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: 496VN

Calculation Name: 3G67-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G67

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DFA3

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1721129.312936
FMO2-HF: Nuclear repulsion 1636011.92678
FMO2-HF: Total energy -85117.386155
FMO2-MP2: Total energy -85363.9903


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:41:ARG)


Summations of interaction energy for fragment #1(A:41:ARG)
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.
-183.244-187.31228.107-12.903-11.138-0.145
Interaction energy analysis for fragmet #1(A:41:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.889
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].
3A43GLU-1-0.776-0.8753.608-28.096-26.443-0.004-0.619-1.0300.000
4A44GLU-1-0.727-0.8161.724-129.471-135.73928.103-12.206-9.630-0.145
5A45VAL0-0.048-0.0283.3760.7211.1560.009-0.073-0.3720.000
6A46LYS10.8200.9135.98227.51427.5140.0000.0000.0000.000
7A47GLU-1-0.913-0.9608.417-26.620-26.6200.0000.0000.0000.000
8A48ARG10.7900.8793.86050.83050.942-0.001-0.005-0.1060.000
9A49PHE00.0150.0019.7842.1432.1430.0000.0000.0000.000
10A50VAL00.0590.03512.1991.7751.7750.0000.0000.0000.000
11A51ASN00.0060.00513.6962.6962.6960.0000.0000.0000.000
12A52LEU0-0.025-0.01811.7250.9790.9790.0000.0000.0000.000
13A53ASN00.009-0.00515.6251.4441.4440.0000.0000.0000.000
14A54ARG10.7980.89417.97416.43216.4320.0000.0000.0000.000
15A55LEU0-0.020-0.01017.0300.7030.7030.0000.0000.0000.000
16A56PHE0-0.009-0.00119.7330.7340.7340.0000.0000.0000.000
17A57GLN00.012-0.01421.4221.2331.2330.0000.0000.0000.000
18A58GLU-1-0.860-0.91423.315-13.019-13.0190.0000.0000.0000.000
19A59LEU0-0.033-0.02223.1130.5500.5500.0000.0000.0000.000
20A60VAL0-0.0090.00125.1410.5300.5300.0000.0000.0000.000
21A61GLY00.0060.00227.4530.4770.4770.0000.0000.0000.000
22A62ASP-1-0.964-0.97929.108-9.682-9.6820.0000.0000.0000.000
23A63PHE00.0050.00029.9210.4320.4320.0000.0000.0000.000
24A64GLN0-0.027-0.02830.8740.6370.6370.0000.0000.0000.000
25A65ALA00.0280.02133.5150.3520.3520.0000.0000.0000.000
26A66LYS10.9150.96034.6328.9238.9230.0000.0000.0000.000
27A67SER00.0410.01435.3810.3810.3810.0000.0000.0000.000
28A68ASP-1-0.822-0.91337.188-8.010-8.0100.0000.0000.0000.000
29A69GLN0-0.070-0.02939.2600.1840.1840.0000.0000.0000.000
30A70LEU0-0.034-0.02037.9450.2310.2310.0000.0000.0000.000
31A71VAL00.0120.00840.7480.2170.2170.0000.0000.0000.000
32A72SER0-0.050-0.02843.1340.2250.2250.0000.0000.0000.000
33A73VAL00.001-0.00744.9960.1860.1860.0000.0000.0000.000
34A74ILE0-0.033-0.01143.2710.1650.1650.0000.0000.0000.000
35A75GLN00.0230.01146.7350.1410.1410.0000.0000.0000.000
