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

tag_button

FMODB ID: KGY23

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2223349.29771
FMO2-HF: Nuclear repulsion 2141528.546534
FMO2-HF: Total energy -81820.751176
FMO2-MP2: Total energy -82060.410696


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.
-4.7-1.1872.722-2.454-3.78-0.007
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 : -0.002 / q_NPA : -0.005
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].
3B7SER00.0260.0252.101-2.1490.4811.772-1.763-2.6390.003
4B8ALA00.0250.0132.675-2.090-1.2070.950-0.691-1.141-0.010
5B9THR00.000-0.0195.4540.2920.2920.0000.0000.0000.000
6B10LYS10.8460.9456.9310.6520.6520.0000.0000.0000.000
7B11LEU0-0.010-0.00310.5560.0860.0860.0000.0000.0000.000
8B12PHE0-0.031-0.03013.139-0.005-0.0050.0000.0000.0000.000
9B13SER0-0.005-0.00516.6210.0370.0370.0000.0000.0000.000
10B14VAL00.0370.01520.015-0.008-0.0080.0000.0000.0000.000
11B15LYS10.9590.99523.7550.1300.1300.0000.0000.0000.000
12B16LEU00.0220.00626.695-0.003-0.0030.0000.0000.0000.000
13B17GLY0-0.083-0.04130.0750.0030.0030.0000.0000.0000.000
14B18ALA0-0.001-0.00133.1420.0070.0070.0000.0000.0000.000
15B19THR00.0630.03731.387-0.003-0.0030.0000.0000.0000.000
16B20ARG10.8370.92633.6260.0600.0600.0000.0000.0000.000
17B21VAL00.0130.00436.869-0.001-0.0010.0000.0000.0000.000
18B22ILE00.0000.00839.4200.0010.0010.0000.0000.0000.000
19B23TYR00.0020.00043.182-0.002-0.0020.0000.0000.0000.000
20B24HIS00.0730.03045.0830.0030.0030.0000.0000.0000.000
21B25ALA00.0190.01548.640-0.001-0.0010.0000.0000.0000.000
22B26GLY00.0540.01951.079-0.001-0.0010.0000.0000.0000.000
23B27THR0-0.075-0.03448.9330.0000.0000.0000.0000.0000.000
24B28ALA0-0.029-0.01949.214-0.002-0.0020.0000.0000.0000.000
25B29GLY00.0010.02045.769-0.001-0.0010.0000.0000.0000.000
26B30ALA00.0170.00142.2190.0020.0020.0000.0000.0000.000
27B31THR0-0.031-0.01839.748-0.002-0.0020.0000.0000.0000.000
28B32LEU0-0.0050.00033.2160.0030.0030.0000.0000.0000.000
29B33SER0-0.047-0.03033.521-0.005-0.0050.0000.0000.0000.000
30B34VAL00.0510.01628.625-0.001-0.0010.0000.0000.0000.000
31B35SER0-0.038-0.03927.6610.0050.0050.0000.0000.0000.000
32B36ASN0-0.006-0.01423.023-0.016-0.0160.0000.0000.0000.000
33B37PRO0-0.0150.01221.0700.0040.0040.0000.0000.0000.000
34B38GLN00.0180.01918.112-0.025-0.0250.0000.0000.0000.000
35B39ASN00.0200.00219.5640.0490.0490.0000.0000.0000.000
36B40TYR00.0260.00115.947-0.001-0.0010.0000.0000.0000.000
37B41PRO0-0.017-0.00821.6920.0090.0090.0000.0000.0000.000
38B42ILE0-0.0050.01321.346-0.025-0.0250.0000.0000.0000.000
39B43LEU0-0.023-0.01523.8780.0240.0240.0000.0000.0000.000
