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: G6RQ1

Calculation Name: 1VE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VE2

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WA2

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401360.650451
FMO2-HF: Nuclear repulsion 2319582.610054
FMO2-HF: Total energy -81778.040397
FMO2-MP2: Total energy -82022.50022


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-10.702-1.9676.673-5.248-10.161-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.003
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].
3A3GLY00.0350.0242.112-1.6911.4561.032-1.777-2.4030.003
4A4LYS10.7800.8773.2770.2081.2200.111-0.497-0.626-0.005
5A5VAL00.0150.0165.917-0.147-0.1470.0000.0000.0000.000
6A6TYR00.0010.0029.085-0.191-0.1910.0000.0000.0000.000
7A7LEU0-0.018-0.00412.3600.0380.0380.0000.0000.0000.000
8A8VAL00.010-0.02315.263-0.055-0.0550.0000.0000.0000.000
9A9GLY00.0090.02518.1720.0210.0210.0000.0000.0000.000
10A10ALA0-0.010-0.03021.851-0.018-0.0180.0000.0000.0000.000
11A11GLY00.0010.01724.301-0.010-0.0100.0000.0000.0000.000
12A12PHE0-0.006-0.01927.2430.0110.0110.0000.0000.0000.000
13A13GLY00.0220.00130.4960.0040.0040.0000.0000.0000.000
14A14GLY00.0260.02730.2040.0020.0020.0000.0000.0000.000
15A15PRO00.027-0.01528.1750.0000.0000.0000.0000.0000.000
16A16GLU-1-0.897-0.92828.550-0.029-0.0290.0000.0000.0000.000
17A17HIS0-0.060-0.03529.808-0.006-0.0060.0000.0000.0000.000
18A18LEU0-0.060-0.00223.5450.0030.0030.0000.0000.0000.000
19A19THR00.0170.00622.343-0.016-0.0160.0000.0000.0000.000
20A20LEU00.0910.02023.499-0.003-0.0030.0000.0000.0000.000
21A21LYS10.8460.92314.9820.1840.1840.0000.0000.0000.000
22A22ALA00.0080.00118.709-0.014-0.0140.0000.0000.0000.000
23A23LEU00.0450.02619.8120.0040.0040.0000.0000.0000.000
24A24ARG10.9941.00713.8860.3660.3660.0000.0000.0000.000
25A25VAL0-0.071-0.04714.251-0.024-0.0240.0000.0000.0000.000
26A26LEU0-0.004-0.00116.2800.0110.0110.0000.0000.0000.000
27A27GLU-1-0.830-0.88318.889-0.156-0.1560.0000.0000.0000.000
28A28VAL0-0.057-0.04113.796-0.023-0.0230.0000.0000.0000.000
29A29ALA0-0.073-0.02613.074-0.025-0.0250.0000.0000.0000.000
30A30GLU-1-0.734-0.8549.966-0.248-0.2480.0000.0000.0000.000
31A31VAL0-0.0020.00113.0130.0320.0320.0000.0000.0000.000
32A32VAL00.0160.00214.2400.0290.0290.0000.0000.0000.000
33A33LEU0-0.0010.01214.262-0.010-0.0100.0000.0000.0000.000
34A34HIS00.015-0.00917.6470.0010.0010.0000.0000.0000.000
35A35ASP-1-0.771-0.87420.8830.1550.1550.0000.0000.0000.000
36A36ARG10.9270.95923.671-0.144-0.1440.0000.0000.0000.000
37A37LEU0-0.025-0.01226.798-0.008-0.0080.0000.0000.0000.000
38A38VAL00.0030.01723.715-0.007-0.0070.0000.0000.0000.000
