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: N9MJQ

Calculation Name: 3GUY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GUY

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2236130.966669
FMO2-HF: Nuclear repulsion 2158093.311229
FMO2-HF: Total energy -78037.655439
FMO2-MP2: Total energy -78263.220094


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:LEU)


Summations of interaction energy for fragment #1(A:1: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.
-13.9610.2276.733-6.491-14.428-0.028
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.038
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].
3A3VAL00.0380.0232.658-2.0041.2650.426-1.255-2.4410.004
4A4ILE0-0.0120.0064.249-0.223-0.1040.000-0.020-0.0990.000
5A5THR00.014-0.0077.8370.0640.0640.0000.0000.0000.000
6A6GLY00.0150.00410.8930.0070.0070.0000.0000.0000.000
7A7ALA00.0090.00510.7960.0130.0130.0000.0000.0000.000
8A8SER0-0.009-0.00812.7130.0170.0170.0000.0000.0000.000
9A9SER00.002-0.01615.2360.0160.0160.0000.0000.0000.000
10A10GLY0-0.0070.00316.933-0.012-0.0120.0000.0000.0000.000
11A11LEU00.0630.02216.1280.0070.0070.0000.0000.0000.000
12A12GLY00.0840.04713.242-0.005-0.0050.0000.0000.0000.000
13A13ALA0-0.044-0.01712.276-0.001-0.0010.0000.0000.0000.000
14A14GLU-1-0.802-0.88613.2670.0040.0040.0000.0000.0000.000
15A15LEU00.000-0.00111.8610.0100.0100.0000.0000.0000.000
16A16ALA00.000-0.0029.011-0.002-0.0020.0000.0000.0000.000
17A17LYS10.8250.8919.7630.0480.0480.0000.0000.0000.000
18A18LEU0-0.0080.00812.5000.0350.0350.0000.0000.0000.000
19A19TYR0-0.018-0.0217.501-0.044-0.0440.0000.0000.0000.000
20A20ASP-1-0.756-0.8638.4350.4690.4690.0000.0000.0000.000
21A21ALA00.0130.0149.3330.0680.0680.0000.0000.0000.000
22A22GLU-1-0.835-0.89710.163-0.053-0.0530.0000.0000.0000.000
23A23GLY0-0.009-0.0089.9310.0170.0170.0000.0000.0000.000
24A24LYS10.7360.8675.2520.2930.2930.0000.0000.0000.000
25A25ALA00.0620.0333.014-1.001-0.2000.176-0.281-0.6950.000
26A26THR00.010-0.0042.675-3.473-0.9661.504-1.958-2.053-0.024
27A27TYR00.0370.0192.227-1.362-0.1921.467-0.360-2.278-0.005
28A28LEU0-0.035-0.0163.702-0.088-0.0470.0060.029-0.0760.000
29A29THR00.0290.0067.415-0.008-0.0080.0000.0000.0000.000
30A30GLY0-0.007-0.02110.2630.0030.0030.0000.0000.0000.000
31A31ARG10.9460.98614.0440.0940.0940.0000.0000.0000.000
32A32SER0-0.037-0.01217.2360.0070.0070.0000.0000.0000.000
33A33GLU-1-0.822-0.92115.469-0.065-0.0650.0000.0000.0000.000
34A34SER00.0200.01215.9500.0050.0050.0000.0000.0000.000
35A35LYS10.9760.97717.5890.0500.0500.0000.0000.0000.000
36A36LEU0-0.0130.00611.0260.0060.0060.0000.0000.0000.000
37A37SER00.0010.01412.9490.0180.0180.0000.0000.0000.000
38A38THR0-0.071-0.04014.7850.0150.0150.0000.0000.0000.000
39A39VAL0-0.012-0.02011.9820.0100.0100.0000.0000.0000.000
40A40THR0-0.013-0.0249.1940.0130.0130.0000.0000.0000.000
41A41ASN0-0.0040.01511.6500.0360.0360.0000.0000.0000.000
42A42CYS0-0.089-0.03414.6200.0040.0040.0000.0000.0000.000
43A43LEU0-0.086-0.0278.8420.0030.0030.0000.0000.0000.000
44A44SER0-0.022-0.02311.213-0.017-0.0170.0000.0000.0000.000
45A45ASN0-0.072-0.0407.5220.0750.0750.0000.0000.0000.000
46A46ASN0-0.046-0.0245.8110.2010.2010.0000.0000.0000.000
