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: J2M99

Calculation Name: 1VI7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VI7

Chain ID: A

ChEMBL ID:

UniProt ID: P27862

Base Structure: X-ray

Registration Date: 2023-09-26

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1959982.925509
FMO2-HF: Nuclear repulsion 1882648.524732
FMO2-HF: Total energy -77334.400777
FMO2-MP2: Total energy -77559.419013


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:3:LEU)


Summations of interaction energy for fragment #1(A:3: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.
-6.312-0.9496.474-3.526-8.308-0.017
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023
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].
3A5GLU-1-0.909-0.9593.493-1.1790.5380.018-0.848-0.887-0.001
4A6SER00.002-0.0066.2030.4460.4460.0000.0000.0000.000
5A7TRP0-0.027-0.0152.844-1.606-0.2800.890-0.572-1.643-0.006
6A8LEU0-0.005-0.0048.0170.0610.0610.0000.0000.0000.000
7A9ILE00.0140.0199.3220.0340.0340.0000.0000.0000.000
8A10PRO0-0.001-0.02011.848-0.031-0.0310.0000.0000.0000.000
9A11ALA00.0070.00215.4730.0150.0150.0000.0000.0000.000
10A12ALA0-0.026-0.00917.8070.0020.0020.0000.0000.0000.000
11A13PRO0-0.0130.00019.5380.0000.0000.0000.0000.0000.000
12A14VAL0-0.013-0.00221.212-0.008-0.0080.0000.0000.0000.000
13A15THR0-0.006-0.00623.3560.0040.0040.0000.0000.0000.000
14A16VAL00.0160.01726.196-0.004-0.0040.0000.0000.0000.000
15A17VAL00.001-0.00628.5970.0020.0020.0000.0000.0000.000
16A18GLU-1-0.865-0.93030.640-0.014-0.0140.0000.0000.0000.000
17A19GLU-1-0.835-0.90133.4200.0020.0020.0000.0000.0000.000
18A20ILE00.0090.01432.668-0.003-0.0030.0000.0000.0000.000
19A21LYS10.8470.90637.1550.0080.0080.0000.0000.0000.000
20A22LYS10.9850.97940.6960.0010.0010.0000.0000.0000.000
21A23SER0-0.0170.00936.2920.0020.0020.0000.0000.0000.000
22A24ARG10.8240.89934.786-0.007-0.0070.0000.0000.0000.000
23A25PHE00.0240.00530.3890.0020.0020.0000.0000.0000.000
24A26ILE00.0150.00328.996-0.003-0.0030.0000.0000.0000.000
25A27THR0-0.0240.00023.8780.0030.0030.0000.0000.0000.000
26A28MET0-0.029-0.01124.005-0.003-0.0030.0000.0000.0000.000
27A29LEU00.019-0.00718.6860.0030.0030.0000.0000.0000.000
28A30ALA00.0130.00618.132-0.006-0.0060.0000.0000.0000.000
29A31HIS0-0.015-0.01311.034-0.025-0.0250.0000.0000.0000.000
30A32THR0-0.075-0.07313.168-0.007-0.0070.0000.0000.0000.000
31A33ASP-1-0.866-0.9208.5540.5220.5220.0000.0000.0000.000
32A34GLY00.0750.0459.481-0.017-0.0170.0000.0000.0000.000
33A35VAL0-0.021-0.03510.358-0.050-0.0500.0000.0000.0000.000
34A36GLU-1-0.954-0.96712.9730.1490.1490.0000.0000.0000.000
