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: 72Y7K

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2887249.558578
FMO2-HF: Nuclear repulsion 2798300.865381
FMO2-HF: Total energy -88948.693197
FMO2-MP2: Total energy -89213.8317


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.
-13.811-8.2660.261-2.819-2.989-0.008
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 : 0.022 / q_NPA : 0.010
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-1-0.933-0.9563.697-2.1270.685-0.009-1.375-1.4280.007
4A4VAL0-0.035-0.0115.6170.1460.1460.0000.0000.0000.000
5A5LYS10.9931.0089.1731.2801.2800.0000.0000.0000.000
6A6LYS10.9400.95011.7460.2750.2750.0000.0000.0000.000
7A7HIS00.0270.03615.4740.0300.0300.0000.0000.0000.000
8A8LYS10.9470.97917.7420.3640.3640.0000.0000.0000.000
9A9PHE0-0.033-0.02821.0900.0440.0440.0000.0000.0000.000
10A10PRO00.0360.01021.011-0.033-0.0330.0000.0000.0000.000
11A11GLY00.0370.01120.5130.0120.0120.0000.0000.0000.000
12A12VAL0-0.032-0.01118.653-0.030-0.0300.0000.0000.0000.000
13A13TYR0-0.010-0.01613.6870.0550.0550.0000.0000.0000.000
14A14THR0-0.046-0.02512.1730.0560.0560.0000.0000.0000.000
15A15VAL0-0.029-0.0188.7220.0220.0220.0000.0000.0000.000
16A16ILE0-0.019-0.0326.9270.4790.4790.0000.0000.0000.000
17A17ASP-1-0.858-0.9214.552-4.175-4.051-0.001-0.029-0.0940.000
18A18ASP-1-0.879-0.9392.913-12.085-9.5470.272-1.414-1.397-0.015
19A19ASP-1-0.984-0.9855.278-0.399-0.328-0.001-0.001-0.0700.000
20A20GLY0-0.067-0.0418.6460.4490.4490.0000.0000.0000.000
21A21SER00.0230.0068.326-0.185-0.1850.0000.0000.0000.000
22A22GLU-1-0.988-0.99410.503-0.542-0.5420.0000.0000.0000.000
23A23ARG10.9250.98712.5891.4611.4610.0000.0000.0000.000
24A24ILE00.0150.01313.948-0.073-0.0730.0000.0000.0000.000
25A25ALA0-0.008-0.02014.819-0.015-0.0150.0000.0000.0000.000
26A26THR0-0.036-0.00616.8540.0330.0330.0000.0000.0000.000
27A27LYS10.8680.94115.9820.3240.3240.0000.0000.0000.000
28A28ASN0-0.050-0.03518.0290.0610.0610.0000.0000.0000.000
29A29LEU0-0.017-0.00220.1300.0150.0150.0000.0000.0000.000
30A30VAL0-0.048-0.02423.2530.0280.0280.0000.0000.0000.000
31A31PRO0-0.032-0.01319.396-0.012-0.0120.0000.0000.0000.000
32A32GLY00.0310.01020.2990.0330.0330.0000.0000.0000.000
33A33GLN0-0.020-0.00921.864-0.009-0.0090.0000.0000.0000.000
34A34ARG10.9080.96420.9220.2260.2260.0000.0000.0000.000
35A35VAL0-0.0020.01222.4810.0210.0210.0000.0000.0000.000
36A36TYR00.016-0.01522.859-0.027-0.0270.0000.0000.0000.000
37A37GLY0-0.007-0.00322.0280.0030.0030.0000.0000.0000.000
38A38GLU-1-0.895-0.93519.061-0.439-0.4390.0000.0000.0000.000
39A39ARG10.9040.95115.4830.7370.7370.0000.0000.0000.000
40A40VAL00.001-0.00714.635-0.045-0.0450.0000.0000.0000.000
41A41ILE00.0320.0238.8190.0010.0010.0000.0000.0000.000
42A42LYS10.9330.95810.7920.4890.4890.0000.0000.0000.000
