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: 85JZY

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 OptAll
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 -2013389.051962
FMO2-HF: Nuclear repulsion 1929565.060153
FMO2-HF: Total energy -83823.991809
FMO2-MP2: Total energy -84065.398989


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.
-16.713-22.2417.278-6.034-5.7170.06
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 : -0.911 / q_NPA : -0.946
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].
3A27THR0-0.056-0.0593.8415.6787.700-0.010-1.073-0.9390.002
4A28LYS10.8070.9041.895-96.827-104.48417.289-4.937-4.6950.058
5A29LEU00.0130.0006.582-2.070-2.0700.0000.0000.0000.000
6A30ASP-1-0.785-0.87610.00619.83619.8360.0000.0000.0000.000
7A31ASP-1-0.879-0.95312.75120.79620.7960.0000.0000.0000.000
8A32ASP-1-0.925-0.94514.31414.31114.3110.0000.0000.0000.000
9A33PHE0-0.020-0.01313.424-0.352-0.3520.0000.0000.0000.000
10A34LYS10.8340.8898.348-23.956-23.9560.0000.0000.0000.000
11A35GLU-1-0.798-0.86414.03913.88613.8860.0000.0000.0000.000
12A36MET0-0.023-0.00317.450-0.777-0.7770.0000.0000.0000.000
13A37GLU-1-0.820-0.90912.34920.72820.7280.0000.0000.0000.000
14A38ARG10.8280.87916.183-14.890-14.8900.0000.0000.0000.000
15A39LYS10.9430.98017.570-12.556-12.5560.0000.0000.0000.000
16A40VAL00.0330.03519.378-0.624-0.6240.0000.0000.0000.000
17A41ASP-1-0.797-0.85918.27014.21014.2100.0000.0000.0000.000
18A42VAL0-0.049-0.02920.338-0.536-0.5360.0000.0000.0000.000
19A43THR0-0.011-0.01522.654-0.611-0.6110.0000.0000.0000.000
20A44SER0-0.026-0.01023.295-0.343-0.3430.0000.0000.0000.000
21A45ARG10.7930.84519.937-13.908-13.9080.0000.0000.0000.000
22A46ALA00.0100.01225.460-0.373-0.3730.0000.0000.0000.000
23A47VAL00.0180.01128.105-0.393-0.3930.0000.0000.0000.000
24A48MET00.0120.01628.307-0.453-0.4530.0000.0000.0000.000
25A49GLU-1-0.859-0.90129.5279.5549.5540.0000.0000.0000.000
26A50ILE00.0150.00231.231-0.346-0.3460.0000.0000.0000.000
27A51MET0-0.0120.02732.668-0.404-0.4040.0000.0000.0000.000
28A52THR0-0.022-0.02732.852-0.283-0.2830.0000.0000.0000.000
29A53LYS10.8580.89132.804-9.256-9.2560.0000.0000.0000.000
30A54THR0-0.009-0.00637.041-0.266-0.2660.0000.0000.0000.000
31A55ILE0-0.010-0.01037.696-0.262-0.2620.0000.0000.0000.000
32A56GLU-1-0.903-0.94237.3697.8477.8470.0000.0000.0000.000
33A57TYR0-0.029-0.00940.992-0.168-0.1680.0000.0000.0000.000
34A58LEU0-0.0120.00643.026-0.167-0.1670.0000.0000.0000.000
35A59GLN0-0.069-0.05144.149-0.223-0.2230.0000.0000.0000.000
36A60PRO00.0410.03144.1440.1140.1140.0000.0000.0000.000
37A61ASN00.019-0.00144.4740.1580.1580.0000.0000.0000.000
38A62PRO00.032-0.00342.4580.0150.0150.0000.0000.0000.000
39A63ALA0-0.047-0.02244.0940.0420.0420.0000.0000.0000.000
40A64SER00.0100.01546.708-0.119-0.1190.0000.0000.0000.000
41A65ARG10.7610.87639.513-7.472-7.4720.0000.0000.0000.000
42A66ALA0-0.036-0.01043.3540.1490.1490.0000.0000.0000.000
43A67LYS10.8360.91242.257-6.785-6.7850.0000.0000.0000.000
44A87PRO00.0090.00452.403-0.024-0.0240.0000.0000.0000.000
45A88GLN0-0.0010.00250.6990.1460.1460.0000.0000.0000.000
46A89ALA00.014-0.00253.430-0.097-0.0970.0000.0000.0000.000
47A90GLU-1-0.849-0.93654.0585.6935.6930.0000.0000.0000.000