35A37ALA00.0610.03013.787-0.027-0.0270.0000.0000.0000.000
36A38ALA0-0.001-0.00113.797-0.024-0.0240.0000.0000.0000.000
37A39LYS10.9030.94315.727-0.136-0.1360.0000.0000.0000.000
38A40ALA00.0210.00918.468-0.015-0.0150.0000.0000.0000.000
39A41PHE00.0340.02018.641-0.011-0.0110.0000.0000.0000.000
40A42VAL0-0.014-0.00820.228-0.012-0.0120.0000.0000.0000.000
41A43GLU-1-0.929-0.95522.9670.0550.0550.0000.0000.0000.000
42A44SER00.0440.01824.765-0.006-0.0060.0000.0000.0000.000
43A45VAL00.0200.00224.537-0.006-0.0060.0000.0000.0000.000
44A46ARG10.7680.85724.608-0.059-0.0590.0000.0000.0000.000
45A47ALA0-0.014-0.00429.219-0.004-0.0040.0000.0000.0000.000
46A48GLU-1-0.891-0.93329.3430.0360.0360.0000.0000.0000.000
47A49HIS0-0.047-0.01629.994-0.007-0.0070.0000.0000.0000.000
48A50PRO00.0290.02632.8870.0000.0000.0000.0000.0000.000
49A51ASP-1-0.923-0.96934.7150.0220.0220.0000.0000.0000.000
50A52ALA0-0.070-0.02232.842-0.003-0.0030.0000.0000.0000.000
51A53ARG10.8260.89533.882-0.010-0.0100.0000.0000.0000.000
52A54HIS0-0.036-0.00430.101-0.003-0.0030.0000.0000.0000.000
53A55HIS10.8950.93827.358-0.035-0.0350.0000.0000.0000.000
54A56CYS0-0.058-0.01525.4070.0050.0050.0000.0000.0000.000
55A57VAL00.0180.00619.1690.0010.0010.0000.0000.0000.000
56A58ALA0-0.003-0.01317.590-0.007-0.0070.0000.0000.0000.000
57A59TRP0-0.0270.00012.035-0.024-0.0240.0000.0000.0000.000
58A60VAL00.0460.0188.988-0.012-0.0120.0000.0000.0000.000
59A61ALA0-0.006-0.0018.096-0.003-0.0030.0000.0000.0000.000
60A62GLY0-0.0070.0066.1370.0170.0170.0000.0000.0000.000
61A63ALA00.0310.0402.216-0.348-0.3173.521-1.174-2.379-0.001
62A64PRO0-0.045-0.0153.085-1.110-0.7560.1170.417-0.888-0.007
63A65ASP-1-0.813-0.9566.1880.0940.0940.0000.0000.0000.000
64A66ASP-1-0.914-0.9492.346-2.671-2.1051.503-0.961-1.108-0.002
65A67SER0-0.021-0.0022.475-1.351-0.3010.427-0.355-1.1210.000
66A68GLN00.0420.0164.331-0.0890.0420.000-0.024-0.1060.000
67A69GLN0-0.038-0.0244.612-0.253-0.186-0.001-0.001-0.0640.000
68A70LEU0-0.015-0.0128.990-0.013-0.0130.0000.0000.0000.000
69A71GLY00.0030.00112.1100.0030.0030.0000.0000.0000.000
70A72PHE0-0.003-0.02215.720-0.016-0.0160.0000.0000.0000.000
71A73SER00.0040.00119.3250.0000.0000.0000.0000.0000.000
72A74ASP-1-0.712-0.85422.9150.0110.0110.0000.0000.0000.000
73A75ASP-1-0.789-0.87126.2480.0370.0370.0000.0000.0000.000
74A76GLY00.0550.03727.981-0.001-0.0010.0000.0000.0000.000
75A77GLU-1-0.775-0.84229.5860.0050.0050.0000.0000.0000.000
76A78PRO0-0.045-0.03730.4950.0010.0010.0000.0000.0000.000
77A79ALA00.0340.01728.030-0.001-0.0010.0000.0000.0000.000
