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: 2J4QR

Calculation Name: 1G8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G8A

Chain ID: A

ChEMBL ID:

UniProt ID: O57811

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2888450.552805
FMO2-HF: Nuclear repulsion 2799500.862073
FMO2-HF: Total energy -88949.690731
FMO2-MP2: Total energy -89214.830758


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.
-16.801-9.8690.461-3.705-3.687-0.02
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 : 0.008 / q_NPA : 0.006
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].
3A3GLU-1-0.851-0.9003.798-2.1000.578-0.012-1.310-1.3550.008
4A4VAL0-0.022-0.0025.7650.1270.1270.0000.0000.0000.000
5A5LYS10.9070.9529.3051.5751.5750.0000.0000.0000.000
6A6LYS10.9420.95311.8910.2710.2710.0000.0000.0000.000
7A7HIS00.0310.02715.6140.0440.0440.0000.0000.0000.000
8A8LYS10.8700.95017.8740.3760.3760.0000.0000.0000.000
9A9PHE0-0.032-0.02221.1060.0480.0480.0000.0000.0000.000
10A10PRO00.0430.01721.152-0.034-0.0340.0000.0000.0000.000
11A11GLY00.0290.00720.6490.0110.0110.0000.0000.0000.000
12A12VAL0-0.037-0.01818.922-0.032-0.0320.0000.0000.0000.000
13A13TYR0-0.010-0.01313.8560.0550.0550.0000.0000.0000.000
14A14THR0-0.005-0.01412.7410.0590.0590.0000.0000.0000.000
15A15VAL0-0.040-0.0198.9420.0190.0190.0000.0000.0000.000
16A16ILE0-0.036-0.0276.8640.4280.4280.0000.0000.0000.000
17A17ASP-1-0.821-0.9094.549-4.351-4.215-0.001-0.030-0.1050.000
18A18ASP-1-0.884-0.9372.661-15.603-11.5570.475-2.364-2.157-0.028
19A19ASP-1-0.918-0.9565.286-0.435-0.363-0.001-0.001-0.0700.000
20A20GLY0-0.048-0.0708.7000.4600.4600.0000.0000.0000.000
21A21SER0-0.006-0.0047.897-0.106-0.1060.0000.0000.0000.000
22A22GLU-1-0.984-0.99110.510-0.572-0.5720.0000.0000.0000.000
23A23ARG10.8460.97712.4551.6001.6000.0000.0000.0000.000
24A24ILE00.0110.00813.955-0.068-0.0680.0000.0000.0000.000
25A25ALA0-0.013-0.01514.880-0.016-0.0160.0000.0000.0000.000
26A26THR0-0.037-0.01716.8540.0370.0370.0000.0000.0000.000
27A27LYS10.8160.90515.9170.3480.3480.0000.0000.0000.000
28A28ASN0-0.040-0.03218.0990.0640.0640.0000.0000.0000.000
29A29LEU0-0.0040.00320.1980.0160.0160.0000.0000.0000.000
30A30VAL0-0.045-0.02223.3290.0290.0290.0000.0000.0000.000
31A31PRO0-0.021-0.01619.354-0.014-0.0140.0000.0000.0000.000
32A32GLY00.0090.00320.3600.0350.0350.0000.0000.0000.000
33A33GLN0-0.028-0.01921.882-0.009-0.0090.0000.0000.0000.000
34A34ARG10.8980.96220.7820.2510.2510.0000.0000.0000.000
35A35VAL00.0130.01722.4910.0220.0220.0000.0000.0000.000
36A36TYR00.003-0.01822.866-0.031-0.0310.0000.0000.0000.000
37A37GLY0-0.0010.00222.0280.0040.0040.0000.0000.0000.000
38A38GLU-1-0.899-0.93718.744-0.473-0.4730.0000.0000.0000.000
39A39ARG10.9220.95415.5940.7780.7780.0000.0000.0000.000
40A40VAL0-0.015-0.01414.781-0.037-0.0370.0000.0000.0000.000
