Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: YY8K2

Calculation Name: 3AQ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AQ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q44522

Base Structure: X-ray

Registration Date: 2023-06-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2255708.983225
FMO2-HF: Nuclear repulsion 2178549.151389
FMO2-HF: Total energy -77159.831836
FMO2-MP2: Total energy -77384.716743


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-17.896-12.3413.645-8.19-11.008-0.044
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.000
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].
3A3VAL00.0980.0393.739-2.2800.619-0.004-1.542-1.3530.008
4A4PRO0-0.043-0.0246.3360.2050.2050.0000.0000.0000.000
5A5THR0-0.055-0.0322.311-3.647-1.6372.803-1.479-3.334-0.011
6A6TRP0-0.048-0.0114.638-0.244-0.033-0.001-0.015-0.1940.000
7A7GLN0-0.010-0.0015.9680.3960.3960.0000.0000.0000.000
8A8VAL00.0040.0119.053-0.075-0.0750.0000.0000.0000.000
9A9ARG10.8180.8927.7451.3631.3630.0000.0000.0000.000
10A10ASP-1-0.765-0.87613.758-0.363-0.3630.0000.0000.0000.000
11A11LEU0-0.046-0.02916.5970.0490.0490.0000.0000.0000.000
12A12ARG10.7640.84919.5710.3380.3380.0000.0000.0000.000
13A13ARG10.9270.96522.2510.2090.2090.0000.0000.0000.000
14A14ILE0-0.0240.00720.3690.0240.0240.0000.0000.0000.000
15A15LEU00.0570.01723.672-0.017-0.0170.0000.0000.0000.000
16A16ARG10.8880.94426.7780.1730.1730.0000.0000.0000.000
17A17VAL00.0390.01226.315-0.017-0.0170.0000.0000.0000.000
18A18SER0-0.015-0.01325.977-0.017-0.0170.0000.0000.0000.000
19A19GLU-1-0.838-0.90423.626-0.206-0.2060.0000.0000.0000.000
20A20LEU00.0340.02721.039-0.033-0.0330.0000.0000.0000.000
21A21SER0-0.017-0.00320.997-0.048-0.0480.0000.0000.0000.000
22A22GLN0-0.033-0.02420.565-0.038-0.0380.0000.0000.0000.000
23A23HIS00.022-0.00417.282-0.026-0.0260.0000.0000.0000.000
24A24LEU0-0.0080.00216.227-0.084-0.0840.0000.0000.0000.000
25A25ARG10.9450.97516.1540.3010.3010.0000.0000.0000.000
26A26GLN0-0.030-0.02711.744-0.010-0.0100.0000.0000.0000.000
27A27ALA00.0390.02812.016-0.115-0.1150.0000.0000.0000.000
28A28ARG10.8930.93111.1300.7830.7830.0000.0000.0000.000
29A29THR0-0.050-0.03311.450-0.209-0.2090.0000.0000.0000.000
30A30ASP-1-0.793-0.8507.933-1.053-1.0530.0000.0000.0000.000
31A31PHE00.0180.0166.532-0.695-0.6950.0000.0000.0000.000
32A32ARG10.8610.9236.6220.5030.5030.0000.0000.0000.000
33A33SER0-0.092-0.0686.800-0.201-0.2010.0000.0000.0000.000
34A34THR0-0.050-0.0342.358-1.0070.1401.358-0.707-1.7980.001
35A35LEU0-0.0090.0101.881-10.909-11.7819.490-4.483-4.134-0.042
36A36SER0-0.0090.0103.5701.4001.561-0.0010.036-0.1950.000
37A37GLN00.0490.0206.108-0.206-0.2060.0000.0000.0000.000
38A38LEU0-0.038-0.0098.0700.2580.2580.0000.0000.0000.000
39A39VAL0-0.0090.0006.111-0.398-0.3980.0000.0000.0000.000
40A40TYR00.0770.0577.8710.3990.3990.0000.0000.0000.000
41A41PHE0-0.039-0.0458.176-0.596-0.5960.0000.0000.0000.000
42A42ASN0-0.015-0.01510.5000.1020.1020.0000.0000.0000.000