40B44VAL00.017-0.00125.725-0.006-0.0060.0000.0000.0000.000
41B45GLN00.0390.02128.3380.0100.0100.0000.0000.0000.000
42B46SER00.0160.00830.255-0.002-0.0020.0000.0000.0000.000
43B47SER0-0.060-0.02632.9100.0060.0060.0000.0000.0000.000
44B48VAL00.0460.00935.055-0.001-0.0010.0000.0000.0000.000
45B49LYS10.8900.96633.2080.1040.1040.0000.0000.0000.000
46B50ALA00.0900.03137.6150.0020.0020.0000.0000.0000.000
47B51ALA00.0280.00538.620-0.003-0.0030.0000.0000.0000.000
48B52ASP-1-0.776-0.86438.740-0.066-0.0660.0000.0000.0000.000
49B53LYS10.8810.94732.6160.0690.0690.0000.0000.0000.000
50B54SER0-0.061-0.02634.490-0.007-0.0070.0000.0000.0000.000
51B55SER0-0.005-0.02936.662-0.003-0.0030.0000.0000.0000.000
52B56PRO0-0.054-0.01539.210-0.002-0.0020.0000.0000.0000.000
53B57ALA00.0220.01240.1540.0050.0050.0000.0000.0000.000
54B58PRO00.0010.01242.126-0.003-0.0030.0000.0000.0000.000
55B59PHE00.007-0.01341.5340.0020.0020.0000.0000.0000.000
56B60LEU00.0040.00840.273-0.003-0.0030.0000.0000.0000.000
57B61VAL0-0.013-0.00235.7030.0030.0030.0000.0000.0000.000
58B62MET0-0.0140.02438.553-0.003-0.0030.0000.0000.0000.000
59B63PRO00.032-0.01034.9250.0030.0030.0000.0000.0000.000
60B64PRO00.0310.01335.417-0.004-0.0040.0000.0000.0000.000
61B65LEU0-0.024-0.02730.025-0.006-0.0060.0000.0000.0000.000
62B66PHE00.0030.00131.3990.0040.0040.0000.0000.0000.000
63B67ARG10.8970.94525.5750.2190.2190.0000.0000.0000.000
64B68LEU0-0.0080.01927.4370.0100.0100.0000.0000.0000.000
65B69GLU-1-0.768-0.91126.692-0.225-0.2250.0000.0000.0000.000
66B70ALA0-0.0040.01524.2280.0010.0010.0000.0000.0000.000
67B71ASN0-0.038-0.02924.2000.0140.0140.0000.0000.0000.000
68B72GLN00.0100.03326.2400.0100.0100.0000.0000.0000.000
69B73GLN00.0220.01228.844-0.002-0.0020.0000.0000.0000.000
70B74SER0-0.022-0.01131.3950.0070.0070.0000.0000.0000.000
71B75GLN00.0120.00133.8150.0020.0020.0000.0000.0000.000
72B76LEU00.0050.01932.4720.0000.0000.0000.0000.0000.000
73B77ARG10.9060.95636.8590.0780.0780.0000.0000.0000.000
74B78ILE00.006-0.00337.574-0.003-0.0030.0000.0000.0000.000
75B79VAL00.001-0.00941.2390.0040.0040.0000.0000.0000.000
76B80ARG10.9240.97144.2710.0490.0490.0000.0000.0000.000
77B81THR0-0.050-0.03944.8360.0020.0020.0000.0000.0000.000
78B82GLY00.0400.01047.5750.0020.0020.0000.0000.0000.000
79B83GLY0-0.021-0.00649.1800.0000.0000.0000.0000.0000.000
80B84ASP-1-0.939-0.97150.075-0.039-0.0390.0000.0000.0000.000
81B85MET0-0.067-0.02346.8010.0000.0000.0000.0000.0000.000
82B86PRO00.0490.03750.4890.0020.0020.0000.0000.0000.000
83B87THR00.004-0.02153.069-0.001-0.0010.0000.0000.0000.000
84B88ASP-1-0.814-0.87255.462-0.031-0.0310.0000.0000.0000.000
