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: 5J8JZ

Calculation Name: 3B8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8O

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG01

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2377263.661692
FMO2-HF: Nuclear repulsion 2287038.989893
FMO2-HF: Total energy -90224.671799
FMO2-MP2: Total energy -90486.947512


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:55:GLU)


Summations of interaction energy for fragment #1(A:55: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.
-23.409-10.4273.991-7.661-9.310.035
Interaction energy analysis for fragmet #1(A:55:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.895 / q_NPA : -0.961
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].
3A57SER0-0.027-0.0313.888-3.284-1.637-0.019-0.905-0.7230.002
4A58SER00.0200.0196.861-2.255-2.2550.0000.0000.0000.000
5A59THR0-0.059-0.05010.330-0.170-0.1700.0000.0000.0000.000
6A60ALA0-0.0070.00213.585-0.382-0.3820.0000.0000.0000.000
7A61ILE00.003-0.00616.9410.0400.0400.0000.0000.0000.000
8A62THR0-0.033-0.00420.289-0.054-0.0540.0000.0000.0000.000
9A63ASP-1-0.823-0.89223.0769.9149.9140.0000.0000.0000.000
10A64ARG10.8920.91226.701-9.065-9.0650.0000.0000.0000.000
11A65PRO0-0.051-0.00929.491-0.011-0.0110.0000.0000.0000.000
12A66THR0-0.010-0.04130.883-0.263-0.2630.0000.0000.0000.000
13A67VAL00.0580.00334.2470.0670.0670.0000.0000.0000.000
14A68ASN0-0.004-0.00935.768-0.193-0.1930.0000.0000.0000.000
15A69MET0-0.0750.00328.915-0.029-0.0290.0000.0000.0000.000
16A70LEU00.0420.02332.7180.1250.1250.0000.0000.0000.000
17A71GLY00.0480.03834.855-0.062-0.0620.0000.0000.0000.000
18A72GLY0-0.023-0.02337.435-0.117-0.1170.0000.0000.0000.000
19A73TYR00.0510.03736.402-0.176-0.1760.0000.0000.0000.000
20A74TYR00.0230.00138.548-0.134-0.1340.0000.0000.0000.000
21A75SER0-0.035-0.03439.783-0.173-0.1730.0000.0000.0000.000
22A76GLN00.0610.04041.790-0.173-0.1730.0000.0000.0000.000
23A77GLN00.0870.04439.377-0.197-0.1970.0000.0000.0000.000
24A78GLN0-0.039-0.03442.3070.0150.0150.0000.0000.0000.000
25A79PHE0-0.046-0.01044.822-0.150-0.1500.0000.0000.0000.000
26A80LEU00.022-0.00544.070-0.131-0.1310.0000.0000.0000.000
27A81ARG10.9360.98640.040-7.224-7.2240.0000.0000.0000.000
28A82ASN0-0.050-0.00846.888-0.069-0.0690.0000.0000.0000.000
29A83LEU0-0.042-0.02949.824-0.152-0.1520.0000.0000.0000.000
30A84ASP-1-1.020-0.99147.0946.2446.2440.0000.0000.0000.000
31A85VAL0-0.0060.00450.653-0.046-0.0460.0000.0000.0000.000
32A95PRO00.0130.01238.120-0.045-0.0450.0000.0000.0000.000
33A96SER00.023-0.00437.042-0.101-0.1010.0000.0000.0000.000
34A97VAL00.0500.03136.9640.1060.1060.0000.0000.0000.000