39A39HIS00.0780.04227.159-0.002-0.0020.0000.0000.0000.000
40A40PRO00.0510.00528.384-0.001-0.0010.0000.0000.0000.000
41A41GLY00.0120.00829.086-0.003-0.0030.0000.0000.0000.000
42A42VAL0-0.005-0.00124.411-0.009-0.0090.0000.0000.0000.000
43A43LEU0-0.012-0.01423.831-0.005-0.0050.0000.0000.0000.000
44A44ALA0-0.025-0.00824.516-0.004-0.0040.0000.0000.0000.000
45A45LEU0-0.025-0.01324.543-0.010-0.0100.0000.0000.0000.000
46A46ALA0-0.054-0.02020.228-0.017-0.0170.0000.0000.0000.000
47A47LYS10.8290.90020.1250.1330.1330.0000.0000.0000.000
48A48GLY00.0210.03017.292-0.015-0.0150.0000.0000.0000.000
49A49GLU-1-0.993-1.00017.2340.1800.1800.0000.0000.0000.000
50A50LEU0-0.017-0.00718.2150.0330.0330.0000.0000.0000.000
51A51VAL00.003-0.00417.8460.0050.0050.0000.0000.0000.000
52A52PRO0-0.0080.00520.3320.0140.0140.0000.0000.0000.000
53A53VAL0-0.057-0.06018.925-0.004-0.0040.0000.0000.0000.000
54A61LYS11.0081.00326.104-0.122-0.1220.0000.0000.0000.000
55A62THR0-0.036-0.01321.207-0.004-0.0040.0000.0000.0000.000
56A63PRO00.0410.03121.6600.0000.0000.0000.0000.0000.000
57A64GLN00.012-0.01116.688-0.012-0.0120.0000.0000.0000.000
58A65GLU-1-0.863-0.94617.2450.2860.2860.0000.0000.0000.000
59A66ALA0-0.009-0.00216.2300.0560.0560.0000.0000.0000.000
60A67ILE0-0.0030.00415.9140.0580.0580.0000.0000.0000.000
61A68THR00.024-0.00612.2940.0680.0680.0000.0000.0000.000
62A69ALA00.0090.01611.6660.1510.1510.0000.0000.0000.000
63A70ARG10.8750.93011.415-0.453-0.4530.0000.0000.0000.000
64A71LEU00.0120.00910.3610.1100.1100.0000.0000.0000.000
65A72ILE0-0.008-0.0106.3270.3630.3630.0000.0000.0000.000
66A73ALA0-0.033-0.0226.6750.7220.7220.0000.0000.0000.000
67A74LEU00.0130.0068.0240.2010.2010.0000.0000.0000.000
68A75ALA00.0200.0154.243-0.330-0.1130.015-0.069-0.1630.000
69A76ARG10.9060.9373.665-2.582-0.8730.346-0.749-1.306-0.004
70A77GLU-1-0.852-0.8984.710-0.224-0.2520.0000.069-0.0410.000
71A78GLY0-0.037-0.0123.717-0.709-0.5750.001-0.042-0.0940.000
72A79ARG10.8930.9454.780-0.906-0.893-0.001-0.003-0.0080.000
73A80VAL0-0.036-0.0176.5140.3400.3400.0000.0000.0000.000
74A81VAL00.004-0.0068.7180.0060.0060.0000.0000.0000.000
75A82ALA00.007-0.00711.1430.0020.0020.0000.0000.0000.000
76A83ARG10.7660.88813.926-0.222-0.2220.0000.0000.0000.000
77A84LEU0-0.018-0.00915.850-0.030-0.0300.0000.0000.0000.000
78A85LYS10.7840.88318.416-0.179-0.1790.0000.0000.0000.000
79A86GLY00.0130.02421.925-0.018-0.0180.0000.0000.0000.000
80A87GLY0-0.032-0.01025.0770.0070.0070.0000.0000.0000.000
81A88ASP-1-0.783-0.91223.1430.0330.0330.0000.0000.0000.000
82A89PRO0-0.0050.00018.7160.0130.0130.0000.0000.0000.000
83A90MET0-0.016-0.01917.2690.0390.0390.0000.0000.0000.000
84A91VAL0-0.030-0.00121.402-0.001-0.0010.0000.0000.0000.000
