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: VQJ51

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2383815.893163
FMO2-HF: Nuclear repulsion 2293588.564654
FMO2-HF: Total energy -90227.328509
FMO2-MP2: Total energy -90489.447197


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.
-69.786-66.30126.01-14.692-14.8010.089
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 : -0.822 / 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].
3A57SER0-0.027-0.0463.892-3.317-1.855-0.014-0.728-0.7200.002
4A58SER0-0.022-0.0146.771-1.888-1.8880.0000.0000.0000.000
5A59THR0-0.017-0.03910.244-0.392-0.3920.0000.0000.0000.000
6A60ALA0-0.050-0.00413.476-0.367-0.3670.0000.0000.0000.000
7A61ILE00.009-0.00816.9120.0250.0250.0000.0000.0000.000
8A62THR0-0.020-0.00920.3670.0170.0170.0000.0000.0000.000
9A63ASP-1-0.753-0.85723.2719.6249.6240.0000.0000.0000.000
10A64ARG10.8400.90127.052-9.005-9.0050.0000.0000.0000.000
11A65PRO0-0.0410.00829.6640.0350.0350.0000.0000.0000.000
12A66THR00.008-0.02730.940-0.316-0.3160.0000.0000.0000.000
13A67VAL00.0540.00734.2380.0700.0700.0000.0000.0000.000
14A68ASN0-0.009-0.01435.694-0.154-0.1540.0000.0000.0000.000
15A69MET0-0.066-0.00328.425-0.048-0.0480.0000.0000.0000.000
16A70LEU00.0470.02832.6680.1120.1120.0000.0000.0000.000
17A71GLY00.0230.02234.666-0.081-0.0810.0000.0000.0000.000
18A72GLY0-0.001-0.00937.197-0.157-0.1570.0000.0000.0000.000
19A73TYR00.0430.01535.937-0.129-0.1290.0000.0000.0000.000
20A74TYR00.0280.01138.193-0.197-0.1970.0000.0000.0000.000
21A75SER00.002-0.00239.657-0.158-0.1580.0000.0000.0000.000
22A76GLN00.0320.02341.740-0.230-0.2300.0000.0000.0000.000
23A77GLN00.0470.02239.266-0.027-0.0270.0000.0000.0000.000
24A78GLN00.015-0.01642.0480.0130.0130.0000.0000.0000.000
25A79PHE0-0.034-0.00544.443-0.142-0.1420.0000.0000.0000.000
26A80LEU00.007-0.00343.901-0.130-0.1300.0000.0000.0000.000
27A81ARG10.8350.92540.691-7.203-7.2030.0000.0000.0000.000
28A82ASN0-0.042-0.00546.989-0.077-0.0770.0000.0000.0000.000
29A83LEU0-0.044-0.02850.023-0.148-0.1480.0000.0000.0000.000
30A84ASP-1-0.915-0.95247.1106.2396.2390.0000.0000.0000.000
31A85VAL0-0.0300.00150.803-0.056-0.0560.0000.0000.0000.000
32A95PRO00.0290.02237.744-0.045-0.0450.0000.0000.0000.000
33A96SER0-0.010-0.04437.161-0.097-0.0970.0000.0000.0000.000
34A97VAL00.0350.00436.6390.1210.1210.0000.0000.0000.000
35A98MET00.0240.01133.5170.0880.0880.0000.0000.0000.000
36A99ASP-1-0.786-0.84732.6558.5858.5850.0000.0000.0000.000
37A100GLU-1-0.817-0.89032.6318.3698.3690.0000.0000.0000.000
38A101ALA00.0250.00932.0010.1800.1800.0000.0000.0000.000