47A47VAL00.0070.0052.635-0.550-0.1950.905-0.207-1.053-0.001
48A48GLY00.0190.0145.447-0.193-0.1930.0000.0000.0000.000
49A49TYR00.015-0.0066.3520.0090.0090.0000.0000.0000.000
50A50ARG10.9320.9768.5260.1950.1950.0000.0000.0000.000
51A51ALA00.0200.02310.769-0.014-0.0140.0000.0000.0000.000
52A52ARG10.7450.86011.3130.1470.1470.0000.0000.0000.000
53A53ASP-1-0.859-0.92714.572-0.108-0.1080.0000.0000.0000.000
54A54LEU0-0.025-0.03312.580-0.007-0.0070.0000.0000.0000.000
55A55ALA00.0150.02216.452-0.009-0.0090.0000.0000.0000.000
56A56SER00.0290.02318.6570.0030.0030.0000.0000.0000.000
57A57HIS00.012-0.01017.478-0.022-0.0220.0000.0000.0000.000
58A58GLN00.0500.02516.935-0.019-0.0190.0000.0000.0000.000
59A59GLU-1-0.815-0.90315.364-0.139-0.1390.0000.0000.0000.000
60A60VAL00.010-0.00412.450-0.021-0.0210.0000.0000.0000.000
61A61GLU-1-0.891-0.93411.979-0.204-0.2040.0000.0000.0000.000
62A62GLN0-0.016-0.01812.271-0.024-0.0240.0000.0000.0000.000
63A63LEU0-0.040-0.0157.550-0.010-0.0100.0000.0000.0000.000
64A64PHE00.004-0.0216.494-0.035-0.0350.0000.0000.0000.000
65A65GLU-1-0.863-0.8867.843-0.314-0.3140.0000.0000.0000.000
66A66GLN0-0.034-0.0178.5950.0030.0030.0000.0000.0000.000
67A67LEU0-0.051-0.0182.498-0.689-0.1250.574-0.205-0.932-0.001
68A68ASP-1-0.850-0.9083.635-2.053-1.5740.008-0.178-0.308-0.001
69A69SER0-0.068-0.0342.883-1.2190.1040.323-0.620-1.026-0.005
70A70ILE0-0.041-0.0244.116-0.517-0.2510.000-0.053-0.2140.000
71A71PRO0-0.0050.0122.257-1.709-0.4151.058-0.874-1.4780.003
72A72SER0-0.014-0.0122.684-0.8530.8940.287-0.464-1.5690.002
73A73THR0-0.035-0.0304.3170.6490.902-0.001-0.045-0.2060.000
74A74VAL0-0.0020.0005.308-0.279-0.2790.0000.0000.0000.000
75A75VAL00.0050.0087.4610.1020.1020.0000.0000.0000.000
76A76HIS00.0570.0409.8680.0160.0160.0000.0000.0000.000
77A77SER0-0.041-0.04812.3990.0320.0320.0000.0000.0000.000
78A78ALA0-0.029-0.00414.6070.0260.0260.0000.0000.0000.000
79A79GLY00.0250.01116.250-0.004-0.0040.0000.0000.0000.000
80A80SER0-0.065-0.03820.0160.0030.0030.0000.0000.0000.000
81A81GLY00.0440.02523.278-0.003-0.0030.0000.0000.0000.000
82A82TYR00.0320.01326.7460.0020.0020.0000.0000.0000.000
83A83PHE0-0.026-0.01428.172-0.002-0.0020.0000.0000.0000.000
84A84GLY00.0620.03633.3150.0020.0020.0000.0000.0000.000
85A85LEU0-0.020-0.01036.953-0.003-0.0030.0000.0000.0000.000
86A86LEU0-0.0060.00036.7160.0000.0000.0000.0000.0000.000
87A87GLN0-0.034-0.03939.106-0.002-0.0020.0000.0000.0000.000
88A88GLU-1-0.864-0.92040.197-0.030-0.0300.0000.0000.0000.000
89A89GLN0-0.103-0.02334.015-0.003-0.0030.0000.0000.0000.000
90A90ASP-1-0.784-0.90035.688-0.042-0.0420.0000.0000.0000.000
91A91PRO0-0.002-0.02434.967-0.003-0.0030.0000.0000.0000.000
92A92GLU-1-0.911-0.94733.476-0.047-0.0470.0000.0000.0000.000
93A93GLN0-0.009-0.00430.725-0.007-0.0070.0000.0000.0000.000
94A94ILE0-0.038-0.01530.137-0.005-0.0050.0000.0000.0000.000
95A95GLN0-0.026-0.02128.263-0.003-0.0030.0000.0000.0000.000
96A96THR00.0140.01026.091-0.006-0.0060.0000.0000.0000.000
97A97LEU0-0.062-0.02225.572-0.008-0.0080.0000.0000.0000.000
98A98ILE00.0240.00425.157-0.009-0.0090.0000.0000.0000.000
99A99GLU-1-0.851-0.90523.491-0.089-0.0890.0000.0000.0000.000
