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: MVQ3Z

Calculation Name: 2C46-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C46

Chain ID: A

ChEMBL ID:

UniProt ID: O60942

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2533868.767944
FMO2-HF: Nuclear repulsion 2449247.221889
FMO2-HF: Total energy -84621.546055
FMO2-MP2: Total energy -84863.997072


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:-5:ASN)


Summations of interaction energy for fragment #1(A:-5:ASN)
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.
-34.164-22.5958.894-8.342-12.121-0.014
Interaction energy analysis for fragmet #1(A:-5:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.006
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].
3A-3TYR00.0010.0332.474-10.575-5.6851.477-2.672-3.6940.023
4A-2PHE0-0.029-0.0182.457-3.342-1.7971.376-0.713-2.2080.003
5A-1GLN00.0080.0064.212-2.329-2.253-0.001-0.040-0.0350.000
6A0SER00.007-0.0067.7530.6070.6070.0000.0000.0000.000
7A1MET00.0180.03410.5090.3230.3230.0000.0000.0000.000
8A2ALA0-0.0190.00112.0710.0390.0390.0000.0000.0000.000
9A3HIS00.0410.02214.4090.0230.0230.0000.0000.0000.000
10A4ASN0-0.022-0.0159.1380.1240.1240.0000.0000.0000.000
11A5LYS11.0331.03213.132-0.602-0.6020.0000.0000.0000.000
12A6ILE00.0070.01114.2110.2210.2210.0000.0000.0000.000
13A7PRO0-0.026-0.02313.879-0.072-0.0720.0000.0000.0000.000
14A8PRO00.0730.04516.733-0.043-0.0430.0000.0000.0000.000
15A9ARG10.8720.93220.347-0.347-0.3470.0000.0000.0000.000
16A10TRP0-0.024-0.01615.082-0.038-0.0380.0000.0000.0000.000
17A11LEU0-0.019-0.02119.528-0.009-0.0090.0000.0000.0000.000
18A12ASN00.0710.03621.128-0.010-0.0100.0000.0000.0000.000
19A13CYS0-0.0460.02820.750-0.011-0.0110.0000.0000.0000.000
20A14PRO00.0380.02821.8100.0150.0150.0000.0000.0000.000
21A15ARG10.8280.88219.271-0.292-0.2920.0000.0000.0000.000
22A16ARG10.8830.93719.380-0.182-0.1820.0000.0000.0000.000
23A17GLY00.0200.01821.487-0.027-0.0270.0000.0000.0000.000
24A18GLN0-0.019-0.00524.0740.0000.0000.0000.0000.0000.000
25A19PRO00.008-0.01424.7970.0210.0210.0000.0000.0000.000
26A20VAL00.0260.01325.703-0.018-0.0180.0000.0000.0000.000
27A21ALA00.0490.02127.5270.0010.0010.0000.0000.0000.000
28A22GLY0-0.031-0.01128.199-0.010-0.0100.0000.0000.0000.000
29A23ARG10.8510.92525.941-0.165-0.1650.0000.0000.0000.000
30A24PHE00.0620.01721.8330.0120.0120.0000.0000.0000.000
31A25LEU0-0.034-0.00519.031-0.023-0.0230.0000.0000.0000.000
32A26PRO00.0220.02719.7020.0580.0580.0000.0000.0000.000
33A27LEU0-0.012-0.02314.776-0.060-0.0600.0000.0000.0000.000
34A28LYS10.8340.94316.690-0.539-0.5390.0000.0000.0000.000
35A29THR0-0.048-0.03111.0480.1210.1210.0000.0000.0000.000
36A30MET00.0110.03010.818-0.233-0.2330.0000.0000.0000.000
37A31LEU0-0.007-0.00410.4450.4240.4240.0000.0000.0000.000
38A32GLY00.028-0.0098.838-0.332-0.3320.0000.0000.0000.000
39A33PRO00.004-0.0179.6000.0350.0350.0000.0000.0000.000
40A34ARG10.8780.9448.421-0.646-0.6460.0000.0000.0000.000
41A35TYR0-0.023-0.0338.538-0.236-0.2360.0000.0000.0000.000
42A36ASP-1-0.739-0.85213.4830.2960.2960.0000.0000.0000.000
43A37SER0-0.037-0.01316.442-0.014-0.0140.0000.0000.0000.000
44A38GLN0-0.026-0.02515.0180.0050.0050.0000.0000.0000.000