43A43TRP00.0390.0125.188-0.004-0.0040.0000.0000.0000.000
44A44GLU-1-0.898-0.9607.833-0.263-0.2630.0000.0000.0000.000
45A45GLY0-0.0210.00010.0600.0620.0620.0000.0000.0000.000
46A46GLU-1-0.868-0.92512.821-0.317-0.3170.0000.0000.0000.000
47A47GLU-1-0.848-0.93413.411-0.510-0.5100.0000.0000.0000.000
48A48TYR00.0080.00912.4140.0520.0520.0000.0000.0000.000
49A49ARG10.8170.89314.6120.3660.3660.0000.0000.0000.000
50A50ILE00.0200.01012.7920.0170.0170.0000.0000.0000.000
51A51TRP0-0.065-0.06416.6780.0970.0970.0000.0000.0000.000
52A52ASN0-0.023-0.01219.612-0.024-0.0240.0000.0000.0000.000
53A53PRO00.0820.04120.3500.0480.0480.0000.0000.0000.000
54A54ASN00.0080.00223.3050.0310.0310.0000.0000.0000.000
55A55ARG10.9270.96623.9800.3950.3950.0000.0000.0000.000
56A56SER0-0.0140.00124.9330.0150.0150.0000.0000.0000.000
57A57LYS10.9520.96426.4230.2230.2230.0000.0000.0000.000
58A58LEU00.0130.01727.247-0.003-0.0030.0000.0000.0000.000
59A59GLY00.0100.01223.535-0.012-0.0120.0000.0000.0000.000
60A60ALA00.020-0.00423.265-0.029-0.0290.0000.0000.0000.000
61A61ALA00.0130.01125.266-0.003-0.0030.0000.0000.0000.000
62A62ILE0-0.026-0.02421.4500.0010.0010.0000.0000.0000.000
63A63MET0-0.057-0.02717.958-0.007-0.0070.0000.0000.0000.000
64A64ASN0-0.035-0.00321.941-0.033-0.0330.0000.0000.0000.000
65A65GLY0-0.007-0.00123.9150.0280.0280.0000.0000.0000.000
66A66LEU0-0.054-0.00825.0880.0250.0250.0000.0000.0000.000
67A67LYS10.8670.91426.1910.1810.1810.0000.0000.0000.000
68A68ASN0-0.093-0.05528.4820.0100.0100.0000.0000.0000.000
69A69PHE00.0580.02025.007-0.003-0.0030.0000.0000.0000.000
70A70PRO0-0.019-0.02628.606-0.001-0.0010.0000.0000.0000.000
71A71ILE00.0010.01727.9180.0120.0120.0000.0000.0000.000
72A72LYS10.9360.96126.7940.1740.1740.0000.0000.0000.000
73A73PRO00.011-0.00124.4400.0100.0100.0000.0000.0000.000
74A74GLY00.0130.00627.2680.0120.0120.0000.0000.0000.000
75A75LYS10.8750.95830.6230.1630.1630.0000.0000.0000.000
76A76SER0-0.009-0.00132.697-0.003-0.0030.0000.0000.0000.000
77A77VAL0-0.007-0.02831.949-0.001-0.0010.0000.0000.0000.000
78A78LEU00.0090.02635.3160.0010.0010.0000.0000.0000.000
79A79TYR00.008-0.01431.012-0.015-0.0150.0000.0000.0000.000
80A80LEU00.0100.01036.5940.0030.0030.0000.0000.0000.000
81A81GLY00.0720.04137.670-0.007-0.0070.0000.0000.0000.000
82A82ILE0-0.072-0.04733.481-0.013-0.0130.0000.0000.0000.000
83A83ALA0-0.012-0.01233.315-0.013-0.0130.0000.0000.0000.000
84A84SER0-0.0450.00033.321-0.013-0.0130.0000.0000.0000.000
85A85GLY00.0060.00329.660-0.011-0.0110.0000.0000.0000.000
86A86THR0-0.008-0.02524.731-0.007-0.0070.0000.0000.0000.000
87A87THR00.0190.02026.243-0.028-0.0280.0000.0000.0000.000
88A88ALA00.0890.06427.553-0.007-0.0070.0000.0000.0000.000
89A89SER00.0230.00425.038-0.011-0.0110.0000.0000.0000.000