85B89ARG10.8470.87950.9700.0330.0330.0000.0000.0000.000
86B90GLU-1-0.785-0.88146.431-0.045-0.0450.0000.0000.0000.000
87B91THR0-0.022-0.01645.4700.0010.0010.0000.0000.0000.000
88B92LEU0-0.0270.00438.773-0.002-0.0020.0000.0000.0000.000
89B93GLN0-0.033-0.03140.0300.0020.0020.0000.0000.0000.000
90B94TRP0-0.022-0.02033.3520.0010.0010.0000.0000.0000.000
91B95VAL00.0330.02634.450-0.002-0.0020.0000.0000.0000.000
92B96CYS0-0.128-0.06127.2560.0010.0010.0000.0000.0000.000
93B97ILE00.0590.02028.143-0.001-0.0010.0000.0000.0000.000
94B98LYS10.8890.94625.2930.1590.1590.0000.0000.0000.000
95B99ALA00.001-0.00123.2850.0030.0030.0000.0000.0000.000
96B100VAL0-0.008-0.01921.391-0.009-0.0090.0000.0000.0000.000
97B101PRO0-0.0110.01917.1850.0200.0200.0000.0000.0000.000
98B102PRO0-0.007-0.00618.9070.0180.0180.0000.0000.0000.000
99B103GLU-1-0.886-0.93717.252-0.449-0.4490.0000.0000.0000.000
100B104ASN0-0.071-0.06011.7610.0550.0550.0000.0000.0000.000
101B105GLU-1-0.935-0.96314.455-0.499-0.4990.0000.0000.0000.000
102B106PRO00.0130.00412.400-0.118-0.1180.0000.0000.0000.000
103B107SER0-0.043-0.03412.649-0.060-0.0600.0000.0000.0000.000
104B108ASP-1-0.749-0.8588.249-1.753-1.7530.0000.0000.0000.000
105B109THR00.011-0.0047.9480.1230.1230.0000.0000.0000.000
106B110GLN0-0.041-0.0166.4750.4120.4120.0000.0000.0000.000
107B111ALA0-0.0130.0046.3380.2900.2900.0000.0000.0000.000
108B112LYS10.8020.8907.9830.7220.7220.0000.0000.0000.000
109B113GLY00.0580.0349.7770.1420.1420.0000.0000.0000.000
110B114ALA0-0.043-0.0109.471-0.084-0.0840.0000.0000.0000.000
111B115THR0-0.055-0.0476.4930.0510.0510.0000.0000.0000.000
112B116LEU0-0.020-0.0106.2220.1720.1720.0000.0000.0000.000
113B117ASP-1-0.797-0.8747.103-1.181-1.1810.0000.0000.0000.000
114B118LEU0-0.0100.0066.2840.1780.1780.0000.0000.0000.000
115B119ASN00.0570.01010.260-0.056-0.0560.0000.0000.0000.000
116B120LEU0-0.041-0.01313.5290.0470.0470.0000.0000.0000.000
117B121SER00.0040.00316.3300.0090.0090.0000.0000.0000.000
118B122ILE0-0.0130.00319.1330.0110.0110.0000.0000.0000.000
119B123ASN0-0.009-0.02821.8170.0110.0110.0000.0000.0000.000
120B124ALA00.0280.03125.4840.0060.0060.0000.0000.0000.000
121B126ASP-1-0.765-0.87630.694-0.091-0.0910.0000.0000.0000.000
122B127LYS10.8070.90333.6440.0560.0560.0000.0000.0000.000
123B128LEU00.0100.01037.071-0.001-0.0010.0000.0000.0000.000
124B129ILE0-0.009-0.01239.6380.0010.0010.0000.0000.0000.000
125B130PHE00.0090.00742.8760.0000.0000.0000.0000.0000.000
126B131ARG10.7860.84645.6930.0440.0440.0000.0000.0000.000
127B132PRO0-0.0030.00148.9530.0000.0000.0000.0000.0000.000
128B133ASP-1-0.867-0.93852.482-0.036-0.0360.0000.0000.0000.000
