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: VQKM1

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2148454.342608
FMO2-HF: Nuclear repulsion 2074449.420944
FMO2-HF: Total energy -74004.921664
FMO2-MP2: Total energy -74222.770969


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.
-13.406-5.92811.933-7.241-12.174-0.051
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 : -0.063 / q_NPA : -0.025
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].
3A4TYR0-0.003-0.0033.814-1.8820.339-0.028-1.036-1.1580.003
4A5PRO00.0170.0292.466-1.592-0.1250.968-0.391-2.0450.000
5A6GLU-1-0.782-0.8884.330-0.279-0.1570.000-0.029-0.0940.000
6A7LEU0-0.036-0.0186.868-0.021-0.0210.0000.0000.0000.000
7A8PRO0-0.0170.0007.3040.0000.0000.0000.0000.0000.000
8A9LEU00.0490.0079.5710.0240.0240.0000.0000.0000.000
9A10GLU-1-0.912-0.98412.786-0.061-0.0610.0000.0000.0000.000
10A11SER0-0.093-0.02511.6030.0180.0180.0000.0000.0000.000
11A12PRO00.0450.00113.699-0.003-0.0030.0000.0000.0000.000
12A13LEU00.0060.01615.846-0.009-0.0090.0000.0000.0000.000
13A14ILE0-0.046-0.00313.0880.0120.0120.0000.0000.0000.000
14A15ASP-1-0.762-0.88217.680-0.028-0.0280.0000.0000.0000.000
15A16ALA0-0.002-0.00820.5240.0000.0000.0000.0000.0000.000
16A17GLU-1-0.882-0.93322.723-0.012-0.0120.0000.0000.0000.000
17A18LEU0-0.023-0.00222.7600.0010.0010.0000.0000.0000.000
18A19PRO0-0.009-0.00527.1530.0020.0020.0000.0000.0000.000
19A20ASP-1-0.706-0.83429.627-0.040-0.0400.0000.0000.0000.000
20A21PRO0-0.042-0.03330.9000.0030.0030.0000.0000.0000.000
21A22ARG10.7880.88433.3820.0380.0380.0000.0000.0000.000
22A23GLY0-0.026-0.00835.6640.0020.0020.0000.0000.0000.000
23A24GLY0-0.025-0.01035.693-0.001-0.0010.0000.0000.0000.000
24A25ARG10.8330.89828.4460.0130.0130.0000.0000.0000.000
25A26TYR00.0150.00729.3760.0010.0010.0000.0000.0000.000
26A27ARG10.9340.97026.3670.0080.0080.0000.0000.0000.000
27A28LEU0-0.017-0.01221.287-0.001-0.0010.0000.0000.0000.000
28A29SER0-0.035-0.04324.641-0.001-0.0010.0000.0000.0000.000
29A30GLN0-0.0080.00826.0240.0030.0030.0000.0000.0000.000
30A31PHE0-0.026-0.00826.9830.0010.0010.0000.0000.0000.000
31A32HIS00.0220.00828.278-0.002-0.0020.0000.0000.0000.000
32A33GLU-1-0.914-0.93929.833-0.031-0.0310.0000.0000.0000.000
33A34PRO00.0170.01428.735-0.001-0.0010.0000.0000.0000.000
34A35LEU00.0190.01925.133-0.002-0.0020.0000.0000.0000.000
35A36LEU0-0.0090.00722.9210.0030.0030.0000.0000.0000.000
36A37ALA00.0140.00622.844-0.008-0.0080.0000.0000.0000.000
37A38VAL00.0200.01320.0970.0050.0050.0000.0000.0000.000
38A39VAL0-0.010-0.02120.629-0.013-0.0130.0000.0000.0000.000
39A40PHE00.0310.03617.4810.0060.0060.0000.0000.0000.000
40A41MET0-0.026-0.04520.862-0.007-0.0070.0000.0000.0000.000
41A42CYS0-0.044-0.00823.670-0.001-0.0010.0000.0000.0000.000
42A43ASN00.0420.02126.2280.0000.0000.0000.0000.0000.000
43A44HIS0-0.063-0.06724.364-0.004-0.0040.0000.0000.0000.000