100A100ASN0-0.018-0.03721.048-0.016-0.0160.0000.0000.0000.000
101A101ASN0-0.075-0.01819.998-0.017-0.0170.0000.0000.0000.000
102A102LEU00.0390.02420.626-0.011-0.0110.0000.0000.0000.000
103A103SER00.0210.00721.322-0.010-0.0100.0000.0000.0000.000
104A104SER0-0.021-0.02017.041-0.016-0.0160.0000.0000.0000.000
105A105ALA0-0.0060.00316.648-0.021-0.0210.0000.0000.0000.000
106A106ILE00.0200.00317.240-0.018-0.0180.0000.0000.0000.000
107A107ASN0-0.060-0.03916.675-0.011-0.0110.0000.0000.0000.000
108A108VAL00.0030.00011.448-0.017-0.0170.0000.0000.0000.000
109A109LEU00.0280.01813.045-0.036-0.0360.0000.0000.0000.000
110A110ARG10.9720.97615.1770.1550.1550.0000.0000.0000.000
111A111GLU-1-0.786-0.88211.783-0.243-0.2430.0000.0000.0000.000
112A112LEU00.004-0.0058.581-0.027-0.0270.0000.0000.0000.000
113A113VAL00.0190.00811.834-0.015-0.0150.0000.0000.0000.000
114A114LYS10.7170.85214.8210.2240.2240.0000.0000.0000.000
115A115ARG10.7520.84010.0440.3280.3280.0000.0000.0000.000
116A116TYR00.0290.0036.763-0.011-0.0110.0000.0000.0000.000
117A117LYS10.9150.95711.7460.1840.1840.0000.0000.0000.000
118A118ASP-1-0.863-0.92214.762-0.171-0.1710.0000.0000.0000.000
119A119GLN00.0200.0079.6230.0300.0300.0000.0000.0000.000
120A120PRO00.0060.0118.990-0.009-0.0090.0000.0000.0000.000
121A121VAL0-0.0050.0057.311-0.064-0.0640.0000.0000.0000.000
122A122ASN0-0.042-0.0188.5000.2610.2610.0000.0000.0000.000
123A123VAL00.0610.0209.716-0.117-0.1170.0000.0000.0000.000
124A124VAL00.0090.00411.3290.0770.0770.0000.0000.0000.000
125A125MET0-0.017-0.00513.086-0.006-0.0060.0000.0000.0000.000
126A126ILE0-0.025-0.01314.3470.0260.0260.0000.0000.0000.000
127A127MET0-0.0120.00617.3530.0100.0100.0000.0000.0000.000
128A128SER00.007-0.01020.8910.0080.0080.0000.0000.0000.000
129A129THR00.0270.00823.992-0.002-0.0020.0000.0000.0000.000
130A130ALA0-0.015-0.01127.1530.0040.0040.0000.0000.0000.000
131A131ALA00.000-0.00924.9540.0020.0020.0000.0000.0000.000
132A132GLN0-0.015-0.00227.010-0.003-0.0030.0000.0000.0000.000
133A133GLN00.0140.02329.5460.0020.0020.0000.0000.0000.000
134A134PRO00.0230.01332.169-0.002-0.0020.0000.0000.0000.000
135A135LYS10.8970.94229.7470.0640.0640.0000.0000.0000.000
136A136ALA00.0160.00035.284-0.001-0.0010.0000.0000.0000.000
137A137GLN0-0.026-0.01636.6400.0000.0000.0000.0000.0000.000
138A138GLU-1-0.786-0.90530.722-0.059-0.0590.0000.0000.0000.000
139A139SER00.0160.02332.325-0.004-0.0040.0000.0000.0000.000
140A140THR00.042-0.00831.454-0.004-0.0040.0000.0000.0000.000
141A141TYR00.0260.01324.488-0.009-0.0090.0000.0000.0000.000
142A142CYS0-0.017-0.01427.871-0.005-0.0050.0000.0000.0000.000
143A143ALA0-0.0130.00929.066-0.005-0.0050.0000.0000.0000.000
144A144VAL00.000-0.00125.152-0.005-0.0050.0000.0000.0000.000
145A145LYS10.8950.94720.8700.1080.1080.0000.0000.0000.000
146A146TRP0-0.044-0.02324.995-0.007-0.0070.0000.0000.0000.000
147A147ALA0-0.0300.00726.007-0.004-0.0040.0000.0000.0000.000
148A148VAL0-0.019-0.00819.844-0.006-0.0060.0000.0000.0000.000
149A149LYS10.9490.97322.3310.0920.0920.0000.0000.0000.000
150A150GLY00.0090.00624.124-0.003-0.0030.0000.0000.0000.000
151A151LEU00.0080.01319.8670.0000.0000.0000.0000.0000.000
152A152ILE0-0.006-0.01318.803-0.007-0.0070.0000.0000.0000.000