78A80GLY0-0.031-0.01424.920-0.005-0.0050.0000.0000.0000.000
79A81THR0-0.031-0.01625.849-0.007-0.0070.0000.0000.0000.000
80A82ALA00.009-0.01026.418-0.003-0.0030.0000.0000.0000.000
81A83GLY00.0360.00722.7230.0000.0000.0000.0000.0000.000
82A84LYS10.9160.95419.4230.0060.0060.0000.0000.0000.000
83A85PRO0-0.024-0.00820.389-0.006-0.0060.0000.0000.0000.000
84A86MET00.0050.01120.610-0.005-0.0050.0000.0000.0000.000
85A87LEU00.0160.01114.130-0.003-0.0030.0000.0000.0000.000
86A88ALA0-0.004-0.00816.241-0.005-0.0050.0000.0000.0000.000
87A89GLN0-0.052-0.00917.652-0.022-0.0220.0000.0000.0000.000
88A90LEU0-0.0160.00314.368-0.012-0.0120.0000.0000.0000.000
89A91MET00.0470.03410.546-0.001-0.0010.0000.0000.0000.000
90A92GLY0-0.049-0.00913.223-0.042-0.0420.0000.0000.0000.000
91A93SER0-0.090-0.06414.449-0.011-0.0110.0000.0000.0000.000
92A94GLY00.0340.02911.057-0.017-0.0170.0000.0000.0000.000
93A95VAL0-0.092-0.03410.781-0.019-0.0190.0000.0000.0000.000
94A96GLY00.0280.0087.6750.0260.0260.0000.0000.0000.000
95A97GLU-1-0.767-0.8727.1710.4310.4310.0000.0000.0000.000
96A98ILE00.0620.0509.911-0.051-0.0510.0000.0000.0000.000
97A99THR0-0.029-0.01913.2470.0160.0160.0000.0000.0000.000
98A100ALA00.0010.00816.203-0.011-0.0110.0000.0000.0000.000
99A101VAL00.001-0.00419.6370.0040.0040.0000.0000.0000.000
100A102VAL0-0.044-0.02222.968-0.006-0.0060.0000.0000.0000.000
101A103VAL0-0.0040.01226.2050.0010.0010.0000.0000.0000.000
102A104ARG10.8020.88429.385-0.010-0.0100.0000.0000.0000.000
103A105TYR00.0420.00432.5540.0000.0000.0000.0000.0000.000
104A106TYR0-0.075-0.04836.102-0.003-0.0030.0000.0000.0000.000
105A107GLY00.0780.03238.2500.0000.0000.0000.0000.0000.000
106A108GLY0-0.031-0.01541.015-0.001-0.0010.0000.0000.0000.000
107A109ILE0-0.055-0.02042.312-0.001-0.0010.0000.0000.0000.000
108A110LEU00.0540.03639.6270.0000.0000.0000.0000.0000.000
109A111LEU0-0.012-0.02235.028-0.002-0.0020.0000.0000.0000.000
110A112GLY00.0610.04037.0260.0010.0010.0000.0000.0000.000
111A113THR00.0360.01131.447-0.002-0.0020.0000.0000.0000.000
112A114GLY00.0640.02431.9230.0000.0000.0000.0000.0000.000
113A115GLY0-0.016-0.01332.085-0.002-0.0020.0000.0000.0000.000
114A116LEU0-0.0090.00031.1850.0000.0000.0000.0000.0000.000
115A117VAL00.0310.02326.8380.0010.0010.0000.0000.0000.000
116A118LYS10.8730.93227.7840.0300.0300.0000.0000.0000.000
117A119ALA00.0320.02329.397-0.001-0.0010.0000.0000.0000.000
118A120TYR0-0.046-0.05525.8430.0020.0020.0000.0000.0000.000
119A121GLY00.0150.01123.9560.0020.0020.0000.0000.0000.000
120A122GLY0-0.009-0.00824.517-0.003-0.0030.0000.0000.0000.000
121A123GLY00.0590.03226.380-0.001-0.0010.0000.0000.0000.000