41A41ILE00.0320.0238.8190.0120.0120.0000.0000.0000.000
42A42LYS10.8760.92710.8130.5650.5650.0000.0000.0000.000
43A43TRP00.031-0.0035.2000.0530.0530.0000.0000.0000.000
44A44GLU-1-0.899-0.9547.741-0.222-0.2220.0000.0000.0000.000
45A45GLY0-0.0140.00010.2560.0650.0650.0000.0000.0000.000
46A46GLU-1-0.807-0.87613.013-0.354-0.3540.0000.0000.0000.000
47A47GLU-1-0.822-0.91413.443-0.533-0.5330.0000.0000.0000.000
48A48TYR00.0040.00112.4210.0530.0530.0000.0000.0000.000
49A49ARG10.8170.89014.6280.3820.3820.0000.0000.0000.000
50A50ILE00.0370.01912.7270.0300.0300.0000.0000.0000.000
51A51TRP0-0.073-0.06116.6780.1020.1020.0000.0000.0000.000
52A52ASN0-0.006-0.00819.616-0.035-0.0350.0000.0000.0000.000
53A53PRO00.0740.04420.3400.0530.0530.0000.0000.0000.000
54A54ASN00.0160.00123.2990.0270.0270.0000.0000.0000.000
55A55ARG10.9110.95524.5210.4100.4100.0000.0000.0000.000
56A56SER0-0.001-0.00424.9990.0170.0170.0000.0000.0000.000
57A57LYS10.9100.94726.4270.2280.2280.0000.0000.0000.000
58A58LEU00.0150.01627.286-0.004-0.0040.0000.0000.0000.000
59A59GLY00.0130.01423.540-0.012-0.0120.0000.0000.0000.000
60A60ALA00.013-0.00723.272-0.029-0.0290.0000.0000.0000.000
61A61ALA00.0120.01025.273-0.003-0.0030.0000.0000.0000.000
62A62ILE0-0.032-0.02521.5010.0030.0030.0000.0000.0000.000
63A63MET0-0.042-0.01618.149-0.011-0.0110.0000.0000.0000.000
64A64ASN0-0.057-0.02821.947-0.034-0.0340.0000.0000.0000.000
65A65GLY00.0030.00723.9230.0290.0290.0000.0000.0000.000
66A66LEU0-0.0410.00025.0940.0270.0270.0000.0000.0000.000
67A67LYS10.9050.93626.1970.1890.1890.0000.0000.0000.000
68A68ASN0-0.079-0.05228.4380.0110.0110.0000.0000.0000.000
69A69PHE00.0630.02025.844-0.005-0.0050.0000.0000.0000.000
70A70PRO0-0.017-0.02628.751-0.001-0.0010.0000.0000.0000.000
71A71ILE0-0.0120.01428.0150.0130.0130.0000.0000.0000.000
72A72LYS10.9290.95926.9210.1870.1870.0000.0000.0000.000
73A73PRO00.0370.00924.5840.0100.0100.0000.0000.0000.000
74A74GLY00.0130.01027.3810.0130.0130.0000.0000.0000.000
75A75LYS10.7980.91030.7360.1610.1610.0000.0000.0000.000
76A76SER00.003-0.01932.809-0.003-0.0030.0000.0000.0000.000
77A77VAL0-0.013-0.03332.025-0.001-0.0010.0000.0000.0000.000
78A78LEU00.0130.03235.4340.0010.0010.0000.0000.0000.000
79A79TYR00.002-0.02331.273-0.016-0.0160.0000.0000.0000.000
80A80LEU00.0130.01636.6950.0030.0030.0000.0000.0000.000
81A81GLY00.0670.03837.670-0.007-0.0070.0000.0000.0000.000
82A82ILE0-0.071-0.03933.428-0.014-0.0140.0000.0000.0000.000
83A83ALA0-0.007-0.01633.327-0.014-0.0140.0000.0000.0000.000
84A84SER0-0.094-0.02633.330-0.014-0.0140.0000.0000.0000.000
85A85GLY00.0160.00429.661-0.011-0.0110.0000.0000.0000.000
86A86THR0-0.008-0.02524.757-0.007-0.0070.0000.0000.0000.000
87A87THR00.0150.02226.252-0.029-0.0290.0000.0000.0000.000
88A88ALA00.0700.05827.553-0.006-0.0060.0000.0000.0000.000
