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: YYK42

Calculation Name: 5BVL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BVL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200139.142204
FMO2-HF: Nuclear repulsion 2125147.427795
FMO2-HF: Total energy -74991.714409
FMO2-MP2: Total energy -75214.530793


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
160.884165.6385.672-5.232-5.197-0.025
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.869 / q_NPA : -0.920
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].
3A3ASP-1-0.907-0.9522.03227.87431.8885.673-5.124-4.564-0.025
4A4GLU-1-0.906-0.9573.45822.43522.8690.001-0.089-0.3470.000
5A5ALA00.0300.0185.298-3.924-3.809-0.001-0.008-0.1060.000
6A6TRP0-0.044-0.0317.267-3.479-3.4790.0000.0000.0000.000
7A7LYS10.8110.8987.969-22.571-22.5710.0000.0000.0000.000
8A8CYS0-0.026-0.0199.049-2.828-2.8280.0000.0000.0000.000
9A9VAL00.0410.01911.433-1.885-1.8850.0000.0000.0000.000
10A10GLU-1-0.833-0.88112.82816.91016.9100.0000.0000.0000.000
11A11GLN0-0.035-0.02013.769-2.128-2.1280.0000.0000.0000.000
12A12LEU00.0470.01115.479-1.112-1.1120.0000.0000.0000.000
13A13ARG10.7980.87417.340-16.081-16.0810.0000.0000.0000.000
14A14ARG10.7300.85317.874-15.103-15.1030.0000.0000.0000.000
15A15GLU-1-0.806-0.89019.47612.48912.4890.0000.0000.0000.000
16A16GLY0-0.0260.00821.696-0.557-0.5570.0000.0000.0000.000
17A17ALA0-0.046-0.02620.100-0.194-0.1940.0000.0000.0000.000
18A18THR0-0.025-0.01321.976-0.260-0.2600.0000.0000.0000.000
19A19GLN0-0.031-0.02822.088-0.460-0.4600.0000.0000.0000.000
20A20ILE0-0.0230.00315.7130.2660.2660.0000.0000.0000.000
21A21ALA0-0.028-0.01616.409-0.366-0.3660.0000.0000.0000.000
22A22TYR0-0.065-0.0676.8910.7580.7580.0000.0000.0000.000
23A23ARG10.8850.93810.599-24.899-24.8990.0000.0000.0000.000
24A24SER0-0.044-0.0507.4504.4954.4950.0000.0000.0000.000
25A25ASP-1-0.869-0.9328.11627.84927.8490.0000.0000.0000.000
26A26ASP-1-0.792-0.8798.60726.19026.1900.0000.0000.0000.000
27A27TRP00.0590.01410.419-0.460-0.4600.0000.0000.0000.000
28A28ARG10.8910.94312.251-20.288-20.2880.0000.0000.0000.000
29A29ASP-1-0.726-0.8107.33139.30039.3000.0000.0000.0000.000
30A30LEU00.0230.02810.130-1.143-1.1430.0000.0000.0000.000
31A31LYS10.8370.91112.616-16.875-16.8750.0000.0000.0000.000
32A32GLU-1-0.837-0.92812.11017.95817.9580.0000.0000.0000.000
33A33ALA00.0480.04111.406-0.679-0.6790.0000.0000.0000.000
34A34TRP00.0130.02513.390-1.209-1.2090.0000.0000.0000.000
35A35LYS10.7850.89016.816-18.134-18.1340.0000.0000.0000.000
36A36LYS10.7430.83513.413-21.130-21.1300.0000.0000.0000.000
37A37GLY0-0.057-0.03516.722-0.644-0.6440.0000.0000.0000.000
38A38ALA00.0550.04214.1280.0750.0750.0000.0000.0000.000
39A39ASP-1-0.769-0.85816.28314.79514.7950.0000.0000.0000.000
40A40ILE0-0.029-0.00618.237-0.581-0.5810.0000.0000.0000.000
41A41LEU0-0.039-0.02714.8821.2751.2750.0000.0000.0000.000