35A98MET00.005-0.01233.7680.1340.1340.0000.0000.0000.000
36A99ASP-1-0.885-0.94632.7418.5848.5840.0000.0000.0000.000
37A100GLU-1-0.889-0.95432.5588.3968.3960.0000.0000.0000.000
38A101ALA0-0.024-0.00231.6590.1510.1510.0000.0000.0000.000
39A102TYR0-0.027-0.01324.8890.3300.3300.0000.0000.0000.000
40A103LYS10.9430.98027.725-8.296-8.2960.0000.0000.0000.000
41A104GLU-1-0.822-0.90028.18510.02610.0260.0000.0000.0000.000
42A105PHE00.0000.00621.3340.3340.3340.0000.0000.0000.000
43A106VAL0-0.029-0.01123.4730.4940.4940.0000.0000.0000.000
44A107MET0-0.0180.00223.1450.4030.4030.0000.0000.0000.000
45A108GLN0-0.036-0.03523.6940.7330.7330.0000.0000.0000.000
46A109LEU0-0.008-0.00418.5460.5620.5620.0000.0000.0000.000
47A110ALA00.0060.03718.8440.8150.8150.0000.0000.0000.000
48A111SER00.0010.02019.8500.4110.4110.0000.0000.0000.000
49A112TRP00.0350.01017.3270.6330.6330.0000.0000.0000.000
50A113ASP-1-0.879-0.93719.48712.03512.0350.0000.0000.0000.000
51A114THR0-0.043-0.02819.6200.0500.0500.0000.0000.0000.000
52A115ARG10.8710.94214.855-15.630-15.6300.0000.0000.0000.000
53A116ARG10.9770.99016.479-12.347-12.3470.0000.0000.0000.000
54A117GLU-1-0.939-0.98918.37811.96011.9600.0000.0000.0000.000
55A118PHE0-0.0010.00512.938-0.109-0.1090.0000.0000.0000.000
56A119TRP00.0580.0159.3380.3830.3830.0000.0000.0000.000
57A120LEU0-0.017-0.00915.4490.1760.1760.0000.0000.0000.000
58A121GLN0-0.071-0.02218.4860.0290.0290.0000.0000.0000.000
59A122THR0-0.0330.01613.2730.2000.2000.0000.0000.0000.000
60A123ASP-1-0.916-0.97516.56715.55115.5510.0000.0000.0000.000
61A124TYR00.0510.0136.2751.0641.0640.0000.0000.0000.000
62A125TYR00.012-0.04212.6470.5280.5280.0000.0000.0000.000
63A126LYS10.9380.95913.606-14.547-14.5470.0000.0000.0000.000
64A127GLN0-0.039-0.01814.0000.7850.7850.0000.0000.0000.000
65A128ARG10.8570.9377.814-30.571-30.5710.0000.0000.0000.000
66A129MET0-0.092-0.01213.582-0.232-0.2320.0000.0000.0000.000
67A130VAL0-0.032-0.02415.816-0.163-0.1630.0000.0000.0000.000
68A131GLY0-0.0050.00618.499-0.756-0.7560.0000.0000.0000.000
69A132ASN0-0.042-0.01520.046-0.866-0.8660.0000.0000.0000.000
70A133SER00.0380.01620.5090.5690.5690.0000.0000.0000.000
71A134LYS11.0030.99519.483-14.283-14.2830.0000.0000.0000.000
72A135ALA0-0.022-0.02116.8750.3760.3760.0000.0000.0000.000
73A136ASP-1-0.719-0.85916.39117.27717.2770.0000.0000.0000.000
74A137ALA0-0.019-0.00116.9240.4600.4600.0000.0000.0000.000
75A138ALA0-0.048-0.02715.6160.1180.1180.0000.0000.0000.000
76A139LEU00.0690.04010.4360.6360.6360.0000.0000.0000.000
77A140LEU0-0.030-0.01212.2760.8560.8560.0000.0000.0000.000
78A141ASP-1-0.932-0.97614.18617.08517.0850.0000.0000.0000.000
79A142GLU-1-0.929-0.9607.77129.40129.4010.0000.0000.0000.000