44A45CYS0-0.0950.00419.736-0.011-0.0110.0000.0000.0000.000
45A46PRO00.028-0.00726.7870.0020.0020.0000.0000.0000.000
46A47TYR00.047-0.00124.0570.0030.0030.0000.0000.0000.000
47A48VAL00.0430.03824.7000.0000.0000.0000.0000.0000.000
48A49LYS10.9160.95326.8600.0630.0630.0000.0000.0000.000
49A50GLY0-0.0210.00729.5660.0040.0040.0000.0000.0000.000
50A51SER00.004-0.01826.6390.0010.0010.0000.0000.0000.000
51A52ILE00.0030.00629.0090.0010.0010.0000.0000.0000.000
52A53GLY00.0120.01230.3080.0030.0030.0000.0000.0000.000
53A54GLU-1-0.799-0.88029.325-0.071-0.0710.0000.0000.0000.000
54A55LEU00.016-0.00625.4350.0010.0010.0000.0000.0000.000
55A56VAL0-0.0050.00929.5110.0020.0020.0000.0000.0000.000
56A57ALA00.0050.00732.7650.0030.0030.0000.0000.0000.000
57A58LEU0-0.021-0.01128.0650.0020.0020.0000.0000.0000.000
58A59ALA00.0050.01030.9930.0020.0020.0000.0000.0000.000
59A60GLU-1-0.891-0.94432.280-0.031-0.0310.0000.0000.0000.000
60A61ARG10.9330.96434.5390.0460.0460.0000.0000.0000.000
61A62TYR0-0.098-0.08530.7230.0010.0010.0000.0000.0000.000
62A63ARG10.9340.97533.3190.0330.0330.0000.0000.0000.000
63A64GLY0-0.036-0.01434.5580.0010.0010.0000.0000.0000.000
64A65LYS10.8950.94532.3980.0350.0350.0000.0000.0000.000
65A66VAL00.0310.00427.029-0.001-0.0010.0000.0000.0000.000
66A67ALA0-0.0160.01528.2270.0010.0010.0000.0000.0000.000
67A68PHE00.014-0.00326.733-0.005-0.0050.0000.0000.0000.000
68A69VAL00.0180.01124.9790.0050.0050.0000.0000.0000.000
69A70GLY0-0.0170.00524.850-0.008-0.0080.0000.0000.0000.000
70A71ILE0-0.0010.00021.0820.0060.0060.0000.0000.0000.000
71A72ASN0-0.004-0.04023.086-0.017-0.0170.0000.0000.0000.000
72A73ALA00.0390.01320.1760.0060.0060.0000.0000.0000.000
73A74ASN0-0.021-0.01721.959-0.011-0.0110.0000.0000.0000.000
74A75ASP-1-0.818-0.91223.335-0.045-0.0450.0000.0000.0000.000
75A76TYR0-0.031-0.04024.954-0.001-0.0010.0000.0000.0000.000
76A77GLU-1-0.846-0.89228.289-0.031-0.0310.0000.0000.0000.000
77A78LYS10.9100.96223.6320.0780.0780.0000.0000.0000.000
78A79TYR0-0.044-0.03124.437-0.006-0.0060.0000.0000.0000.000
79A80PRO00.0820.03928.807-0.001-0.0010.0000.0000.0000.000
80A81GLU-1-0.975-0.99430.984-0.053-0.0530.0000.0000.0000.000
81A82ASP-1-0.736-0.84526.648-0.073-0.0730.0000.0000.0000.000
82A83ALA00.0430.02029.3280.0000.0000.0000.0000.0000.000
83A84PRO00.0590.01030.674-0.001-0.0010.0000.0000.0000.000
84A85GLU-1-0.921-0.95932.531-0.026-0.0260.0000.0000.0000.000
85A86LYS10.9290.96433.2410.0360.0360.0000.0000.0000.000
86A87MET0-0.0570.02528.506-0.002-0.0020.0000.0000.0000.000
87A88ALA00.0130.01632.742-0.001-0.0010.0000.0000.0000.000
88A89ALA00.0650.03335.9390.0000.0000.0000.0000.0000.000
89A90PHE0-0.015-0.00730.271-0.001-0.0010.0000.0000.0000.000
90A91ALA0-0.008-0.02133.914-0.001-0.0010.0000.0000.0000.000
91A92GLU-1-0.929-0.96835.074-0.030-0.0300.0000.0000.0000.000