36A76ASP-1-0.951-0.96349.301-5.963-5.9630.0000.0000.0000.000
37A77MET0-0.005-0.00849.9070.1930.1930.0000.0000.0000.000
38A78GLU-1-0.780-0.87349.335-6.479-6.4790.0000.0000.0000.000
39A79LYS10.8260.91252.7085.6885.6880.0000.0000.0000.000
40A80ILE00.0250.01154.7830.1620.1620.0000.0000.0000.000
41A81SER00.002-0.01554.4680.0890.0890.0000.0000.0000.000
42A82GLU-1-0.914-0.95456.512-5.447-5.4470.0000.0000.0000.000
43A83ASN00.0260.01358.8400.0860.0860.0000.0000.0000.000
44A84ILE00.0670.03157.7150.1030.1030.0000.0000.0000.000
45A85MET0-0.054-0.02158.0480.0890.0890.0000.0000.0000.000
46A86GLU-1-0.947-0.96362.225-4.940-4.9400.0000.0000.0000.000
47A87GLU-1-0.928-0.96762.996-5.050-5.0500.0000.0000.0000.000
48A88LEU0-0.033-0.00961.7960.1030.1030.0000.0000.0000.000
49A89LYS10.8680.92963.4865.1695.1690.0000.0000.0000.000
50A90LYS10.8540.92668.0624.4524.4520.0000.0000.0000.000
51A91SER0-0.011-0.02068.5540.0960.0960.0000.0000.0000.000
52A92GLY0-0.0010.00169.9500.0550.0550.0000.0000.0000.000
53A93THR00.0200.00871.4350.0740.0740.0000.0000.0000.000
54A94ASN0-0.009-0.00373.7860.0910.0910.0000.0000.0000.000
55A95VAL00.0050.00972.6740.0660.0660.0000.0000.0000.000
56A96ASP-1-0.874-0.93675.075-4.294-4.2940.0000.0000.0000.000
57A97GLN0-0.041-0.04077.5680.0210.0210.0000.0000.0000.000
58A98ILE0-0.027-0.00876.9120.0700.0700.0000.0000.0000.000
59A99VAL00.002-0.00178.0810.0560.0560.0000.0000.0000.000
60A100GLU-1-0.817-0.89280.946-3.839-3.8390.0000.0000.0000.000
61A101ARG10.8630.90683.5713.8163.8160.0000.0000.0000.000
62A102VAL00.0210.01582.4650.0480.0480.0000.0000.0000.000
63A103LYS10.8110.90784.2143.8973.8970.0000.0000.0000.000
64A104GLU-1-0.852-0.89887.520-3.624-3.6240.0000.0000.0000.000
65A105ALA00.0210.00988.0520.0490.0490.0000.0000.0000.000
66A106SER0-0.010-0.02988.1070.0370.0370.0000.0000.0000.000
67A107SER0-0.003-0.00190.7660.0450.0450.0000.0000.0000.000
68A108GLN00.0050.00792.1360.0160.0160.0000.0000.0000.000
69A109ILE00.0060.02592.1540.0480.0480.0000.0000.0000.000
70A110GLY00.0130.00294.9830.0380.0380.0000.0000.0000.000
71A111GLU-1-0.947-0.97696.837-3.270-3.2700.0000.0000.0000.000
72A112THR0-0.023-0.02297.6640.0510.0510.0000.0000.0000.000
73A113LEU0-0.0010.00097.6280.0400.0400.0000.0000.0000.000
74A114GLU-1-0.997-0.980100.390-3.066-3.0660.0000.0000.0000.000
75A115ASN00.0370.007102.7310.0610.0610.0000.0000.0000.000
76A116ILE0-0.009-0.002102.1660.0410.0410.0000.0000.0000.000
77A117ARG10.9330.959102.1293.2043.2040.0000.0000.0000.000
78A118SER0-0.033-0.007106.6030.0510.0510.0000.0000.0000.000
79A119ILE00.005-0.007106.6140.0410.0410.0000.0000.0000.000
80A120GLU-1-0.881-0.949106.724-3.039-3.0390.0000.0000.0000.000
