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: G6QK1

Calculation Name: 2C08-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C08

Chain ID: A

ChEMBL ID:

UniProt ID: O35179

Base Structure: X-ray

Registration Date: 2023-06-21

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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010091.097237
FMO2-HF: Nuclear repulsion 1926268.104642
FMO2-HF: Total energy -83822.992595
FMO2-MP2: Total energy -84064.790835


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:25:GLU)


Summations of interaction energy for fragment #1(A:25:GLU)
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.
-16.078-11.6015.221-4.475-5.2220.051
Interaction energy analysis for fragmet #1(A:25:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.973
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].
3A27THR00.003-0.0163.8161.2643.696-0.029-1.342-1.0600.001
4A28LYS10.7990.9102.205-89.689-87.7115.251-3.124-4.1050.050
5A29LEU00.0260.0267.145-1.456-1.4560.0000.0000.0000.000
6A30ASP-1-0.790-0.89010.60018.94818.9480.0000.0000.0000.000
7A31ASP-1-0.881-0.95513.04320.38920.3890.0000.0000.0000.000
8A32ASP-1-0.924-0.94514.56414.19014.1900.0000.0000.0000.000
9A33PHE00.0020.00413.708-0.245-0.2450.0000.0000.0000.000
10A34LYS10.8710.9208.546-23.493-23.4930.0000.0000.0000.000
11A35GLU-1-0.791-0.85714.02213.78413.7840.0000.0000.0000.000
12A36MET0-0.024-0.00617.315-0.683-0.6830.0000.0000.0000.000
13A37GLU-1-0.835-0.93212.96819.65019.6500.0000.0000.0000.000
14A38ARG10.8110.87016.419-14.859-14.8590.0000.0000.0000.000
15A39LYS10.9280.96917.890-12.561-12.5610.0000.0000.0000.000
16A40VAL00.0470.04519.862-0.617-0.6170.0000.0000.0000.000
17A41ASP-1-0.821-0.88018.80413.92413.9240.0000.0000.0000.000
18A42VAL0-0.066-0.03820.839-0.517-0.5170.0000.0000.0000.000
19A43THR0-0.010-0.01923.133-0.570-0.5700.0000.0000.0000.000
20A44SER0-0.0170.00223.699-0.369-0.3690.0000.0000.0000.000
21A45ARG10.8270.87020.414-13.731-13.7310.0000.0000.0000.000
22A46ALA0-0.0150.00325.850-0.393-0.3930.0000.0000.0000.000
23A47VAL00.0370.02328.526-0.379-0.3790.0000.0000.0000.000
24A48MET00.0120.01228.505-0.443-0.4430.0000.0000.0000.000
25A49GLU-1-0.857-0.90629.6799.4889.4880.0000.0000.0000.000
26A50ILE00.0150.00431.459-0.354-0.3540.0000.0000.0000.000
27A51MET0-0.0050.02933.187-0.408-0.4080.0000.0000.0000.000
28A52THR0-0.026-0.02433.182-0.280-0.2800.0000.0000.0000.000
29A53LYS10.8640.89233.027-9.228-9.2280.0000.0000.0000.000
30A54THR0-0.005-0.00137.348-0.258-0.2580.0000.0000.0000.000
31A55ILE0-0.020-0.01438.019-0.274-0.2740.0000.0000.0000.000