129B134ALA0-0.012-0.00855.0420.0010.0010.0000.0000.0000.000
130B135VAL0-0.038-0.00451.4560.0020.0020.0000.0000.0000.000
131B136LYS10.8470.92653.1080.0310.0310.0000.0000.0000.000
132B137GLY00.0300.02353.0140.0010.0010.0000.0000.0000.000
133B138THR0-0.062-0.05847.661-0.002-0.0020.0000.0000.0000.000
134B139PRO00.0390.00345.2150.0020.0020.0000.0000.0000.000
135B140GLU-1-0.883-0.96146.032-0.029-0.0290.0000.0000.0000.000
136B141ASP-1-0.843-0.89447.938-0.027-0.0270.0000.0000.0000.000
137B142VAL0-0.023-0.02450.9830.0020.0020.0000.0000.0000.000
138B143ALA00.0230.01747.3740.0010.0010.0000.0000.0000.000
139B144GLY00.0150.00549.4110.0010.0010.0000.0000.0000.000
140B145ASN0-0.057-0.03751.8590.0020.0020.0000.0000.0000.000
141B146LEU0-0.076-0.01546.5660.0000.0000.0000.0000.0000.000
142B147ARG10.9090.95651.0010.0190.0190.0000.0000.0000.000
143B148TRP00.0110.00044.730-0.001-0.0010.0000.0000.0000.000
144B149VAL00.0100.00950.8620.0010.0010.0000.0000.0000.000
145B150GLU-1-0.818-0.90149.718-0.004-0.0040.0000.0000.0000.000
146B151THR0-0.034-0.02450.3960.0000.0000.0000.0000.0000.000
147B152GLY00.0330.02349.803-0.001-0.0010.0000.0000.0000.000
148B153ASN00.0000.00144.860-0.002-0.0020.0000.0000.0000.000
149B154LYS10.8710.92542.5300.0100.0100.0000.0000.0000.000
150B155LEU00.0110.00345.3780.0010.0010.0000.0000.0000.000
151B156LYS10.8090.90546.1200.0160.0160.0000.0000.0000.000
152B157VAL00.0050.00645.1400.0010.0010.0000.0000.0000.000
153B158GLU-1-0.784-0.88348.342-0.018-0.0180.0000.0000.0000.000
154B159ASN0-0.009-0.00748.0760.0020.0020.0000.0000.0000.000
155B160PRO0-0.046-0.01350.657-0.001-0.0010.0000.0000.0000.000
156B161THR0-0.013-0.02750.5030.0000.0000.0000.0000.0000.000
157B162PRO00.0530.02351.762-0.001-0.0010.0000.0000.0000.000
158B163PHE00.0360.00947.450-0.002-0.0020.0000.0000.0000.000
159B164TYR0-0.018-0.01843.1250.0010.0010.0000.0000.0000.000
160B165MET0-0.0160.02144.446-0.001-0.0010.0000.0000.0000.000
161B166ASN0-0.005-0.01339.126-0.003-0.0030.0000.0000.0000.000
162B167LEU00.0450.02940.1330.0000.0000.0000.0000.0000.000
163B168ALA0-0.0160.00337.110-0.003-0.0030.0000.0000.0000.000
164B169SER0-0.008-0.01536.7470.0010.0010.0000.0000.0000.000
165B170VAL00.0420.01739.1290.0000.0000.0000.0000.0000.000
166B171THR0-0.047-0.00740.0200.0020.0020.0000.0000.0000.000
167B172VAL00.0360.01042.3730.0000.0000.0000.0000.0000.000
168B173GLY00.006-0.00144.2330.0020.0020.0000.0000.0000.000
169B174GLY00.0200.01242.8700.0020.0020.0000.0000.0000.000
170B175LYS10.8310.91539.742-0.008-0.0080.0000.0000.0000.000
171B176PRO00.0260.00336.065-0.002-0.0020.0000.0000.0000.000
172B177ILE0-0.0210.00238.1940.0020.0020.0000.0000.0000.000
