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: QVRNY

Calculation Name: 2CO6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CO6

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZRK3

Base Structure: X-ray

Registration Date: 2023-09-24

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2223215.997973
FMO2-HF: Nuclear repulsion 2141396.306224
FMO2-HF: Total energy -81819.691749
FMO2-MP2: Total energy -82059.402937


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(B:5:LEU)


Summations of interaction energy for fragment #1(B:5: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.
-5.162-1.3491.19-1.908-3.095-0.014
Interaction energy analysis for fragmet #1(B:5:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.033
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].
3B7SER00.0230.0342.514-1.5330.9680.342-1.046-1.798-0.001
4B8ALA00.0430.0292.607-3.101-1.8690.849-0.862-1.219-0.013
5B9THR00.004-0.0145.3750.2140.294-0.0010.000-0.0780.000
6B10LYS10.8990.9837.1680.6920.6920.0000.0000.0000.000
7B11LEU0-0.007-0.00610.6950.0560.0560.0000.0000.0000.000
8B12PHE0-0.042-0.03513.3020.0200.0200.0000.0000.0000.000
9B13SER0-0.010-0.00716.8150.0280.0280.0000.0000.0000.000
10B14VAL00.0450.01720.1580.0030.0030.0000.0000.0000.000
11B15LYS10.9560.99223.9170.1680.1680.0000.0000.0000.000
12B16LEU00.0250.00526.8140.0030.0030.0000.0000.0000.000
13B17GLY0-0.085-0.04030.1880.0000.0000.0000.0000.0000.000
14B18ALA0-0.002-0.00233.2230.0060.0060.0000.0000.0000.000
15B19THR00.0680.04031.416-0.002-0.0020.0000.0000.0000.000
16B20ARG10.8610.93933.6440.1010.1010.0000.0000.0000.000
17B21VAL00.0260.01136.9070.0000.0000.0000.0000.0000.000
18B22ILE0-0.0020.00839.5000.0010.0010.0000.0000.0000.000
19B23TYR0-0.0110.00043.253-0.001-0.0010.0000.0000.0000.000
20B24HIS00.0620.02245.1950.0040.0040.0000.0000.0000.000
21B25ALA00.0060.00748.7440.0000.0000.0000.0000.0000.000
22B26GLY00.0660.02851.2050.0000.0000.0000.0000.0000.000
23B27THR0-0.090-0.03748.7820.0000.0000.0000.0000.0000.000
24B28ALA0-0.015-0.02249.334-0.001-0.0010.0000.0000.0000.000
25B29GLY0-0.0210.00245.951-0.002-0.0020.0000.0000.0000.000
26B30ALA00.0310.01542.3130.0010.0010.0000.0000.0000.000
27B31THR0-0.068-0.04140.010-0.002-0.0020.0000.0000.0000.000
28B32LEU00.0390.02533.3680.0010.0010.0000.0000.0000.000
29B33SER0-0.044-0.00733.590-0.004-0.0040.0000.0000.0000.000
30B34VAL00.0540.01628.816-0.005-0.0050.0000.0000.0000.000
31B35SER0-0.030-0.03228.0680.0090.0090.0000.0000.0000.000
32B36ASN00.002-0.00723.013-0.032-0.0320.0000.0000.0000.000
33B37PRO0-0.0200.01421.2960.0080.0080.0000.0000.0000.000
34B38GLN00.0100.01118.254-0.042-0.0420.0000.0000.0000.000
35B39ASN00.021-0.00319.6140.0500.0500.0000.0000.0000.000