85A92PHE00.0300.01125.0230.0020.0020.0000.0000.0000.000
86A93GLY00.0620.02023.3330.0070.0070.0000.0000.0000.000
87A94ARG10.9040.95619.829-0.156-0.1560.0000.0000.0000.000
88A95GLY00.0770.03118.1290.0280.0280.0000.0000.0000.000
89A96GLY0-0.015-0.00716.8120.0250.0250.0000.0000.0000.000
90A97GLU-1-0.871-0.94416.5840.2080.2080.0000.0000.0000.000
91A98GLU-1-0.751-0.85514.1300.3280.3280.0000.0000.0000.000
92A99ALA00.0280.01012.2940.0800.0800.0000.0000.0000.000
93A100LEU0-0.026-0.01411.7060.0270.0270.0000.0000.0000.000
94A101ALA0-0.006-0.00111.605-0.001-0.0010.0000.0000.0000.000
95A102LEU00.0210.0107.8830.0560.0560.0000.0000.0000.000
96A103ARG10.9330.9706.890-0.144-0.1440.0000.0000.0000.000
97A104ARG10.9490.9658.095-0.291-0.2910.0000.0000.0000.000
98A105ALA0-0.0160.0206.351-0.026-0.0260.0000.0000.0000.000
99A106GLY00.0050.0084.402-0.294-0.169-0.001-0.032-0.0910.000
100A107ILE0-0.031-0.0162.432-3.555-1.5521.922-1.200-2.725-0.009
101A108PRO00.0090.0032.339-1.889-1.4863.248-0.948-2.7040.001
102A109PHE0-0.019-0.0205.4920.2940.2940.0000.0000.0000.000
103A110GLU-1-0.819-0.8868.847-0.640-0.6400.0000.0000.0000.000
104A111VAL00.0150.00712.0070.0690.0690.0000.0000.0000.000
105A112VAL0-0.061-0.03715.549-0.055-0.0550.0000.0000.0000.000
106A113PRO00.0210.00218.0000.0200.0200.0000.0000.0000.000
107A114GLY00.0130.01521.613-0.011-0.0110.0000.0000.0000.000
108A115VAL00.0140.02824.3920.0050.0050.0000.0000.0000.000
109A116THR00.023-0.00727.5810.0070.0070.0000.0000.0000.000
110A117SER00.0660.00828.892-0.005-0.0050.0000.0000.0000.000
111A118ALA00.0200.02230.999-0.001-0.0010.0000.0000.0000.000
112A119VAL00.0320.00232.685-0.003-0.0030.0000.0000.0000.000
113A120GLY00.0100.01232.047-0.005-0.0050.0000.0000.0000.000
114A121ALA00.0340.02533.014-0.004-0.0040.0000.0000.0000.000
115A122LEU00.015-0.00335.387-0.002-0.0020.0000.0000.0000.000
116A123SER00.004-0.00735.696-0.003-0.0030.0000.0000.0000.000
117A124ALA0-0.0130.01735.596-0.003-0.0030.0000.0000.0000.000
118A125LEU0-0.045-0.03637.568-0.002-0.0020.0000.0000.0000.000
119A126GLY00.0110.01840.3310.0000.0000.0000.0000.0000.000
120A127LEU0-0.038-0.01641.1760.0010.0010.0000.0000.0000.000
121A128PRO0-0.0110.01140.7410.0000.0000.0000.0000.0000.000
122A129LEU00.0470.01637.2040.0030.0030.0000.0000.0000.000
123A130THR0-0.033-0.01040.8980.0010.0010.0000.0000.0000.000
124A131HIS00.0670.02043.274-0.003-0.0030.0000.0000.0000.000
125A132ARG10.9870.99846.5190.0110.0110.0000.0000.0000.000
126A133GLY0-0.002-0.00849.1960.0000.0000.0000.0000.0000.000
127A134LEU0-0.057-0.00948.6850.0010.0010.0000.0000.0000.000
128A135ALA00.0130.00144.3180.0020.0020.0000.0000.0000.000
