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: 7GJ5K

Calculation Name: 5BVL-A-Xray323

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2204386.935155
FMO2-HF: Nuclear repulsion 2129226.670284
FMO2-HF: Total energy -75160.264871
FMO2-MP2: Total energy -75383.67312


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:0:ACE )


Summations of interaction energy for fragment #1(A:0:ACE )
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.
-0.2281.7410.04-0.926-1.084-0.004
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.028
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].
3A2LYS 10.9911.0173.8421.4452.308-0.005-0.414-0.444-0.001
4A3ASP -1-0.966-0.9993.424-0.7280.0820.041-0.465-0.386-0.003
5A4GLU -1-0.965-0.9733.6040.9411.2170.004-0.045-0.2360.000
6A5ALA 00.0270.0065.2830.1270.1470.000-0.002-0.0180.000
7A6TRP 0-0.062-0.0318.1540.1310.1310.0000.0000.0000.000
8A7LYS 10.8090.8998.252-0.285-0.2850.0000.0000.0000.000
9A8CYS 00.0150.0059.5490.0150.0150.0000.0000.0000.000
10A9VAL 00.0740.04611.9740.0100.0100.0000.0000.0000.000
11A10GLU -1-0.871-0.90213.3180.2390.2390.0000.0000.0000.000
12A11GLN 00.0130.02013.794-0.022-0.0220.0000.0000.0000.000
13A12LEU 00.012-0.00215.800-0.002-0.0020.0000.0000.0000.000
14A13ARG 10.9740.99017.8780.0020.0020.0000.0000.0000.000
15A14ARG 10.7490.86218.000-0.083-0.0830.0000.0000.0000.000
16A15GLU -1-0.893-0.94919.5890.0530.0530.0000.0000.0000.000
17A16GLY 0-0.0160.00522.109-0.005-0.0050.0000.0000.0000.000
18A17ALA 0-0.029-0.02221.420-0.006-0.0060.0000.0000.0000.000
19A18THR 0-0.0040.01022.8580.0020.0020.0000.0000.0000.000
20A19GLN 0-0.031-0.01623.9310.0030.0030.0000.0000.0000.000
21A20ILE 0-0.028-0.00617.435-0.005-0.0050.0000.0000.0000.000
22A21ALA 00.000-0.00118.8660.0000.0000.0000.0000.0000.000
23A22TYR 0-0.055-0.03010.480-0.021-0.0210.0000.0000.0000.000
24A23ARG 10.9290.97214.9710.2800.2800.0000.0000.0000.000
25A24SER 0-0.052-0.05013.916-0.052-0.0520.0000.0000.0000.000
26A25ASP -1-0.827-0.92014.352-0.301-0.3010.0000.0000.0000.000
27A26ASP -1-0.825-0.90414.649-0.208-0.2080.0000.0000.0000.000
28A27TRP 00.0380.01216.4310.0160.0160.0000.0000.0000.000
29A28ARG 10.8780.93817.1670.1410.1410.0000.0000.0000.000
30A29ASP -1-0.835-0.89812.672-0.349-0.3490.0000.0000.0000.000
31A30LEU 00.0700.04515.1170.0270.0270.0000.0000.0000.000
32A31LYS 10.8770.93417.6470.1020.1020.0000.0000.0000.000
33A32GLU -1-0.856-0.93115.510-0.025-0.0250.0000.0000.0000.000
34A33ALA 0-0.011-0.00615.1530.0270.0270.0000.0000.0000.000
35A34TRP 0-0.0060.03816.9090.0160.0160.0000.0000.0000.000
36A35LYS 10.8380.89018.8400.0430.0430.0000.0000.0000.000
37A36LYS 10.7670.86114.6450.0720.0720.0000.0000.0000.000
38A37GLY 0-0.069-0.04117.4150.0180.0180.0000.0000.0000.000
39A38ALA 00.0070.02617.463-0.002-0.0020.0000.0000.0000.000
40A39ASP -1-0.826-0.91119.395-0.051-0.0510.0000.0000.0000.000
41A40ILE 0-0.050-0.02021.6070.0000.0000.0000.0000.0000.000