36B40TYR00.0340.01416.1190.0080.0080.0000.0000.0000.000
37B41PRO00.003-0.00121.607-0.001-0.0010.0000.0000.0000.000
38B42ILE0-0.0120.00821.193-0.021-0.0210.0000.0000.0000.000
39B43LEU0-0.027-0.02123.7510.0250.0250.0000.0000.0000.000
40B44VAL00.0160.00025.636-0.012-0.0120.0000.0000.0000.000
41B45GLN0-0.005-0.00928.2890.0160.0160.0000.0000.0000.000
42B46SER00.0090.00730.292-0.007-0.0070.0000.0000.0000.000
43B47SER0-0.051-0.02032.8650.0080.0080.0000.0000.0000.000
44B48VAL00.0370.00435.174-0.003-0.0030.0000.0000.0000.000
45B49LYS10.8870.96633.3650.1240.1240.0000.0000.0000.000
46B50ALA00.0910.03437.7110.0010.0010.0000.0000.0000.000
47B51ALA00.0260.00338.655-0.005-0.0050.0000.0000.0000.000
48B52ASP-1-0.782-0.86238.713-0.088-0.0880.0000.0000.0000.000
49B53LYS10.8820.94532.1870.1130.1130.0000.0000.0000.000
50B54SER0-0.038-0.01934.439-0.007-0.0070.0000.0000.0000.000
51B55SER0-0.024-0.03836.6270.0000.0000.0000.0000.0000.000
52B56PRO0-0.045-0.01439.238-0.003-0.0030.0000.0000.0000.000
53B57ALA00.0220.01140.1610.0050.0050.0000.0000.0000.000
54B58PRO0-0.0010.01342.249-0.001-0.0010.0000.0000.0000.000
55B59PHE00.014-0.00841.6920.0020.0020.0000.0000.0000.000
56B60LEU0-0.0060.00140.320-0.003-0.0030.0000.0000.0000.000
57B61VAL0-0.0090.00335.7700.0010.0010.0000.0000.0000.000
58B62MET0-0.0060.03938.549-0.001-0.0010.0000.0000.0000.000
59B63PRO00.027-0.02634.9420.0020.0020.0000.0000.0000.000
60B64PRO00.0300.01335.397-0.005-0.0050.0000.0000.0000.000
61B65LEU0-0.017-0.02229.902-0.008-0.0080.0000.0000.0000.000
62B66PHE00.003-0.00131.2690.0070.0070.0000.0000.0000.000
63B67ARG10.9840.99724.7890.1800.1800.0000.0000.0000.000
64B68LEU0-0.0220.00327.2840.0100.0100.0000.0000.0000.000
65B69GLU-1-0.847-0.94226.578-0.184-0.1840.0000.0000.0000.000
66B70ALA0-0.0160.00324.139-0.007-0.0070.0000.0000.0000.000
67B71ASN0-0.039-0.02524.3600.0060.0060.0000.0000.0000.000
68B72GLN00.0170.03226.3610.0080.0080.0000.0000.0000.000
69B73GLN00.014-0.00328.988-0.005-0.0050.0000.0000.0000.000
70B74SER0-0.047-0.02731.5830.0110.0110.0000.0000.0000.000
71B75GLN00.0230.00934.0000.0000.0000.0000.0000.0000.000
72B76LEU0-0.0010.01532.6070.0020.0020.0000.0000.0000.000
73B77ARG10.9290.96137.0050.0860.0860.0000.0000.0000.000
74B78ILE00.0090.00537.714-0.002-0.0020.0000.0000.0000.000
75B79VAL0-0.002-0.00641.4180.0040.0040.0000.0000.0000.000
76B80ARG10.9460.98444.3970.0590.0590.0000.0000.0000.000
77B81THR0-0.039-0.03944.6040.0020.0020.0000.0000.0000.000
78B82GLY00.0290.00547.6500.0030.0030.0000.0000.0000.000
79B83GLY0-0.031-0.01549.342-0.001-0.0010.0000.0000.0000.000
80B84ASP-1-0.946-0.97250.227-0.050-0.0500.0000.0000.0000.000
81B85MET0-0.081-0.03246.515-0.001-0.0010.0000.0000.0000.000
