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: G5Y11

Calculation Name: 2CVB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CVB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SKQ0

Base Structure: X-ray

Registration Date: 2023-09-22

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152534.117319
FMO2-HF: Nuclear repulsion 2078528.303618
FMO2-HF: Total energy -74005.813701
FMO2-MP2: Total energy -74223.736601


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-16.06-6.7249.055-6.648-11.744-0.037
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.009
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].
3A4TYR00.011-0.0043.891-0.6921.443-0.016-1.058-1.0610.004
4A5PRO00.0320.0312.347-1.3470.0061.590-0.462-2.4810.000
5A6GLU-1-0.773-0.8544.352-0.173-0.0500.000-0.029-0.0940.000
6A7LEU0-0.0030.0116.818-0.020-0.0200.0000.0000.0000.000
7A8PRO0-0.0180.0037.3880.0400.0400.0000.0000.0000.000
8A9LEU00.0580.0239.546-0.023-0.0230.0000.0000.0000.000
9A10GLU-1-0.778-0.86612.5900.0100.0100.0000.0000.0000.000
10A11SER0-0.068-0.03411.572-0.017-0.0170.0000.0000.0000.000
11A12PRO00.033-0.00813.7130.0010.0010.0000.0000.0000.000
12A13LEU0-0.0160.00315.928-0.023-0.0230.0000.0000.0000.000
13A14ILE0-0.040-0.00312.973-0.004-0.0040.0000.0000.0000.000
14A15ASP-1-0.769-0.86217.618-0.146-0.1460.0000.0000.0000.000
15A16ALA00.0160.00520.503-0.025-0.0250.0000.0000.0000.000
16A17GLU-1-0.835-0.89322.624-0.121-0.1210.0000.0000.0000.000
17A18LEU0-0.0050.01222.813-0.009-0.0090.0000.0000.0000.000
18A19PRO00.0170.00227.2510.0110.0110.0000.0000.0000.000
19A20ASP-1-0.723-0.82729.533-0.105-0.1050.0000.0000.0000.000
20A21PRO0-0.053-0.04330.7650.0040.0040.0000.0000.0000.000
21A22ARG10.7480.86133.4420.0870.0870.0000.0000.0000.000
22A23GLY0-0.021-0.00735.6730.0060.0060.0000.0000.0000.000
23A24GLY0-0.0090.00535.6260.0010.0010.0000.0000.0000.000
24A25ARG10.7700.84327.9390.1390.1390.0000.0000.0000.000
25A26TYR0-0.0040.00029.3370.0090.0090.0000.0000.0000.000
26A27ARG10.8980.94225.6010.1330.1330.0000.0000.0000.000
27A28LEU0-0.009-0.00321.2990.0100.0100.0000.0000.0000.000
28A29SER0-0.008-0.04024.8010.0110.0110.0000.0000.0000.000
29A30GLN0-0.046-0.01926.1610.0020.0020.0000.0000.0000.000
30A31PHE0-0.0150.00127.1100.0070.0070.0000.0000.0000.000
31A32HIS00.0080.01228.0910.0000.0000.0000.0000.0000.000
32A33GLU-1-0.888-0.93629.906-0.058-0.0580.0000.0000.0000.000
33A34PRO00.0060.01328.822-0.004-0.0040.0000.0000.0000.000
34A35LEU00.0390.02824.877-0.002-0.0020.0000.0000.0000.000
35A36LEU0-0.018-0.00823.155-0.002-0.0020.0000.0000.0000.000
36A37ALA00.0170.01122.652-0.004-0.0040.0000.0000.0000.000
37A38VAL00.0180.01519.956-0.001-0.0010.0000.0000.0000.000
38A39VAL0-0.023-0.02720.6740.0000.0000.0000.0000.0000.000
39A40PHE00.0420.03717.281-0.005-0.0050.0000.0000.0000.000
40A41MET0-0.030-0.03920.6690.0150.0150.0000.0000.0000.000