42A41LEU 0-0.014-0.00919.429-0.017-0.0170.0000.0000.0000.000
43A42ILE 0-0.024-0.01518.8700.0120.0120.0000.0000.0000.000
44A43VAL 00.0220.01218.963-0.029-0.0290.0000.0000.0000.000
45A44ASP -1-0.853-0.92417.387-0.308-0.3080.0000.0000.0000.000
46A45ALA 0-0.070-0.03119.6880.0080.0080.0000.0000.0000.000
47A46THR 00.0380.01418.953-0.006-0.0060.0000.0000.0000.000
48A47ASP -1-0.880-0.93021.694-0.146-0.1460.0000.0000.0000.000
49A48LYS 10.8930.94324.7110.1240.1240.0000.0000.0000.000
50A49ASP -1-0.945-0.95926.995-0.107-0.1070.0000.0000.0000.000
51A50GLU -1-0.859-0.93221.843-0.153-0.1530.0000.0000.0000.000
52A51ALA 00.004-0.00223.3610.0010.0010.0000.0000.0000.000
53A52TRP 0-0.021-0.03124.3120.0100.0100.0000.0000.0000.000
54A53LYS 11.0051.00826.3250.1150.1150.0000.0000.0000.000
55A54GLN 0-0.036-0.02919.5420.0080.0080.0000.0000.0000.000
56A55VAL 00.0060.01824.3190.0060.0060.0000.0000.0000.000
57A56GLU -1-0.947-0.97126.494-0.078-0.0780.0000.0000.0000.000
58A57GLN 0-0.056-0.02324.8880.0110.0110.0000.0000.0000.000
59A58LEU 00.008-0.01421.8450.0090.0090.0000.0000.0000.000
60A59ARG 11.0050.99425.9930.0730.0730.0000.0000.0000.000
61A60ARG 10.8240.90929.6000.0870.0870.0000.0000.0000.000
62A61GLU -1-0.890-0.93825.320-0.069-0.0690.0000.0000.0000.000
63A62GLY 0-0.0200.00528.2550.0050.0050.0000.0000.0000.000
64A63ALA 0-0.035-0.02625.0750.0030.0030.0000.0000.0000.000
65A64THR 0-0.030-0.02726.871-0.002-0.0020.0000.0000.0000.000
66A65GLN 00.0270.02125.8000.0030.0030.0000.0000.0000.000
67A66ILE 0-0.0150.01424.845-0.012-0.0120.0000.0000.0000.000
68A67ALA 00.0190.00323.1930.0080.0080.0000.0000.0000.000
69A68TYR 0-0.006-0.00723.827-0.008-0.0080.0000.0000.0000.000
70A69ARG 10.8310.91018.8800.2540.2540.0000.0000.0000.000
71A70SER 0-0.030-0.02324.261-0.008-0.0080.0000.0000.0000.000
72A71ASP -1-0.854-0.92026.333-0.128-0.1280.0000.0000.0000.000
73A72ASP -1-0.752-0.85228.347-0.084-0.0840.0000.0000.0000.000
74A73TRP 00.024-0.01531.1730.0000.0000.0000.0000.0000.000
75A74ARG 10.7660.87433.3750.0870.0870.0000.0000.0000.000
76A75ASP -1-0.834-0.92629.151-0.116-0.1160.0000.0000.0000.000
77A76LEU 0-0.016-0.00227.9550.0000.0000.0000.0000.0000.000
78A77LYS 10.8740.93130.9160.0650.0650.0000.0000.0000.000
79A78GLU -1-0.908-0.97132.496-0.076-0.0760.0000.0000.0000.000
80A79ALA 00.0040.00628.6040.0010.0010.0000.0000.0000.000
81A80TRP 0-0.032-0.00630.5460.0020.0020.0000.0000.0000.000
82A81LYS 10.8380.92332.9070.0710.0710.0000.0000.0000.000
83A82LYS 10.8330.93531.0210.0890.0890.0000.0000.0000.000
84A83GLY 0-0.055-0.03431.371-0.001-0.0010.0000.0000.0000.000
85A84ALA 0-0.0160.01328.2600.0000.0000.0000.0000.0000.000
86A85ASP -1-0.873-0.94529.072-0.070-0.0700.0000.0000.0000.000
87A86ILE 0-0.035-0.02026.2970.0030.0030.0000.0000.0000.000
88A87LEU 0-0.042-0.03027.376-0.011-0.0110.0000.0000.0000.000
89A88ILE 0-0.013-0.01422.8040.0040.0040.0000.0000.0000.000
90A89VAL 00.0270.01626.577-0.008-0.0080.0000.0000.0000.000