82B86PRO00.0690.03950.5850.0020.0020.0000.0000.0000.000
83B87THR0-0.009-0.01953.156-0.001-0.0010.0000.0000.0000.000
84B88ASP-1-0.817-0.88655.556-0.048-0.0480.0000.0000.0000.000
85B89ARG10.8420.89451.0410.0510.0510.0000.0000.0000.000
86B90GLU-1-0.784-0.88246.377-0.070-0.0700.0000.0000.0000.000
87B91THR0-0.014-0.00945.2950.0010.0010.0000.0000.0000.000
88B92LEU0-0.044-0.00938.790-0.002-0.0020.0000.0000.0000.000
89B93GLN0-0.017-0.01139.9720.0040.0040.0000.0000.0000.000
90B94TRP0-0.025-0.02533.615-0.003-0.0030.0000.0000.0000.000
91B95VAL00.0330.02934.4680.0010.0010.0000.0000.0000.000
92B96CYS0-0.120-0.05827.3670.0030.0030.0000.0000.0000.000
93B97ILE00.0590.01928.1960.0040.0040.0000.0000.0000.000
94B98LYS10.9320.97425.1210.1770.1770.0000.0000.0000.000
95B99ALA0-0.004-0.00423.4130.0090.0090.0000.0000.0000.000
96B100VAL0-0.006-0.01921.182-0.016-0.0160.0000.0000.0000.000
97B101PRO0-0.0110.01417.0490.0270.0270.0000.0000.0000.000
98B102PRO0-0.017-0.00718.9600.0190.0190.0000.0000.0000.000
99B103GLU-1-0.924-0.95717.317-0.393-0.3930.0000.0000.0000.000
100B104ASN0-0.086-0.07411.8630.0430.0430.0000.0000.0000.000
101B105GLU-1-0.929-0.96214.582-0.299-0.2990.0000.0000.0000.000
102B106PRO00.0080.00712.713-0.090-0.0900.0000.0000.0000.000
103B107SER0-0.049-0.04112.990-0.023-0.0230.0000.0000.0000.000
104B108ASP-1-0.755-0.8598.445-0.548-0.5480.0000.0000.0000.000
105B109THR00.008-0.0068.4720.1060.1060.0000.0000.0000.000
106B110GLN0-0.041-0.0166.5010.5130.5130.0000.0000.0000.000
107B111ALA0-0.011-0.0036.410-0.080-0.0800.0000.0000.0000.000
108B112LYS10.8120.9018.175-0.515-0.5150.0000.0000.0000.000
109B113GLY00.0590.0369.7150.0330.0330.0000.0000.0000.000
110B114ALA0-0.037-0.0089.384-0.077-0.0770.0000.0000.0000.000
111B115THR0-0.065-0.0536.632-0.037-0.0370.0000.0000.0000.000
112B116LEU0-0.015-0.0136.0720.1460.1460.0000.0000.0000.000
113B117ASP-1-0.832-0.8977.278-0.980-0.9800.0000.0000.0000.000
114B118LEU00.0010.0046.4990.1430.1430.0000.0000.0000.000
115B119ASN00.0900.01910.174-0.050-0.0500.0000.0000.0000.000
116B120LEU0-0.057-0.01913.5150.0310.0310.0000.0000.0000.000
117B121SER0-0.0060.00416.3300.0240.0240.0000.0000.0000.000
118B122ILE0-0.0120.00119.3930.0010.0010.0000.0000.0000.000
119B123ASN00.002-0.02722.0010.0240.0240.0000.0000.0000.000
120B124ALA00.0210.03325.643-0.001-0.0010.0000.0000.0000.000
121B126ASP-1-0.766-0.87930.787-0.135-0.1350.0000.0000.0000.000
122B127LYS10.8120.90833.7110.1010.1010.0000.0000.0000.000
123B128LEU00.0090.01137.1240.0000.0000.0000.0000.0000.000
124B129ILE0-0.003-0.01339.7310.0020.0020.0000.0000.0000.000
125B130PHE00.0030.00042.9410.0010.0010.0000.0000.0000.000
126B131ARG10.8090.86245.8440.0680.0680.0000.0000.0000.000