80A143MET0-0.041-0.0199.1460.8450.8450.0000.0000.0000.000
81A144ILE0-0.0170.00510.655-0.153-0.1530.0000.0000.0000.000
82A145ASN0-0.064-0.03811.398-1.090-1.0900.0000.0000.0000.000
83A146ASN0-0.0040.0106.4040.6620.6620.0000.0000.0000.000
84A147ILE0-0.0120.0088.9930.8360.8360.0000.0000.0000.000
85A148GLN0-0.002-0.0039.016-0.466-0.4660.0000.0000.0000.000
86A149PHE00.0170.00113.3940.0410.0410.0000.0000.0000.000
87A150ILE0-0.047-0.02414.4360.0420.0420.0000.0000.0000.000
88A151PRO0-0.0210.00118.752-0.187-0.1870.0000.0000.0000.000
89A152GLY00.026-0.00922.4710.1690.1690.0000.0000.0000.000
90A153ASP-1-0.848-0.88124.3209.5449.5440.0000.0000.0000.000
91A154PHE0-0.002-0.02927.364-0.025-0.0250.0000.0000.0000.000
92A155THR0-0.074-0.06630.313-0.286-0.2860.0000.0000.0000.000
93A156ARG10.8880.95125.875-10.449-10.4490.0000.0000.0000.000
94A157ALA0-0.016-0.00328.4630.0870.0870.0000.0000.0000.000
95A158VAL0-0.0390.00122.2270.2120.2120.0000.0000.0000.000
96A159ASN00.0260.00923.661-0.450-0.4500.0000.0000.0000.000
97A160ASP-1-0.755-0.86421.97911.72811.7280.0000.0000.0000.000
98A161SER0-0.064-0.03617.4730.3130.3130.0000.0000.0000.000
99A162VAL00.0210.01714.4770.0350.0350.0000.0000.0000.000
100A163LYS10.9510.9717.965-25.532-25.5320.0000.0000.0000.000
101A164LEU0-0.0040.0047.770-0.598-0.5980.0000.0000.0000.000
102A165ILE0-0.015-0.0113.127-0.5650.2630.513-0.509-0.8310.005
103A166ALA0-0.007-0.0094.089-2.843-2.535-0.001-0.044-0.2640.000
104A167GLU-1-0.843-0.9392.48342.58144.8991.301-1.719-1.900-0.017
105A168THR0-0.051-0.0603.1957.3988.2190.093-0.278-0.636-0.004
106A169ALA00.0600.0175.387-2.946-2.922-0.001-0.002-0.0200.000
107A170PRO00.0500.0097.871-1.980-1.9800.0000.0000.0000.000
108A171ASP-1-0.876-0.9047.68927.11927.1190.0000.0000.0000.000
109A172ALA00.0030.0056.427-1.958-1.9580.0000.0000.0000.000
110A173ASN00.0440.0278.320-2.604-2.6040.0000.0000.0000.000
111A174ASN0-0.015-0.01211.898-2.290-2.2900.0000.0000.0000.000
112A175LEU00.0060.0179.293-1.328-1.3280.0000.0000.0000.000
113A176LEU00.0040.01511.843-1.251-1.2510.0000.0000.0000.000
114A177ARG10.8270.88013.357-17.171-17.1710.0000.0000.0000.000
115A178GLN0-0.002-0.00215.888-0.686-0.6860.0000.0000.0000.000
116A179TYR0-0.033-0.05514.894-0.822-0.8220.0000.0000.0000.000
117A180VAL0-0.001-0.00816.797-0.765-0.7650.0000.0000.0000.000
118A181ALA0-0.013-0.00619.011-0.714-0.7140.0000.0000.0000.000
119A182PHE0-0.014-0.00619.524-0.654-0.6540.0000.0000.0000.000
120A183ALA00.0200.01120.392-0.524-0.5240.0000.0000.0000.000
121A184SER00.032-0.00622.153-0.606-0.6060.0000.0000.0000.000
122A185GLN0-0.0210.00324.638-0.349-0.3490.0000.0000.0000.000
123A186ARG10.8540.93123.045-12.169-12.1690.0000.0000.0000.000