43A43ARG10.8550.9428.7210.6940.6940.0000.0000.0000.000
44A44SER0-0.015-0.03114.8870.0450.0450.0000.0000.0000.000
45A45VAL0-0.029-0.03118.0380.0360.0360.0000.0000.0000.000
46A46VAL0-0.037-0.00521.2460.0470.0470.0000.0000.0000.000
47A47ASN0-0.011-0.02918.6880.0630.0630.0000.0000.0000.000
48A48PRO00.0430.02117.643-0.045-0.0450.0000.0000.0000.000
49A49ASN0-0.079-0.03614.789-0.001-0.0010.0000.0000.0000.000
50A50GLU-1-0.919-0.93913.270-0.309-0.3090.0000.0000.0000.000
51A51TYR0-0.075-0.0506.833-0.048-0.0480.0000.0000.0000.000
52A52ASP-1-0.777-0.87913.573-0.704-0.7040.0000.0000.0000.000
53A53ASP-1-0.806-0.91014.984-0.579-0.5790.0000.0000.0000.000
54A54GLU-1-0.832-0.84215.706-0.785-0.7850.0000.0000.0000.000
55A55TYR0-0.007-0.02111.789-0.124-0.1240.0000.0000.0000.000
56A56LEU0-0.053-0.03410.8420.1420.1420.0000.0000.0000.000
57A57LEU00.0240.03211.438-0.139-0.1390.0000.0000.0000.000
58A58SER0-0.010-0.0319.0170.2440.2440.0000.0000.0000.000
59A59ASP-1-0.844-0.89312.050-0.996-0.9960.0000.0000.0000.000
60A60GLN0-0.050-0.02914.4620.2330.2330.0000.0000.0000.000
61A61ARG10.9280.95016.1330.3830.3830.0000.0000.0000.000
62A62LEU00.0100.00815.053-0.035-0.0350.0000.0000.0000.000
63A63THR0-0.041-0.03818.3990.0660.0660.0000.0000.0000.000
64A64TYR0-0.012-0.01220.072-0.068-0.0680.0000.0000.0000.000
65A65VAL00.0540.03121.7970.0300.0300.0000.0000.0000.000
66A66TYR0-0.022-0.02523.584-0.004-0.0040.0000.0000.0000.000
67A67VAL00.0150.03023.5950.0020.0020.0000.0000.0000.000
68A68ASP-1-0.709-0.82726.771-0.264-0.2640.0000.0000.0000.000
69A69GLU-1-0.860-0.93525.611-0.264-0.2640.0000.0000.0000.000
70A70VAL0-0.013-0.00625.398-0.012-0.0120.0000.0000.0000.000
71A71THR00.002-0.03724.325-0.016-0.0160.0000.0000.0000.000
72A72ALA0-0.0060.00222.240-0.039-0.0390.0000.0000.0000.000
73A73GLN00.0180.01820.690-0.045-0.0450.0000.0000.0000.000
74A74LEU00.0000.00720.400-0.019-0.0190.0000.0000.0000.000
75A75CYS00.0100.00619.813-0.020-0.0200.0000.0000.0000.000
76A76GLY00.013-0.00416.678-0.079-0.0790.0000.0000.0000.000
77A77LEU0-0.069-0.04015.344-0.070-0.0700.0000.0000.0000.000
78A78ASN0-0.069-0.04015.9820.0400.0400.0000.0000.0000.000
79A79ARG10.8520.95210.5671.0261.0260.0000.0000.0000.000
80A80LEU00.0460.02115.035-0.014-0.0140.0000.0000.0000.000
81A81LEU0-0.008-0.00618.292-0.017-0.0170.0000.0000.0000.000
82A82PRO00.0120.01220.1310.0220.0220.0000.0000.0000.000
83A83SER0-0.027-0.01523.970-0.021-0.0210.0000.0000.0000.000
84A84ASN0-0.032-0.04126.6130.0130.0130.0000.0000.0000.000
85A85SER00.0550.01429.0590.0250.0250.0000.0000.0000.000
86A86PRO00.0080.01630.907-0.010-0.0100.0000.0000.0000.000
87A87ALA0-0.004-0.01331.831-0.011-0.0110.0000.0000.0000.000
88A88PHE0-0.020-0.01027.079-0.013-0.0130.0000.0000.0000.000
89A89GLY00.0450.04226.641-0.029-0.0290.0000.0000.0000.000
90A90THR0-0.047-0.04222.7160.0070.0070.0000.0000.0000.000
91A91VAL0-0.047-0.02225.156-0.023-0.0230.0000.0000.0000.000
92A92ALA0-0.0040.00222.714-0.007-0.0070.0000.0000.0000.000