39A102TYR0-0.028-0.03625.1990.3680.3680.0000.0000.0000.000
40A103LYS10.8250.89927.902-8.071-8.0710.0000.0000.0000.000
41A104GLU-1-0.815-0.89728.3549.9829.9820.0000.0000.0000.000
42A105PHE0-0.016-0.01321.5900.3330.3330.0000.0000.0000.000
43A106VAL0-0.007-0.00323.7000.4790.4790.0000.0000.0000.000
44A107MET0-0.0090.00623.3670.3840.3840.0000.0000.0000.000
45A108GLN0-0.043-0.03923.6910.7280.7280.0000.0000.0000.000
46A109LEU0-0.009-0.00618.1060.5080.5080.0000.0000.0000.000
47A110ALA00.0160.02318.8110.7890.7890.0000.0000.0000.000
48A111SER0-0.0040.01219.8470.3840.3840.0000.0000.0000.000
49A112TRP0-0.0020.01517.1120.6770.6770.0000.0000.0000.000
50A113ASP-1-0.873-0.94819.34012.06512.0650.0000.0000.0000.000
51A114THR0-0.003-0.00419.6780.0130.0130.0000.0000.0000.000
52A115ARG10.8520.92314.897-15.120-15.1200.0000.0000.0000.000
53A116ARG10.9590.98616.488-11.651-11.6510.0000.0000.0000.000
54A117GLU-1-0.844-0.91318.46011.54911.5490.0000.0000.0000.000
55A118PHE0-0.0110.00212.580-0.055-0.0550.0000.0000.0000.000
56A119TRP00.030-0.0089.1890.3520.3520.0000.0000.0000.000
57A120LEU0-0.029-0.01515.4150.1020.1020.0000.0000.0000.000
58A121GLN0-0.021-0.00118.6470.1680.1680.0000.0000.0000.000
59A122THR0-0.0130.01013.4840.0210.0210.0000.0000.0000.000
60A123ASP-1-0.833-0.92516.02415.05215.0520.0000.0000.0000.000
61A124TYR0-0.039-0.0366.0710.5190.5190.0000.0000.0000.000
62A125TYR00.060-0.00312.0990.6090.6090.0000.0000.0000.000
63A126LYS10.8050.88213.475-14.424-14.4240.0000.0000.0000.000
64A127GLN0-0.042-0.02913.1850.7800.7800.0000.0000.0000.000
65A128ARG10.7780.8648.187-27.236-27.2360.0000.0000.0000.000
66A129MET0-0.0660.00113.655-0.204-0.2040.0000.0000.0000.000
67A130VAL0-0.041-0.03316.114-0.068-0.0680.0000.0000.0000.000
68A131GLY0-0.0060.00718.847-0.616-0.6160.0000.0000.0000.000
69A132ASN0-0.023-0.01520.125-0.760-0.7600.0000.0000.0000.000
70A133SER00.0620.03020.1810.3900.3900.0000.0000.0000.000
71A134LYS10.9420.97019.243-13.552-13.5520.0000.0000.0000.000
72A135ALA0-0.010-0.00816.8000.2820.2820.0000.0000.0000.000
73A136ASP-1-0.705-0.85416.06215.96515.9650.0000.0000.0000.000
74A137ALA0-0.0100.00016.3880.4600.4600.0000.0000.0000.000
75A138ALA0-0.060-0.02815.424-0.040-0.0400.0000.0000.0000.000
76A139LEU00.0540.03610.0060.4990.4990.0000.0000.0000.000
77A140LEU0-0.026-0.00812.0870.7350.7350.0000.0000.0000.000
78A141ASP-1-0.902-0.95114.09116.41516.4150.0000.0000.0000.000
79A142GLU-1-0.893-0.9538.26125.59325.5930.0000.0000.0000.000
80A143MET0-0.016-0.0039.0320.9170.9170.0000.0000.0000.000
81A144ILE0-0.030-0.00510.5370.1370.1370.0000.0000.0000.000
82A145ASN0-0.018-0.01411.962-0.692-0.6920.0000.0000.0000.000
