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

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FMODB ID: Q839Y

Calculation Name: 2ZZ8-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZZ8

Chain ID: A

ChEMBL ID:

UniProt ID: O34094

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 233
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2755955.129118
FMO2-HF: Nuclear repulsion 2667678.311159
FMO2-HF: Total energy -88276.817959
FMO2-MP2: Total energy -88537.249853


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:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
0.3491.052-0.005-0.371-0.3260
Interaction energy analysis for fragmet #1(A:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.011
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].
3A7LEU 0-0.039-0.0063.8591.4022.105-0.005-0.371-0.3260.000
4A8PRO 00.0190.0126.8690.0750.0750.0000.0000.0000.000
5A9SER 00.0400.0188.683-0.037-0.0370.0000.0000.0000.000
6A10LEU 00.0050.01310.8390.0570.0570.0000.0000.0000.000
7A11LYS 10.9080.96413.9400.1020.1020.0000.0000.0000.000
8A12SER 00.0420.01216.9780.0060.0060.0000.0000.0000.000
9A13SER 0-0.139-0.11320.6170.0130.0130.0000.0000.0000.000
10A14PHE 00.0460.02423.2890.0100.0100.0000.0000.0000.000
11A15VAL 0-0.037-0.02522.727-0.003-0.0030.0000.0000.0000.000
12A16LEU 0-0.035-0.01119.9000.0010.0010.0000.0000.0000.000
13A17SER 00.0190.00123.1510.0030.0030.0000.0000.0000.000
14A18GLU -1-0.857-0.90623.824-0.001-0.0010.0000.0000.0000.000
15A19ASP -1-0.873-0.91623.8290.0270.0270.0000.0000.0000.000
16A20THR 0-0.007-0.00925.9030.0000.0000.0000.0000.0000.000
17A21ILE 00.016-0.00524.6510.0060.0060.0000.0000.0000.000
18A22PRO 00.0130.00425.882-0.004-0.0040.0000.0000.0000.000
19A23GLY 0-0.023-0.01028.8920.0030.0030.0000.0000.0000.000
20A24THR 0-0.0380.00429.685-0.003-0.0030.0000.0000.0000.000
21A25ASN 0-0.068-0.04431.874-0.004-0.0040.0000.0000.0000.000
22A26GLU -1-0.898-0.95328.2130.0350.0350.0000.0000.0000.000
23A27THR 0-0.019-0.00427.3020.0050.0050.0000.0000.0000.000
24A28VAL 0-0.001-0.00320.708-0.001-0.0010.0000.0000.0000.000
25A29LYS 10.8280.89723.2780.0050.0050.0000.0000.0000.000
26A30THR 00.0040.00618.3130.0010.0010.0000.0000.0000.000
27A31LEU 0-0.043-0.02618.578-0.006-0.0060.0000.0000.0000.000
28A32LEU 00.0380.01818.390-0.001-0.0010.0000.0000.0000.000
29A33PRO 0-0.0130.00714.927-0.008-0.0080.0000.0000.0000.000
30A34TYR 0-0.014-0.03616.9760.0130.0130.0000.0000.0000.000
31A35GLY 00.0090.01316.860-0.019-0.0190.0000.0000.0000.000
32A36SER 00.0040.00118.070-0.007-0.0070.0000.0000.0000.000
33A37VAL 0-0.019-0.01413.5860.0220.0220.0000.0000.0000.000
34A38ILE 00.0350.03415.413-0.025-0.0250.0000.0000.0000.000
35A39ASN 0-0.033-0.00711.0870.1120.1120.0000.0000.0000.000
36A40TYR 00.0240.01514.019-0.004-0.0040.0000.0000.0000.000