90A90HIS10.8330.90920.1260.4840.4840.0000.0000.0000.000
91A91VAL00.0610.03324.353-0.003-0.0030.0000.0000.0000.000
92A92SER0-0.030-0.02927.1540.0070.0070.0000.0000.0000.000
93A93ASP-1-0.696-0.82021.750-0.386-0.3860.0000.0000.0000.000
94A94ILE0-0.076-0.02322.7740.0050.0050.0000.0000.0000.000
95A95VAL0-0.0420.01324.3770.0140.0140.0000.0000.0000.000
96A96GLY00.0690.03826.2680.0160.0160.0000.0000.0000.000
97A97TRP00.011-0.02026.1980.0110.0110.0000.0000.0000.000
98A98GLU-1-0.949-0.96029.351-0.119-0.1190.0000.0000.0000.000
99A99GLY00.0010.00030.7800.0080.0080.0000.0000.0000.000
100A100LYS10.8620.93232.2660.1270.1270.0000.0000.0000.000
101A101ILE0-0.0110.00729.973-0.002-0.0020.0000.0000.0000.000
102A102PHE00.0190.00134.5350.0040.0040.0000.0000.0000.000
103A103GLY00.0190.00037.062-0.004-0.0040.0000.0000.0000.000
104A104ILE00.0020.01737.7450.0060.0060.0000.0000.0000.000
105A105GLU-1-0.826-0.93038.070-0.176-0.1760.0000.0000.0000.000
106A106PHE00.0860.04641.6760.0060.0060.0000.0000.0000.000
107A107SER00.0110.00943.2350.0070.0070.0000.0000.0000.000
108A108PRO00.0580.01243.225-0.005-0.0050.0000.0000.0000.000
109A109ARG10.8330.92142.4310.1140.1140.0000.0000.0000.000
110A110VAL00.1110.05738.365-0.003-0.0030.0000.0000.0000.000
111A111LEU00.0290.01738.563-0.007-0.0070.0000.0000.0000.000
112A112ARG10.9180.95638.7910.1170.1170.0000.0000.0000.000
113A113GLU-1-0.959-0.98837.096-0.154-0.1540.0000.0000.0000.000
114A114LEU00.0120.01933.192-0.010-0.0100.0000.0000.0000.000
115A115VAL0-0.007-0.00434.002-0.008-0.0080.0000.0000.0000.000
116A116PRO00.0120.00532.109-0.003-0.0030.0000.0000.0000.000
117A117ILE0-0.0290.00028.430-0.014-0.0140.0000.0000.0000.000
118A118VAL0-0.033-0.03929.379-0.014-0.0140.0000.0000.0000.000
119A119GLU-1-0.940-0.94631.753-0.158-0.1580.0000.0000.0000.000
120A120GLU-1-0.872-0.93927.775-0.190-0.1900.0000.0000.0000.000
121A121ARG10.8150.90623.4180.3040.3040.0000.0000.0000.000
122A122ARG10.9200.93130.1410.1460.1460.0000.0000.0000.000
123A123ASN0-0.0220.02028.2600.0080.0080.0000.0000.0000.000
124A124ILE0-0.003-0.00430.167-0.002-0.0020.0000.0000.0000.000
125A125VAL0-0.025-0.01633.8820.0070.0070.0000.0000.0000.000
126A126PRO0-0.031-0.02136.4650.0000.0000.0000.0000.0000.000
127A127ILE0-0.007-0.00638.9220.0080.0080.0000.0000.0000.000
128A128LEU0-0.029-0.01542.399-0.004-0.0040.0000.0000.0000.000
129A129GLY00.001-0.01544.8710.0050.0050.0000.0000.0000.000
130A130ASP-1-0.816-0.87745.620-0.112-0.1120.0000.0000.0000.000
131A131ALA00.0290.00543.7450.0030.0030.0000.0000.0000.000
132A132THR0-0.064-0.06045.7940.0020.0020.0000.0000.0000.000
133A133LYS10.9430.98748.9260.0910.0910.0000.0000.0000.000
134A134PRO00.0570.03246.9880.0000.0000.0000.0000.0000.000
135A135GLU-1-0.890-0.96248.456-0.088-0.0880.0000.0000.0000.000