93A93THR00.0200.01424.7220.0210.0210.0000.0000.0000.000
94A94ALA00.010-0.00524.130-0.036-0.0360.0000.0000.0000.000
95A95MET0-0.058-0.01425.1840.0070.0070.0000.0000.0000.000
96A96PRO00.0010.01424.978-0.016-0.0160.0000.0000.0000.000
97A97PRO00.0460.01323.7780.0310.0310.0000.0000.0000.000
98A98TRP0-0.0030.00023.0830.0170.0170.0000.0000.0000.000
99A99LEU0-0.115-0.03729.4030.0210.0210.0000.0000.0000.000
100A100LEU00.0380.01131.3540.0170.0170.0000.0000.0000.000
101A101ASP-1-0.785-0.87932.659-0.195-0.1950.0000.0000.0000.000
102A102PRO00.021-0.00431.640-0.006-0.0060.0000.0000.0000.000
103A103GLN0-0.042-0.03333.6240.0020.0020.0000.0000.0000.000
104A104GLU-1-0.877-0.93236.395-0.186-0.1860.0000.0000.0000.000
105A105MET0-0.016-0.01629.831-0.005-0.0050.0000.0000.0000.000
106A106ASN0-0.029-0.01333.9780.0040.0040.0000.0000.0000.000
107A107ALA00.0330.02235.1960.0000.0000.0000.0000.0000.000
108A108ILE0-0.009-0.00434.0170.0010.0010.0000.0000.0000.000
109A109LEU0-0.027-0.00729.694-0.007-0.0070.0000.0000.0000.000
110A110GLN0-0.040-0.02433.6740.0010.0010.0000.0000.0000.000
111A111GLN0-0.034-0.00136.7520.0080.0080.0000.0000.0000.000
112A112SER0-0.062-0.03432.603-0.001-0.0010.0000.0000.0000.000
113A113CYS0-0.0290.02530.585-0.017-0.0170.0000.0000.0000.000
114A114GLY00.0380.03333.7430.0150.0150.0000.0000.0000.000
115A115GLN0-0.012-0.01134.666-0.008-0.0080.0000.0000.0000.000
116A116GLY0-0.003-0.02035.2270.0030.0030.0000.0000.0000.000
117A117GLY00.0010.02630.878-0.001-0.0010.0000.0000.0000.000
118A118PHE0-0.038-0.02627.1050.0140.0140.0000.0000.0000.000
119A119VAL0-0.035-0.00827.0140.0140.0140.0000.0000.0000.000
120A120ASN00.023-0.01329.985-0.003-0.0030.0000.0000.0000.000
121A121TYR00.028-0.03427.7220.0050.0050.0000.0000.0000.000
122A122HIS00.010-0.00734.2710.0180.0180.0000.0000.0000.000
123A123HIS0-0.0340.00335.7400.0160.0160.0000.0000.0000.000
124A124GLY00.0290.03137.2170.0100.0100.0000.0000.0000.000
125A125PRO00.0180.00434.983-0.012-0.0120.0000.0000.0000.000
126A126SER0-0.0140.01233.453-0.012-0.0120.0000.0000.0000.000
127A127THR0-0.037-0.04531.615-0.017-0.0170.0000.0000.0000.000
128A128ASN0-0.007-0.01029.180-0.013-0.0130.0000.0000.0000.000
129A129GLY00.0330.02229.558-0.005-0.0050.0000.0000.0000.000
130A130PHE0-0.021-0.02224.5100.0040.0040.0000.0000.0000.000
131A131PHE00.0230.00419.847-0.004-0.0040.0000.0000.0000.000
132A132LEU00.0320.02218.872-0.011-0.0110.0000.0000.0000.000
133A133ALA0-0.027-0.01717.1930.0260.0260.0000.0000.0000.000
134A134ILE00.0230.00115.616-0.119-0.1190.0000.0000.0000.000
135A135LEU0-0.0220.00011.8020.0570.0570.0000.0000.0000.000
136A136MET0-0.0010.04415.199-0.035-0.0350.0000.0000.0000.000
137A137SER00.032-0.02515.475-0.056-0.0560.0000.0000.0000.000
138A138GLN00.002-0.01916.4170.0250.0250.0000.0000.0000.000
139A139LEU0-0.039-0.00718.5600.0740.0740.0000.0000.0000.000
140A140PHE0-0.064-0.03218.8590.0480.0480.0000.0000.0000.000
141A141ILE00.0520.04522.276-0.010-0.0100.0000.0000.0000.000
142A142ARG10.7960.87025.3400.3450.3450.0000.0000.0000.000