129A136ARG10.9170.95843.919-0.005-0.0050.0000.0000.0000.000
130A137SER0-0.037-0.03640.1140.0000.0000.0000.0000.0000.000
131A138PHE00.025-0.00134.3680.0000.0000.0000.0000.0000.000
132A139ALA00.0080.01335.9460.0010.0010.0000.0000.0000.000
133A140VAL0-0.007-0.01132.464-0.001-0.0010.0000.0000.0000.000
134A141ALA00.0000.00533.0400.0030.0030.0000.0000.0000.000
135A142THR0-0.0020.00030.476-0.002-0.0020.0000.0000.0000.000
136A143GLY00.0560.02933.872-0.002-0.0020.0000.0000.0000.000
137A144HIS0-0.044-0.03032.4040.0010.0010.0000.0000.0000.000
138A145ASP-1-0.904-0.93632.6530.0810.0810.0000.0000.0000.000
139A146PRO00.004-0.01135.810-0.003-0.0030.0000.0000.0000.000
140A147ALA0-0.021-0.00538.855-0.003-0.0030.0000.0000.0000.000
141A148LEU0-0.020-0.00534.464-0.002-0.0020.0000.0000.0000.000
142A149PRO0-0.018-0.01338.620-0.002-0.0020.0000.0000.0000.000
143A150LEU00.0460.04038.2670.0020.0020.0000.0000.0000.000
144A151PRO00.0290.02136.250-0.002-0.0020.0000.0000.0000.000
145A152ARG10.9430.96238.758-0.026-0.0260.0000.0000.0000.000
146A153ALA00.0080.01039.6430.0000.0000.0000.0000.0000.000
147A154ASP-1-0.848-0.89541.7860.0090.0090.0000.0000.0000.000
148A155THR0-0.016-0.02041.3480.0000.0000.0000.0000.0000.000
149A156LEU0-0.022-0.00138.4140.0010.0010.0000.0000.0000.000
150A157VAL00.008-0.00136.260-0.001-0.0010.0000.0000.0000.000
151A158LEU0-0.006-0.01036.4860.0030.0030.0000.0000.0000.000
152A159LEU0-0.022-0.01830.656-0.002-0.0020.0000.0000.0000.000
153A160MET0-0.066-0.04132.4900.0060.0060.0000.0000.0000.000
154A161PRO00.0110.02136.0320.0030.0030.0000.0000.0000.000
155A162LEU00.023-0.00738.6740.0010.0010.0000.0000.0000.000
156A163HIS0-0.0240.00439.907-0.002-0.0020.0000.0000.0000.000
157A164THR0-0.006-0.02443.6850.0000.0000.0000.0000.0000.000
158A165LEU0-0.004-0.00346.3960.0000.0000.0000.0000.0000.000
159A166GLY00.0150.01046.0250.0010.0010.0000.0000.0000.000
160A167GLY0-0.003-0.01145.866-0.002-0.0020.0000.0000.0000.000
161A168LEU0-0.013-0.00741.9500.0000.0000.0000.0000.0000.000
162A169LYS10.8830.92744.933-0.026-0.0260.0000.0000.0000.000
163A170GLU-1-0.825-0.90347.8320.0270.0270.0000.0000.0000.000
164A171ARG10.9070.93742.729-0.040-0.0400.0000.0000.0000.000
165A172LEU0-0.035-0.00842.910-0.001-0.0010.0000.0000.0000.000
166A173LEU00.0690.04246.023-0.002-0.0020.0000.0000.0000.000
167A174GLU-1-0.908-0.92345.9460.0320.0320.0000.0000.0000.000
168A175ARG10.6580.80741.753-0.031-0.0310.0000.0000.0000.000
169A176PHE0-0.040-0.02743.652-0.002-0.0020.0000.0000.0000.000
170A177PRO00.0320.03649.0250.0010.0010.0000.0000.0000.000
171A178PRO00.0700.03051.9370.0000.0000.0000.0000.0000.000
172A179GLU-1-0.800-0.90153.7410.0130.0130.0000.0000.0000.000
173A180THR0-0.118-0.05048.669-0.002-0.0020.0000.0000.0000.000