45A39VAL0-0.035-0.01116.1640.0310.0310.0000.0000.0000.000
46A40ALA00.0430.03319.154-0.032-0.0320.0000.0000.0000.000
47A41GLU-1-0.828-0.92420.4240.1860.1860.0000.0000.0000.000
48A42GLU-1-0.814-0.90921.4590.2210.2210.0000.0000.0000.000
49A43ASN0-0.035-0.00821.1080.0100.0100.0000.0000.0000.000
50A44ARG10.7750.90216.949-0.168-0.1680.0000.0000.0000.000
51A45PHE00.033-0.01615.883-0.074-0.0740.0000.0000.0000.000
52A46HIS10.8250.90312.248-0.169-0.1690.0000.0000.0000.000
53A47PRO00.1040.0358.233-0.039-0.0390.0000.0000.0000.000
54A48SER00.0100.00311.442-0.011-0.0110.0000.0000.0000.000
55A49MET0-0.0190.00913.859-0.005-0.0050.0000.0000.0000.000
56A50LEU00.0200.01613.654-0.013-0.0130.0000.0000.0000.000
57A51SER0-0.009-0.02314.359-0.001-0.0010.0000.0000.0000.000
58A52ASN0-0.005-0.01216.334-0.053-0.0530.0000.0000.0000.000
59A53TYR00.0430.02219.2320.0000.0000.0000.0000.0000.000
60A54LEU00.0100.02116.839-0.008-0.0080.0000.0000.0000.000
61A55LYS10.9100.94816.7590.1560.1560.0000.0000.0000.000
62A56SER0-0.078-0.04022.297-0.001-0.0010.0000.0000.0000.000
63A57LEU0-0.032-0.02323.937-0.003-0.0030.0000.0000.0000.000
64A58LYS10.8810.94725.086-0.028-0.0280.0000.0000.0000.000
65A59VAL00.0260.01723.1660.0000.0000.0000.0000.0000.000
66A60LYS10.8130.92617.8950.0510.0510.0000.0000.0000.000
67A61MET00.0150.03316.2460.0470.0470.0000.0000.0000.000
68A62GLY00.0650.02517.636-0.052-0.0520.0000.0000.0000.000
69A63LEU0-0.067-0.03014.966-0.037-0.0370.0000.0000.0000.000
70A64LEU00.0130.01610.734-0.013-0.0130.0000.0000.0000.000
71A65VAL00.002-0.00713.2510.0780.0780.0000.0000.0000.000
72A66ASP-1-0.748-0.8208.9562.8992.8990.0000.0000.0000.000
73A67LEU00.0250.00112.4580.0770.0770.0000.0000.0000.000
74A68THR0-0.103-0.06210.4990.1010.1010.0000.0000.0000.000
75A69ASN00.0410.00310.9040.1780.1780.0000.0000.0000.000
76A70THR0-0.007-0.0037.5070.2850.2850.0000.0000.0000.000
77A71SER00.0620.0302.839-2.746-1.0070.408-1.007-1.141-0.001
78A72ARG10.9070.9443.4583.6404.2470.064-0.207-0.4640.000
79A73PHE00.0060.0195.923-0.883-0.8830.0000.0000.0000.000
80A74TYR0-0.014-0.0425.985-1.074-1.0740.0000.0000.0000.000
81A75ASP-1-0.750-0.8592.028-16.725-15.3705.402-3.333-3.424-0.041
82A76ARG10.8460.8852.967-2.608-1.4450.168-0.307-1.0240.002
83A77ASN00.024-0.0073.4831.3101.5040.000-0.063-0.1310.000
84A78ASP-1-0.905-0.9695.493-0.149-0.1490.0000.0000.0000.000
85A79ILE0-0.070-0.0427.4290.3760.3760.0000.0000.0000.000
86A80GLU-1-0.801-0.8796.875-0.874-0.8740.0000.0000.0000.000
87A81LYS10.8270.9389.0641.0161.0160.0000.0000.0000.000
88A82GLU-1-0.833-0.89411.067-0.281-0.2810.0000.0000.0000.000
89A83GLY00.0040.00913.1830.1030.1030.0000.0000.0000.000
90A84ILE0-0.097-0.03312.7430.1010.1010.0000.0000.0000.000
91A85LYS10.9640.97912.177-0.170-0.1700.0000.0000.0000.000
92A86TYR0-0.005-0.0367.5540.3270.3270.0000.0000.0000.000
93A87ILE0-0.028-0.02410.961-0.042-0.0420.0000.0000.0000.000
94A88LYS10.7700.8977.248-3.151-3.1510.0000.0000.0000.000
95A89LEU0-0.009-0.00711.037-0.177-0.1770.0000.0000.0000.000
96A90GLN0-0.0020.00110.7220.1380.1380.0000.0000.0000.000
97A91CYS0-0.021-0.00214.317-0.136-0.1360.0000.0000.0000.000
98A92LYS10.8420.90717.636-0.377-0.3770.0000.0000.0000.000
99A93GLY00.0150.00419.5480.0220.0220.0000.0000.0000.000