143A143ILE00.0050.00327.3330.0210.0210.0000.0000.0000.000
144A144ARG10.8000.86630.4780.2860.2860.0000.0000.0000.000
145A145THR0-0.046-0.03430.706-0.030-0.0300.0000.0000.0000.000
146A146ASP-1-0.750-0.82432.360-0.240-0.2400.0000.0000.0000.000
147A147VAL0-0.001-0.02033.315-0.012-0.0120.0000.0000.0000.000
148A148ILE00.0240.01534.3050.0120.0120.0000.0000.0000.000
149A149ARG10.8510.89933.4430.2060.2060.0000.0000.0000.000
150A150GLY00.0180.01136.8200.0000.0000.0000.0000.0000.000
151A151GLN0-0.0280.00231.866-0.012-0.0120.0000.0000.0000.000
152A152GLY00.0280.02132.1400.0030.0030.0000.0000.0000.000
153A153TYR0-0.055-0.04328.060-0.024-0.0240.0000.0000.0000.000
154A154GLY00.0060.00927.3090.0150.0150.0000.0000.0000.000
155A155TRP0-0.004-0.01527.454-0.026-0.0260.0000.0000.0000.000
156A156TYR00.0390.00324.0740.0170.0170.0000.0000.0000.000
157A157ALA00.0270.01926.0970.0020.0020.0000.0000.0000.000
158A158ARG10.8080.89519.6420.6060.6060.0000.0000.0000.000
159A159GLN00.0390.00224.1550.0440.0440.0000.0000.0000.000
160A160GLY00.0710.02526.8140.0030.0030.0000.0000.0000.000
161A161ASN0-0.115-0.05430.1500.0070.0070.0000.0000.0000.000
162A162TYR0-0.002-0.00130.0320.0140.0140.0000.0000.0000.000
163A163VAL0-0.005-0.00431.614-0.002-0.0020.0000.0000.0000.000
164A164GLU-1-0.894-0.94627.101-0.377-0.3770.0000.0000.0000.000
165A165GLU-1-0.802-0.88730.719-0.269-0.2690.0000.0000.0000.000
166A166GLY0-0.078-0.04132.3820.0080.0080.0000.0000.0000.000
167A180GLU-1-0.827-0.89925.112-0.382-0.3820.0000.0000.0000.000
168A181THR0-0.007-0.01625.5580.0160.0160.0000.0000.0000.000
169A182ARG10.7910.88220.8120.4490.4490.0000.0000.0000.000
170A183GLU-1-0.770-0.84520.201-0.392-0.3920.0000.0000.0000.000
171A184PHE0-0.005-0.01319.484-0.070-0.0700.0000.0000.0000.000
172A185GLN0-0.016-0.00417.2140.0990.0990.0000.0000.0000.000
173A186LEU00.0340.01621.727-0.018-0.0180.0000.0000.0000.000
174A187SER00.017-0.00124.1130.0400.0400.0000.0000.0000.000
175A188ASP-1-0.791-0.87525.641-0.320-0.3200.0000.0000.0000.000
176A189LEU0-0.052-0.01722.731-0.010-0.0100.0000.0000.0000.000
177A190ILE0-0.0290.01119.3760.0150.0150.0000.0000.0000.000
178A191HIS00.0060.00412.376-0.115-0.1150.0000.0000.0000.000
179A192TYR00.001-0.03414.879-0.035-0.0350.0000.0000.0000.000
180A193PRO0-0.007-0.00710.1980.0180.0180.0000.0000.0000.000
181A194ILE0-0.0030.01712.3450.0790.0790.0000.0000.0000.000
182A195VAL0-0.034-0.00611.667-0.111-0.1110.0000.0000.0000.000
183A196ALA00.003-0.02212.6190.0170.0170.0000.0000.0000.000
184A197LEU00.0150.03015.3910.0040.0040.0000.0000.0000.000
185A198GLY00.016-0.00418.7520.0160.0160.0000.0000.0000.000
186A199SER00.0320.02221.8620.0080.0080.0000.0000.0000.000
187A200CYS0-0.025-0.01525.641-0.023-0.0230.0000.0000.0000.000
188A201HIS0-0.0360.00328.2150.0200.0200.0000.0000.0000.000
189A202LEU0-0.016-0.00126.1520.0080.0080.0000.0000.0000.000
190A203THR00.0200.00930.1960.0190.0190.0000.0000.0000.000
191A204ARG10.9510.97331.0560.1740.1740.0000.0000.0000.000