81A121LYS10.9180.965110.4072.9032.9030.0000.0000.0000.000
82A122LEU0-0.020-0.011112.2190.0400.0400.0000.0000.0000.000
83A123ILE00.0330.014111.9940.0360.0360.0000.0000.0000.000
84A124GLN0-0.022-0.012111.9370.0430.0430.0000.0000.0000.000
85A125ASN00.0040.003116.4020.0480.0480.0000.0000.0000.000
86A126ILE00.0350.021116.1230.0300.0300.0000.0000.0000.000
87A127MET00.0340.027115.9080.0260.0260.0000.0000.0000.000
88A128ARG10.7410.841119.9632.6532.6530.0000.0000.0000.000
89A129ILE00.0350.014122.0730.0260.0260.0000.0000.0000.000
90A130ALA00.0290.034122.4830.0270.0270.0000.0000.0000.000
91A131ARG10.9080.943118.8092.7402.7400.0000.0000.0000.000
92A132GLU-1-0.824-0.882125.804-2.551-2.5510.0000.0000.0000.000
93A133THR0-0.002-0.018127.3570.0290.0290.0000.0000.0000.000
94A134ASN00.0210.011127.5780.0280.0280.0000.0000.0000.000
95A135ILE0-0.013-0.009129.6150.0210.0210.0000.0000.0000.000
96A136LEU0-0.0090.008131.9530.0270.0270.0000.0000.0000.000
97A137ALA00.0200.014132.2520.0230.0230.0000.0000.0000.000
98A138LEU00.0160.008133.2960.0170.0170.0000.0000.0000.000
99A139ASN0-0.028-0.018135.2110.0340.0340.0000.0000.0000.000
100A140ALA00.0020.012137.3290.0220.0220.0000.0000.0000.000
101A141THR0-0.050-0.044136.3210.0180.0180.0000.0000.0000.000
102A142ILE0-0.0040.000138.6470.0190.0190.0000.0000.0000.000
103A143GLU-1-0.792-0.876141.624-2.240-2.2400.0000.0000.0000.000
104A144ALA0-0.020-0.001141.7490.0200.0200.0000.0000.0000.000
105A145ALA0-0.042-0.027143.1310.0120.0120.0000.0000.0000.000
106A146ARG10.8140.869144.9152.2622.2620.0000.0000.0000.000
107A147ALA0-0.0160.006147.1370.0190.0190.0000.0000.0000.000
108A148GLY00.0420.025148.9490.0060.0060.0000.0000.0000.000
109A149GLU-1-0.885-0.937148.599-2.178-2.1780.0000.0000.0000.000
110A150ALA00.0240.004148.176-0.018-0.0180.0000.0000.0000.000
111A151GLY0-0.0020.006145.932-0.016-0.0160.0000.0000.0000.000
112A152LYS10.8210.891143.8902.2272.2270.0000.0000.0000.000
113A153GLY00.0120.014142.539-0.015-0.0150.0000.0000.0000.000
114A154PHE0-0.011-0.019140.845-0.020-0.0200.0000.0000.0000.000
115A155MET0-0.0200.003139.340-0.021-0.0210.0000.0000.0000.000
116A156ILE00.0170.022136.512-0.020-0.0200.0000.0000.0000.000
117A157VAL00.0140.012135.036-0.022-0.0220.0000.0000.0000.000
118A158ALA0-0.0040.005134.507-0.021-0.0210.0000.0000.0000.000
119A159ASN0-0.005-0.026133.873-0.006-0.0060.0000.0000.0000.000
120A160GLU-1-0.832-0.902128.680-2.564-2.5640.0000.0000.0000.000
121A161VAL0-0.005-0.001129.712-0.026-0.0260.0000.0000.0000.000
122A162GLN00.0060.017129.180-0.014-0.0140.0000.0000.0000.000
123A163ASN0-0.031-0.021127.449-0.025-0.0250.0000.0000.0000.000
124A164LEU00.0340.021125.199-0.029-0.0290.0000.0000.0000.000