32A56GLU-1-0.907-0.95137.8307.7617.7610.0000.0000.0000.000
33A57TYR0-0.038-0.00741.217-0.164-0.1640.0000.0000.0000.000
34A58LEU0-0.0150.00143.095-0.167-0.1670.0000.0000.0000.000
35A59GLN0-0.080-0.04244.419-0.224-0.2240.0000.0000.0000.000
36A60PRO00.0350.02244.4870.1210.1210.0000.0000.0000.000
37A61ASN00.0110.00345.3620.0960.0960.0000.0000.0000.000
38A62PRO00.016-0.01142.7320.0050.0050.0000.0000.0000.000
39A63ALA0-0.069-0.02644.5520.0470.0470.0000.0000.0000.000
40A64SER0-0.009-0.00546.966-0.133-0.1330.0000.0000.0000.000
41A65ARG10.8270.91040.008-7.417-7.4170.0000.0000.0000.000
42A66ALA0-0.029-0.01043.8940.1410.1410.0000.0000.0000.000
43A67LYS10.8950.95042.786-6.799-6.7990.0000.0000.0000.000
44A87PRO00.0050.00252.475-0.022-0.0220.0000.0000.0000.000
45A88GLN00.002-0.01651.3510.1460.1460.0000.0000.0000.000
46A89ALA00.0190.00953.764-0.103-0.1030.0000.0000.0000.000
47A90GLU-1-0.855-0.93654.4365.6525.6520.0000.0000.0000.000
48A91ALA00.0430.02257.607-0.115-0.1150.0000.0000.0000.000
49A92LEU0-0.011-0.00556.387-0.100-0.1000.0000.0000.0000.000
50A93LEU0-0.018-0.00959.694-0.103-0.1030.0000.0000.0000.000
51A94ALA00.0400.01461.526-0.103-0.1030.0000.0000.0000.000
52A95GLU-1-0.966-0.97563.1514.8444.8440.0000.0000.0000.000
53A96ALA0-0.008-0.00664.095-0.103-0.1030.0000.0000.0000.000
54A97MET0-0.031-0.01264.228-0.090-0.0900.0000.0000.0000.000
55A98LEU00.0170.01667.317-0.102-0.1020.0000.0000.0000.000
56A99LYS10.7530.86668.684-4.564-4.5640.0000.0000.0000.000
57A100PHE00.023-0.01067.549-0.068-0.0680.0000.0000.0000.000
58A101GLY00.0220.02471.538-0.067-0.0670.0000.0000.0000.000
59A102ARG10.9090.94970.023-4.496-4.4960.0000.0000.0000.000
60A103GLU-1-0.917-0.93673.6574.2904.2900.0000.0000.0000.000
61A104LEU0-0.065-0.02674.797-0.050-0.0500.0000.0000.0000.000
62A105GLY00.0020.01077.491-0.062-0.0620.0000.0000.0000.000
63A106ASP-1-0.956-1.01179.2243.9213.9210.0000.0000.0000.000
64A107ASP-1-0.954-0.95681.5253.7403.7400.0000.0000.0000.000
65A108CYS0-0.070-0.01779.3030.0110.0110.0000.0000.0000.000
66A109ASN00.0470.01378.547-0.013-0.0130.0000.0000.0000.000
67A110PHE00.006-0.01371.0760.0420.0420.0000.0000.0000.000
68A111GLY00.0920.04674.2140.0590.0590.0000.0000.0000.000
69A112PRO00.0290.01374.2690.0740.0740.0000.0000.0000.000
70A113ALA00.0100.01273.0290.0500.0500.0000.0000.0000.000
71A114LEU0-0.048-0.01969.1660.0810.0810.0000.0000.0000.000
72A115GLY00.0250.01269.6810.0710.0710.0000.0000.0000.000
73A116GLU-1-0.816-0.88770.1634.2874.2870.0000.0000.0000.000
74A117VAL00.000-0.00965.8420.0640.0640.0000.0000.0000.000
75A118GLY00.0510.01865.8520.0900.0900.0000.0000.0000.000
76A119GLU-1-0.867-0.92465.3184.6894.6890.0000.0000.0000.000