42A42ILE0-0.013-0.01014.142-1.040-1.0400.0000.0000.0000.000
43A43VAL00.0300.01313.3192.0392.0390.0000.0000.0000.000
44A44ASP-1-0.777-0.86712.07622.74222.7420.0000.0000.0000.000
45A45ALA0-0.021-0.00714.009-0.479-0.4790.0000.0000.0000.000
46A46THR0-0.027-0.01712.4410.4570.4570.0000.0000.0000.000
47A47ASP-1-0.875-0.94415.02916.09816.0980.0000.0000.0000.000
48A48LYS10.8460.91318.028-14.041-14.0410.0000.0000.0000.000
49A49ASP-1-0.854-0.90220.34713.91413.9140.0000.0000.0000.000
50A50GLU-1-0.838-0.91615.56718.50018.5000.0000.0000.0000.000
51A51ALA00.0360.01616.676-0.029-0.0290.0000.0000.0000.000
52A52TRP0-0.018-0.03217.580-0.477-0.4770.0000.0000.0000.000
53A53LYS10.8520.92119.870-14.860-14.8600.0000.0000.0000.000
54A54GLN0-0.081-0.05412.8490.0230.0230.0000.0000.0000.000
55A55VAL0-0.0150.00317.911-0.159-0.1590.0000.0000.0000.000
56A56GLU-1-0.839-0.91620.18512.30212.3020.0000.0000.0000.000
57A57GLN0-0.048-0.00819.173-1.030-1.0300.0000.0000.0000.000
58A58LEU00.0180.00015.829-0.316-0.3160.0000.0000.0000.000
59A59ARG10.9751.00420.037-11.913-11.9130.0000.0000.0000.000
60A60ARG10.7400.84722.811-13.682-13.6820.0000.0000.0000.000
61A61GLU-1-0.881-0.93519.89114.80514.8050.0000.0000.0000.000
62A62GLY0-0.032-0.00422.8270.0610.0610.0000.0000.0000.000
63A63ALA0-0.017-0.01320.121-0.157-0.1570.0000.0000.0000.000
64A64THR0-0.022-0.02722.082-0.132-0.1320.0000.0000.0000.000
65A65GLN00.0290.01822.109-0.339-0.3390.0000.0000.0000.000
66A66ILE0-0.0260.01119.1381.0301.0300.0000.0000.0000.000
67A67ALA0-0.007-0.01218.348-0.758-0.7580.0000.0000.0000.000
68A68TYR0-0.021-0.02017.8100.7950.7950.0000.0000.0000.000
69A69ARG10.7620.84414.193-21.553-21.5530.0000.0000.0000.000
70A70SER0-0.016-0.02118.9550.7420.7420.0000.0000.0000.000
71A71ASP-1-0.867-0.91721.18914.23014.2300.0000.0000.0000.000
72A72ASP-1-0.806-0.86623.37510.96010.9600.0000.0000.0000.000
73A73TRP00.051-0.00925.7060.1860.1860.0000.0000.0000.000
74A74ARG10.7820.86428.226-11.084-11.0840.0000.0000.0000.000
75A75ASP-1-0.745-0.85523.10213.62413.6240.0000.0000.0000.000
76A76LEU0-0.0080.01122.5250.1480.1480.0000.0000.0000.000
77A77LYS10.8620.91625.192-9.698-9.6980.0000.0000.0000.000
78A78GLU-1-0.839-0.90826.13610.91210.9120.0000.0000.0000.000
79A79ALA00.0280.01622.3980.0010.0010.0000.0000.0000.000
80A80TRP0-0.0240.00824.210-0.069-0.0690.0000.0000.0000.000
81A81LYS10.7920.88026.898-10.514-10.5140.0000.0000.0000.000
82A82LYS10.8180.91724.221-12.329-12.3290.0000.0000.0000.000
83A83GLY0-0.048-0.04524.9290.0530.0530.0000.0000.0000.000
84A84ALA0-0.0050.00822.0130.1890.1890.0000.0000.0000.000
85A85ASP-1-0.853-0.92623.44712.28812.2880.0000.0000.0000.000
86A86ILE0-0.038-0.01922.192-0.398-0.3980.0000.0000.0000.000
87A87LEU0-0.044-0.02822.3880.6250.6250.0000.0000.0000.000
88A88ILE00.001-0.00518.153-0.399-0.3990.0000.0000.0000.000
89A89VAL00.0170.00421.7590.3830.3830.0000.0000.0000.000
90A90ASP-1-0.794-0.88518.12618.12318.1230.0000.0000.0000.000