122A124VAL00.0340.00219.8680.0020.0020.0000.0000.0000.000
123A125ASN0-0.0110.00522.191-0.001-0.0010.0000.0000.0000.000
124A126GLN0-0.032-0.03023.686-0.007-0.0070.0000.0000.0000.000
125A127ALA0-0.0010.01022.4560.0000.0000.0000.0000.0000.000
126A128LEU00.0240.00717.3540.0020.0020.0000.0000.0000.000
127A129ARG10.8160.91120.9540.0380.0380.0000.0000.0000.000
128A130GLN0-0.069-0.04623.2440.0000.0000.0000.0000.0000.000
129A131LEU0-0.0090.01315.9790.0070.0070.0000.0000.0000.000
130A132THR00.0070.01319.678-0.010-0.0100.0000.0000.0000.000
131A133THR0-0.034-0.01414.9760.0070.0070.0000.0000.0000.000
132A134GLN00.0170.00714.189-0.015-0.0150.0000.0000.0000.000
133A135ARG10.8820.9339.5960.3090.3090.0000.0000.0000.000
134A136LYS10.8040.9007.589-0.457-0.4570.0000.0000.0000.000
135A137THR00.012-0.0078.111-0.052-0.0520.0000.0000.0000.000
136A138PRO0-0.0210.0114.327-0.122-0.001-0.001-0.008-0.1120.000
137A139LEU0-0.031-0.0187.163-0.068-0.0680.0000.0000.0000.000
138A140THR0-0.019-0.0097.9990.0640.0640.0000.0000.0000.000
139A141GLU-1-0.769-0.8628.5390.4840.4840.0000.0000.0000.000
140A142TYR0-0.011-0.01710.8440.0040.0040.0000.0000.0000.000
141A143THR0-0.010-0.00414.1090.0000.0000.0000.0000.0000.000
142A144LEU00.0030.00217.109-0.014-0.0140.0000.0000.0000.000
143A145GLN00.0270.02120.8420.0040.0040.0000.0000.0000.000
144A146CYS0-0.026-0.00524.209-0.004-0.0040.0000.0000.0000.000
145A147GLU-1-0.891-0.95327.1150.0680.0680.0000.0000.0000.000
146A148TYR00.016-0.02829.9570.0030.0030.0000.0000.0000.000
147A149HIS0-0.051-0.01431.5560.0000.0000.0000.0000.0000.000
148A150GLN00.0100.00329.3830.0030.0030.0000.0000.0000.000
149A151LEU00.0470.03124.7620.0010.0010.0000.0000.0000.000
150A152THR00.0560.02326.5870.0040.0040.0000.0000.0000.000
151A153GLY0-0.0200.00028.045-0.001-0.0010.0000.0000.0000.000
152A154ILE00.0230.00722.8950.0000.0000.0000.0000.0000.000
153A155GLU-1-0.891-0.95922.9810.1180.1180.0000.0000.0000.000
154A156ALA0-0.022-0.00823.4250.0030.0030.0000.0000.0000.000
155A157LEU0-0.038-0.02724.475-0.002-0.0020.0000.0000.0000.000
156A158LEU00.0040.00717.274-0.001-0.0010.0000.0000.0000.000
157A159GLY00.0130.01520.0590.0050.0050.0000.0000.0000.000
158A160GLN0-0.048-0.02721.753-0.005-0.0050.0000.0000.0000.000
159A161CYS0-0.090-0.01219.537-0.011-0.0110.0000.0000.0000.000
160A162ASP-1-0.844-0.91717.1160.0950.0950.0000.0000.0000.000
161A163GLY00.0400.01015.7340.0200.0200.0000.0000.0000.000
162A164LYS10.8240.91414.729-0.236-0.2360.0000.0000.0000.000
163A165ILE00.0700.02915.7340.0240.0240.0000.0000.0000.000