124A187ALA00.0230.01426.426-0.337-0.3370.0000.0000.0000.000
125A188ALA0-0.0060.00728.192-0.377-0.3770.0000.0000.0000.000
126A189SER0-0.056-0.03729.633-0.360-0.3600.0000.0000.0000.000
127A190HIS00.0840.05030.622-0.229-0.2290.0000.0000.0000.000
128A191LEU0-0.035-0.01131.711-0.301-0.3010.0000.0000.0000.000
129A192ASN0-0.046-0.04634.279-0.431-0.4310.0000.0000.0000.000
130A193ASP-1-0.915-0.94934.7708.0718.0710.0000.0000.0000.000
131A194GLU-1-0.939-0.96035.8577.5957.5950.0000.0000.0000.000
132A195LEU0-0.048-0.01538.262-0.262-0.2620.0000.0000.0000.000
133A196LYS10.9230.95939.942-7.455-7.4550.0000.0000.0000.000
134A197GLY00.007-0.00141.006-0.212-0.2120.0000.0000.0000.000
135A198ALA00.0300.01342.449-0.179-0.1790.0000.0000.0000.000
136A199TRP0-0.004-0.01744.189-0.155-0.1550.0000.0000.0000.000
137A200ALA0-0.0090.00045.685-0.191-0.1910.0000.0000.0000.000
138A201ALA00.0090.01646.849-0.167-0.1670.0000.0000.0000.000
139A202ARG10.9200.94748.376-5.936-5.9360.0000.0000.0000.000
140A203THR00.004-0.01449.702-0.160-0.1600.0000.0000.0000.000
141A204ILE0-0.001-0.00450.464-0.160-0.1600.0000.0000.0000.000
142A205GLN0-0.0170.01152.275-0.212-0.2120.0000.0000.0000.000
143A206MET00.0470.02354.408-0.140-0.1400.0000.0000.0000.000
144A207LYS10.9210.96154.742-5.693-5.6930.0000.0000.0000.000
145A208ALA0-0.017-0.01557.560-0.112-0.1120.0000.0000.0000.000
146A209GLN0-0.032-0.01558.876-0.032-0.0320.0000.0000.0000.000
147A210VAL00.0540.02760.506-0.086-0.0860.0000.0000.0000.000
148A211LYS10.9130.96862.143-4.969-4.9690.0000.0000.0000.000
149A212ARG10.9830.98359.718-5.110-5.1100.0000.0000.0000.000
150A213GLN00.0360.01263.674-0.008-0.0080.0000.0000.0000.000
151A214GLU-1-0.864-0.93665.7904.6634.6630.0000.0000.0000.000
152A215GLU-1-0.958-0.97168.1984.2724.2720.0000.0000.0000.000
153A216VAL0-0.008-0.00468.922-0.076-0.0760.0000.0000.0000.000
154A217ALA00.0240.01071.063-0.077-0.0770.0000.0000.0000.000
155A218LYS10.9550.98072.693-4.242-4.2420.0000.0000.0000.000
156A219ALA00.0310.02574.128-0.066-0.0660.0000.0000.0000.000
157A220ILE0-0.081-0.05173.988-0.077-0.0770.0000.0000.0000.000
158A221TYR0-0.052-0.02277.106-0.063-0.0630.0000.0000.0000.000
159A222ASP-1-0.808-0.90478.2523.9473.9470.0000.0000.0000.000
160A223ARG10.9210.97277.330-4.039-4.0390.0000.0000.0000.000
161A224ARG10.9250.96281.718-3.781-3.7810.0000.0000.0000.000
162A225MET00.0140.00882.996-0.044-0.0440.0000.0000.0000.000
163A226ASN00.0640.03884.612-0.070-0.0700.0000.0000.0000.000
164A227SER0-0.120-0.07486.183-0.052-0.0520.0000.0000.0000.000
165A228ILE0-0.069-0.04086.720-0.033-0.0330.0000.0000.0000.000
166A229GLU-1-0.923-0.95387.4763.5523.5520.0000.0000.0000.000