100A94HIS00.0440.01120.165-0.045-0.0450.0000.0000.0000.000
101A95GLY0-0.0010.00322.163-0.035-0.0350.0000.0000.0000.000
102A96GLU-1-0.758-0.84523.7270.3950.3950.0000.0000.0000.000
103A97CYS0-0.0120.02823.6290.0400.0400.0000.0000.0000.000
104A98PRO0-0.038-0.01121.6970.0120.0120.0000.0000.0000.000
105A99THR00.040-0.00623.117-0.023-0.0230.0000.0000.0000.000
106A100THR00.0560.01124.9580.0120.0120.0000.0000.0000.000
107A101GLU-1-0.822-0.87723.3720.3570.3570.0000.0000.0000.000
108A102ASN0-0.0010.00519.8640.0220.0220.0000.0000.0000.000
109A103THR00.0600.02221.6660.0300.0300.0000.0000.0000.000
110A104GLU-1-0.756-0.84424.2800.2560.2560.0000.0000.0000.000
111A105THR0-0.075-0.04818.5260.0000.0000.0000.0000.0000.000
112A106PHE0-0.007-0.02219.3660.0090.0090.0000.0000.0000.000
113A107ILE00.0590.03021.263-0.014-0.0140.0000.0000.0000.000
114A108ARG10.8260.89423.133-0.253-0.2530.0000.0000.0000.000
115A109LEU0-0.058-0.02016.644-0.032-0.0320.0000.0000.0000.000
116A110CYS00.0350.01620.956-0.027-0.0270.0000.0000.0000.000
117A111GLU-1-0.816-0.87522.4500.1650.1650.0000.0000.0000.000
118A112ARG10.8560.92518.905-0.263-0.2630.0000.0000.0000.000
119A113PHE0-0.061-0.03518.283-0.027-0.0270.0000.0000.0000.000
120A114ASN00.0040.01023.410-0.024-0.0240.0000.0000.0000.000
121A115GLU-1-0.833-0.93626.0810.1040.1040.0000.0000.0000.000
122A116ARG10.7920.90821.622-0.078-0.0780.0000.0000.0000.000
123A117ASN00.0190.00028.331-0.005-0.0050.0000.0000.0000.000
124A118PRO0-0.0140.00926.925-0.001-0.0010.0000.0000.0000.000
125A119PRO00.0100.01126.6130.0040.0040.0000.0000.0000.000
126A120GLU-1-0.822-0.91520.8440.0080.0080.0000.0000.0000.000
127A121LEU0-0.034-0.00621.3330.0240.0240.0000.0000.0000.000
128A122ILE00.0020.00118.742-0.010-0.0100.0000.0000.0000.000
129A123GLY0-0.011-0.01416.8920.0010.0010.0000.0000.0000.000
130A124VAL00.000-0.00716.9570.0430.0430.0000.0000.0000.000
131A125HIS00.0190.03511.0110.0730.0730.0000.0000.0000.000
132A126CYM-1-0.761-0.78314.9730.9210.9210.0000.0000.0000.000
133A127THR0-0.009-0.01214.7770.0850.0850.0000.0000.0000.000
134A128HIS00.017-0.02315.8170.0370.0370.0000.0000.0000.000
135A129GLY00.0430.00718.844-0.056-0.0560.0000.0000.0000.000
136A130PHE0-0.012-0.02519.861-0.048-0.0480.0000.0000.0000.000
137A131ASN00.0440.01822.715-0.050-0.0500.0000.0000.0000.000
138A132ARG10.9670.97218.506-0.726-0.7260.0000.0000.0000.000
139A133THR00.001-0.06919.102-0.007-0.0070.0000.0000.0000.000
140A134GLY00.0500.01821.074-0.033-0.0330.0000.0000.0000.000
141A135PHE00.0290.00324.149-0.025-0.0250.0000.0000.0000.000
142A136LEU00.004-0.00419.756-0.025-0.0250.0000.0000.0000.000
143A137ILE0-0.030-0.01622.130-0.029-0.0290.0000.0000.0000.000
144A138CYS0-0.025-0.01125.309-0.035-0.0350.0000.0000.0000.000
145A139ALA00.0630.03326.613-0.022-0.0220.0000.0000.0000.000
146A140PHE0-0.037-0.01125.488-0.020-0.0200.0000.0000.0000.000
147A141LEU0-0.043-0.03327.993-0.022-0.0220.0000.0000.0000.000
148A142VAL00.0130.01930.807-0.016-0.0160.0000.0000.0000.000
149A143GLU-1-0.879-0.91529.8590.2590.2590.0000.0000.0000.000
150A144LYS10.7870.88229.354-0.191-0.1910.0000.0000.0000.000
151A145MET0-0.122-0.06930.501-0.010-0.0100.0000.0000.0000.000
152A146ASP-1-0.883-0.91833.6060.1330.1330.0000.0000.0000.000