48A91ALA00.0390.02057.255-0.114-0.1140.0000.0000.0000.000
49A92LEU0-0.007-0.00155.806-0.100-0.1000.0000.0000.0000.000
50A93LEU0-0.019-0.01359.339-0.096-0.0960.0000.0000.0000.000
51A94ALA00.0400.01761.199-0.101-0.1010.0000.0000.0000.000
52A95GLU-1-0.974-0.97862.7714.8594.8590.0000.0000.0000.000
53A96ALA0-0.008-0.00863.643-0.098-0.0980.0000.0000.0000.000
54A97MET0-0.046-0.01163.987-0.082-0.0820.0000.0000.0000.000
55A98LEU00.0350.01866.339-0.102-0.1020.0000.0000.0000.000
56A99LYS10.7180.85168.282-4.571-4.5710.0000.0000.0000.000
57A100PHE00.024-0.01467.243-0.066-0.0660.0000.0000.0000.000
58A101GLY00.0140.01371.061-0.063-0.0630.0000.0000.0000.000
59A102ARG10.9100.95469.289-4.525-4.5250.0000.0000.0000.000
60A103GLU-1-0.905-0.92573.2464.3054.3050.0000.0000.0000.000
61A104LEU0-0.034-0.01174.278-0.045-0.0450.0000.0000.0000.000
62A105GLY0-0.0050.01677.393-0.057-0.0570.0000.0000.0000.000
63A106ASP-1-0.918-0.99179.1213.9583.9580.0000.0000.0000.000
64A107ASP-1-0.954-0.96181.1453.7493.7490.0000.0000.0000.000
65A108CYS0-0.083-0.02479.1850.0030.0030.0000.0000.0000.000
66A109ASN00.0510.00478.1840.0060.0060.0000.0000.0000.000
67A110PHE00.007-0.00471.1500.0480.0480.0000.0000.0000.000
68A111GLY00.0670.03474.0110.0610.0610.0000.0000.0000.000
69A112PRO00.0170.01374.0130.0740.0740.0000.0000.0000.000
70A113ALA00.0180.02272.7990.0500.0500.0000.0000.0000.000
71A114LEU0-0.031-0.01568.7200.0830.0830.0000.0000.0000.000
72A115GLY00.0190.01069.2840.0710.0710.0000.0000.0000.000
73A116GLU-1-0.816-0.88569.8114.2974.2970.0000.0000.0000.000
74A117VAL0-0.006-0.01065.3660.0570.0570.0000.0000.0000.000
75A118GLY00.0470.00865.5200.0880.0880.0000.0000.0000.000
76A119GLU-1-0.872-0.92765.0884.7074.7070.0000.0000.0000.000
77A120ALA00.0040.00164.6210.0590.0590.0000.0000.0000.000
78A121MET0-0.034-0.00758.6570.0980.0980.0000.0000.0000.000
79A122ARG10.7270.82860.508-4.755-4.7550.0000.0000.0000.000
80A123GLU-1-0.875-0.92060.7154.9574.9570.0000.0000.0000.000
81A124LEU0-0.015-0.01657.9830.0930.0930.0000.0000.0000.000
82A125SER00.001-0.00356.4940.1260.1260.0000.0000.0000.000
83A126GLU-1-0.876-0.91955.9435.1815.1810.0000.0000.0000.000
84A127VAL0-0.008-0.00155.3270.0880.0880.0000.0000.0000.000
85A128LYS10.8250.90948.865-6.131-6.1310.0000.0000.0000.000
86A129ASP-1-0.837-0.91951.5255.8895.8890.0000.0000.0000.000
87A130SER0-0.085-0.05351.6290.1060.1060.0000.0000.0000.000
88A131LEU00.0250.02547.5170.1090.1090.0000.0000.0000.000
89A132ASP-1-0.766-0.86247.3516.6536.6530.0000.0000.0000.000
90A133MET0-0.034-0.01346.8420.1790.1790.0000.0000.0000.000
91A134GLU-1-0.862-0.93147.0396.4506.4500.0000.0000.0000.000
92A135VAL00.013-0.00142.5070.1560.1560.0000.0000.0000.000
93A136LYS10.7790.87042.000-6.960-6.9600.0000.0000.0000.000
94A137GLN0-0.020-0.01942.1590.0920.0920.0000.0000.0000.000
95A138ASN0-0.018-0.01842.7610.1420.1420.0000.0000.0000.000
96A139PHE0-0.022-0.00736.8140.1110.1110.0000.0000.0000.000
97A140ILE0-0.029-0.01338.0110.2110.2110.0000.0000.0000.000
98A141ASP-1-0.785-0.87037.3017.5447.5440.0000.0000.0000.000
99A142PRO0-0.027-0.00837.2510.1920.1920.0000.0000.0000.000
100A143LEU00.0380.02733.0310.2700.2700.0000.0000.0000.000