92A93GLU-1-0.998-0.98836.734-0.043-0.0430.0000.0000.0000.000
93A94HIS10.8170.90334.2680.0490.0490.0000.0000.0000.000
94A95GLY00.0500.03735.904-0.001-0.0010.0000.0000.0000.000
95A96ILE0-0.028-0.01130.899-0.001-0.0010.0000.0000.0000.000
96A97PHE0-0.022-0.01334.2910.0020.0020.0000.0000.0000.000
97A98PHE0-0.0390.00228.3590.0020.0020.0000.0000.0000.000
98A99PRO00.0250.01029.5370.0000.0000.0000.0000.0000.000
99A100TYR0-0.029-0.02426.889-0.008-0.0080.0000.0000.0000.000
100A101LEU00.015-0.01625.9650.0030.0030.0000.0000.0000.000
101A102LEU00.0080.01126.200-0.007-0.0070.0000.0000.0000.000
102A103ASP-1-0.824-0.93219.959-0.063-0.0630.0000.0000.0000.000
103A104GLU-1-0.862-0.94623.047-0.035-0.0350.0000.0000.0000.000
104A105THR0-0.021-0.02521.530-0.006-0.0060.0000.0000.0000.000
105A106GLN0-0.018-0.00518.532-0.003-0.0030.0000.0000.0000.000
106A107GLU-1-0.865-0.93217.000-0.031-0.0310.0000.0000.0000.000
107A108VAL00.0240.02216.336-0.008-0.0080.0000.0000.0000.000
108A109ALA00.006-0.00416.142-0.016-0.0160.0000.0000.0000.000
109A110LYS10.8930.94712.9200.0740.0740.0000.0000.0000.000
110A111ALA0-0.0210.00011.637-0.039-0.0390.0000.0000.0000.000
111A112TYR0-0.035-0.05312.136-0.017-0.0170.0000.0000.0000.000
112A113ARG10.8080.8996.8170.2930.2930.0000.0000.0000.000
113A114ALA00.0040.03310.697-0.046-0.0460.0000.0000.0000.000
114A115LEU0-0.025-0.0409.549-0.013-0.0130.0000.0000.0000.000
115A116ARG10.8410.92613.1520.2820.2820.0000.0000.0000.000
116A117THR00.0010.04017.3070.0080.0080.0000.0000.0000.000
117A118PRO0-0.037-0.03620.8060.0020.0020.0000.0000.0000.000
118A119GLU-1-0.761-0.87213.713-0.258-0.2580.0000.0000.0000.000
119A120VAL0-0.020-0.00818.5100.0080.0080.0000.0000.0000.000
120A121PHE00.009-0.00413.043-0.015-0.0150.0000.0000.0000.000
121A122LEU0-0.0040.00218.2610.0110.0110.0000.0000.0000.000
122A123PHE00.006-0.00916.651-0.007-0.0070.0000.0000.0000.000
123A124ASP-1-0.757-0.88821.021-0.050-0.0500.0000.0000.0000.000
124A125GLU-1-0.842-0.92523.506-0.040-0.0400.0000.0000.0000.000
125A126ARG10.8430.94121.2810.0430.0430.0000.0000.0000.000
126A127ARG10.7660.85921.5930.0430.0430.0000.0000.0000.000
127A128LEU0-0.0030.00717.7710.0010.0010.0000.0000.0000.000
128A129LEU0-0.088-0.03313.012-0.003-0.0030.0000.0000.0000.000
129A130ARG10.8890.93716.5210.0650.0650.0000.0000.0000.000
130A131TYR0-0.016-0.02917.857-0.007-0.0070.0000.0000.0000.000
131A132HIS10.8320.90511.3400.2550.2550.0000.0000.0000.000
132A133GLY0-0.033-0.01115.538-0.015-0.0150.0000.0000.0000.000
133A134ARG10.8450.93216.6950.1620.1620.0000.0000.0000.000
134A135VAL00.0490.04819.8130.0040.0040.0000.0000.0000.000
135A136ASN00.010-0.01123.3450.0020.0020.0000.0000.0000.000
136A137ASP-1-0.786-0.90923.331-0.101-0.1010.0000.0000.0000.000
137A138ASN0-0.062-0.03624.434-0.003-0.0030.0000.0000.0000.000
138A139PRO0-0.0100.01123.0130.0060.0060.0000.0000.0000.000
139A140LYS10.8760.93826.3500.0940.0940.0000.0000.0000.000
