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: QYMGY

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1716083.703923
FMO2-HF: Nuclear repulsion 1630969.047403
FMO2-HF: Total energy -85114.65652
FMO2-MP2: Total energy -85361.462144


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.
-129.026-121.981.052-3.175-4.922-0.024
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 : 0.992 / q_NPA : 0.989
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-1-0.853-0.9412.770-28.609-26.0810.089-0.907-1.710-0.001
4A44GLU-1-0.893-0.9312.661-70.378-66.3710.942-2.161-2.788-0.023
5A45VAL0-0.062-0.0283.2562.0392.5500.021-0.107-0.4240.000
6A46LYS10.8820.9515.95827.93127.9310.0000.0000.0000.000
7A47GLU-1-0.881-0.9427.915-22.782-22.7820.0000.0000.0000.000
8A48ARG10.8630.9355.85240.38640.3860.0000.0000.0000.000
9A49PHE00.001-0.0169.7381.8091.8090.0000.0000.0000.000
10A50VAL00.0590.05412.1101.6971.6970.0000.0000.0000.000
11A51ASN0-0.022-0.00713.6532.4002.4000.0000.0000.0000.000
12A52LEU00.002-0.01312.5200.9710.9710.0000.0000.0000.000
13A53ASN00.0360.02215.8821.3141.3140.0000.0000.0000.000
14A54ARG10.9040.96017.81415.99615.9960.0000.0000.0000.000
15A55LEU0-0.009-0.01218.1620.6560.6560.0000.0000.0000.000
16A56PHE0-0.019-0.00719.7560.6430.6430.0000.0000.0000.000
17A57GLN0-0.016-0.02421.3361.2531.2530.0000.0000.0000.000
18A58GLU-1-0.966-0.97523.778-12.237-12.2370.0000.0000.0000.000
19A59LEU0-0.033-0.01223.0740.5090.5090.0000.0000.0000.000
20A60VAL00.0050.01325.2760.5370.5370.0000.0000.0000.000
21A61GLY00.0120.00227.7770.4670.4670.0000.0000.0000.000
22A62ASP-1-0.942-0.96929.460-9.521-9.5210.0000.0000.0000.000
23A63PHE0-0.015-0.01630.4340.4380.4380.0000.0000.0000.000
24A64GLN0-0.006-0.02931.2490.5950.5950.0000.0000.0000.000
25A65ALA00.0280.03833.9590.3360.3360.0000.0000.0000.000
26A66LYS10.9330.95735.3198.7128.7120.0000.0000.0000.000
27A67SER00.001-0.00335.5410.3780.3780.0000.0000.0000.000
28A68ASP-1-0.854-0.93537.460-7.971-7.9710.0000.0000.0000.000
29A69GLN0-0.051-0.02039.9180.3100.3100.0000.0000.0000.000
30A70LEU0-0.029-0.00238.4470.2100.2100.0000.0000.0000.000
31A71VAL00.0380.02040.9300.1980.1980.0000.0000.0000.000
32A72SER0-0.052-0.03543.4650.2110.2110.0000.0000.0000.000
33A73VAL00.0270.01245.5410.1730.1730.0000.0000.0000.000
34A74ILE0-0.042-0.01843.1870.1510.1510.0000.0000.0000.000
35A75GLN00.015-0.00347.0450.1300.1300.0000.0000.0000.000
36A76ASP-1-0.965-0.96449.476-5.907-5.9070.0000.0000.0000.000
37A77MET00.007-0.01049.9890.1970.1970.0000.0000.0000.000
38A78GLU-1-0.834-0.92349.420-6.381-6.3810.0000.0000.0000.000