153A153GLU-1-0.865-0.92921.229-0.131-0.1310.0000.0000.0000.000
154A154SER0-0.050-0.03624.2800.0060.0060.0000.0000.0000.000
155A155VAL00.0370.01118.5500.0000.0000.0000.0000.0000.000
156A156ARG10.7520.84919.7440.1600.1600.0000.0000.0000.000
157A157LEU0-0.063-0.02821.6950.0040.0040.0000.0000.0000.000
158A158GLU-1-0.955-0.97522.132-0.136-0.1360.0000.0000.0000.000
159A159LEU0-0.043-0.01616.843-0.002-0.0020.0000.0000.0000.000
160A160LYS10.9620.97820.1520.0900.0900.0000.0000.0000.000
161A161GLY0-0.056-0.02222.0220.0050.0050.0000.0000.0000.000
162A162LYS10.8360.92017.5260.1660.1660.0000.0000.0000.000
163A163PRO0-0.021-0.00813.6240.0040.0040.0000.0000.0000.000
164A164MET0-0.0190.03312.739-0.023-0.0230.0000.0000.0000.000
165A165LYS10.8560.92813.0870.3520.3520.0000.0000.0000.000
166A166ILE00.0200.01413.837-0.051-0.0510.0000.0000.0000.000
167A167ILE0-0.045-0.01913.9640.0340.0340.0000.0000.0000.000
168A168ALA0-0.0220.00716.586-0.012-0.0120.0000.0000.0000.000
169A169VAL00.0490.01016.6440.0140.0140.0000.0000.0000.000
170A170TYR0-0.003-0.01919.6390.0020.0020.0000.0000.0000.000
171A171PRO00.0310.02920.4190.0110.0110.0000.0000.0000.000
172A172GLY00.027-0.00823.2070.0010.0010.0000.0000.0000.000
173A173GLY0-0.038-0.01625.310-0.003-0.0030.0000.0000.0000.000
174A174MET0-0.0090.00420.7410.0020.0020.0000.0000.0000.000
175A191PHE0-0.024-0.01728.4570.0000.0000.0000.0000.0000.000
176A192MET0-0.021-0.00724.3090.0050.0050.0000.0000.0000.000
177A193SER0-0.005-0.01424.327-0.001-0.0010.0000.0000.0000.000
178A194ALA00.006-0.01819.618-0.005-0.0050.0000.0000.0000.000
179A195GLU-1-0.894-0.94519.505-0.011-0.0110.0000.0000.0000.000
180A196ASP-1-0.843-0.89520.367-0.030-0.0300.0000.0000.0000.000
181A197ALA0-0.024-0.01920.934-0.004-0.0040.0000.0000.0000.000
182A198ALA0-0.004-0.00516.100-0.013-0.0130.0000.0000.0000.000
183A199LEU00.0580.02917.068-0.012-0.0120.0000.0000.0000.000
184A200MET0-0.0110.00418.7750.0000.0000.0000.0000.0000.000
185A201ILE0-0.046-0.04215.648-0.008-0.0080.0000.0000.0000.000
186A202HIS0-0.075-0.04611.593-0.019-0.0190.0000.0000.0000.000
187A203GLY00.0230.01514.973-0.005-0.0050.0000.0000.0000.000
188A204ALA0-0.048-0.01817.5780.0050.0050.0000.0000.0000.000
189A205LEU0-0.058-0.02413.794-0.006-0.0060.0000.0000.0000.000
190A206ALA00.0600.02814.3460.0030.0030.0000.0000.0000.000
191A207ASN0-0.011-0.02112.680-0.016-0.0160.0000.0000.0000.000
192A208ILE00.0320.02214.7050.0140.0140.0000.0000.0000.000
193A209GLY00.0100.00717.5320.0010.0010.0000.0000.0000.000
194A210ASN0-0.031-0.02418.339-0.014-0.0140.0000.0000.0000.000
195A211GLY00.0060.01319.384-0.004-0.0040.0000.0000.0000.000
196A212TYR0-0.026-0.02415.997-0.013-0.0130.0000.0000.0000.000
197A213VAL00.0040.01717.2760.0130.0130.0000.0000.0000.000
198A214SER00.013-0.01617.418-0.024-0.0240.0000.0000.0000.000
199A215ASP-1-0.800-0.87519.564-0.153-0.1530.0000.0000.0000.000
200A216ILE0-0.0110.00918.2590.0140.0140.0000.0000.0000.000
201A217THR0-0.016-0.01522.183-0.005-0.0050.0000.0000.0000.000
202A218VAL00.0110.01621.5830.0070.0070.0000.0000.0000.000
203A219ASN00.022-0.01324.767-0.001-0.0010.0000.0000.0000.000
204A220ARG10.9871.01227.8170.0300.0300.0000.0000.0000.000