153A147TRP0-0.065-0.03833.059-0.001-0.0010.0000.0000.0000.000
154A148SER00.042-0.00536.3090.0050.0050.0000.0000.0000.000
155A149ILE00.0510.01232.1100.0120.0120.0000.0000.0000.000
156A150GLU-1-0.792-0.86935.0340.1850.1850.0000.0000.0000.000
157A151ALA0-0.017-0.00436.4390.0060.0060.0000.0000.0000.000
158A152ALA0-0.0120.01531.4190.0070.0070.0000.0000.0000.000
159A153VAL00.012-0.01231.4920.0170.0170.0000.0000.0000.000
160A154ALA00.0190.01732.1480.0110.0110.0000.0000.0000.000
161A155THR0-0.024-0.02531.019-0.004-0.0040.0000.0000.0000.000
162A156PHE0-0.049-0.01023.7800.0100.0100.0000.0000.0000.000
163A157ALA00.020-0.00128.8910.0140.0140.0000.0000.0000.000
164A158GLN0-0.037-0.00831.109-0.008-0.0080.0000.0000.0000.000
165A159ALA0-0.047-0.02127.788-0.004-0.0040.0000.0000.0000.000
166A160ARG10.7770.88320.992-0.470-0.4700.0000.0000.0000.000
167A161PRO00.0570.06227.1960.0210.0210.0000.0000.0000.000
168A162PRO0-0.021-0.02427.8110.0160.0160.0000.0000.0000.000
169A163GLY00.0300.01027.991-0.014-0.0140.0000.0000.0000.000
170A164ILE0-0.076-0.04126.5190.0260.0260.0000.0000.0000.000
171A165TYR00.0640.01724.241-0.013-0.0130.0000.0000.0000.000
172A166LYS10.8170.92726.086-0.415-0.4150.0000.0000.0000.000
173A167GLY00.0640.02129.060-0.005-0.0050.0000.0000.0000.000
174A168ASP-1-0.792-0.91929.7440.3240.3240.0000.0000.0000.000
175A169TYR0-0.117-0.09723.0780.0230.0230.0000.0000.0000.000
176A170LEU00.0050.00929.193-0.002-0.0020.0000.0000.0000.000
177A171LYS10.9550.98032.212-0.224-0.2240.0000.0000.0000.000
178A172GLU-1-0.745-0.82529.3360.2780.2780.0000.0000.0000.000
179A173LEU0-0.057-0.02528.454-0.005-0.0050.0000.0000.0000.000
180A174PHE00.0480.01032.201-0.005-0.0050.0000.0000.0000.000
181A175ARG10.8410.90332.322-0.255-0.2550.0000.0000.0000.000
182A176ARG10.6980.83327.148-0.335-0.3350.0000.0000.0000.000
183A177TYR0-0.078-0.09529.8260.0040.0040.0000.0000.0000.000
184A178GLY00.0110.01335.951-0.007-0.0070.0000.0000.0000.000
185A179ASP-1-0.823-0.89539.0670.1500.1500.0000.0000.0000.000
186A180ILE0-0.063-0.04437.4170.0080.0080.0000.0000.0000.000
187A181GLU-1-0.932-0.97839.7240.1660.1660.0000.0000.0000.000
188A182GLU-1-0.978-0.97941.5600.1440.1440.0000.0000.0000.000
189A183ALA0-0.060-0.01936.7350.0060.0060.0000.0000.0000.000
190A184PRO0-0.0170.00235.481-0.005-0.0050.0000.0000.0000.000
191A185PRO0-0.032-0.02136.7410.0110.0110.0000.0000.0000.000
192A186PRO00.004-0.02033.1710.0060.0060.0000.0000.0000.000
193A187PRO0-0.0260.01032.139-0.013-0.0130.0000.0000.0000.000
194A188LEU00.010-0.00234.3860.0060.0060.0000.0000.0000.000
195A189LEU0-0.0060.00029.9460.0110.0110.0000.0000.0000.000
196A190PRO0-0.024-0.01928.955-0.015-0.0150.0000.0000.0000.000
197A191ASP-1-0.868-0.94430.6340.2700.2700.0000.0000.0000.000
198A192TRP00.0210.00823.2570.0290.0290.0000.0000.0000.000
199A193CYS0-0.136-0.06026.0600.0340.0340.0000.0000.0000.000
200A194PHE00.0490.01727.442-0.019-0.0190.0000.0000.0000.000
201A195GLU-1-0.998-1.00327.5390.3500.3500.0000.0000.0000.000
202A196ASP-1-0.807-0.92528.3510.2550.2550.0000.0000.0000.000
203A197ASP-1-0.930-0.96727.6980.3770.3770.0000.0000.0000.000
204A198GLU-1-1.004-0.99328.6040.2510.2510.0000.0000.0000.000
205A199ASP-1-1.007-0.97226.6080.3610.3610.0000.0000.0000.000