91A91ALA0-0.035-0.01121.534-0.215-0.2150.0000.0000.0000.000
92A92THR0-0.015-0.01220.4690.4760.4760.0000.0000.0000.000
93A93ASP-1-0.837-0.90623.56810.49810.4980.0000.0000.0000.000
94A94LYS10.7970.87826.883-10.531-10.5310.0000.0000.0000.000
95A95ASP-1-0.863-0.95029.4549.3439.3430.0000.0000.0000.000
96A96GLU-1-0.857-0.91729.2029.8039.8030.0000.0000.0000.000
97A97ALA00.0350.02926.5090.1240.1240.0000.0000.0000.000
98A98TRP0-0.022-0.03428.137-0.148-0.1480.0000.0000.0000.000
99A99LYS10.8630.92231.187-9.616-9.6160.0000.0000.0000.000
100A100GLN0-0.015-0.00526.868-0.203-0.2030.0000.0000.0000.000
101A101VAL00.0020.01528.8640.0280.0280.0000.0000.0000.000
102A102GLU-1-0.834-0.90330.9348.8288.8280.0000.0000.0000.000
103A103GLN0-0.032-0.00932.233-0.324-0.3240.0000.0000.0000.000
104A104LEU00.0300.00527.175-0.199-0.1990.0000.0000.0000.000
105A105ARG10.8950.95931.878-9.419-9.4190.0000.0000.0000.000
106A106ARG10.7450.86534.677-9.285-9.2850.0000.0000.0000.000
107A107GLU-1-0.817-0.88933.0119.0559.0550.0000.0000.0000.000
108A108GLY0-0.021-0.00235.066-0.012-0.0120.0000.0000.0000.000
109A109ALA0-0.028-0.02129.7400.0490.0490.0000.0000.0000.000
110A110THR00.0100.00029.445-0.084-0.0840.0000.0000.0000.000
111A111GLN0-0.016-0.00926.9650.0480.0480.0000.0000.0000.000
112A112ILE0-0.0190.00726.3840.5660.5660.0000.0000.0000.000
113A113ALA0-0.0010.00123.311-0.149-0.1490.0000.0000.0000.000
114A114TYR00.015-0.00724.660-0.037-0.0370.0000.0000.0000.000
115A115ARG10.7690.86315.876-18.698-18.6980.0000.0000.0000.000
116A116SER0-0.013-0.01622.064-0.365-0.3650.0000.0000.0000.000
117A117ASP-1-0.826-0.90621.83413.41413.4140.0000.0000.0000.000
118A118ASP-1-0.752-0.83523.02310.26910.2690.0000.0000.0000.000
119A119TRP00.0270.00026.815-0.277-0.2770.0000.0000.0000.000
120A120ARG10.7800.85728.664-10.412-10.4120.0000.0000.0000.000
121A121ASP-1-0.767-0.85628.17310.69310.6930.0000.0000.0000.000
122A122LEU00.0080.01524.636-0.212-0.2120.0000.0000.0000.000
123A123LYS10.8520.90828.946-8.912-8.9120.0000.0000.0000.000
124A124GLU-1-0.851-0.91132.6048.5338.5330.0000.0000.0000.000
125A125ALA00.0280.00829.447-0.186-0.1860.0000.0000.0000.000
126A126TRP0-0.0240.00131.416-0.144-0.1440.0000.0000.0000.000
127A127LYS10.7680.86532.613-8.839-8.8390.0000.0000.0000.000
128A128LYS10.8070.90933.555-9.292-9.2920.0000.0000.0000.000
129A129GLY0-0.038-0.03133.542-0.112-0.1120.0000.0000.0000.000
130A130ALA0-0.011-0.00728.2100.1630.1630.0000.0000.0000.000
131A131ASP-1-0.869-0.93929.9999.8169.8160.0000.0000.0000.000
132A132ILE0-0.034-0.00523.7030.0930.0930.0000.0000.0000.000
133A133LEU0-0.024-0.02226.0710.1440.1440.0000.0000.0000.000
134A134ILE0-0.014-0.01019.2480.1480.1480.0000.0000.0000.000
135A135VAL00.0380.01621.573-0.015-0.0150.0000.0000.0000.000
136A136ASP-1-0.815-0.89716.62820.02620.0260.0000.0000.0000.000
137A137ALA0-0.0040.01417.253-0.718-0.7180.0000.0000.0000.000