37A41TYR 00.0590.0218.5830.0160.0160.0000.0000.0000.000
38A42GLY 0-0.010-0.00815.3440.0400.0400.0000.0000.0000.000
39A43TYR 0-0.010-0.02417.874-0.007-0.0070.0000.0000.0000.000
40A44VAL 0-0.0380.00420.4110.0120.0120.0000.0000.0000.000
41A45LYS 10.9981.00223.6840.1300.1300.0000.0000.0000.000
42A46PRO 00.0470.00325.4420.0050.0050.0000.0000.0000.000
43A47GLY 0-0.020-0.00228.3680.0010.0010.0000.0000.0000.000
44A48GLN 00.0060.01526.547-0.001-0.0010.0000.0000.0000.000
45A49ALA 00.0080.00130.3590.0010.0010.0000.0000.0000.000
46A50PRO 0-0.048-0.01930.900-0.005-0.0050.0000.0000.0000.000
47A51ASP -1-0.792-0.88429.292-0.104-0.1040.0000.0000.0000.000
48A52GLY 0-0.028-0.01332.4390.0050.0050.0000.0000.0000.000
49A53LEU 0-0.024-0.00933.372-0.002-0.0020.0000.0000.0000.000
50A54VAL 00.001-0.00931.4540.0000.0000.0000.0000.0000.000
51A55ASP -1-0.831-0.91234.460-0.045-0.0450.0000.0000.0000.000
52A56GLY 0-0.0010.01536.5760.0030.0030.0000.0000.0000.000
53A57ASN 0-0.004-0.00235.862-0.001-0.0010.0000.0000.0000.000
54A58LYS 10.7720.88931.1360.0520.0520.0000.0000.0000.000
55A59LYS 10.9580.97630.6150.0670.0670.0000.0000.0000.000
56A60ALA 00.0050.02829.052-0.005-0.0050.0000.0000.0000.000
57A61TYR 0-0.014-0.01325.8690.0040.0040.0000.0000.0000.000
58A62TYR 0-0.034-0.03827.005-0.002-0.0020.0000.0000.0000.000
59A63LEU 0-0.0080.00220.456-0.006-0.0060.0000.0000.0000.000
60A64TYR 0-0.029-0.01125.1980.0120.0120.0000.0000.0000.000
61A65VAL 00.0350.00423.391-0.015-0.0150.0000.0000.0000.000
62A66TRP 0-0.014-0.00825.7330.0160.0160.0000.0000.0000.000
63A67ILE 0-0.002-0.00925.680-0.014-0.0140.0000.0000.0000.000
64A68PRO 00.0620.02626.1830.0120.0120.0000.0000.0000.000
65A69ALA 00.0180.00228.9910.0090.0090.0000.0000.0000.000
66A70VAL 0-0.006-0.00129.533-0.004-0.0040.0000.0000.0000.000
67A71ILE 0-0.024-0.00425.861-0.004-0.0040.0000.0000.0000.000
68A72ALA 0-0.002-0.01626.9970.0080.0080.0000.0000.0000.000
69A73GLU -1-0.766-0.85423.364-0.096-0.0960.0000.0000.0000.000
70A74MET 00.0300.03622.640-0.013-0.0130.0000.0000.0000.000
71A75GLY 0-0.0170.00620.4020.0150.0150.0000.0000.0000.000
72A76VAL 00.0110.00319.639-0.025-0.0250.0000.0000.0000.000
73A77ARG 10.8710.92411.0800.4680.4680.0000.0000.0000.000
74A78MET 0-0.0330.00317.138-0.040-0.0400.0000.0000.0000.000
75A79ILE 0-0.023-0.00511.3380.0270.0270.0000.0000.0000.000
76A80SER 0-0.0460.00715.020-0.025-0.0250.0000.0000.0000.000
77A81PRO 00.0210.01514.6480.0260.0260.0000.0000.0000.000
78A82THR 0-0.063-0.06611.1450.0050.0050.0000.0000.0000.000
79A83GLY 00.0250.03110.204-0.048-0.0480.0000.0000.0000.000
80A84GLU -1-0.953-0.99310.825-0.205-0.2050.0000.0000.0000.000
81A85ILE 0-0.033-0.0307.8800.0120.0120.0000.0000.0000.000
82A86GLY 0-0.0190.0097.406-0.275-0.2750.0000.0000.0000.000