41A42CYS0-0.048-0.01923.474-0.010-0.0100.0000.0000.0000.000
42A43ASN00.0590.03426.0340.0080.0080.0000.0000.0000.000
43A44HIS0-0.049-0.05624.2340.0090.0090.0000.0000.0000.000
44A45CYS0-0.0540.02119.6940.0110.0110.0000.0000.0000.000
45A46PRO00.036-0.00126.9040.0050.0050.0000.0000.0000.000
46A47TYR00.035-0.00524.0940.0060.0060.0000.0000.0000.000
47A48VAL00.0370.03424.6430.0020.0020.0000.0000.0000.000
48A49LYS10.7690.86226.9800.0890.0890.0000.0000.0000.000
49A50GLY0-0.0110.01129.6740.0040.0040.0000.0000.0000.000
50A51SER0-0.038-0.03726.6150.0040.0040.0000.0000.0000.000
51A52ILE00.0080.00528.7560.0020.0020.0000.0000.0000.000
52A53GLY00.0420.02230.1960.0010.0010.0000.0000.0000.000
53A54GLU-1-0.793-0.87628.705-0.032-0.0320.0000.0000.0000.000
54A55LEU00.008-0.00725.6560.0020.0020.0000.0000.0000.000
55A56VAL00.0160.01729.401-0.001-0.0010.0000.0000.0000.000
56A57ALA00.0070.00832.6220.0020.0020.0000.0000.0000.000
57A58LEU0-0.029-0.01227.8550.0030.0030.0000.0000.0000.000
58A59ALA00.0160.00830.8730.0020.0020.0000.0000.0000.000
59A60GLU-1-0.850-0.89032.136-0.040-0.0400.0000.0000.0000.000
60A61ARG10.8720.93233.8270.0250.0250.0000.0000.0000.000
61A62TYR0-0.049-0.06931.0180.0020.0020.0000.0000.0000.000
62A63ARG10.8810.91532.8440.0440.0440.0000.0000.0000.000
63A64GLY0-0.015-0.00834.3260.0040.0040.0000.0000.0000.000
64A65LYS10.7840.89132.3510.0340.0340.0000.0000.0000.000
65A66VAL00.006-0.00326.6330.0010.0010.0000.0000.0000.000
66A67ALA00.0000.02527.6490.0000.0000.0000.0000.0000.000
67A68PHE00.012-0.00826.584-0.002-0.0020.0000.0000.0000.000
68A69VAL00.0050.00624.9510.0000.0000.0000.0000.0000.000
69A70GLY0-0.0020.01224.691-0.006-0.0060.0000.0000.0000.000
70A71ILE0-0.015-0.01120.878-0.002-0.0020.0000.0000.0000.000
71A72ASN00.006-0.02322.995-0.016-0.0160.0000.0000.0000.000
72A73ALA00.0460.01919.965-0.004-0.0040.0000.0000.0000.000
73A74ASN0-0.050-0.03121.294-0.041-0.0410.0000.0000.0000.000
74A75ASP-1-0.787-0.89923.339-0.196-0.1960.0000.0000.0000.000
75A76TYR0-0.025-0.05325.0790.0160.0160.0000.0000.0000.000
76A77GLU-1-0.852-0.90328.593-0.160-0.1600.0000.0000.0000.000
77A78LYS10.8380.92921.9000.2480.2480.0000.0000.0000.000
78A79TYR0-0.025-0.02524.4320.0030.0030.0000.0000.0000.000
79A80PRO00.0590.02928.9780.0010.0010.0000.0000.0000.000
80A81GLU-1-0.830-0.90230.973-0.085-0.0850.0000.0000.0000.000
81A82ASP-1-0.729-0.82926.767-0.136-0.1360.0000.0000.0000.000
82A83ALA00.0300.01929.533-0.006-0.0060.0000.0000.0000.000
83A84PRO00.0680.01530.6630.0070.0070.0000.0000.0000.000
84A85GLU-1-0.844-0.89832.554-0.079-0.0790.0000.0000.0000.000
85A86LYS10.8450.89533.4620.0880.0880.0000.0000.0000.000
86A87MET0-0.0760.02328.4480.0000.0000.0000.0000.0000.000
87A88ALA00.0310.02532.6450.0030.0030.0000.0000.0000.000
88A89ALA00.0240.01635.8320.0040.0040.0000.0000.0000.000
89A90PHE00.004-0.00629.9200.0050.0050.0000.0000.0000.000
90A91ALA00.008-0.00633.5700.0030.0030.0000.0000.0000.000