138A138THR0-0.042-0.03314.2741.0891.0890.0000.0000.0000.000
139A139ASP-1-0.870-0.94016.40714.72914.7290.0000.0000.0000.000
140A140LYS10.7600.87513.119-20.587-20.5870.0000.0000.0000.000
141A141ASP-1-0.914-0.96518.34712.03512.0350.0000.0000.0000.000
142A142GLU-1-0.818-0.90121.58511.14011.1400.0000.0000.0000.000
143A143ALA00.0910.03820.931-0.475-0.4750.0000.0000.0000.000
144A144TRP0-0.045-0.02320.163-0.516-0.5160.0000.0000.0000.000
145A145LYS10.8500.91124.628-11.497-11.4970.0000.0000.0000.000
146A146GLN0-0.041-0.02124.591-0.467-0.4670.0000.0000.0000.000
147A147VAL00.0210.01723.958-0.230-0.2300.0000.0000.0000.000
148A148GLU-1-0.843-0.91527.06310.16910.1690.0000.0000.0000.000
149A149GLN0-0.035-0.01130.277-0.655-0.6550.0000.0000.0000.000
150A150LEU00.0270.01327.241-0.336-0.3360.0000.0000.0000.000
151A151ARG10.8420.91229.224-10.728-10.7280.0000.0000.0000.000
152A152ARG10.8380.92032.481-8.781-8.7810.0000.0000.0000.000
153A153GLU-1-0.861-0.92234.0328.4338.4330.0000.0000.0000.000
154A154GLY0-0.0020.01034.790-0.194-0.1940.0000.0000.0000.000
155A155ALA0-0.025-0.00830.974-0.036-0.0360.0000.0000.0000.000
156A156THR0-0.014-0.02331.5940.2090.2090.0000.0000.0000.000
157A157GLN00.0120.01026.9250.0030.0030.0000.0000.0000.000
158A158ILE0-0.0020.01225.3250.3180.3180.0000.0000.0000.000
159A159ALA0-0.015-0.01521.2830.1010.1010.0000.0000.0000.000
160A160TYR00.019-0.00117.675-0.090-0.0900.0000.0000.0000.000
161A161ARG10.7740.88511.317-23.193-23.1930.0000.0000.0000.000
162A162SER0-0.013-0.03114.087-0.242-0.2420.0000.0000.0000.000
163A163ASP-1-0.850-0.9009.07224.20624.2060.0000.0000.0000.000
164A164ASP-1-0.764-0.8789.74919.33819.3380.0000.0000.0000.000
165A165TRP00.035-0.00211.967-1.532-1.5320.0000.0000.0000.000
166A166ARG10.8450.90812.707-18.672-18.6720.0000.0000.0000.000
167A167ASP-1-0.746-0.86015.99816.43316.4330.0000.0000.0000.000
168A168LEU0-0.0110.00414.218-0.930-0.9300.0000.0000.0000.000
169A169LYS10.8540.92518.091-13.521-13.5210.0000.0000.0000.000
170A170GLU-1-0.806-0.90220.37111.24711.2470.0000.0000.0000.000
171A171ALA00.0160.00720.917-0.617-0.6170.0000.0000.0000.000
172A172TRP0-0.0090.00122.048-0.543-0.5430.0000.0000.0000.000
173A173LYS10.7430.86023.711-12.060-12.0600.0000.0000.0000.000
174A174LYS10.7820.89325.836-11.742-11.7420.0000.0000.0000.000
175A175GLY00.0090.00626.872-0.369-0.3690.0000.0000.0000.000
176A176ALA0-0.023-0.00422.725-0.108-0.1080.0000.0000.0000.000
177A177ASP-1-0.833-0.90824.10611.39511.3950.0000.0000.0000.000
178A178ILE0-0.0190.00920.3170.2660.2660.0000.0000.0000.000
179A179LEU0-0.019-0.01718.2490.1010.1010.0000.0000.0000.000
180A180ILE0-0.001-0.00613.9240.6760.6760.0000.0000.0000.000
181A181CYS0-0.0150.00211.205-0.189-0.1890.0000.0000.0000.000
182A182ASP-1-0.795-0.90110.12228.70628.7060.0000.0000.0000.000
183A183ALA00.0020.0016.298-0.718-0.7180.0000.0000.0000.000
184A184THR0-0.0280.0044.78010.15210.343-0.001-0.011-0.1800.000