89A89SER00.0310.00924.987-0.012-0.0120.0000.0000.0000.000
90A90HIS10.8350.90819.9330.5180.5180.0000.0000.0000.000
91A91VAL00.0530.02724.415-0.002-0.0020.0000.0000.0000.000
92A92SER0-0.019-0.02227.2820.0070.0070.0000.0000.0000.000
93A93ASP-1-0.708-0.80721.720-0.414-0.4140.0000.0000.0000.000
94A94ILE0-0.078-0.02322.8560.0060.0060.0000.0000.0000.000
95A95VAL0-0.050-0.00124.4890.0160.0160.0000.0000.0000.000
96A96GLY00.0840.04626.3560.0170.0170.0000.0000.0000.000
97A97TRP00.002-0.02126.2710.0120.0120.0000.0000.0000.000
98A98GLU-1-0.945-0.95829.062-0.128-0.1280.0000.0000.0000.000
99A99GLY0-0.0060.00930.8600.0080.0080.0000.0000.0000.000
100A100LYS10.8630.92932.3650.1350.1350.0000.0000.0000.000
101A101ILE0-0.0140.00630.026-0.002-0.0020.0000.0000.0000.000
102A102PHE00.0220.00734.6370.0040.0040.0000.0000.0000.000
103A103GLY00.021-0.00137.104-0.004-0.0040.0000.0000.0000.000
104A104ILE0-0.0030.01237.8300.0060.0060.0000.0000.0000.000
105A105GLU-1-0.825-0.92238.045-0.187-0.1870.0000.0000.0000.000
106A106PHE00.0770.03641.6880.0070.0070.0000.0000.0000.000
107A107SER00.0030.00343.2190.0080.0080.0000.0000.0000.000
108A108PRO00.0610.01443.236-0.006-0.0060.0000.0000.0000.000
109A109ARG10.8460.94042.5530.1220.1220.0000.0000.0000.000
110A110VAL00.0660.03238.392-0.004-0.0040.0000.0000.0000.000
111A111LEU00.0250.01838.573-0.008-0.0080.0000.0000.0000.000
112A112ARG10.8080.88938.8030.1300.1300.0000.0000.0000.000
113A113GLU-1-0.793-0.90737.011-0.151-0.1510.0000.0000.0000.000
114A114LEU0-0.0070.01133.023-0.012-0.0120.0000.0000.0000.000
115A115VAL0-0.009-0.00434.015-0.009-0.0090.0000.0000.0000.000
116A116PRO00.0200.00932.062-0.004-0.0040.0000.0000.0000.000
117A117ILE0-0.052-0.01028.459-0.015-0.0150.0000.0000.0000.000
118A118VAL0-0.020-0.03329.394-0.015-0.0150.0000.0000.0000.000
119A119GLU-1-0.926-0.93831.769-0.168-0.1680.0000.0000.0000.000
120A120GLU-1-0.826-0.90627.569-0.216-0.2160.0000.0000.0000.000
121A121ARG10.7870.88423.2580.3270.3270.0000.0000.0000.000
122A122ARG10.9180.93230.2060.1570.1570.0000.0000.0000.000
123A123ASN0-0.0390.00028.3990.0060.0060.0000.0000.0000.000
124A124ILE0-0.002-0.00629.943-0.002-0.0020.0000.0000.0000.000
125A125VAL0-0.024-0.01533.9670.0070.0070.0000.0000.0000.000
126A126PRO0-0.023-0.01436.5550.0000.0000.0000.0000.0000.000
127A127ILE0-0.009-0.01338.9390.0090.0090.0000.0000.0000.000
128A128LEU0-0.022-0.00942.416-0.005-0.0050.0000.0000.0000.000
129A129GLY00.002-0.01544.8860.0050.0050.0000.0000.0000.000
130A130ASP-1-0.796-0.86745.620-0.117-0.1170.0000.0000.0000.000
131A131ALA00.0300.00643.7470.0030.0030.0000.0000.0000.000
132A132THR0-0.043-0.04545.7940.0020.0020.0000.0000.0000.000
133A133LYS10.8120.90148.9260.1010.1010.0000.0000.0000.000
134A134PRO00.0490.03247.0500.0000.0000.0000.0000.0000.000
135A135GLU-1-0.895-0.95548.575-0.093-0.0930.0000.0000.0000.000