140A141ASP-1-0.837-0.90628.526-0.059-0.0590.0000.0000.0000.000
141A142PRO00.0520.02531.111-0.001-0.0010.0000.0000.0000.000
142A143SER0-0.084-0.04532.5260.0010.0010.0000.0000.0000.000
143A144LYS10.9040.94631.2360.0690.0690.0000.0000.0000.000
144A145VAL0-0.073-0.01228.325-0.004-0.0040.0000.0000.0000.000
145A146GLN0-0.058-0.03028.7660.0060.0060.0000.0000.0000.000
146A147SER0-0.068-0.02124.7430.0040.0040.0000.0000.0000.000
147A148HIS10.8970.91426.7730.0660.0660.0000.0000.0000.000
148A149ASP-1-0.842-0.93722.037-0.107-0.1070.0000.0000.0000.000
149A150LEU00.0260.02322.7700.0010.0010.0000.0000.0000.000
150A151GLU-1-0.931-0.96824.382-0.055-0.0550.0000.0000.0000.000
151A152ALA0-0.008-0.00825.6790.0040.0040.0000.0000.0000.000
152A153ALA0-0.007-0.00522.6680.0030.0030.0000.0000.0000.000
153A154ILE00.0180.00724.5710.0030.0030.0000.0000.0000.000
154A155GLU-1-0.859-0.92126.999-0.044-0.0440.0000.0000.0000.000
155A156ALA0-0.034-0.00425.7320.0040.0040.0000.0000.0000.000
156A157LEU00.0090.00122.6970.0030.0030.0000.0000.0000.000
157A158LEU0-0.062-0.02026.8600.0050.0050.0000.0000.0000.000
158A159ARG10.8440.93130.1950.0550.0550.0000.0000.0000.000
159A160GLY0-0.0220.00328.5590.0020.0020.0000.0000.0000.000
160A161GLU-1-0.966-0.98427.464-0.052-0.0520.0000.0000.0000.000
161A162GLU-1-0.889-0.93820.678-0.076-0.0760.0000.0000.0000.000
162A163PRO0-0.013-0.01321.0040.0000.0000.0000.0000.0000.000
163A164PRO0-0.024-0.02021.599-0.002-0.0020.0000.0000.0000.000
164A165LEU00.0550.02619.231-0.008-0.0080.0000.0000.0000.000
165A166LYS10.8880.96117.4560.1220.1220.0000.0000.0000.000
166A167GLH0-0.006-0.02210.7690.0020.0020.0000.0000.0000.000
167A168ALA00.0150.01015.798-0.003-0.0030.0000.0000.0000.000
168A169PRO00.0480.02413.0700.0070.0070.0000.0000.0000.000
169A170ALA00.0440.02315.0750.0190.0190.0000.0000.0000.000
170A171ILE0-0.039-0.01216.854-0.014-0.0140.0000.0000.0000.000
171A172GLY00.036-0.00919.6070.0130.0130.0000.0000.0000.000
172A174THR00.0160.00816.3570.0020.0020.0000.0000.0000.000
173A175ILE00.0420.02016.0340.0190.0190.0000.0000.0000.000
174A176LYS10.7740.90718.4020.1130.1130.0000.0000.0000.000
175A177TRP00.0350.00114.2800.0120.0120.0000.0000.0000.000
176A178ARG10.8570.92819.3440.0460.0460.0000.0000.0000.000
177A179PRO00.001-0.01020.252-0.005-0.0050.0000.0000.0000.000
178A180GLY0-0.0100.00918.6300.0120.0120.0000.0000.0000.000
179A181ASN0-0.046-0.02716.7960.0190.0190.0000.0000.0000.000
180A182GLU-1-0.939-0.97614.993-0.113-0.1130.0000.0000.0000.000
181A183PRO0-0.0380.00510.1130.0080.0080.0000.0000.0000.000
182A184GLU-1-0.923-0.9698.945-0.050-0.0500.0000.0000.0000.000
183A185VAL0-0.034-0.0135.549-0.165-0.1650.0000.0000.0000.000
184A186ARG10.8570.9303.2320.3240.9630.061-0.206-0.4940.000
185A187ILE00.0720.0192.306-4.551-3.0763.944-2.326-3.094-0.030
186A188GLY00.0120.0262.163-5.663-4.1096.988-3.253-5.289-0.024