83A87GLU -1-0.936-0.9828.463-0.381-0.3810.0000.0000.0000.000
84A88PRO 0-0.069-0.0258.585-0.201-0.2010.0000.0000.0000.000
85A89GLY 00.0480.0169.4320.0560.0560.0000.0000.0000.000
86A90ASP -1-0.952-0.98310.114-0.387-0.3870.0000.0000.0000.000
87A91GLY 00.0360.02912.2980.0830.0830.0000.0000.0000.000
88A92ASP -1-0.860-0.9279.739-1.102-1.1020.0000.0000.0000.000
89A93LEU 0-0.020-0.00713.2980.0720.0720.0000.0000.0000.000
90A94VAL 00.006-0.00513.821-0.028-0.0280.0000.0000.0000.000
91A95SER 0-0.0100.00316.6590.0380.0380.0000.0000.0000.000
92A96ASP -1-0.808-0.91919.795-0.179-0.1790.0000.0000.0000.000
93A97ALA 0-0.111-0.06322.0910.0080.0080.0000.0000.0000.000
94A98PHE 00.009-0.00812.6820.0180.0180.0000.0000.0000.000
95A99LYS 10.9500.96616.9470.2860.2860.0000.0000.0000.000
96A100ALA 0-0.045-0.01318.9740.0140.0140.0000.0000.0000.000
97A101ALA 0-0.0280.01918.9780.0150.0150.0000.0000.0000.000
98A102THR 00.0330.00119.156-0.011-0.0110.0000.0000.0000.000
99A103PRO 00.033-0.00115.531-0.014-0.0140.0000.0000.0000.000
100A104GLU -1-0.909-0.93916.426-0.055-0.0550.0000.0000.0000.000
101A105GLU -1-0.883-0.94418.955-0.111-0.1110.0000.0000.0000.000
102A106LYS 10.8050.92114.4800.2600.2600.0000.0000.0000.000
103A107SER 00.020-0.01014.708-0.034-0.0340.0000.0000.0000.000
104A108MET 0-0.0230.01315.8640.0260.0260.0000.0000.0000.000
105A109PRO 0-0.026-0.01118.143-0.017-0.0170.0000.0000.0000.000
106A110HIS 00.0390.01519.3020.0170.0170.0000.0000.0000.000
107A111TRP 0-0.072-0.06720.2250.0120.0120.0000.0000.0000.000
108A112PHE 00.0490.01619.958-0.005-0.0050.0000.0000.0000.000
109A113ASP -1-0.811-0.87020.502-0.074-0.0740.0000.0000.0000.000
110A114THR 00.0400.04020.881-0.002-0.0020.0000.0000.0000.000
111A115TRP 0-0.081-0.02723.5310.0050.0050.0000.0000.0000.000
112A116ILE 00.004-0.01621.655-0.006-0.0060.0000.0000.0000.000
113A117ARG 10.8730.93126.3240.0800.0800.0000.0000.0000.000
114A118VAL 0-0.0030.00426.149-0.009-0.0090.0000.0000.0000.000
115A119GLU -1-0.859-0.92228.924-0.070-0.0700.0000.0000.0000.000
116A120ARG 10.8960.96631.6480.0670.0670.0000.0000.0000.000
117A121MET 0-0.025-0.01232.5990.0060.0060.0000.0000.0000.000
118A122SER 0-0.016-0.02135.1280.0000.0000.0000.0000.0000.000
119A123ALA 0-0.036-0.00934.8630.0030.0030.0000.0000.0000.000
120A124ILE 0-0.012-0.00135.930-0.002-0.0020.0000.0000.0000.000
121A125MET 00.0260.02936.130-0.003-0.0030.0000.0000.0000.000
122A126PRO 00.1100.05632.8410.0000.0000.0000.0000.0000.000
123A127ASP -1-0.847-0.91634.407-0.072-0.0720.0000.0000.0000.000
124A128GLN 0-0.007-0.02337.0580.0020.0020.0000.0000.0000.000
125A129ILE 00.0190.01930.7080.0020.0020.0000.0000.0000.000
126A130ALA 00.0160.00334.5830.0000.0000.0000.0000.0000.000
127A131LYS 10.7860.88435.4740.0750.0750.0000.0000.0000.000
128A132ALA 00.0200.01435.8930.0020.0020.0000.0000.0000.000