77A120ALA0-0.0060.00364.9240.0700.0700.0000.0000.0000.000
78A121MET0-0.030-0.01258.9090.1010.1010.0000.0000.0000.000
79A122ARG10.7420.83460.802-4.730-4.7300.0000.0000.0000.000
80A123GLU-1-0.872-0.92661.0934.9234.9230.0000.0000.0000.000
81A124LEU0-0.014-0.01858.1640.0960.0960.0000.0000.0000.000
82A125SER00.0300.01056.9730.1270.1270.0000.0000.0000.000
83A126GLU-1-0.887-0.91956.3125.1525.1520.0000.0000.0000.000
84A127VAL0-0.011-0.00355.2680.0980.0980.0000.0000.0000.000
85A128LYS10.8070.91148.939-6.122-6.1220.0000.0000.0000.000
86A129ASP-1-0.841-0.90851.8895.8615.8610.0000.0000.0000.000
87A130SER0-0.091-0.06051.8450.1100.1100.0000.0000.0000.000
88A131LEU00.0250.02048.0160.1070.1070.0000.0000.0000.000
89A132ASP-1-0.778-0.87547.6036.6436.6430.0000.0000.0000.000
90A133MET0-0.051-0.03147.0500.1860.1860.0000.0000.0000.000
91A134GLU-1-0.892-0.94747.6166.3636.3630.0000.0000.0000.000
92A135VAL00.004-0.00442.9240.1630.1630.0000.0000.0000.000
93A136LYS10.7690.85242.197-6.942-6.9420.0000.0000.0000.000
94A137GLN0-0.043-0.02942.6490.0840.0840.0000.0000.0000.000
95A138ASN0-0.001-0.00343.2430.1130.1130.0000.0000.0000.000
96A139PHE0-0.019-0.00636.8890.1230.1230.0000.0000.0000.000
97A140ILE0-0.024-0.01338.3080.2040.2040.0000.0000.0000.000
98A141ASP-1-0.775-0.86437.5767.5407.5400.0000.0000.0000.000
99A142PRO0-0.0110.00837.5010.1980.1980.0000.0000.0000.000
100A143LEU00.0540.03833.1420.2680.2680.0000.0000.0000.000
101A144GLN0-0.032-0.02832.9780.3190.3190.0000.0000.0000.000
102A145ASN0-0.040-0.03633.2250.1520.1520.0000.0000.0000.000
103A146LEU00.0090.00730.0270.1770.1770.0000.0000.0000.000
104A147HIS0-0.007-0.01426.4370.4030.4030.0000.0000.0000.000
105A148ASP-1-0.935-0.96028.6869.3989.3980.0000.0000.0000.000
106A149LYS10.8540.92429.307-8.237-8.2370.0000.0000.0000.000
107A150ASP-1-0.782-0.89128.7509.8119.8110.0000.0000.0000.000
108A151LEU00.0310.02624.6610.5120.5120.0000.0000.0000.000
109A152ARG10.9610.99024.376-9.798-9.7980.0000.0000.0000.000
110A153GLU-1-0.942-0.95224.65711.06411.0640.0000.0000.0000.000
111A154ILE00.0500.02121.1040.5300.5300.0000.0000.0000.000
112A155GLN0-0.0130.00020.0970.3520.3520.0000.0000.0000.000
113A156HIS0-0.082-0.04519.8790.8340.8340.0000.0000.0000.000
114A157HIS0-0.026-0.03620.4150.9510.9510.0000.0000.0000.000
115A158LEU00.0490.02915.1010.6740.6740.0000.0000.0000.000
116A159LYS10.9140.96615.791-13.186-13.1860.0000.0000.0000.000
117A160LYS10.9110.95316.246-12.269-12.2690.0000.0000.0000.000
118A161LEU00.0160.01613.8730.5390.5390.0000.0000.0000.000
119A162GLU-1-0.776-0.8629.27427.60227.6020.0000.0000.0000.000