127B132PRO0-0.0050.00049.0190.0010.0010.0000.0000.0000.000
128B133ASP-1-0.862-0.93652.563-0.051-0.0510.0000.0000.0000.000
129B134ALA0-0.044-0.02355.1220.0010.0010.0000.0000.0000.000
130B135VAL0-0.0280.00051.6150.0010.0010.0000.0000.0000.000
131B136LYS10.8760.93553.1340.0460.0460.0000.0000.0000.000
132B137GLY00.0440.03052.9950.0000.0000.0000.0000.0000.000
133B138THR0-0.039-0.02047.583-0.002-0.0020.0000.0000.0000.000
134B139PRO00.0300.00145.4200.0020.0020.0000.0000.0000.000
135B140GLU-1-0.919-0.97645.963-0.064-0.0640.0000.0000.0000.000
136B141ASP-1-0.864-0.91947.840-0.052-0.0520.0000.0000.0000.000
137B142VAL0-0.034-0.03050.8970.0020.0020.0000.0000.0000.000
138B143ALA00.0270.01747.2620.0010.0010.0000.0000.0000.000
139B144GLY00.0040.00649.2850.0000.0000.0000.0000.0000.000
140B145ASN0-0.044-0.03251.7010.0020.0020.0000.0000.0000.000
141B146LEU0-0.084-0.02246.4650.0010.0010.0000.0000.0000.000
142B147ARG10.9470.98550.8510.0440.0440.0000.0000.0000.000
143B148TRP00.0210.00944.484-0.003-0.0030.0000.0000.0000.000
144B149VAL00.0060.00950.6740.0020.0020.0000.0000.0000.000
145B150GLU-1-0.837-0.92249.650-0.043-0.0430.0000.0000.0000.000
146B151THR0-0.048-0.03350.1560.0020.0020.0000.0000.0000.000
147B152GLY00.0230.02149.610-0.001-0.0010.0000.0000.0000.000
148B153ASN00.0150.00644.382-0.001-0.0010.0000.0000.0000.000
149B154LYS10.8790.94042.5250.0520.0520.0000.0000.0000.000
150B155LEU00.0330.01244.7520.0020.0020.0000.0000.0000.000
151B156LYS10.9280.97345.9230.0440.0440.0000.0000.0000.000
152B157VAL00.0050.01044.8620.0010.0010.0000.0000.0000.000
153B158GLU-1-0.894-0.95848.179-0.044-0.0440.0000.0000.0000.000
154B159ASN0-0.003-0.00747.8550.0020.0020.0000.0000.0000.000
155B160PRO0-0.039-0.00750.5550.0000.0000.0000.0000.0000.000
156B161THR0-0.015-0.03050.4170.0010.0010.0000.0000.0000.000
157B162PRO00.0530.02551.717-0.001-0.0010.0000.0000.0000.000
158B163PHE00.0330.00347.354-0.002-0.0020.0000.0000.0000.000
159B164TYR0-0.014-0.00943.1060.0000.0000.0000.0000.0000.000
160B165MET0-0.0160.02144.366-0.002-0.0020.0000.0000.0000.000
161B166ASN0-0.010-0.02238.968-0.004-0.0040.0000.0000.0000.000
162B167LEU00.0550.03139.987-0.001-0.0010.0000.0000.0000.000
163B168ALA0-0.024-0.00236.958-0.004-0.0040.0000.0000.0000.000
164B169SER0-0.017-0.01736.556-0.003-0.0030.0000.0000.0000.000
165B170VAL00.0530.02138.9180.0030.0030.0000.0000.0000.000
166B171THR0-0.0280.00239.799-0.001-0.0010.0000.0000.0000.000
167B172VAL00.0370.01542.1650.0030.0030.0000.0000.0000.000
168B173GLY0-0.003-0.00844.2070.0000.0000.0000.0000.0000.000
169B174GLY00.0190.00842.8520.0010.0010.0000.0000.0000.000
170B175LYS10.9090.95339.5750.0490.0490.0000.0000.0000.000
171B176PRO00.0250.00935.9250.0010.0010.0000.0000.0000.000