125A165SER0-0.035-0.021124.263-0.026-0.0260.0000.0000.0000.000
126A166ASN0-0.068-0.031123.290-0.043-0.0430.0000.0000.0000.000
127A167GLU-1-0.842-0.922119.947-2.755-2.7550.0000.0000.0000.000
128A168THR0-0.038-0.027119.640-0.032-0.0320.0000.0000.0000.000
129A169ASN0-0.097-0.057118.775-0.038-0.0380.0000.0000.0000.000
130A170GLU-1-0.785-0.866115.311-2.867-2.8670.0000.0000.0000.000
131A171VAL00.0780.035114.395-0.034-0.0340.0000.0000.0000.000
132A172THR0-0.043-0.033113.769-0.033-0.0330.0000.0000.0000.000
133A173LYS10.7770.864112.8322.8162.8160.0000.0000.0000.000
134A174GLN0-0.040-0.018110.114-0.053-0.0530.0000.0000.0000.000
135A175ILE00.0100.006108.793-0.035-0.0350.0000.0000.0000.000
136A176VAL0-0.010-0.006108.374-0.027-0.0270.0000.0000.0000.000
137A177GLU-1-0.816-0.881104.494-3.152-3.1520.0000.0000.0000.000
138A178LYS10.8030.871102.7593.1283.1280.0000.0000.0000.000
139A179ALA00.0130.014103.615-0.034-0.0340.0000.0000.0000.000
140A180ARG10.8360.882100.3013.1673.1670.0000.0000.0000.000
141A181GLU-1-0.811-0.883100.279-3.244-3.2440.0000.0000.0000.000
142A182ILE00.0020.00498.936-0.047-0.0470.0000.0000.0000.000
143A183LEU0-0.0250.00398.595-0.044-0.0440.0000.0000.0000.000
144A184GLU-1-0.847-0.89596.073-3.402-3.4020.0000.0000.0000.000
145A185SER0-0.038-0.02394.649-0.062-0.0620.0000.0000.0000.000
146A186SER00.001-0.01493.706-0.043-0.0430.0000.0000.0000.000
147A187GLN0-0.077-0.04392.933-0.001-0.0010.0000.0000.0000.000
148A188ARG10.9310.95290.2273.4823.4820.0000.0000.0000.000
149A189SER0-0.067-0.04489.385-0.053-0.0530.0000.0000.0000.000
150A190LEU00.0100.00388.732-0.045-0.0450.0000.0000.0000.000
151A191GLU-1-0.845-0.91287.569-3.652-3.6520.0000.0000.0000.000
152A192ASN0-0.034-0.01384.438-0.079-0.0790.0000.0000.0000.000
153A193LEU0-0.003-0.01483.948-0.061-0.0610.0000.0000.0000.000
154A194GLU-1-0.943-0.95884.038-3.874-3.8740.0000.0000.0000.000
155A195PHE00.0190.01177.645-0.071-0.0710.0000.0000.0000.000
156A196MET0-0.019-0.01579.731-0.050-0.0500.0000.0000.0000.000
157A197ALA0-0.0060.00879.211-0.061-0.0610.0000.0000.0000.000
158A198ASN0-0.020-0.02278.211-0.082-0.0820.0000.0000.0000.000
159A199LEU00.0050.00975.137-0.076-0.0760.0000.0000.0000.000
160A200PHE00.0080.00574.435-0.081-0.0810.0000.0000.0000.000
161A201GLU-1-0.752-0.84574.462-4.438-4.4380.0000.0000.0000.000
162A202THR0-0.073-0.04171.174-0.087-0.0870.0000.0000.0000.000
163A203VAL00.0070.01470.146-0.099-0.0990.0000.0000.0000.000
164A204GLY00.0480.03069.722-0.071-0.0710.0000.0000.0000.000
165A205LYS10.7950.85468.7434.3724.3720.0000.0000.0000.000
166A206THR0-0.049-0.02765.077-0.105-0.1050.0000.0000.0000.000
167A207LEU00.0160.00465.083-0.102-0.1020.0000.0000.0000.000