167A230GLN0-0.098-0.03589.998-0.075-0.0750.0000.0000.0000.000
168A266GLN00.031-0.00193.4330.0240.0240.0000.0000.0000.000
169A267ALA00.0850.04391.6300.0300.0300.0000.0000.0000.000
170A268ARG10.9140.95384.235-3.631-3.6310.0000.0000.0000.000
171A269LEU00.0690.04387.4170.0460.0460.0000.0000.0000.000
172A270GLU-1-0.881-0.93586.9243.4933.4930.0000.0000.0000.000
173A271ASN0-0.057-0.03885.1360.0260.0260.0000.0000.0000.000
174A272LEU0-0.051-0.01881.5860.0500.0500.0000.0000.0000.000
175A273GLN0-0.012-0.03082.1930.0330.0330.0000.0000.0000.000
176A274ALA0-0.011-0.00282.0890.0250.0250.0000.0000.0000.000
177A275VAL0-0.059-0.00378.4930.0320.0320.0000.0000.0000.000
178A276GLY0-0.0010.01176.8530.0590.0590.0000.0000.0000.000
179A277PRO0-0.027-0.02973.971-0.031-0.0310.0000.0000.0000.000
180A278ALA0-0.024-0.00374.7030.0240.0240.0000.0000.0000.000
181A279PHE00.003-0.01369.3480.0300.0300.0000.0000.0000.000
182A280ASP-1-0.882-0.93668.2414.5334.5330.0000.0000.0000.000
183A281LEU00.027-0.00166.2030.0410.0410.0000.0000.0000.000
184A282ASP-1-0.887-0.94963.3284.9344.9340.0000.0000.0000.000
185A283TYR0-0.089-0.03363.6240.0870.0870.0000.0000.0000.000
186A284ASP-1-0.898-0.95463.9744.6674.6670.0000.0000.0000.000
187A285GLN0-0.044-0.03661.2890.0940.0940.0000.0000.0000.000
188A286ASN00.0310.01959.5210.1440.1440.0000.0000.0000.000
189A287ARG10.9300.98059.072-4.736-4.7360.0000.0000.0000.000
190A288ALA0-0.024-0.01559.7090.0680.0680.0000.0000.0000.000
191A289MET00.0230.01454.4530.1290.1290.0000.0000.0000.000
192A290LEU0-0.014-0.02655.0060.1070.1070.0000.0000.0000.000
193A291ASN0-0.052-0.01655.3550.0930.0930.0000.0000.0000.000
194A292THR0-0.040-0.01052.2150.1140.1140.0000.0000.0000.000
195A293LEU00.0720.02449.7290.1100.1100.0000.0000.0000.000
196A294ASN0-0.027-0.01450.5680.1900.1900.0000.0000.0000.000
197A295VAL0-0.097-0.02049.4300.0250.0250.0000.0000.0000.000
198A296GLY0-0.0310.00147.8050.0890.0890.0000.0000.0000.000
199A297PRO00.0190.00443.013-0.009-0.0090.0000.0000.0000.000
200A298THR0-0.067-0.05441.6990.0280.0280.0000.0000.0000.000
201A299LEU0-0.0090.00338.6280.1190.1190.0000.0000.0000.000
202A300ASP-1-0.817-0.90635.8068.3108.3100.0000.0000.0000.000
203A301PRO0-0.041-0.02932.7160.0830.0830.0000.0000.0000.000
204A302ARG10.9240.95431.549-7.810-7.8100.0000.0000.0000.000
205A303PHE0-0.052-0.00131.2980.2110.2110.0000.0000.0000.000
206A304GLN00.0060.00826.4460.1840.1840.0000.0000.0000.000
207A305THR00.0280.00426.377-0.387-0.3870.0000.0000.0000.000
208A306TYR00.0250.00422.623-0.042-0.0420.0000.0000.0000.000
209A307ARG10.9330.95926.190-9.847-9.8470.0000.0000.0000.000
210A308TYR00.0610.01518.6570.1030.1030.0000.0000.0000.000
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