172B177ILE0-0.0040.00938.0560.0010.0010.0000.0000.0000.000
173B178THR0-0.023-0.01832.698-0.004-0.0040.0000.0000.0000.000
174B179GLY0-0.016-0.01833.5810.0030.0030.0000.0000.0000.000
175B180LEU0-0.0110.00734.6640.0030.0030.0000.0000.0000.000
176B181GLU-1-0.860-0.91636.056-0.089-0.0890.0000.0000.0000.000
177B182TYR0-0.051-0.02838.0370.0000.0000.0000.0000.0000.000
178B183VAL00.0320.00740.6750.0010.0010.0000.0000.0000.000
179B184PRO0-0.035-0.01844.154-0.001-0.0010.0000.0000.0000.000
180B185PRO00.0060.01846.0420.0020.0020.0000.0000.0000.000
181B186PHE0-0.066-0.02849.4900.0000.0000.0000.0000.0000.000
182B187ALA00.0100.01948.3580.0010.0010.0000.0000.0000.000
183B188ASP-1-0.818-0.92948.962-0.049-0.0490.0000.0000.0000.000
184B189LYS10.7790.87740.5390.0720.0720.0000.0000.0000.000
185B190THR0-0.011-0.00644.3780.0020.0020.0000.0000.0000.000
186B191LEU0-0.0050.01841.361-0.003-0.0030.0000.0000.0000.000
187B192ASN00.013-0.00937.9960.0070.0070.0000.0000.0000.000
188B193MET00.0240.02341.046-0.001-0.0010.0000.0000.0000.000
189B194PRO0-0.0020.00539.7500.0000.0000.0000.0000.0000.000
190B195GLY0-0.044-0.02440.9530.0000.0000.0000.0000.0000.000
191B196SER00.0130.03143.0160.0020.0020.0000.0000.0000.000
192B197ALA00.008-0.01145.3890.0010.0010.0000.0000.0000.000
193B198HIS10.7720.88147.7720.0420.0420.0000.0000.0000.000
194B199GLY00.0460.02548.8510.0010.0010.0000.0000.0000.000
195B200ASP-1-0.836-0.91249.308-0.041-0.0410.0000.0000.0000.000
196B201ILE0-0.065-0.04546.132-0.002-0.0020.0000.0000.0000.000
197B202GLU-1-0.911-0.95442.921-0.059-0.0590.0000.0000.0000.000
198B203TRP0-0.037-0.03443.264-0.003-0.0030.0000.0000.0000.000
199B204ARG10.9911.01140.1490.0710.0710.0000.0000.0000.000
200B205VAL00.013-0.00541.465-0.002-0.0020.0000.0000.0000.000
201B206ILE0-0.047-0.02535.591-0.001-0.0010.0000.0000.0000.000
202B207THR00.0320.01139.7770.0000.0000.0000.0000.0000.000
203B208ASP-1-0.782-0.89240.602-0.076-0.0760.0000.0000.0000.000
204B209PHE0-0.037-0.02940.459-0.003-0.0030.0000.0000.0000.000
205B210GLY0-0.053-0.01636.938-0.004-0.0040.0000.0000.0000.000
206B211GLY00.0120.01736.608-0.004-0.0040.0000.0000.0000.000
207B212GLU-1-0.945-0.97836.005-0.089-0.0890.0000.0000.0000.000
208B213SER00.0330.01539.8090.0010.0010.0000.0000.0000.000
209B214HIS0-0.016-0.00642.984-0.003-0.0030.0000.0000.0000.000
210B215PRO0-0.035-0.00944.455-0.001-0.0010.0000.0000.0000.000
211B216PHE0-0.024-0.00845.7930.0030.0030.0000.0000.0000.000
212B217HIS00.0470.01247.711-0.001-0.0010.0000.0000.0000.000
213B218TYR0-0.0010.00150.2660.0010.0010.0000.0000.0000.000
214B219VAL00.0260.01151.4880.0000.0000.0000.0000.0000.000
215B220LEU0-0.055-0.01749.8380.0010.0010.0000.0000.0000.000