136A136GLU-1-0.936-0.97150.376-0.087-0.0870.0000.0000.0000.000
137A137TYR0-0.021-0.01544.4830.0010.0010.0000.0000.0000.000
138A138ARG10.8910.94746.9580.0780.0780.0000.0000.0000.000
139A139ALA0-0.046-0.01448.4940.0010.0010.0000.0000.0000.000
140A140LEU0-0.049-0.02044.6740.0010.0010.0000.0000.0000.000
141A141VAL0-0.0120.00541.499-0.004-0.0040.0000.0000.0000.000
142A142PRO0-0.0090.01441.0160.0050.0050.0000.0000.0000.000
143A143LYS10.9100.93542.9850.0870.0870.0000.0000.0000.000
144A144VAL0-0.010-0.01338.245-0.001-0.0010.0000.0000.0000.000
145A145ASP-1-0.854-0.92735.477-0.128-0.1280.0000.0000.0000.000
146A146VAL0-0.024-0.02333.186-0.002-0.0020.0000.0000.0000.000
147A147ILE00.0450.04736.3680.0010.0010.0000.0000.0000.000
148A148PHE0-0.051-0.04132.199-0.008-0.0080.0000.0000.0000.000
149A149GLU-1-0.803-0.93335.579-0.143-0.1430.0000.0000.0000.000
150A150ASP-1-0.855-0.91634.041-0.228-0.2280.0000.0000.0000.000
151A151VAL00.0480.01836.8520.0010.0010.0000.0000.0000.000
152A152ALA0-0.025-0.00139.6350.0040.0040.0000.0000.0000.000
153A153GLN0-0.012-0.02241.3560.0020.0020.0000.0000.0000.000
154A154PRO00.0520.01245.036-0.002-0.0020.0000.0000.0000.000
155A155THR00.0010.00447.5760.0010.0010.0000.0000.0000.000
156A156GLN00.0150.00640.838-0.004-0.0040.0000.0000.0000.000
157A157ALA00.0630.04444.054-0.003-0.0030.0000.0000.0000.000
158A158LYS10.9500.96645.1280.0940.0940.0000.0000.0000.000
159A159ILE0-0.045-0.00343.8500.0030.0030.0000.0000.0000.000
160A160LEU00.0290.02740.2950.0010.0010.0000.0000.0000.000
161A161ILE0-0.002-0.00743.7870.0010.0010.0000.0000.0000.000
162A162ASP-1-0.820-0.90546.620-0.094-0.0940.0000.0000.0000.000
163A163ASN0-0.047-0.04043.6650.0020.0020.0000.0000.0000.000
164A164ALA0-0.021-0.01643.5800.0010.0010.0000.0000.0000.000
165A165GLU-1-0.873-0.89244.810-0.084-0.0840.0000.0000.0000.000
166A166VAL0-0.046-0.00847.6780.0040.0040.0000.0000.0000.000
167A167TYR0-0.041-0.05643.2240.0030.0030.0000.0000.0000.000
168A168LEU0-0.0570.01539.347-0.001-0.0010.0000.0000.0000.000
169A169LYS10.8690.93138.8210.1200.1200.0000.0000.0000.000
170A170ARG11.0301.01442.6240.0770.0770.0000.0000.0000.000
171A171GLY0-0.062-0.03041.2950.0010.0010.0000.0000.0000.000
172A172GLY00.0130.01038.479-0.006-0.0060.0000.0000.0000.000
173A173TYR0-0.026-0.03235.5070.0030.0030.0000.0000.0000.000
174A174GLY00.0520.03437.6070.0010.0010.0000.0000.0000.000
175A175MET0-0.065-0.02630.112-0.007-0.0070.0000.0000.0000.000
176A176ILE00.0600.04435.603-0.001-0.0010.0000.0000.0000.000
177A177ALA0-0.023-0.00933.667-0.006-0.0060.0000.0000.0000.000
178A178VAL00.0280.02035.5440.0060.0060.0000.0000.0000.000
179A179LYS10.9690.99937.6330.1680.1680.0000.0000.0000.000
180A180SER00.0840.03738.9340.0110.0110.0000.0000.0000.000
181A181ARG10.9750.97141.3400.1470.1470.0000.0000.0000.000