39A79LYS10.9630.99652.9945.6035.6030.0000.0000.0000.000
40A80ILE0-0.018-0.01155.2000.1490.1490.0000.0000.0000.000
41A81SER0-0.009-0.01654.8840.1150.1150.0000.0000.0000.000
42A82GLU-1-0.976-0.98656.913-5.429-5.4290.0000.0000.0000.000
43A83ASN00.0500.01759.1510.1320.1320.0000.0000.0000.000
44A84ILE00.0490.02958.1770.0990.0990.0000.0000.0000.000
45A85MET0-0.040-0.01358.0290.1070.1070.0000.0000.0000.000
46A86GLU-1-0.944-0.97362.336-4.963-4.9630.0000.0000.0000.000
47A87GLU-1-0.962-0.97664.087-4.933-4.9330.0000.0000.0000.000
48A88LEU0-0.070-0.04361.7070.0940.0940.0000.0000.0000.000
49A89LYS10.9310.95763.1285.1105.1100.0000.0000.0000.000
50A90LYS10.9320.99268.2174.4454.4450.0000.0000.0000.000
51A91SER00.004-0.01068.9220.1000.1000.0000.0000.0000.000
52A92GLY0-0.0010.00670.2420.0510.0510.0000.0000.0000.000
53A93THR00.0090.00771.5560.0570.0570.0000.0000.0000.000
54A94ASN00.001-0.01173.9270.0890.0890.0000.0000.0000.000
55A95VAL0-0.003-0.00872.7690.0670.0670.0000.0000.0000.000
56A96ASP-1-0.867-0.92875.192-4.254-4.2540.0000.0000.0000.000
57A97GLN0-0.074-0.04377.5460.0240.0240.0000.0000.0000.000
58A98ILE0-0.023-0.01276.9820.0690.0690.0000.0000.0000.000
59A99VAL00.0020.01277.8020.0520.0520.0000.0000.0000.000
60A100GLU-1-0.891-0.96580.818-3.825-3.8250.0000.0000.0000.000
61A101ARG10.8690.93083.3703.8093.8090.0000.0000.0000.000
62A102VAL00.0180.01582.2020.0530.0530.0000.0000.0000.000
63A103LYS10.9020.96284.8023.8353.8350.0000.0000.0000.000
64A104GLU-1-0.894-0.93387.292-3.579-3.5790.0000.0000.0000.000
65A105ALA00.005-0.00687.9890.0510.0510.0000.0000.0000.000
66A106SER0-0.003-0.01288.1990.0370.0370.0000.0000.0000.000
67A107SER0-0.015-0.00190.7960.0450.0450.0000.0000.0000.000
68A108GLN0-0.021-0.01891.9740.0170.0170.0000.0000.0000.000
69A109ILE0-0.0140.00992.0000.0440.0440.0000.0000.0000.000
70A110GLY00.027-0.00195.1380.0380.0380.0000.0000.0000.000
71A111GLU-1-0.920-0.95996.952-3.239-3.2390.0000.0000.0000.000
72A112THR0-0.040-0.00898.2730.0500.0500.0000.0000.0000.000
73A113LEU0-0.027-0.01696.7950.0410.0410.0000.0000.0000.000
74A114GLU-1-0.987-0.979100.594-3.070-3.0700.0000.0000.0000.000
75A115ASN00.0700.019102.6390.0640.0640.0000.0000.0000.000
76A116ILE0-0.028-0.012102.3720.0410.0410.0000.0000.0000.000
77A117ARG10.9870.992100.4703.2083.2080.0000.0000.0000.000
78A118SER0-0.058-0.016106.5310.0480.0480.0000.0000.0000.000
79A119ILE00.026-0.003106.7520.0410.0410.0000.0000.0000.000
80A120GLU-1-0.898-0.944106.985-3.017-3.0170.0000.0000.0000.000
81A121LYS10.9240.977110.6202.8772.8770.0000.0000.0000.000
82A122LEU0-0.049-0.040112.1500.0410.0410.0000.0000.0000.000