91A92GLU-1-0.839-0.92434.761-0.068-0.0680.0000.0000.0000.000
92A93GLU-1-0.927-0.95436.332-0.060-0.0600.0000.0000.0000.000
93A94HIS10.7430.86433.6660.0680.0680.0000.0000.0000.000
94A95GLY00.0400.03335.6260.0010.0010.0000.0000.0000.000
95A96ILE0-0.018-0.00830.7260.0010.0010.0000.0000.0000.000
96A97PHE0-0.019-0.01634.291-0.004-0.0040.0000.0000.0000.000
97A98PHE0-0.035-0.00128.2860.0010.0010.0000.0000.0000.000
98A99PRO00.0170.00429.595-0.002-0.0020.0000.0000.0000.000
99A100TYR0-0.023-0.04726.750-0.007-0.0070.0000.0000.0000.000
100A101LEU00.0180.00025.5690.0000.0000.0000.0000.0000.000
101A102LEU00.0040.00126.242-0.004-0.0040.0000.0000.0000.000
102A103ASP-1-0.790-0.91319.475-0.297-0.2970.0000.0000.0000.000
103A104GLU-1-0.804-0.87522.446-0.202-0.2020.0000.0000.0000.000
104A105THR0-0.023-0.05521.0920.0000.0000.0000.0000.0000.000
105A106GLN0-0.039-0.01418.438-0.071-0.0710.0000.0000.0000.000
106A107GLU-1-0.850-0.89316.849-0.350-0.3500.0000.0000.0000.000
107A108VAL00.0100.00716.113-0.036-0.0360.0000.0000.0000.000
108A109ALA00.001-0.01215.895-0.015-0.0150.0000.0000.0000.000
109A110LYS10.8170.90212.5210.5630.5630.0000.0000.0000.000
110A111ALA0-0.017-0.00311.384-0.092-0.0920.0000.0000.0000.000
111A112TYR0-0.021-0.05011.883-0.012-0.0120.0000.0000.0000.000
112A113ARG10.7660.8846.8220.6210.6210.0000.0000.0000.000
113A114ALA00.0000.03310.5840.0300.0300.0000.0000.0000.000
114A115LEU0-0.024-0.0369.592-0.059-0.0590.0000.0000.0000.000
115A116ARG10.8000.89914.0590.1510.1510.0000.0000.0000.000
116A117THR00.0220.04017.283-0.005-0.0050.0000.0000.0000.000
117A118PRO0-0.038-0.02420.8610.0080.0080.0000.0000.0000.000
118A119GLU-1-0.762-0.88113.757-0.248-0.2480.0000.0000.0000.000
119A120VAL0-0.027-0.00318.296-0.010-0.0100.0000.0000.0000.000
120A121PHE0-0.001-0.01312.7740.0050.0050.0000.0000.0000.000
121A122LEU0-0.0090.00817.985-0.002-0.0020.0000.0000.0000.000
122A123PHE00.016-0.00316.4030.0050.0050.0000.0000.0000.000
123A124ASP-1-0.717-0.84520.755-0.031-0.0310.0000.0000.0000.000
124A125GLU-1-0.832-0.91323.416-0.037-0.0370.0000.0000.0000.000
125A126ARG10.6510.78620.1760.0110.0110.0000.0000.0000.000
126A127ARG10.7370.83921.8220.0630.0630.0000.0000.0000.000
127A128LEU0-0.027-0.00317.645-0.017-0.0170.0000.0000.0000.000
128A129LEU0-0.055-0.02012.9610.0050.0050.0000.0000.0000.000
129A130ARG10.8380.87716.0840.0170.0170.0000.0000.0000.000
130A131TYR0-0.012-0.03017.3330.0180.0180.0000.0000.0000.000
131A132HIS10.8180.89011.2290.1430.1430.0000.0000.0000.000
132A133GLY0-0.019-0.00615.3900.0180.0180.0000.0000.0000.000
133A134ARG10.8020.91016.836-0.008-0.0080.0000.0000.0000.000
134A135VAL00.0540.03919.9260.0040.0040.0000.0000.0000.000
135A136ASN0-0.019-0.02823.5340.0060.0060.0000.0000.0000.000
136A137ASP-1-0.772-0.90523.234-0.012-0.0120.0000.0000.0000.000
137A138ASN0-0.034-0.02024.320-0.004-0.0040.0000.0000.0000.000
138A139PRO00.0030.01223.006-0.001-0.0010.0000.0000.0000.000