136A136GLU-1-0.850-0.91150.437-0.093-0.0930.0000.0000.0000.000
137A137TYR0-0.009-0.01944.4620.0000.0000.0000.0000.0000.000
138A138ARG10.8990.94547.0620.0810.0810.0000.0000.0000.000
139A139ALA0-0.053-0.01648.5990.0010.0010.0000.0000.0000.000
140A140LEU0-0.048-0.01744.7120.0010.0010.0000.0000.0000.000
141A141VAL0-0.0130.00341.615-0.004-0.0040.0000.0000.0000.000
142A142PRO0-0.0040.01741.1360.0050.0050.0000.0000.0000.000
143A143LYS10.8920.91843.0990.0920.0920.0000.0000.0000.000
144A144VAL0-0.009-0.01538.355-0.001-0.0010.0000.0000.0000.000
145A145ASP-1-0.863-0.90635.616-0.132-0.1320.0000.0000.0000.000
146A146VAL0-0.010-0.01733.240-0.001-0.0010.0000.0000.0000.000
147A147ILE00.0430.04736.4990.0010.0010.0000.0000.0000.000
148A148PHE0-0.045-0.03631.904-0.008-0.0080.0000.0000.0000.000
149A149GLU-1-0.798-0.93035.670-0.150-0.1500.0000.0000.0000.000
150A150ASP-1-0.813-0.89234.173-0.243-0.2430.0000.0000.0000.000
151A151VAL00.0360.01636.8520.0000.0000.0000.0000.0000.000
152A152ALA0-0.0240.00239.5570.0040.0040.0000.0000.0000.000
153A153GLN00.002-0.01541.3600.0020.0020.0000.0000.0000.000
154A154PRO00.0600.02545.040-0.003-0.0030.0000.0000.0000.000
155A155THR00.0060.00947.5810.0010.0010.0000.0000.0000.000
156A156GLN00.005-0.01541.002-0.005-0.0050.0000.0000.0000.000
157A157ALA00.0480.03744.054-0.003-0.0030.0000.0000.0000.000
158A158LYS10.9310.93545.1350.1000.1000.0000.0000.0000.000
159A159ILE0-0.0390.00143.8800.0030.0030.0000.0000.0000.000
160A160LEU00.0350.03040.0670.0010.0010.0000.0000.0000.000
161A161ILE0-0.001-0.00543.8230.0020.0020.0000.0000.0000.000
162A162ASP-1-0.825-0.88546.748-0.099-0.0990.0000.0000.0000.000
163A163ASN0-0.032-0.03543.8020.0020.0020.0000.0000.0000.000
164A164ALA0-0.020-0.01643.6530.0010.0010.0000.0000.0000.000
165A165GLU-1-0.877-0.89944.944-0.089-0.0890.0000.0000.0000.000
166A166VAL0-0.034-0.00247.8510.0050.0050.0000.0000.0000.000
167A167TYR0-0.025-0.03843.3100.0030.0030.0000.0000.0000.000
168A168LEU0-0.0550.01339.518-0.001-0.0010.0000.0000.0000.000
169A169LYS10.8890.94138.5540.1290.1290.0000.0000.0000.000
170A170ARG11.0311.01342.7600.0790.0790.0000.0000.0000.000
171A171GLY0-0.045-0.02041.4340.0010.0010.0000.0000.0000.000
172A172GLY00.0000.00538.616-0.007-0.0070.0000.0000.0000.000
173A173TYR0-0.026-0.03335.6580.0040.0040.0000.0000.0000.000
174A174GLY00.0520.03637.7490.0010.0010.0000.0000.0000.000
175A175MET0-0.068-0.02830.056-0.007-0.0070.0000.0000.0000.000
176A176ILE00.0610.03935.685-0.001-0.0010.0000.0000.0000.000
177A177ALA0-0.026-0.00833.655-0.006-0.0060.0000.0000.0000.000
178A178VAL00.0250.01735.5510.0060.0060.0000.0000.0000.000
179A179LYS10.9661.00037.6400.1880.1880.0000.0000.0000.000
180A180SER00.0630.03438.9400.0120.0120.0000.0000.0000.000
181A181ARG10.9370.95441.3260.1560.1560.0000.0000.0000.000