83A146ASN0-0.054-0.0236.2212.5852.5850.0000.0000.0000.000
84A147ILE0-0.014-0.0048.7581.2131.2130.0000.0000.0000.000
85A148GLN0-0.038-0.0258.748-0.459-0.4590.0000.0000.0000.000
86A149PHE00.0180.00513.4630.1230.1230.0000.0000.0000.000
87A150ILE0-0.026-0.01314.8170.0260.0260.0000.0000.0000.000
88A151PRO00.0040.00718.842-0.129-0.1290.0000.0000.0000.000
89A152GLY0-0.003-0.00422.6810.1920.1920.0000.0000.0000.000
90A153ASP-1-0.822-0.90424.7829.4639.4630.0000.0000.0000.000
91A154PHE0-0.013-0.01027.6750.0150.0150.0000.0000.0000.000
92A155THR0-0.064-0.04030.517-0.309-0.3090.0000.0000.0000.000
93A156ARG10.8830.94926.663-10.454-10.4540.0000.0000.0000.000
94A157ALA0-0.028-0.02028.3230.2090.2090.0000.0000.0000.000
95A158VAL0-0.035-0.00222.7700.2470.2470.0000.0000.0000.000
96A159ASN00.0150.00124.199-0.499-0.4990.0000.0000.0000.000
97A160ASP-1-0.757-0.86222.40011.64711.6470.0000.0000.0000.000
98A161SER0-0.046-0.02717.6640.3130.3130.0000.0000.0000.000
99A162VAL00.0070.00614.430-0.129-0.1290.0000.0000.0000.000
100A163LYS10.8670.9286.929-27.540-27.5400.0000.0000.0000.000
101A164LEU0-0.0110.0097.633-0.847-0.8470.0000.0000.0000.000
102A165ILE0-0.043-0.0252.933-0.5640.1600.664-0.511-0.8770.006
103A166ALA00.0120.0113.754-3.081-2.5930.003-0.150-0.3410.000
104A167GLU-1-0.755-0.8392.10634.42834.9965.035-2.653-2.949-0.032
105A168THR0-0.036-0.0433.26711.08312.2880.152-0.430-0.928-0.003
106A169ALA00.0540.0235.110-4.053-4.013-0.001-0.002-0.0360.000
107A170PRO00.0530.0187.447-2.473-2.4730.0000.0000.0000.000
108A171ASP-1-0.839-0.8866.99127.68327.6830.0000.0000.0000.000
109A172ALA00.0080.0035.987-2.429-2.4290.0000.0000.0000.000
110A173ASN0-0.024-0.0047.899-2.942-2.9420.0000.0000.0000.000
111A174ASN0-0.045-0.04411.582-2.819-2.8190.0000.0000.0000.000
112A175LEU00.0030.0098.563-1.563-1.5630.0000.0000.0000.000
113A176LEU00.0110.01711.588-1.285-1.2850.0000.0000.0000.000
114A177ARG10.7900.86313.188-17.914-17.9140.0000.0000.0000.000
115A178GLN00.0040.00314.845-1.007-1.0070.0000.0000.0000.000
116A179TYR0-0.017-0.02214.613-0.837-0.8370.0000.0000.0000.000
117A180VAL00.0240.00516.607-0.805-0.8050.0000.0000.0000.000
118A181ALA0-0.015-0.00318.901-0.763-0.7630.0000.0000.0000.000
119A182PHE00.000-0.00119.479-0.679-0.6790.0000.0000.0000.000
120A183ALA00.0420.01420.409-0.548-0.5480.0000.0000.0000.000
121A184SER00.006-0.00922.174-0.618-0.6180.0000.0000.0000.000
122A185GLN0-0.040-0.02024.515-0.330-0.3300.0000.0000.0000.000
123A186ARG10.7950.89123.006-12.010-12.0100.0000.0000.0000.000
124A187ALA00.0560.03226.434-0.372-0.3720.0000.0000.0000.000
125A188ALA0-0.001-0.00128.301-0.369-0.3690.0000.0000.0000.000