83A123ILE00.0400.023112.3140.0340.0340.0000.0000.0000.000
84A124GLN0-0.005-0.009113.3470.0370.0370.0000.0000.0000.000
85A125ASN0-0.066-0.029116.6380.0520.0520.0000.0000.0000.000
86A126ILE00.1050.047116.7560.0310.0310.0000.0000.0000.000
87A127MET00.0290.007116.1790.0170.0170.0000.0000.0000.000
88A128ARG10.8610.926120.1762.6632.6630.0000.0000.0000.000
89A129ILE00.0190.020122.3790.0240.0240.0000.0000.0000.000
90A130ALA00.0460.033122.8630.0260.0260.0000.0000.0000.000
91A131ARG10.9000.960119.2932.7142.7140.0000.0000.0000.000
92A132GLU-1-0.949-0.980126.118-2.524-2.5240.0000.0000.0000.000
93A133THR00.002-0.006127.7460.0270.0270.0000.0000.0000.000
94A134ASN00.0220.017128.0730.0170.0170.0000.0000.0000.000
95A135ILE0-0.011-0.014130.0250.0200.0200.0000.0000.0000.000
96A136LEU0-0.0170.005132.1310.0260.0260.0000.0000.0000.000
97A137ALA00.0180.014132.6360.0220.0220.0000.0000.0000.000
98A138LEU0-0.016-0.012133.5760.0170.0170.0000.0000.0000.000
99A139ASN0-0.020-0.030135.6380.0280.0280.0000.0000.0000.000
100A140ALA00.0090.020137.7180.0220.0220.0000.0000.0000.000
101A141THR0-0.010-0.012137.1660.0210.0210.0000.0000.0000.000
102A142ILE0-0.0140.000139.3070.0220.0220.0000.0000.0000.000
103A143GLU-1-0.845-0.934142.110-2.235-2.2350.0000.0000.0000.000
104A144ALA0-0.0310.000142.7230.0190.0190.0000.0000.0000.000
105A145ALA0-0.053-0.048143.5210.0170.0170.0000.0000.0000.000
106A146ARG10.8090.907145.4292.2572.2570.0000.0000.0000.000
107A147ALA0-0.0210.010147.7400.0180.0180.0000.0000.0000.000
108A148GLY00.0310.022148.9410.0190.0190.0000.0000.0000.000
109A149GLU-1-0.929-0.982148.752-2.169-2.1690.0000.0000.0000.000
110A150ALA00.0180.011148.742-0.015-0.0150.0000.0000.0000.000
111A151GLY00.0120.010146.173-0.012-0.0120.0000.0000.0000.000
112A152LYS10.9320.954144.2462.2262.2260.0000.0000.0000.000
113A153GLY00.0360.016142.508-0.017-0.0170.0000.0000.0000.000
114A154PHE0-0.002-0.010140.953-0.019-0.0190.0000.0000.0000.000
115A155MET0-0.036-0.003139.703-0.018-0.0180.0000.0000.0000.000
116A156ILE00.0190.019136.962-0.019-0.0190.0000.0000.0000.000
117A157VAL00.0030.011135.689-0.022-0.0220.0000.0000.0000.000
118A158ALA00.0090.008134.749-0.022-0.0220.0000.0000.0000.000
119A159ASN00.001-0.014134.177-0.002-0.0020.0000.0000.0000.000
120A160GLU-1-0.867-0.929129.300-2.546-2.5460.0000.0000.0000.000
121A161VAL00.0100.007130.115-0.025-0.0250.0000.0000.0000.000
122A162GLN0-0.021-0.001129.379-0.004-0.0040.0000.0000.0000.000
123A163ASN00.0340.012127.768-0.025-0.0250.0000.0000.0000.000
124A164LEU00.0220.020125.901-0.028-0.0280.0000.0000.0000.000
125A165SER0-0.060-0.040124.657-0.026-0.0260.0000.0000.0000.000