91A90ASP -1-0.877-0.96322.779-0.181-0.1810.0000.0000.0000.000
92A91ALA 0-0.011-0.00326.0100.0040.0040.0000.0000.0000.000
93A92THR 0-0.004-0.00224.549-0.004-0.0040.0000.0000.0000.000
94A93ASP -1-0.864-0.94227.445-0.076-0.0760.0000.0000.0000.000
95A94LYS 10.8860.94331.1570.0750.0750.0000.0000.0000.000
96A95ASP -1-0.890-0.96232.934-0.058-0.0580.0000.0000.0000.000
97A96GLU -1-0.876-0.92733.586-0.072-0.0720.0000.0000.0000.000
98A97ALA 00.0030.02331.047-0.001-0.0010.0000.0000.0000.000
99A98TRP 0-0.018-0.02832.7170.0020.0020.0000.0000.0000.000
100A99LYS 11.0041.01535.4880.0650.0650.0000.0000.0000.000
101A100GLN 0-0.043-0.01631.9670.0010.0010.0000.0000.0000.000
102A101VAL 00.0190.01232.8630.0010.0010.0000.0000.0000.000
103A102GLU -1-0.895-0.94935.090-0.051-0.0510.0000.0000.0000.000
104A103GLN 0-0.031-0.00437.3320.0050.0050.0000.0000.0000.000
105A104LEU 00.020-0.00232.4030.0030.0030.0000.0000.0000.000
106A105ARG 10.9821.01536.9540.0500.0500.0000.0000.0000.000
107A106ARG 10.7510.86339.1390.0590.0590.0000.0000.0000.000
108A107GLU -1-0.879-0.92238.718-0.056-0.0560.0000.0000.0000.000
109A108GLY 0-0.008-0.00740.7030.0010.0010.0000.0000.0000.000
110A109ALA 0-0.042-0.02634.8900.0000.0000.0000.0000.0000.000
111A110THR 0-0.024-0.01635.0920.0010.0010.0000.0000.0000.000
112A111GLN 00.0260.01430.9470.0010.0010.0000.0000.0000.000
113A112ILE 00.0010.02430.995-0.008-0.0080.0000.0000.0000.000
114A113ALA 00.0160.00026.8750.0030.0030.0000.0000.0000.000
115A114TYR 00.010-0.01428.222-0.002-0.0020.0000.0000.0000.000
116A115ARG 10.8480.94118.6680.2030.2030.0000.0000.0000.000
117A116SER 00.025-0.00525.3410.0000.0000.0000.0000.0000.000
118A117ASP -1-0.857-0.92424.014-0.099-0.0990.0000.0000.0000.000
119A118ASP -1-0.755-0.85825.307-0.054-0.0540.0000.0000.0000.000
120A119TRP 00.029-0.00729.0030.0020.0020.0000.0000.0000.000
121A120ARG 10.8170.91030.6840.0550.0550.0000.0000.0000.000
122A121ASP -1-0.796-0.90730.814-0.070-0.0700.0000.0000.0000.000
123A122LEU 00.0100.01226.9860.0020.0020.0000.0000.0000.000
124A123LYS 10.8950.95131.4230.0410.0410.0000.0000.0000.000
125A124GLU -1-0.929-0.97034.824-0.045-0.0450.0000.0000.0000.000
126A125ALA 00.0240.00232.5520.0020.0020.0000.0000.0000.000
127A126TRP 0-0.026-0.00734.1350.0020.0020.0000.0000.0000.000
128A127LYS 10.8520.93735.3600.0450.0450.0000.0000.0000.000
129A128LYS 10.7990.91437.3310.0550.0550.0000.0000.0000.000
130A129GLY 0-0.044-0.03337.4720.0000.0000.0000.0000.0000.000
131A130ALA 0-0.0310.00531.731-0.002-0.0020.0000.0000.0000.000
132A131ASP -1-0.857-0.93633.026-0.052-0.0520.0000.0000.0000.000
133A132ILE 0-0.083-0.04026.5520.0000.0000.0000.0000.0000.000
134A133LEU 0-0.037-0.02328.499-0.006-0.0060.0000.0000.0000.000
135A134ILE 0-0.020-0.02522.0160.0000.0000.0000.0000.0000.000
136A135VAL 00.0090.00623.119-0.003-0.0030.0000.0000.0000.000
137A136ASP -1-0.895-0.95819.041-0.203-0.2030.0000.0000.0000.000
138A137ALA 00.0100.02018.4680.0100.0100.0000.0000.0000.000