173B178THR0-0.013-0.01133.023-0.003-0.0030.0000.0000.0000.000
174B179GLY0-0.013-0.01633.7870.0000.0000.0000.0000.0000.000
175B180LEU0-0.0100.00634.851-0.001-0.0010.0000.0000.0000.000
176B181GLU-1-0.838-0.90636.188-0.043-0.0430.0000.0000.0000.000
177B182TYR0-0.040-0.02837.7070.0000.0000.0000.0000.0000.000
178B183VAL00.0380.01140.7550.0000.0000.0000.0000.0000.000
179B184PRO0-0.027-0.01444.126-0.001-0.0010.0000.0000.0000.000
180B185PRO0-0.0010.01846.0800.0020.0020.0000.0000.0000.000
181B186PHE0-0.065-0.02649.5210.0000.0000.0000.0000.0000.000
182B187ALA00.0120.02148.4280.0000.0000.0000.0000.0000.000
183B188ASP-1-0.785-0.90949.068-0.021-0.0210.0000.0000.0000.000
184B189LYS10.7700.87540.6830.0340.0340.0000.0000.0000.000
185B190THR0-0.016-0.00844.5260.0020.0020.0000.0000.0000.000
186B191LEU00.0170.02341.150-0.002-0.0020.0000.0000.0000.000
187B192ASN00.010-0.00338.3990.0030.0030.0000.0000.0000.000
188B193MET00.0350.02741.3020.0000.0000.0000.0000.0000.000
189B194PRO00.0250.02539.9610.0010.0010.0000.0000.0000.000
190B195GLY0-0.007-0.00740.9910.0030.0030.0000.0000.0000.000
191B196SER0-0.0040.01542.9400.0020.0020.0000.0000.0000.000
192B197ALA00.037-0.00645.3170.0000.0000.0000.0000.0000.000
193B198HIS10.7720.88347.7050.0010.0010.0000.0000.0000.000
194B199GLY00.0630.03148.8470.0010.0010.0000.0000.0000.000
195B200ASP-1-0.841-0.91649.344-0.003-0.0030.0000.0000.0000.000
196B201ILE0-0.064-0.04146.3880.0000.0000.0000.0000.0000.000
197B202GLU-1-0.794-0.88543.451-0.011-0.0110.0000.0000.0000.000
198B203TRP0-0.049-0.04043.4820.0000.0000.0000.0000.0000.000
199B204ARG10.9210.96940.4780.0170.0170.0000.0000.0000.000
200B205VAL00.001-0.01041.620-0.001-0.0010.0000.0000.0000.000
201B206ILE0-0.042-0.02635.729-0.001-0.0010.0000.0000.0000.000
202B207THR00.0330.01639.876-0.002-0.0020.0000.0000.0000.000
203B208ASP-1-0.759-0.87340.646-0.046-0.0460.0000.0000.0000.000
204B209PHE0-0.030-0.02540.488-0.004-0.0040.0000.0000.0000.000
205B210GLY0-0.051-0.01436.978-0.002-0.0020.0000.0000.0000.000
206B211GLY00.0110.01536.6890.0000.0000.0000.0000.0000.000
207B212GLU-1-0.949-0.98036.486-0.030-0.0300.0000.0000.0000.000
208B213SER00.0200.00839.9530.0000.0000.0000.0000.0000.000
209B214HIS0-0.023-0.00443.1630.0010.0010.0000.0000.0000.000
210B215PRO0-0.056-0.01644.724-0.001-0.0010.0000.0000.0000.000
211B216PHE0-0.036-0.00946.0080.0010.0010.0000.0000.0000.000
212B217HIS00.0330.00547.6080.0010.0010.0000.0000.0000.000
213B218TYR00.004-0.00350.508-0.001-0.0010.0000.0000.0000.000
214B219VAL00.0120.00851.7430.0010.0010.0000.0000.0000.000
215B220LEU0-0.049-0.01450.2680.0000.0000.0000.0000.0000.000