168A208GLN00.0660.04065.261-0.111-0.1110.0000.0000.0000.000
169A209ASN00.0190.00462.499-0.083-0.0830.0000.0000.0000.000
170A210MET0-0.0130.00460.207-0.131-0.1310.0000.0000.0000.000
171A211VAL0-0.0090.00460.423-0.091-0.0910.0000.0000.0000.000
172A212ARG10.8650.92460.1095.0175.0170.0000.0000.0000.000
173A213PHE00.0010.01253.066-0.093-0.0930.0000.0000.0000.000
174A214MET00.0250.01955.486-0.132-0.1320.0000.0000.0000.000
175A215GLU-1-0.791-0.90156.118-5.333-5.3330.0000.0000.0000.000
176A216ASN0-0.117-0.07253.969-0.103-0.1030.0000.0000.0000.000
177A217ASN00.0060.00651.527-0.212-0.2120.0000.0000.0000.000
178A218VAL00.0420.02051.156-0.139-0.1390.0000.0000.0000.000
179A219LYS10.8790.94451.4005.7845.7840.0000.0000.0000.000
180A220LEU00.0570.03745.491-0.124-0.1240.0000.0000.0000.000
181A221LEU0-0.018-0.00246.623-0.175-0.1750.0000.0000.0000.000
182A222GLN00.0110.00146.594-0.142-0.1420.0000.0000.0000.000
183A223GLU-1-1.012-0.99644.362-7.171-7.1710.0000.0000.0000.000
184A224VAL0-0.008-0.01741.375-0.213-0.2130.0000.0000.0000.000
185A225ARG10.7770.86241.6786.6986.6980.0000.0000.0000.000
186A226ASN00.0380.01842.228-0.134-0.1340.0000.0000.0000.000
187A227SER0-0.0170.00739.029-0.230-0.2300.0000.0000.0000.000
188A228LEU00.0040.00737.156-0.268-0.2680.0000.0000.0000.000
189A229ASP-1-0.828-0.93537.619-7.850-7.8500.0000.0000.0000.000
190A230THR00.015-0.00238.234-0.227-0.2270.0000.0000.0000.000
191A231SER0-0.047-0.02234.073-0.327-0.3270.0000.0000.0000.000
192A232LYS10.8070.92333.4067.8297.8290.0000.0000.0000.000
193A233GLU-1-0.898-0.94033.339-8.560-8.5600.0000.0000.0000.000
194A234SER0-0.040-0.03532.820-0.373-0.3730.0000.0000.0000.000
195A235LEU00.0190.01727.078-0.396-0.3960.0000.0000.0000.000
196A236SER00.0040.01228.563-0.404-0.4040.0000.0000.0000.000
197A237GLU-1-0.896-0.92929.066-10.241-10.2410.0000.0000.0000.000
198A238LYS10.8570.91025.93710.29410.2940.0000.0000.0000.000
199A239SER0-0.051-0.03924.282-0.550-0.5500.0000.0000.0000.000
200A240ALA00.0710.03823.768-0.567-0.5670.0000.0000.0000.000
201A241GLU-1-0.956-0.96023.343-12.548-12.5480.0000.0000.0000.000
202A242ILE0-0.012-0.01719.542-0.553-0.5530.0000.0000.0000.000
203A243ASP-1-0.858-0.89419.200-14.944-14.9440.0000.0000.0000.000
204A244SER0-0.013-0.01919.894-0.391-0.3910.0000.0000.0000.000
205A245ALA0-0.038-0.01818.247-0.301-0.3010.0000.0000.0000.000
206A246THR0-0.050-0.03914.642-1.262-1.2620.0000.0000.0000.000
207A247LYS10.8230.90115.59814.12914.1290.0000.0000.0000.000
208A248VAL00.010-0.00116.815-0.174-0.1740.0000.0000.0000.000
209A249LEU0-0.029-0.00412.484-0.448-0.4480.0000.0000.0000.000
210A250GLU-1-0.890-0.92811.808-18.341-18.3410.0000.0000.0000.000
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