164A166ILE0-0.065-0.01512.059-0.016-0.0160.0000.0000.0000.000
165A167ASN0-0.027-0.03415.5330.0140.0140.0000.0000.0000.000
166A168SER00.0120.00718.3800.0060.0060.0000.0000.0000.000
167A169ASP-1-0.837-0.90321.6770.1390.1390.0000.0000.0000.000
168A170TYR0-0.045-0.02323.794-0.001-0.0010.0000.0000.0000.000
169A171GLN0-0.008-0.00524.458-0.011-0.0110.0000.0000.0000.000
170A172ALA0-0.015-0.00629.312-0.004-0.0040.0000.0000.0000.000
171A173PHE0-0.0230.00028.275-0.005-0.0050.0000.0000.0000.000
172A174VAL0-0.026-0.01724.7320.0020.0020.0000.0000.0000.000
173A175LEU00.0100.01420.487-0.001-0.0010.0000.0000.0000.000
174A176LEU00.000-0.01820.1410.0020.0020.0000.0000.0000.000
175A177ARG10.8670.91810.037-0.459-0.4590.0000.0000.0000.000
176A178VAL0-0.041-0.03615.459-0.015-0.0150.0000.0000.0000.000
177A179ALA00.0530.03110.9930.0330.0330.0000.0000.0000.000
178A180LEU00.0350.01612.665-0.033-0.0330.0000.0000.0000.000
179A181PRO00.0180.01512.3860.0290.0290.0000.0000.0000.000
180A182ALA00.0520.02911.079-0.017-0.0170.0000.0000.0000.000
181A183ALA0-0.030-0.01913.151-0.014-0.0140.0000.0000.0000.000
182A184LYS10.8270.91516.429-0.084-0.0840.0000.0000.0000.000
183A185VAL00.0340.03815.6610.0000.0000.0000.0000.0000.000
184A186ALA00.0060.01217.739-0.002-0.0020.0000.0000.0000.000
185A187GLU-1-0.812-0.91320.9210.0640.0640.0000.0000.0000.000
186A188PHE00.0640.00719.199-0.002-0.0020.0000.0000.0000.000
187A189SER0-0.005-0.02020.3710.0020.0020.0000.0000.0000.000
188A190ALA0-0.026-0.00422.916-0.004-0.0040.0000.0000.0000.000
189A191LYS10.8340.90024.130-0.072-0.0720.0000.0000.0000.000
190A192LEU00.0220.01122.569-0.002-0.0020.0000.0000.0000.000
191A193ALA00.0000.02126.218-0.001-0.0010.0000.0000.0000.000
192A194ASP-1-0.887-0.94528.4700.0400.0400.0000.0000.0000.000
193A195PHE0-0.099-0.04628.515-0.002-0.0020.0000.0000.0000.000
194A196SER0-0.015-0.01528.981-0.001-0.0010.0000.0000.0000.000
195A197ARG10.8680.93731.472-0.048-0.0480.0000.0000.0000.000
196A198GLY00.0010.00529.885-0.003-0.0030.0000.0000.0000.000
197A199SER0-0.075-0.04830.2240.0020.0020.0000.0000.0000.000
198A200LEU0-0.026-0.00725.7690.0030.0030.0000.0000.0000.000
199A201GLN0-0.015-0.01722.8630.0000.0000.0000.0000.0000.000
200A202LEU0-0.023-0.00317.7230.0070.0070.0000.0000.0000.000
201A203LEU0-0.003-0.00117.903-0.012-0.0120.0000.0000.0000.000
202A204ALA00.014-0.00412.7110.0160.0160.0000.0000.0000.000
203A205ILE0-0.046-0.0137.996-0.040-0.0400.0000.0000.0000.000
204A206GLU-1-0.935-0.97211.7630.2660.2660.0000.0000.0000.000
205A207GLU-1-0.992-1.00411.7810.2690.2690.0000.0000.0000.000
206A208GLU-1-1.000-0.9817.1830.7930.7930.0000.0000.0000.000