182A182SER0-0.098-0.05042.0320.0040.0040.0000.0000.0000.000
183A183ILE0-0.014-0.01043.3770.0050.0050.0000.0000.0000.000
184A184ASP-1-0.773-0.87445.805-0.108-0.1080.0000.0000.0000.000
185A185VAL0-0.067-0.03245.575-0.005-0.0050.0000.0000.0000.000
186A186THR0-0.089-0.07347.2220.0000.0000.0000.0000.0000.000
187A187LYS10.8570.93847.7770.1120.1120.0000.0000.0000.000
188A188GLU-1-0.868-0.92244.369-0.131-0.1310.0000.0000.0000.000
189A189PRO00.0340.00240.1880.0020.0020.0000.0000.0000.000
190A190GLU-1-0.813-0.90239.975-0.157-0.1570.0000.0000.0000.000
191A191GLN0-0.101-0.06042.0410.0060.0060.0000.0000.0000.000
192A192VAL00.0250.02343.4830.0030.0030.0000.0000.0000.000
193A193PHE0-0.026-0.02037.7150.0000.0000.0000.0000.0000.000
194A194ARG10.9430.95842.1100.1300.1300.0000.0000.0000.000
195A195GLU-1-0.883-0.93544.473-0.106-0.1060.0000.0000.0000.000
196A196VAL00.0360.01942.0580.0030.0030.0000.0000.0000.000
197A197GLU-1-0.858-0.92440.584-0.147-0.1470.0000.0000.0000.000
198A198ARG10.9200.96143.8640.1080.1080.0000.0000.0000.000
199A199GLU-1-0.874-0.92647.106-0.113-0.1130.0000.0000.0000.000
200A200LEU0-0.030-0.02141.4940.0010.0010.0000.0000.0000.000
201A201SER0-0.087-0.05145.5150.0030.0030.0000.0000.0000.000
202A202GLU-1-0.955-0.95746.466-0.088-0.0880.0000.0000.0000.000
203A203TYR0-0.096-0.08645.6630.0020.0020.0000.0000.0000.000
204A204PHE0-0.072-0.05242.793-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.895-0.92841.156-0.116-0.1160.0000.0000.0000.000
206A206VAL00.001-0.03139.447-0.008-0.0080.0000.0000.0000.000
207A207ILE0-0.060-0.02235.1130.0010.0010.0000.0000.0000.000
208A208GLU-1-0.806-0.90530.738-0.244-0.2440.0000.0000.0000.000
209A209ARG10.8690.93535.1670.1610.1610.0000.0000.0000.000
210A210LEU0-0.047-0.01027.9990.0010.0010.0000.0000.0000.000
211A211ASN00.0280.00332.465-0.008-0.0080.0000.0000.0000.000
212A212LEU0-0.002-0.00729.110-0.018-0.0180.0000.0000.0000.000
213A213GLU-1-0.895-0.89728.986-0.262-0.2620.0000.0000.0000.000
214A214PRO0-0.001-0.01525.719-0.006-0.0060.0000.0000.0000.000
215A215TYR0-0.027-0.03422.147-0.009-0.0090.0000.0000.0000.000
216A216GLU-1-0.883-0.94627.573-0.264-0.2640.0000.0000.0000.000
217A217LYS10.9220.95931.0530.2680.2680.0000.0000.0000.000
218A218ASP-1-0.867-0.92234.271-0.185-0.1850.0000.0000.0000.000
219A219HIS0-0.026-0.04333.6780.0130.0130.0000.0000.0000.000
220A220ALA00.0030.01434.212-0.009-0.0090.0000.0000.0000.000
221A221LEU0-0.030-0.01030.3910.0030.0030.0000.0000.0000.000
222A222PHE00.0030.00034.0450.0000.0000.0000.0000.0000.000
223A223VAL0-0.053-0.02232.425-0.004-0.0040.0000.0000.0000.000
224A224VAL00.0340.01435.8080.0070.0070.0000.0000.0000.000
225A225ARG10.8950.94038.4230.1210.1210.0000.0000.0000.000
226A226LYS10.9130.98740.3420.1080.1080.0000.0000.0000.000
227A227THR00.0030.00143.4860.0040.0040.0000.0000.0000.000