0.774-0.7740.0000.0000.0000.000
144A186ASP-1-0.845-0.93811.486-18.273-18.2730.0000.0000.0000.000
145A187GLU-1-0.967-0.98311.887-14.380-14.3800.0000.0000.0000.000
146A188VAL00.0340.01714.375-0.327-0.3270.0000.0000.0000.000
147A189THR0-0.032-0.0308.682-0.668-0.6680.0000.0000.0000.000
148A190GLN0-0.073-0.0518.359-2.403-2.4030.0000.0000.0000.000
149A191LYS10.9771.00310.74113.44913.4490.0000.0000.0000.000
150A192ILE0-0.052-0.01612.1630.0810.0810.0000.0000.0000.000
151A193ARG10.7610.8716.07130.07830.0780.0000.0000.0000.000
152A194GLU-1-0.908-0.93610.481-19.577-19.5770.0000.0000.0000.000
153A195GLY0-0.020-0.00713.2400.8140.8140.0000.0000.0000.000
154A196GLY00.0340.00915.8250.9080.9080.0000.0000.0000.000
155A197ALA0-0.029-0.00917.8350.7190.7190.0000.0000.0000.000
156A198LYS10.8080.87415.78818.34818.3480.0000.0000.0000.000
157A199GLU-1-0.915-0.95121.154-13.272-13.2720.0000.0000.0000.000
158A200ASP-1-0.849-0.94023.916-10.437-10.4370.0000.0000.0000.000
159A201PHE0-0.037-0.00523.0140.3820.3820.0000.0000.0000.000
160A202ARG10.8970.93420.87713.84313.8430.0000.0000.0000.000
161A203LYS10.9240.97926.79710.29810.2980.0000.0000.0000.000
162A204PHE0-0.048-0.04027.2850.4460.4460.0000.0000.0000.000
163A205ALA00.0300.02827.8020.3450.3450.0000.0000.0000.000
164A206GLU-1-0.843-0.91129.853-8.946-8.9460.0000.0000.0000.000
165A207ALA0-0.025-0.01832.5570.3350.3350.0000.0000.0000.000
166A208ASN0-0.020-0.01330.7760.5920.5920.0000.0000.0000.000
167A209SER00.0130.00233.6720.2350.2350.0000.0000.0000.000
168A210LYS10.9150.95635.3738.8128.8120.0000.0000.0000.000
169A211LYS10.8450.93337.7037.8897.8890.0000.0000.0000.000
170A212LEU0-0.025-0.00236.3400.1840.1840.0000.0000.0000.000
171A213GLU-1-0.919-0.96339.107-7.947-7.9470.0000.0000.0000.000
172A214LYS10.8670.94341.2147.1357.1350.0000.0000.0000.000
173A215ASP-1-0.898-0.96642.317-7.097-7.0970.0000.0000.0000.000
174A216GLY00.006-0.00842.6440.1300.1300.0000.0000.0000.000
175A217GLY0-0.081-0.01643.361-0.035-0.0350.0000.0000.0000.000
176A218SER0-0.025-0.01840.877-0.052-0.0520.0000.0000.0000.000
177A219VAL00.0690.04034.386-0.010-0.0100.0000.0000.0000.000
178A220SER0-0.033-0.01335.465-0.041-0.0410.0000.0000.0000.000
179A221SER0-0.008-0.02832.223-0.043-0.0430.0000.0000.0000.000
180A222PRO00.0530.00733.891-0.078-0.0780.0000.0000.0000.000
181A223ARG10.7200.83534.9658.1458.1450.0000.0000.0000.000
182A224VAL00.0530.03336.984-0.156-0.1560.0000.0000.0000.000
183A225PHE0-0.0060.00739.2710.2130.2130.0000.0000.0000.000
184A226ILE00.0200.00341.041-0.137-0.1370.0000.0000.0000.000
185A227ASP-1-0.876-0.94443.375-6.558-6.5580.0000.0000.0000.000
186A228GLY0-0.013-0.01343.7070.1500.1500.0000.0000.0000.000
187A229LYS10.9280.97345.0976.3746.3740.0000.0000.0000.000
188A230GLU-1-0.852-0.90342.237-7.511-7.5110.0000.0000.0000.000
189A231VAL0-0.032-0.02342.6140.2000.2000.0000.0000.0000.000
190A232LYS10.9450.97043.2946.5736.5730.0000.0000.0000.000
191A233ASN0-0.016-0.01145.298-0.051-0.0510.0000.0000.0000.000
192A234GLY00.0650.03045.7380.0150.0150.0000.0000.0000.000
193A235ILE00.0360.00839.6360.0170.0170.0000.0000.0000.000
194A236GLU-1-0.885-0.94939.773-7.827-7.8270.0000.0000.0000.000
195A237THR0-0.017-0.00141.1940.0000.0000.0000.0000.0000.000
196A238TRP00.013-0.00736.0830.2710.2710.0000.0000.0000.000
197A239VAL00.0420.02838.4170.1220.1220.0000.0000.0000.000
198A240GLU-1-0.929-0.96941.562-6.702-6.7020.0000.0000.0000.000
199A241GLN0-0.083-0.04145.0970.2220.2220.0000.0000.0000.000
200A242ALA0-0.046-0.02442.7540.1250.1250.0000.0000.0000.000
201A243THR0-0.078-0.03843.1940.0970.0970.0000.0000.0000.000
202A244SER0-0.050-0.01045.9030.2030.2030.0000.0000.0000.000