139A140LYS10.8680.93626.3010.0480.0480.0000.0000.0000.000
140A141ASP-1-0.776-0.85328.460-0.024-0.0240.0000.0000.0000.000
141A142PRO00.0690.02831.3080.0050.0050.0000.0000.0000.000
142A143SER0-0.104-0.06332.5720.0040.0040.0000.0000.0000.000
143A144LYS10.8190.87931.4310.0200.0200.0000.0000.0000.000
144A145VAL0-0.0760.00228.1420.0030.0030.0000.0000.0000.000
145A146GLN0-0.065-0.04028.6910.0040.0040.0000.0000.0000.000
146A147SER0-0.069-0.04724.8030.0050.0050.0000.0000.0000.000
147A148HIS10.8710.90126.9050.0150.0150.0000.0000.0000.000
148A149ASP-1-0.759-0.86221.679-0.006-0.0060.0000.0000.0000.000
149A150LEU00.0150.02222.4500.0020.0020.0000.0000.0000.000
150A151GLU-1-0.855-0.91724.031-0.022-0.0220.0000.0000.0000.000
151A152ALA0-0.008-0.00925.3540.0020.0020.0000.0000.0000.000
152A153ALA0-0.009-0.00822.2050.0040.0040.0000.0000.0000.000
153A154ILE00.0170.00324.1200.0000.0000.0000.0000.0000.000
154A155GLU-1-0.836-0.89326.645-0.010-0.0100.0000.0000.0000.000
155A156ALA0-0.0310.00025.4460.0020.0020.0000.0000.0000.000
156A157LEU00.0130.01122.3050.0010.0010.0000.0000.0000.000
157A158LEU0-0.038-0.01726.5890.0000.0000.0000.0000.0000.000
158A159ARG10.7600.86329.808-0.002-0.0020.0000.0000.0000.000
159A160GLY0-0.034-0.00928.0800.0030.0030.0000.0000.0000.000
160A161GLU-1-0.907-0.93227.2670.0200.0200.0000.0000.0000.000
161A162GLU-1-0.818-0.88920.6570.0150.0150.0000.0000.0000.000
162A163PRO0-0.019-0.01320.3600.0020.0020.0000.0000.0000.000
163A164PRO0-0.032-0.02321.2560.0100.0100.0000.0000.0000.000
164A165LEU00.0450.02518.7110.0000.0000.0000.0000.0000.000
165A166LYS10.8880.95917.147-0.068-0.0680.0000.0000.0000.000
166A167GLH0-0.012-0.04210.317-0.013-0.0130.0000.0000.0000.000
167A168ALA00.0190.01315.6110.0090.0090.0000.0000.0000.000
168A169PRO00.0310.02112.922-0.022-0.0220.0000.0000.0000.000
169A170ALA00.0290.01815.0280.0110.0110.0000.0000.0000.000
170A171ILE0-0.038-0.00716.992-0.003-0.0030.0000.0000.0000.000
171A172GLY00.0650.01119.4790.0050.0050.0000.0000.0000.000
172A174THR00.0130.00316.3800.0030.0030.0000.0000.0000.000
173A175ILE00.0450.03116.1960.0210.0210.0000.0000.0000.000
174A176LYS10.7920.91718.6980.1590.1590.0000.0000.0000.000
175A177TRP00.0490.01114.478-0.004-0.0040.0000.0000.0000.000
176A178ARG10.8030.86819.5110.2350.2350.0000.0000.0000.000
177A179PRO0-0.044-0.03120.411-0.032-0.0320.0000.0000.0000.000
178A180GLY0-0.0180.00718.7990.0090.0090.0000.0000.0000.000
179A181ASN0-0.014-0.00817.054-0.096-0.0960.0000.0000.0000.000
180A182GLU-1-0.868-0.93315.414-0.396-0.3960.0000.0000.0000.000
181A183PRO0-0.0240.01110.403-0.080-0.0800.0000.0000.0000.000
182A184GLU-1-0.845-0.9198.267-1.077-1.0770.0000.0000.0000.000
183A185VAL0-0.030-0.0106.082-0.537-0.5370.0000.0000.0000.000
184A186ARG10.7820.8753.5581.2931.6940.009-0.108-0.3020.000
185A187ILE00.0380.0102.475-5.160-2.8603.099-2.384-3.015-0.028
186A188GLY00.0150.0222.563-8.030-5.0064.373-2.607-4.791-0.013