126A189SER0-0.067-0.04529.445-0.393-0.3930.0000.0000.0000.000
127A190HIS00.0010.00030.719-0.187-0.1870.0000.0000.0000.000
128A191LEU0-0.0040.00131.431-0.308-0.3080.0000.0000.0000.000
129A192ASN0-0.065-0.05833.975-0.515-0.5150.0000.0000.0000.000
130A193ASP-1-0.816-0.90135.3287.7837.7830.0000.0000.0000.000
131A194GLU-1-0.871-0.92235.7057.6647.6640.0000.0000.0000.000
132A195LEU0-0.068-0.02138.346-0.253-0.2530.0000.0000.0000.000
133A196LYS10.8450.91138.634-7.806-7.8060.0000.0000.0000.000
134A197GLY00.0090.00741.057-0.188-0.1880.0000.0000.0000.000
135A198ALA00.0150.00142.449-0.200-0.2000.0000.0000.0000.000
136A199TRP00.015-0.00944.273-0.136-0.1360.0000.0000.0000.000
137A200ALA0-0.0150.01045.723-0.191-0.1910.0000.0000.0000.000
138A201ALA00.0160.00746.884-0.170-0.1700.0000.0000.0000.000
139A202ARG10.8710.92048.468-5.834-5.8340.0000.0000.0000.000
140A203THR00.013-0.01149.797-0.180-0.1800.0000.0000.0000.000
141A204ILE0-0.026-0.01450.182-0.150-0.1500.0000.0000.0000.000
142A205GLN0-0.018-0.01052.314-0.167-0.1670.0000.0000.0000.000
143A206MET0-0.0020.01754.394-0.147-0.1470.0000.0000.0000.000
144A207LYS10.9170.94953.895-5.689-5.6890.0000.0000.0000.000
145A208ALA0-0.019-0.01057.580-0.113-0.1130.0000.0000.0000.000
146A209GLN0-0.042-0.01657.945-0.014-0.0140.0000.0000.0000.000
147A210VAL00.0710.02960.175-0.089-0.0890.0000.0000.0000.000
148A211LYS10.8400.91561.928-4.822-4.8220.0000.0000.0000.000
149A212ARG10.9570.97559.163-5.107-5.1070.0000.0000.0000.000
150A213GLN00.0160.00963.656-0.022-0.0220.0000.0000.0000.000
151A214GLU-1-0.823-0.88066.0714.6204.6200.0000.0000.0000.000
152A215GLU-1-0.823-0.90668.2824.2164.2160.0000.0000.0000.000
153A216VAL0-0.023-0.00968.908-0.073-0.0730.0000.0000.0000.000
154A217ALA00.0300.02270.914-0.072-0.0720.0000.0000.0000.000
155A218LYS10.8120.89572.611-4.216-4.2160.0000.0000.0000.000
156A219ALA00.0290.01373.913-0.068-0.0680.0000.0000.0000.000
157A220ILE0-0.082-0.03974.139-0.073-0.0730.0000.0000.0000.000
158A221TYR0-0.060-0.03877.012-0.062-0.0620.0000.0000.0000.000
159A222ASP-1-0.800-0.89877.9523.9543.9540.0000.0000.0000.000
160A223ARG10.8700.93077.773-3.996-3.9960.0000.0000.0000.000
161A224ARG10.9380.97181.624-3.769-3.7690.0000.0000.0000.000
162A225MET00.0270.03483.018-0.042-0.0420.0000.0000.0000.000
163A226ASN00.1120.06884.878-0.068-0.0680.0000.0000.0000.000
164A227SER0-0.156-0.09886.241-0.041-0.0410.0000.0000.0000.000
165A228ILE0-0.080-0.04286.586-0.024-0.0240.0000.0000.0000.000
166A229GLU-1-0.909-0.95587.0133.5573.5570.0000.0000.0000.000
167A230GLN0-0.092-0.03889.674-0.070-0.0700.0000.0000.0000.000