129A133ALA 0-0.015-0.00433.2260.0010.0010.0000.0000.0000.000
130A134LYS 10.9290.97134.9870.0680.0680.0000.0000.0000.000
131A135ALA 0-0.048-0.00738.0750.0050.0050.0000.0000.0000.000
132A136LYS 10.8670.92238.2470.0480.0480.0000.0000.0000.000
133A137PRO 00.0360.00435.528-0.001-0.0010.0000.0000.0000.000
134A138VAL 0-0.042-0.01637.1830.0050.0050.0000.0000.0000.000
135A139GLN 00.0250.00338.5380.0030.0030.0000.0000.0000.000
136A140NME 00.0030.02640.8440.0010.0010.0000.0000.0000.000
137A146ACE 0-0.002-0.01439.2990.0010.0010.0000.0000.0000.000
138A147GLY 00.0250.00235.8750.0020.0020.0000.0000.0000.000
139A148ASP -1-0.801-0.88530.298-0.073-0.0730.0000.0000.0000.000
140A149ASP -1-0.855-0.92331.385-0.077-0.0770.0000.0000.0000.000
141A150THR 0-0.036-0.01232.4230.0000.0000.0000.0000.0000.000
142A151TYR 0-0.005-0.01733.403-0.002-0.0020.0000.0000.0000.000
143A152LYS 10.9681.01428.1540.0770.0770.0000.0000.0000.000
144A153GLU -1-0.797-0.89929.824-0.069-0.0690.0000.0000.0000.000
145A154GLU -1-0.894-0.94025.803-0.066-0.0660.0000.0000.0000.000
146A155ARG 10.8940.95027.3190.0460.0460.0000.0000.0000.000
147A156HIS 10.8100.89726.1400.0560.0560.0000.0000.0000.000
148A157ASN 00.0410.04121.217-0.005-0.0050.0000.0000.0000.000
149A158LYS 10.9901.00020.1560.0390.0390.0000.0000.0000.000
150A159TYR 00.012-0.00817.1540.0050.0050.0000.0000.0000.000
151A160ASN 00.0220.01312.152-0.017-0.0170.0000.0000.0000.000
152A161SER 00.0020.00915.958-0.012-0.0120.0000.0000.0000.000
153A162LEU 0-0.041-0.02516.449-0.018-0.0180.0000.0000.0000.000
154A163THR 00.0110.00720.1420.0220.0220.0000.0000.0000.000
155A164ARG 10.7900.87919.4490.1010.1010.0000.0000.0000.000
156A165ILE 0-0.0010.00424.5200.0100.0100.0000.0000.0000.000
157A166LYS 10.9440.94826.1760.0630.0630.0000.0000.0000.000
158A167ILE 00.0360.02729.0550.0030.0030.0000.0000.0000.000
159A168PRO 00.007-0.01132.1380.0020.0020.0000.0000.0000.000
160A169ASN 0-0.038-0.01935.1410.0030.0030.0000.0000.0000.000
161A170PRO 0-0.030-0.00130.1570.0010.0010.0000.0000.0000.000
162A171PRO 00.0440.03831.1260.0040.0040.0000.0000.0000.000
163A172LYS 10.9570.96728.9570.0220.0220.0000.0000.0000.000
164A173SER 00.0210.01028.850-0.004-0.0040.0000.0000.0000.000
165A174PHE 00.0730.01725.462-0.002-0.0020.0000.0000.0000.000
166A175ASP -1-0.876-0.94527.775-0.039-0.0390.0000.0000.0000.000
167A176ASP -1-0.868-0.94130.012-0.029-0.0290.0000.0000.0000.000
168A177LEU 0-0.116-0.06027.972-0.001-0.0010.0000.0000.0000.000
169A178LYS 10.9210.96831.2090.0360.0360.0000.0000.0000.000
170A179ASN 0-0.029-0.01633.8730.0000.0000.0000.0000.0000.000
171A180ILE 0-0.0210.00833.2110.0020.0020.0000.0000.0000.000
172A181ASP -1-0.876-0.94836.362-0.044-0.0440.0000.0000.0000.000
173A182THR 00.0350.00536.098-0.002-0.0020.0000.0000.0000.000
174A183LYS 10.9450.98036.5340.0430.0430.0000.0000.0000.000