126A166ASN0-0.103-0.066123.829-0.038-0.0380.0000.0000.0000.000
127A167GLU-1-0.852-0.921120.524-2.723-2.7230.0000.0000.0000.000
128A168THR00.000-0.008120.143-0.031-0.0310.0000.0000.0000.000
129A169ASN0-0.060-0.039118.917-0.042-0.0420.0000.0000.0000.000
130A170GLU-1-0.942-0.966116.730-2.828-2.8280.0000.0000.0000.000
131A171VAL00.0910.048115.051-0.035-0.0350.0000.0000.0000.000
132A172THR0-0.034-0.030114.086-0.034-0.0340.0000.0000.0000.000
133A173LYS10.8930.948113.3412.7832.7830.0000.0000.0000.000
134A174GLN0-0.034-0.006110.850-0.057-0.0570.0000.0000.0000.000
135A175ILE0-0.003-0.001109.345-0.035-0.0350.0000.0000.0000.000
136A176VAL0-0.023-0.008108.653-0.028-0.0280.0000.0000.0000.000
137A177GLU-1-0.926-0.964104.914-3.119-3.1190.0000.0000.0000.000
138A178LYS10.9710.978104.7743.0683.0680.0000.0000.0000.000
139A179ALA00.002-0.007103.818-0.036-0.0360.0000.0000.0000.000
140A180ARG10.9790.974103.0273.1313.1310.0000.0000.0000.000
141A181GLU-1-0.915-0.949100.650-3.236-3.2360.0000.0000.0000.000
142A182ILE0-0.0130.00599.130-0.045-0.0450.0000.0000.0000.000
143A183LEU0-0.0220.01198.428-0.047-0.0470.0000.0000.0000.000
144A184GLU-1-0.916-0.95296.402-3.369-3.3690.0000.0000.0000.000
145A185SER0-0.054-0.02394.821-0.062-0.0620.0000.0000.0000.000
146A186SER00.024-0.00793.748-0.045-0.0450.0000.0000.0000.000
147A187GLN0-0.035-0.01093.1030.0030.0030.0000.0000.0000.000
148A188ARG10.9520.98190.2673.4633.4630.0000.0000.0000.000
149A189SER0-0.093-0.05989.477-0.057-0.0570.0000.0000.0000.000
150A190LEU00.019-0.00988.824-0.041-0.0410.0000.0000.0000.000
151A191GLU-1-0.873-0.92387.532-3.645-3.6450.0000.0000.0000.000
152A192ASN0-0.061-0.02184.401-0.084-0.0840.0000.0000.0000.000
153A193LEU00.015-0.01784.043-0.059-0.0590.0000.0000.0000.000
154A194GLU-1-0.956-0.95483.923-3.840-3.8400.0000.0000.0000.000
155A195PHE0-0.013-0.02077.713-0.066-0.0660.0000.0000.0000.000
156A196MET00.0010.00479.715-0.055-0.0550.0000.0000.0000.000
157A197ALA0-0.013-0.00679.223-0.065-0.0650.0000.0000.0000.000
158A198ASN00.019-0.00378.036-0.069-0.0690.0000.0000.0000.000
159A199LEU00.0130.01675.316-0.076-0.0760.0000.0000.0000.000
160A200PHE0-0.0100.00074.468-0.081-0.0810.0000.0000.0000.000
161A201GLU-1-0.876-0.93374.499-4.369-4.3690.0000.0000.0000.000
162A202THR0-0.072-0.04071.129-0.082-0.0820.0000.0000.0000.000
163A203VAL0-0.001-0.00369.952-0.090-0.0900.0000.0000.0000.000
164A204GLY00.0710.03269.477-0.071-0.0710.0000.0000.0000.000
165A205LYS10.9160.95668.5864.4134.4130.0000.0000.0000.000
166A206THR0-0.036-0.01964.824-0.102-0.1020.0000.0000.0000.000
167A207LEU00.0100.00864.840-0.102-0.1020.0000.0000.0000.000