101A144GLN0-0.023-0.02332.1650.3390.3390.0000.0000.0000.000
102A145ASN0-0.029-0.02332.6090.1660.1660.0000.0000.0000.000
103A146LEU00.0510.02829.4220.2050.2050.0000.0000.0000.000
104A147HIS00.0180.00625.7780.4140.4140.0000.0000.0000.000
105A148ASP-1-0.893-0.93428.1859.3189.3180.0000.0000.0000.000
106A149LYS10.7760.87630.026-8.576-8.5760.0000.0000.0000.000
107A150ASP-1-0.803-0.90428.1549.9289.9280.0000.0000.0000.000
108A151LEU00.0170.01324.1200.4900.4900.0000.0000.0000.000
109A152ARG10.9450.98423.606-9.832-9.8320.0000.0000.0000.000
110A153GLU-1-0.919-0.94324.07611.11011.1100.0000.0000.0000.000
111A154ILE00.0420.02220.5350.5330.5330.0000.0000.0000.000
112A155GLN0-0.023-0.00719.3960.4700.4700.0000.0000.0000.000
113A156HIS0-0.068-0.03219.2560.7910.7910.0000.0000.0000.000
114A157HIS0-0.025-0.04220.0730.8680.8680.0000.0000.0000.000
115A158LEU00.0430.02714.3660.7050.7050.0000.0000.0000.000
116A159LYS10.9090.96415.210-13.163-13.1630.0000.0000.0000.000
117A160LYS10.8080.89316.035-12.841-12.8410.0000.0000.0000.000
118A161LEU00.0110.00913.4570.3370.3370.0000.0000.0000.000
119A162GLU-1-0.762-0.8488.67728.32128.3210.0000.0000.0000.000
120A163GLY0-0.029-0.01811.8211.2181.2180.0000.0000.0000.000
121A164ARG10.7740.86013.716-14.179-14.1790.0000.0000.0000.000
122A165ARG10.7670.8704.864-32.982-32.874-0.001-0.024-0.0830.000
123A166LEU0-0.025-0.0107.6401.6441.6440.0000.0000.0000.000
124A167ASP-1-0.840-0.93210.05218.22118.2210.0000.0000.0000.000
125A168PHE00.0280.01810.541-0.377-0.3770.0000.0000.0000.000
126A169ASP-1-0.759-0.8546.33235.98235.9820.0000.0000.0000.000
127A170TYR0-0.092-0.0458.7060.3340.3340.0000.0000.0000.000
128A171LYS10.8110.89310.887-17.202-17.2020.0000.0000.0000.000
129A172LYS10.9290.9669.718-22.115-22.1150.0000.0000.0000.000
130A173LYS10.9000.9406.642-32.756-32.7560.0000.0000.0000.000
131A174ARG10.8940.95510.590-17.888-17.8880.0000.0000.0000.000
132A175GLN00.0450.03713.961-0.016-0.0160.0000.0000.0000.000
133A176GLY00.000-0.00215.927-0.838-0.8380.0000.0000.0000.000
134A177LYS10.8660.92718.239-15.779-15.7790.0000.0000.0000.000
135A178ILE0-0.0120.00916.481-0.200-0.2000.0000.0000.0000.000
136A179PRO00.0200.02420.468-0.015-0.0150.0000.0000.0000.000
137A180ASP-1-0.819-0.92219.91214.54214.5420.0000.0000.0000.000
138A181GLU-1-0.752-0.84020.30712.48812.4880.0000.0000.0000.000
139A182GLU-1-0.884-0.94319.34514.88514.8850.0000.0000.0000.000
140A183LEU0-0.019-0.01113.6180.5670.5670.0000.0000.0000.000
141A184ARG10.7480.83817.089-11.901-11.9010.0000.0000.0000.000
142A185GLN0-0.005-0.02019.7110.2030.2030.0000.0000.0000.000
143A186ALA0-0.033-0.01615.4660.0230.0230.0000.0000.0000.000
144A187LEU0-0.0070.00914.6090.5440.5440.0000.0000.0000.000
145A188GLU-1-0.817-0.89516.51512.43812.4380.0000.0000.0000.000
146A189LYS10.8750.93018.630-13.563-13.5630.0000.0000.0000.000
147A190PHE0-0.0050.00511.4790.1670.1670.0000.0000.0000.000
148A191ASP-1-0.834-0.93316.04017.02117.0210.0000.0000.0000.000
149A192GLU-1-0.747-0.84018.09412.96812.9680.0000.0000.0000.000
150A193SER0-0.032-0.04817.576-0.384-0.3840.0000.0000.0000.000
151A194LYS10.7980.90214.005-17.781-17.7810.0000.0000.0000.000
152A195GLU-1-0.895-0.94417.43112.32812.3280.0000.0000.0000.000