175A184LYS 10.9010.93935.7670.0400.0400.0000.0000.0000.000
176A185LEU 0-0.051-0.00831.069-0.002-0.0020.0000.0000.0000.000
177A186LEU 0-0.0060.00828.2900.0020.0020.0000.0000.0000.000
178A187VAL 0-0.032-0.01831.809-0.003-0.0030.0000.0000.0000.000
179A188ARG 10.8620.94131.1900.0820.0820.0000.0000.0000.000
180A189GLY 00.013-0.00430.9800.0070.0070.0000.0000.0000.000
181A190LEU 0-0.0050.00829.555-0.009-0.0090.0000.0000.0000.000
182A191TYR 0-0.046-0.03927.7080.0090.0090.0000.0000.0000.000
183A192ARG 10.8850.93228.1390.0780.0780.0000.0000.0000.000
184A193ILE 00.0130.00422.6870.0060.0060.0000.0000.0000.000
185A194SER 0-0.041-0.02026.622-0.001-0.0010.0000.0000.0000.000
186A195PHE 00.012-0.00322.570-0.001-0.0010.0000.0000.0000.000
187A196THR 00.020-0.03025.8300.0060.0060.0000.0000.0000.000
188A197THR 0-0.027-0.00925.040-0.002-0.0020.0000.0000.0000.000
189A198TYR 0-0.069-0.07627.0680.0080.0080.0000.0000.0000.000
190A199LYS 10.8920.97128.5090.0530.0530.0000.0000.0000.000
191A200PRO 00.005-0.01128.3830.0020.0020.0000.0000.0000.000
192A201GLY 00.0610.03526.068-0.001-0.0010.0000.0000.0000.000
193A202GLU -1-0.971-1.02025.533-0.064-0.0640.0000.0000.0000.000
194A203VAL 0-0.0110.00623.328-0.005-0.0050.0000.0000.0000.000
195A204LYS 10.9200.96023.1650.0810.0810.0000.0000.0000.000
196A205GLY 00.0510.03120.640-0.003-0.0030.0000.0000.0000.000
197A206SER 0-0.012-0.00315.555-0.009-0.0090.0000.0000.0000.000
198A207PHE 00.021-0.00915.8680.0210.0210.0000.0000.0000.000
199A208VAL 00.0230.01311.439-0.034-0.0340.0000.0000.0000.000
200A209ALA 0-0.052-0.02314.6570.0260.0260.0000.0000.0000.000
201A210SER 0-0.033-0.02312.886-0.027-0.0270.0000.0000.0000.000
202A211VAL 00.006-0.00115.6040.0510.0510.0000.0000.0000.000
203A212GLY 0-0.003-0.00617.943-0.028-0.0280.0000.0000.0000.000
204A213LEU 0-0.003-0.00518.7660.0260.0260.0000.0000.0000.000
205A214LEU 0-0.026-0.01721.154-0.008-0.0080.0000.0000.0000.000
206A215PHE 00.0540.03323.2290.0080.0080.0000.0000.0000.000
207A216PRO 00.002-0.00325.9270.0020.0020.0000.0000.0000.000
208A217PRO 00.0250.00827.445-0.004-0.0040.0000.0000.0000.000
209A218GLY 0-0.025-0.00627.6120.0040.0040.0000.0000.0000.000
210A219ILE 0-0.033-0.00728.0110.0020.0020.0000.0000.0000.000
211A220PRO 0-0.006-0.00125.470-0.007-0.0070.0000.0000.0000.000
212A221GLY 00.001-0.00422.7350.0000.0000.0000.0000.0000.000
213A222VAL 00.0320.01223.8170.0030.0030.0000.0000.0000.000
214A223SER 0-0.020-0.01119.761-0.002-0.0020.0000.0000.0000.000
215A224PRO 00.0050.01420.0650.0170.0170.0000.0000.0000.000
216A225LEU 00.0290.03021.647-0.019-0.0190.0000.0000.0000.000
217A226ILE 00.014-0.00919.0910.0120.0120.0000.0000.0000.000
218A227HIS 00.0400.02822.638-0.007-0.0070.0000.0000.0000.000
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