168A208GLN00.0320.00965.137-0.105-0.1050.0000.0000.0000.000
169A209ASN0-0.033-0.02162.353-0.069-0.0690.0000.0000.0000.000
170A210MET0-0.017-0.00260.738-0.136-0.1360.0000.0000.0000.000
171A211VAL0-0.0140.00060.182-0.089-0.0890.0000.0000.0000.000
172A212ARG10.9730.99359.3105.0465.0460.0000.0000.0000.000
173A213PHE0-0.003-0.00252.655-0.091-0.0910.0000.0000.0000.000
174A214MET00.0300.01155.584-0.138-0.1380.0000.0000.0000.000
175A215GLU-1-0.902-0.94555.835-5.373-5.3730.0000.0000.0000.000
176A216ASN0-0.109-0.06353.480-0.184-0.1840.0000.0000.0000.000
177A217ASN00.006-0.01051.092-0.209-0.2090.0000.0000.0000.000
178A218VAL00.0310.01750.913-0.137-0.1370.0000.0000.0000.000
179A219LYS10.9460.98250.7295.8945.8940.0000.0000.0000.000
180A220LEU00.0240.03045.242-0.141-0.1410.0000.0000.0000.000
181A221LEU0-0.004-0.00546.325-0.182-0.1820.0000.0000.0000.000
182A222GLN00.0150.00746.423-0.027-0.0270.0000.0000.0000.000
183A223GLU-1-1.025-1.01443.662-7.188-7.1880.0000.0000.0000.000
184A224VAL0-0.021-0.01541.273-0.215-0.2150.0000.0000.0000.000
185A225ARG10.8640.92741.5216.5286.5280.0000.0000.0000.000
186A226ASN00.0530.02641.934-0.158-0.1580.0000.0000.0000.000
187A227SER0-0.035-0.00938.501-0.248-0.2480.0000.0000.0000.000
188A228LEU0-0.027-0.02037.096-0.281-0.2810.0000.0000.0000.000
189A229ASP-1-0.929-0.96337.506-7.729-7.7290.0000.0000.0000.000
190A230THR00.011-0.00437.789-0.262-0.2620.0000.0000.0000.000
191A231SER0-0.029-0.01933.519-0.333-0.3330.0000.0000.0000.000
192A232LYS10.8570.95232.9747.8597.8590.0000.0000.0000.000
193A233GLU-1-0.916-0.94833.197-8.409-8.4090.0000.0000.0000.000
194A234SER0-0.035-0.01831.951-0.338-0.3380.0000.0000.0000.000
195A235LEU0-0.021-0.00927.121-0.392-0.3920.0000.0000.0000.000
196A236SER0-0.0110.00128.224-0.552-0.5520.0000.0000.0000.000
197A237GLU-1-0.929-0.95228.638-10.617-10.6170.0000.0000.0000.000
198A238LYS10.9940.97625.87110.51010.5100.0000.0000.0000.000
199A239SER0-0.052-0.03024.103-0.576-0.5760.0000.0000.0000.000
200A240ALA00.0850.04123.660-0.548-0.5480.0000.0000.0000.000
201A241GLU-1-0.944-0.95922.836-12.655-12.6550.0000.0000.0000.000
202A242ILE0-0.063-0.03019.363-0.575-0.5750.0000.0000.0000.000
203A243ASP-1-0.896-0.93519.193-14.235-14.2350.0000.0000.0000.000
204A244SER00.004-0.00520.085-0.280-0.2800.0000.0000.0000.000
205A245ALA0-0.011-0.01117.996-0.346-0.3460.0000.0000.0000.000
206A246THR0-0.059-0.04714.782-1.333-1.3330.0000.0000.0000.000
207A247LYS10.8740.93515.63313.70613.7060.0000.0000.0000.000
208A248VAL00.0160.00716.899-0.114-0.1140.0000.0000.0000.000
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