174A181PRO0-0.005-0.00249.7750.0010.0010.0000.0000.0000.000
175A182LEU00.029-0.00545.6400.0010.0010.0000.0000.0000.000
176A183ALA00.0110.01044.474-0.001-0.0010.0000.0000.0000.000
177A184LEU0-0.028-0.01243.0370.0030.0030.0000.0000.0000.000
178A185LEU00.0250.00440.010-0.002-0.0020.0000.0000.0000.000
179A186ALA00.0130.00039.0530.0040.0040.0000.0000.0000.000
180A187ARG10.8450.92735.966-0.032-0.0320.0000.0000.0000.000
181A188VAL00.0620.03336.793-0.002-0.0020.0000.0000.0000.000
182A189GLY0-0.006-0.00235.7600.0020.0020.0000.0000.0000.000
183A190TRP0-0.119-0.04930.550-0.001-0.0010.0000.0000.0000.000
184A191PRO00.0510.02137.016-0.001-0.0010.0000.0000.0000.000
185A192GLY00.0290.00039.6180.0040.0040.0000.0000.0000.000
186A193GLU-1-0.871-0.91040.2510.0080.0080.0000.0000.0000.000
187A194ALA0-0.015-0.01441.605-0.001-0.0010.0000.0000.0000.000
188A195VAL00.0040.00143.0010.0020.0020.0000.0000.0000.000
189A196ARG10.8380.92445.313-0.022-0.0220.0000.0000.0000.000
190A197LEU0-0.011-0.01147.1340.0010.0010.0000.0000.0000.000
191A198GLY00.0500.02249.7190.0000.0000.0000.0000.0000.000
192A199ARG10.8610.93551.348-0.011-0.0110.0000.0000.0000.000
193A200VAL0-0.019-0.01348.0550.0010.0010.0000.0000.0000.000
194A201GLU-1-0.902-0.97350.3550.0160.0160.0000.0000.0000.000
195A202ASP-1-0.840-0.90452.1440.0150.0150.0000.0000.0000.000
196A203LEU0-0.100-0.02246.7290.0010.0010.0000.0000.0000.000
197A204PRO00.037-0.01048.452-0.001-0.0010.0000.0000.0000.000
198A205GLY00.0470.03049.4280.0010.0010.0000.0000.0000.000
199A206LEU00.0020.00049.0200.0000.0000.0000.0000.0000.000
200A207GLY0-0.016-0.01046.7090.0000.0000.0000.0000.0000.000
201A208GLU-1-0.822-0.90347.0870.0310.0310.0000.0000.0000.000
202A209GLY00.0220.00946.597-0.002-0.0020.0000.0000.0000.000
203A210LEU0-0.074-0.02943.308-0.001-0.0010.0000.0000.0000.000
204A211PRO00.0050.00340.8560.0030.0030.0000.0000.0000.000
205A212SER0-0.0160.01337.2580.0020.0020.0000.0000.0000.000
206A213PRO0-0.007-0.02332.8400.0000.0000.0000.0000.0000.000
207A214ALA00.023-0.00835.945-0.004-0.0040.0000.0000.0000.000
208A215LEU0-0.048-0.01834.4630.0050.0050.0000.0000.0000.000
209A216LEU00.0250.02538.209-0.002-0.0020.0000.0000.0000.000
210A217VAL00.0040.00039.8560.0010.0010.0000.0000.0000.000
211A218VAL00.0090.01542.081-0.001-0.0010.0000.0000.0000.000
212A219GLY00.0960.03444.2640.0000.0000.0000.0000.0000.000
213A220LYS10.9640.97046.837-0.008-0.0080.0000.0000.0000.000
214A221VAL0-0.0120.00044.129-0.001-0.0010.0000.0000.0000.000
215A222VAL00.0010.00545.070-0.001-0.0010.0000.0000.0000.000
216A223GLY0-0.025-0.00947.6250.0000.0000.0000.0000.0000.000
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