120A163GLY0-0.034-0.01812.0371.2271.2270.0000.0000.0000.000
121A164ARG10.7680.85413.520-13.703-13.7030.0000.0000.0000.000
122A165ARG10.7950.9065.323-30.831-30.764-0.001-0.009-0.0570.000
123A166LEU0-0.033-0.0167.6141.4681.4680.0000.0000.0000.000
124A167ASP-1-0.895-0.9539.97718.55018.5500.0000.0000.0000.000
125A168PHE00.0370.01710.117-0.347-0.3470.0000.0000.0000.000
126A169ASP-1-0.756-0.8656.43634.38434.3840.0000.0000.0000.000
127A170TYR0-0.081-0.0468.4200.2380.2380.0000.0000.0000.000
128A171LYS10.8180.87310.452-16.691-16.6910.0000.0000.0000.000
129A172LYS10.9210.9729.435-22.854-22.8540.0000.0000.0000.000
130A173LYS10.9380.9526.578-31.856-31.8560.0000.0000.0000.000
131A174ARG10.8280.92610.245-18.154-18.1540.0000.0000.0000.000
132A175GLN00.0860.05913.402-0.075-0.0750.0000.0000.0000.000
133A176GLY0-0.009-0.00815.218-0.847-0.8470.0000.0000.0000.000
134A177LYS10.8920.93417.576-15.916-15.9160.0000.0000.0000.000
135A178ILE0-0.0160.01516.342-0.523-0.5230.0000.0000.0000.000
136A179PRO00.0230.02020.0750.1120.1120.0000.0000.0000.000
137A180ASP-1-0.853-0.93920.03514.04114.0410.0000.0000.0000.000
138A181GLU-1-0.802-0.87320.35312.27712.2770.0000.0000.0000.000
139A182GLU-1-0.851-0.91019.17014.64614.6460.0000.0000.0000.000
140A183LEU0-0.008-0.00213.5170.5030.5030.0000.0000.0000.000
141A184ARG10.8150.88616.924-11.826-11.8260.0000.0000.0000.000
142A185GLN0-0.005-0.02219.2180.3200.3200.0000.0000.0000.000
143A186ALA0-0.051-0.01915.343-0.041-0.0410.0000.0000.0000.000
144A187LEU0-0.0040.00214.1940.4970.4970.0000.0000.0000.000
145A188GLU-1-0.847-0.91416.25512.31912.3190.0000.0000.0000.000
146A189LYS10.8840.93618.440-13.520-13.5200.0000.0000.0000.000
147A190PHE0-0.017-0.00912.1970.1570.1570.0000.0000.0000.000
148A191ASP-1-0.856-0.93216.28816.77616.7760.0000.0000.0000.000
149A192GLU-1-0.795-0.88418.20312.78712.7870.0000.0000.0000.000
150A193SER0-0.045-0.04517.988-0.251-0.2510.0000.0000.0000.000
151A194LYS10.7960.88514.327-17.485-17.4850.0000.0000.0000.000
152A195GLU-1-0.910-0.94817.67412.16812.1680.0000.0000.0000.000
153A196ILE0-0.054-0.02421.191-0.448-0.4480.0000.0000.0000.000
154A197ALA0-0.023-0.01618.316-0.387-0.3870.0000.0000.0000.000
155A198GLU-1-0.794-0.89118.00814.96014.9600.0000.0000.0000.000
156A199SER0-0.0110.00820.856-0.522-0.5220.0000.0000.0000.000
157A200SER00.0100.00623.094-0.216-0.2160.0000.0000.0000.000
158A201MET0-0.033-0.02117.239-0.210-0.2100.0000.0000.0000.000
159A202PHE0-0.0130.00123.164-0.155-0.1550.0000.0000.0000.000
160A203ASN0-0.050-0.05225.115-0.624-0.6240.0000.0000.0000.000
161A204LEU0-0.0030.00825.346-0.291-0.2910.0000.0000.0000.000
162A205LEU0-0.070-0.05622.224-0.201-0.2010.0000.0000.0000.000