182A182SER0-0.115-0.05542.0260.0040.0040.0000.0000.0000.000
183A183ILE00.004-0.00343.5010.0040.0040.0000.0000.0000.000
184A184ASP-1-0.786-0.88045.800-0.102-0.1020.0000.0000.0000.000
185A185VAL0-0.073-0.03645.613-0.005-0.0050.0000.0000.0000.000
186A186THR0-0.108-0.08247.2150.0000.0000.0000.0000.0000.000
187A187LYS10.8800.95147.8060.1060.1060.0000.0000.0000.000
188A188GLU-1-0.923-0.96244.406-0.125-0.1250.0000.0000.0000.000
189A189PRO00.0320.00140.1410.0020.0020.0000.0000.0000.000
190A190GLU-1-0.869-0.94139.425-0.161-0.1610.0000.0000.0000.000
191A191GLN0-0.082-0.03942.0350.0060.0060.0000.0000.0000.000
192A192VAL00.0380.03243.4380.0030.0030.0000.0000.0000.000
193A193PHE0-0.025-0.01937.8570.0000.0000.0000.0000.0000.000
194A194ARG10.9710.98942.1040.1210.1210.0000.0000.0000.000
195A195GLU-1-0.905-0.95344.466-0.101-0.1010.0000.0000.0000.000
196A196VAL00.0380.02241.9680.0030.0030.0000.0000.0000.000
197A197GLU-1-0.886-0.94241.142-0.137-0.1370.0000.0000.0000.000
198A198ARG10.9170.95743.8570.1040.1040.0000.0000.0000.000
199A199GLU-1-0.878-0.92347.122-0.105-0.1050.0000.0000.0000.000
200A200LEU0-0.032-0.02341.4620.0010.0010.0000.0000.0000.000
201A201SER0-0.089-0.05345.5080.0030.0030.0000.0000.0000.000
202A202GLU-1-0.953-0.95746.460-0.084-0.0840.0000.0000.0000.000
203A203TYR0-0.094-0.07845.6900.0020.0020.0000.0000.0000.000
204A204PHE0-0.073-0.05242.647-0.001-0.0010.0000.0000.0000.000
205A205GLU-1-0.912-0.94141.134-0.115-0.1150.0000.0000.0000.000
206A206VAL0-0.007-0.03139.521-0.008-0.0080.0000.0000.0000.000
207A207ILE0-0.053-0.01535.0410.0010.0010.0000.0000.0000.000
208A208GLU-1-0.798-0.89930.599-0.237-0.2370.0000.0000.0000.000
209A209ARG10.9190.96135.1330.1580.1580.0000.0000.0000.000
210A210LEU0-0.039-0.00627.9760.0020.0020.0000.0000.0000.000
211A211ASN00.0790.03932.323-0.010-0.0100.0000.0000.0000.000
212A212LEU0-0.005-0.01729.060-0.016-0.0160.0000.0000.0000.000
213A213GLU-1-0.942-0.93028.980-0.253-0.2530.0000.0000.0000.000
214A214PRO0-0.010-0.02725.691-0.007-0.0070.0000.0000.0000.000
215A215TYR0-0.041-0.03521.3770.0070.0070.0000.0000.0000.000
216A216GLU-1-0.922-0.95727.567-0.265-0.2650.0000.0000.0000.000
217A217LYS10.9430.96431.2720.2440.2440.0000.0000.0000.000
218A218ASP-1-0.882-0.93034.264-0.173-0.1730.0000.0000.0000.000
219A219HIS0-0.038-0.04633.6450.0110.0110.0000.0000.0000.000
220A220ALA00.0030.01034.213-0.008-0.0080.0000.0000.0000.000
221A221LEU0-0.029-0.01030.4130.0030.0030.0000.0000.0000.000
222A222PHE0-0.0010.00034.0380.0000.0000.0000.0000.0000.000
223A223VAL0-0.051-0.01932.449-0.004-0.0040.0000.0000.0000.000
224A224VAL00.0420.02135.7900.0060.0060.0000.0000.0000.000
225A225ARG10.8960.94238.2750.1170.1170.0000.0000.0000.000
226A226LYS10.9010.96940.1930.1040.1040.0000.0000.0000.000
227A227THR00.0110.00243.3410.0040.0040.0000.0000.0000.000