168A266GLN00.021-0.00293.0990.0170.0170.0000.0000.0000.000
169A267ALA00.0820.03991.6550.0380.0380.0000.0000.0000.000
170A268ARG10.8730.92884.632-3.622-3.6220.0000.0000.0000.000
171A269LEU00.0550.03587.4490.0480.0480.0000.0000.0000.000
172A270GLU-1-0.863-0.93786.9683.4673.4670.0000.0000.0000.000
173A271ASN0-0.026-0.01083.9710.0320.0320.0000.0000.0000.000
174A272LEU00.0010.00481.5820.0480.0480.0000.0000.0000.000
175A273GLN00.0100.00582.1200.0380.0380.0000.0000.0000.000
176A274ALA0-0.029-0.00882.3120.0320.0320.0000.0000.0000.000
177A275VAL0-0.076-0.02378.6180.0330.0330.0000.0000.0000.000
178A276GLY00.0230.02577.2400.0570.0570.0000.0000.0000.000
179A277PRO0-0.035-0.04273.867-0.024-0.0240.0000.0000.0000.000
180A278ALA0-0.0100.01174.7090.0270.0270.0000.0000.0000.000
181A279PHE00.006-0.01068.9350.0350.0350.0000.0000.0000.000
182A280ASP-1-0.860-0.93968.2914.5044.5040.0000.0000.0000.000
183A281LEU00.0300.00865.8780.0450.0450.0000.0000.0000.000
184A282ASP-1-0.816-0.88263.1604.9744.9740.0000.0000.0000.000
185A283TYR0-0.043-0.03463.4320.0930.0930.0000.0000.0000.000
186A284ASP-1-0.874-0.94263.8914.6564.6560.0000.0000.0000.000
187A285GLN0-0.047-0.02561.0830.0930.0930.0000.0000.0000.000
188A286ASN0-0.014-0.02459.3540.1850.1850.0000.0000.0000.000
189A287ARG10.8840.94759.230-4.741-4.7410.0000.0000.0000.000
190A288ALA0-0.021-0.01759.8890.0570.0570.0000.0000.0000.000
191A289MET00.0070.00654.3090.1300.1300.0000.0000.0000.000
192A290LEU0-0.010-0.02055.0490.1100.1100.0000.0000.0000.000
193A291ASN0-0.055-0.01855.4850.0790.0790.0000.0000.0000.000
194A292THR00.0400.01751.5230.0670.0670.0000.0000.0000.000
195A293LEU0-0.017-0.00551.0010.1160.1160.0000.0000.0000.000
196A294ASN0-0.026-0.01550.7830.1440.1440.0000.0000.0000.000
197A295VAL0-0.0370.00249.1050.0040.0040.0000.0000.0000.000
198A296GLY0-0.0150.01147.2100.0890.0890.0000.0000.0000.000
199A297PRO00.0010.00342.648-0.020-0.0200.0000.0000.0000.000
200A298THR0-0.028-0.03941.8870.0210.0210.0000.0000.0000.000
201A299LEU0-0.026-0.00638.6330.1460.1460.0000.0000.0000.000
202A300ASP-1-0.797-0.86235.5118.2428.2420.0000.0000.0000.000
203A301PRO00.0100.00532.6580.1460.1460.0000.0000.0000.000
204A302ARG10.8310.88131.334-7.911-7.9110.0000.0000.0000.000
205A303PHE0-0.0490.00431.0550.2190.2190.0000.0000.0000.000
206A304GLN0-0.019-0.01326.0330.2510.2510.0000.0000.0000.000
207A305THR0-0.007-0.01626.811-0.359-0.3590.0000.0000.0000.000
208A306TYR0-0.002-0.01522.088-0.043-0.0430.0000.0000.0000.000
209A307ARG10.8610.92726.226-9.978-9.9780.0000.0000.0000.000
210A308TYR00.0560.01918.9560.3710.3710.0000.0000.0000.000
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