163A206GLU-1-0.936-0.94726.7659.5239.5230.0000.0000.0000.000
164A207MET0-0.0190.00429.705-0.336-0.3360.0000.0000.0000.000
165A208ASP-1-0.883-0.95030.0649.7229.7220.0000.0000.0000.000
166A209ILE0-0.043-0.02332.610-0.244-0.2440.0000.0000.0000.000
167A210GLU-1-0.869-0.94435.0648.0958.0950.0000.0000.0000.000
168A211GLN00.0200.01931.381-0.242-0.2420.0000.0000.0000.000
169A212VAL0-0.015-0.01634.884-0.194-0.1940.0000.0000.0000.000
170A213SER0-0.0090.00437.224-0.262-0.2620.0000.0000.0000.000
171A214GLN0-0.020-0.02034.964-0.201-0.2010.0000.0000.0000.000
172A215LEU0-0.018-0.01135.397-0.169-0.1690.0000.0000.0000.000
173A216SER0-0.019-0.01139.517-0.230-0.2300.0000.0000.0000.000
174A217ALA00.0210.01142.364-0.186-0.1860.0000.0000.0000.000
175A218LEU0-0.0160.00340.334-0.166-0.1660.0000.0000.0000.000
176A219VAL00.004-0.00842.615-0.161-0.1610.0000.0000.0000.000
177A220GLN0-0.055-0.01845.199-0.295-0.2950.0000.0000.0000.000
178A221ALA00.0670.04746.863-0.147-0.1470.0000.0000.0000.000
179A222GLN0-0.047-0.04444.300-0.083-0.0830.0000.0000.0000.000
180A223LEU0-0.030-0.01048.670-0.161-0.1610.0000.0000.0000.000
181A224GLU-1-0.807-0.89651.0655.4725.4720.0000.0000.0000.000
182A225TYR00.0160.00851.503-0.130-0.1300.0000.0000.0000.000
183A226HIS0-0.001-0.01749.503-0.207-0.2070.0000.0000.0000.000
184A227LYS10.8160.91054.330-5.774-5.7740.0000.0000.0000.000
185A228GLN00.0310.02056.870-0.106-0.1060.0000.0000.0000.000
186A229ALA00.003-0.00256.752-0.115-0.1150.0000.0000.0000.000
187A230VAL0-0.009-0.00957.663-0.109-0.1090.0000.0000.0000.000
188A231GLN0-0.007-0.00260.107-0.141-0.1410.0000.0000.0000.000
189A232ILE00.0140.01561.349-0.108-0.1080.0000.0000.0000.000
190A233LEU00.015-0.00159.435-0.095-0.0950.0000.0000.0000.000
191A234GLN0-0.0100.01463.724-0.071-0.0710.0000.0000.0000.000
192A235GLN00.0040.00565.884-0.108-0.1080.0000.0000.0000.000
193A236VAL0-0.003-0.00965.999-0.090-0.0900.0000.0000.0000.000
194A237THR0-0.034-0.02766.162-0.048-0.0480.0000.0000.0000.000
195A238VAL0-0.014-0.01068.759-0.066-0.0660.0000.0000.0000.000
196A239ARG10.8690.92471.651-4.337-4.3370.0000.0000.0000.000
197A240LEU00.0000.00069.063-0.070-0.0700.0000.0000.0000.000
198A241GLU-1-0.846-0.91772.4884.2464.2460.0000.0000.0000.000
199A242GLU-1-0.929-0.96974.2113.9523.9520.0000.0000.0000.000
200A243ARG10.9060.94076.009-4.171-4.1710.0000.0000.0000.000
201A244ILE0-0.070-0.03673.315-0.043-0.0430.0000.0000.0000.000
202A245ARG10.7840.87876.178-4.162-4.1620.0000.0000.0000.000
203A246GLN0-0.100-0.03980.305-0.080-0.0800.0000.0000.0000.000
204A247ALA0-0.0390.00080.911-0.047-0.0470.0000.0000.0000.000