153A196ILE0-0.047-0.01921.034-0.470-0.4700.0000.0000.0000.000
154A197ALA0-0.0190.00217.788-0.377-0.3770.0000.0000.0000.000
155A198GLU-1-0.794-0.89717.74815.17315.1730.0000.0000.0000.000
156A199SER0-0.0050.00520.570-0.551-0.5510.0000.0000.0000.000
157A200SER0-0.015-0.01822.527-0.284-0.2840.0000.0000.0000.000
158A201MET0-0.029-0.02116.630-0.198-0.1980.0000.0000.0000.000
159A202PHE00.0050.00422.792-0.210-0.2100.0000.0000.0000.000
160A203ASN0-0.067-0.05324.949-0.642-0.6420.0000.0000.0000.000
161A204LEU00.0070.01925.206-0.310-0.3100.0000.0000.0000.000
162A205LEU0-0.052-0.04421.991-0.170-0.1700.0000.0000.0000.000
163A206GLU-1-0.932-0.95226.6279.5279.5270.0000.0000.0000.000
164A207MET0-0.0230.00129.486-0.342-0.3420.0000.0000.0000.000
165A208ASP-1-0.873-0.94429.3279.9479.9470.0000.0000.0000.000
166A209ILE0-0.043-0.02531.846-0.246-0.2460.0000.0000.0000.000
167A210GLU-1-0.871-0.94934.6728.1568.1560.0000.0000.0000.000
168A211GLN0-0.0130.00631.004-0.209-0.2090.0000.0000.0000.000
169A212VAL0-0.012-0.01034.508-0.173-0.1730.0000.0000.0000.000
170A213SER0-0.0060.00136.901-0.267-0.2670.0000.0000.0000.000
171A214GLN0-0.038-0.03134.418-0.204-0.2040.0000.0000.0000.000
172A215LEU0-0.008-0.01234.811-0.154-0.1540.0000.0000.0000.000
173A216SER0-0.017-0.00839.049-0.221-0.2210.0000.0000.0000.000
174A217ALA00.0220.00942.009-0.189-0.1890.0000.0000.0000.000
175A218LEU0-0.0110.00840.072-0.155-0.1550.0000.0000.0000.000
176A219VAL00.006-0.00242.533-0.153-0.1530.0000.0000.0000.000
177A220GLN0-0.049-0.02345.032-0.295-0.2950.0000.0000.0000.000
178A221ALA00.0650.04746.497-0.149-0.1490.0000.0000.0000.000
179A222GLN0-0.034-0.04044.100-0.081-0.0810.0000.0000.0000.000
180A223LEU0-0.026-0.00548.503-0.142-0.1420.0000.0000.0000.000
181A224GLU-1-0.793-0.88850.8935.5495.5490.0000.0000.0000.000
182A225TYR00.0090.01251.178-0.118-0.1180.0000.0000.0000.000
183A226HIS00.010-0.00449.295-0.205-0.2050.0000.0000.0000.000
184A227LYS10.7820.87754.068-5.784-5.7840.0000.0000.0000.000
185A228GLN00.0160.01356.586-0.110-0.1100.0000.0000.0000.000
186A229ALA00.0280.01056.256-0.106-0.1060.0000.0000.0000.000
187A230VAL0-0.011-0.01157.256-0.097-0.0970.0000.0000.0000.000
188A231GLN0-0.013-0.00359.704-0.171-0.1710.0000.0000.0000.000
189A232ILE00.0130.01360.904-0.109-0.1090.0000.0000.0000.000
190A233LEU00.0250.01158.886-0.085-0.0850.0000.0000.0000.000
191A234GLN0-0.0250.00563.188-0.065-0.0650.0000.0000.0000.000
192A235GLN0-0.003-0.00165.404-0.115-0.1150.0000.0000.0000.000
193A236VAL00.006-0.00465.565-0.089-0.0890.0000.0000.0000.000
194A237THR0-0.032-0.02665.688-0.054-0.0540.0000.0000.0000.000
195A238VAL0-0.013-0.01568.342-0.065-0.0650.0000.0000.0000.000
196A239ARG10.8610.92471.164-4.366-4.3660.0000.0000.0000.000
197A240LEU0-0.0010.00068.704-0.067-0.0670.0000.0000.0000.000
198A241GLU-1-0.844-0.90172.1994.2574.2570.0000.0000.0000.000
199A242GLU-1-0.909-0.94273.9423.9473.9470.0000.0000.0000.000
200A243ARG10.9330.94575.847-4.165-4.1650.0000.0000.0000.000
201A244ILE0-0.048-0.01773.356-0.037-0.0370.0000.0000.0000.000
202A245ARG10.7610.84975.635-4.188-4.1880.0000.0000.0000.000
203A246GLN0-0.098-0.05280.035-0.083-0.0830.0000.0000.0000.000
204A247ALA0-0.064-0.01480.364-0.056-0.0560.0000.0000.0000.000