139A138THR 0-0.051-0.03416.224-0.025-0.0250.0000.0000.0000.000
140A139ASP -1-0.917-0.95617.619-0.091-0.0910.0000.0000.0000.000
141A140LYS 10.8470.90112.7770.1340.1340.0000.0000.0000.000
142A141ASP -1-0.934-0.95418.693-0.009-0.0090.0000.0000.0000.000
143A142GLU -1-0.848-0.92721.098-0.052-0.0520.0000.0000.0000.000
144A143ALA 00.0660.03721.5300.0040.0040.0000.0000.0000.000
145A144TRP 0-0.023-0.02220.6220.0020.0020.0000.0000.0000.000
146A145LYS 10.9190.96525.0720.0290.0290.0000.0000.0000.000
147A146GLN 0-0.027-0.01825.5250.0010.0010.0000.0000.0000.000
148A147VAL 00.0200.01624.9220.0000.0000.0000.0000.0000.000
149A148GLU -1-0.893-0.95028.026-0.019-0.0190.0000.0000.0000.000
150A149GLN 0-0.065-0.03330.9010.0030.0030.0000.0000.0000.000
151A150LEU 00.0160.00929.0260.0020.0020.0000.0000.0000.000
152A151ARG 10.9350.97330.8950.0320.0320.0000.0000.0000.000
153A152ARG 10.8840.95133.3870.0270.0270.0000.0000.0000.000
154A153GLU -1-0.954-0.98735.853-0.033-0.0330.0000.0000.0000.000
155A154GLY 0-0.0060.01036.4550.0010.0010.0000.0000.0000.000
156A155ALA 0-0.032-0.00632.821-0.001-0.0010.0000.0000.0000.000
157A156THR 0-0.026-0.03133.5840.0000.0000.0000.0000.0000.000
158A157GLN 00.0140.01629.5350.0010.0010.0000.0000.0000.000
159A158ILE 0-0.0050.01426.554-0.005-0.0050.0000.0000.0000.000
160A159ALA 00.0110.00022.9380.0020.0020.0000.0000.0000.000
161A160TYR 00.028-0.00518.7760.0010.0010.0000.0000.0000.000
162A161ARG 10.8300.92414.7420.2880.2880.0000.0000.0000.000
163A162SER 00.0290.00915.4740.0020.0020.0000.0000.0000.000
164A163ASP -1-0.842-0.9089.817-0.274-0.2740.0000.0000.0000.000
165A164ASP -1-0.861-0.93610.5280.0540.0540.0000.0000.0000.000
166A165TRP 00.021-0.01211.9890.0000.0000.0000.0000.0000.000
167A166ARG 10.8790.93813.193-0.138-0.1380.0000.0000.0000.000
168A167ASP -1-0.773-0.90316.602-0.038-0.0380.0000.0000.0000.000
169A168LEU 0-0.030-0.01214.7420.0020.0020.0000.0000.0000.000
170A169LYS 10.9010.95518.556-0.036-0.0360.0000.0000.0000.000
171A170GLU -1-0.934-0.97220.6240.0110.0110.0000.0000.0000.000
172A171ALA 00.0090.00721.7740.0000.0000.0000.0000.0000.000
173A172TRP 0-0.020-0.00522.6940.0070.0070.0000.0000.0000.000
174A173LYS 10.8750.94424.376-0.014-0.0140.0000.0000.0000.000
175A174LYS 10.8160.92626.2940.0190.0190.0000.0000.0000.000
176A175GLY 0-0.023-0.01527.529-0.001-0.0010.0000.0000.0000.000
177A176ALA 0-0.040-0.00924.236-0.003-0.0030.0000.0000.0000.000
178A177ASP -1-0.897-0.95926.021-0.033-0.0330.0000.0000.0000.000
179A178ILE 0-0.058-0.02922.291-0.002-0.0020.0000.0000.0000.000
180A179LEU 0-0.014-0.01018.964-0.004-0.0040.0000.0000.0000.000
181A180ILE 0-0.011-0.01816.666-0.007-0.0070.0000.0000.0000.000
182A181CYS 0-0.030-0.01812.5960.0110.0110.0000.0000.0000.000
183A182ASP -1-0.846-0.93312.879-0.417-0.4170.0000.0000.0000.000
184A183ALA 00.001-0.0087.4620.0430.0430.0000.0000.0000.000
185A184THR 00.0020.0168.048-0.164-0.1640.0000.0000.0000.000
186A185NME 00.0080.0077.672-0.370-0.3700.0000.0000.0000.000