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: N1KNQ

Calculation Name: 2ZZ8-A-Xray372

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: 2023-06-19

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2741559.583555
FMO2-HF: Nuclear repulsion 2653603.390929
FMO2-HF: Total energy -87956.192626
FMO2-MP2: Total energy -88215.683782


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:6:GLY)


Summations of interaction energy for fragment #1(A:6:GLY)
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.
4.6746.515-0.014-1.044-0.7830.006
Interaction energy analysis for fragmet #1(A:6:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.043
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].
3A8PRO00.0320.0153.782-0.6241.159-0.013-1.041-0.7290.006
4A9SER00.0340.0186.6780.5190.5190.0000.0000.0000.000
5A10LEU0-0.0020.0128.6360.0150.0150.0000.0000.0000.000
6A11LYS10.8690.93711.1350.7460.7460.0000.0000.0000.000
7A12SER00.0520.01414.5200.0200.0200.0000.0000.0000.000
8A13SER0-0.104-0.09717.933-0.018-0.0180.0000.0000.0000.000
9A14PHE00.0490.02920.9040.0140.0140.0000.0000.0000.000
10A15VAL0-0.040-0.02420.906-0.027-0.0270.0000.0000.0000.000
11A16LEU0-0.030-0.01018.8830.0200.0200.0000.0000.0000.000
12A17SER0-0.005-0.01922.1130.0330.0330.0000.0000.0000.000
13A18GLU-1-0.812-0.87122.915-0.239-0.2390.0000.0000.0000.000
14A19ASP-1-0.817-0.88223.507-0.177-0.1770.0000.0000.0000.000
15A20THR00.007-0.00225.387-0.014-0.0140.0000.0000.0000.000
16A21ILE00.014-0.00724.2790.0010.0010.0000.0000.0000.000
17A22PRO00.0140.00325.9440.0120.0120.0000.0000.0000.000
18A23GLY0-0.019-0.00628.948-0.004-0.0040.0000.0000.0000.000
19A24THR0-0.011-0.00129.4550.0060.0060.0000.0000.0000.000
20A25ASN0-0.071-0.03531.6770.0040.0040.0000.0000.0000.000
21A26GLU-1-0.912-0.94827.439-0.213-0.2130.0000.0000.0000.000
22A27THR0-0.034-0.01826.588-0.002-0.0020.0000.0000.0000.000
23A28VAL0-0.001-0.00520.168-0.020-0.0200.0000.0000.0000.000
24A29LYS10.8180.89322.0690.2450.2450.0000.0000.0000.000
25A30THR00.0110.00917.424-0.060-0.0600.0000.0000.0000.000
26A31LEU0-0.026-0.01716.9770.0230.0230.0000.0000.0000.000
27A32LEU00.0580.04117.032-0.037-0.0370.0000.0000.0000.000
28A33PRO0-0.0030.00612.946-0.038-0.0380.0000.0000.0000.000
29A34TYR0-0.025-0.05213.9000.0470.0470.0000.0000.0000.000
30A35GLY00.0120.01613.949-0.011-0.0110.0000.0000.0000.000
31A36SER0-0.003-0.00114.8680.0430.0430.0000.0000.0000.000
32A37VAL0-0.016-0.0159.782-0.058-0.0580.0000.0000.0000.000
33A38ILE00.0290.03111.3490.0790.0790.0000.0000.0000.000
34A39ASN0-0.050-0.0166.786-0.509-0.5090.0000.0000.0000.000
35A40TYR00.0170.0089.8980.1690.1690.0000.0000.0000.000
36A41TYR00.0550.0214.963-0.452-0.394-0.001-0.003-0.0540.000
37A42GLY0-0.005-0.00711.2610.0870.0870.0000.0000.0000.000
38A43TYR0-0.085-0.08814.218-0.042-0.0420.0000.0000.0000.000
39A44VAL0-0.0410.00616.8710.0220.0220.0000.0000.0000.000
40A45LYS10.9770.99420.136-0.029-0.0290.0000.0000.0000.000
41A46PRO00.0540.00622.586-0.012-0.0120.0000.0000.0000.000
42A47GLY0-0.015-0.00125.3720.0100.0100.0000.0000.0000.000
43A48GLN00.0050.01522.5290.0090.0090.0000.0000.0000.000
44A49ALA00.0150.01026.812-0.012-0.0120.0000.0000.0000.000
45A50PRO0-0.044-0.02127.054-0.003-0.0030.0000.0000.0000.000
46A51ASP-1-0.791-0.89725.107-0.078-0.0780.0000.0000.0000.000
47A52GLY0-0.017-0.00728.3590.0070.0070.0000.0000.0000.000
48A53LEU0-0.017-0.00429.457-0.008-0.0080.0000.0000.0000.000
49A54VAL00.007-0.00327.7160.0010.0010.0000.0000.0000.000
50A55ASP-1-0.819-0.91430.695-0.144-0.1440.0000.0000.0000.000
51A56GLY0-0.0090.00533.0090.0030.0030.0000.0000.0000.000
52A57ASN0-0.029-0.00632.561-0.003-0.0030.0000.0000.0000.000
53A58LYS10.7940.89827.8500.1550.1550.0000.0000.0000.000
54A59LYS10.8900.94526.6660.1210.1210.0000.0000.0000.000
55A60ALA0-0.0010.01725.201-0.018-0.0180.0000.0000.0000.000
56A61TYR0-0.013-0.01921.9540.0120.0120.0000.0000.0000.000
57A62TYR0-0.040-0.02722.879-0.021-0.0210.0000.0000.0000.000
58A63LEU0-0.024-0.00716.4050.0100.0100.0000.0000.0000.000
59A64TYR0-0.012-0.01020.973-0.013-0.0130.0000.0000.0000.000
60A65VAL00.0300.00419.0380.0070.0070.0000.0000.0000.000
61A66TRP0-0.038-0.02421.561-0.008-0.0080.0000.0000.0000.000
62A67ILE00.005-0.00421.6300.0040.0040.0000.0000.0000.000
63A68PRO00.0680.02522.182-0.001-0.0010.0000.0000.0000.000
64A69ALA00.010-0.00325.0010.0070.0070.0000.0000.0000.000
65A70VAL0-0.005-0.00125.629-0.010-0.0100.0000.0000.0000.000
66A71ILE0-0.031-0.00521.8920.0000.0000.0000.0000.0000.000
67A72ALA00.004-0.01223.8440.0020.0020.0000.0000.0000.000
68A73GLU-1-0.755-0.84620.164-0.305-0.3050.0000.0000.0000.000
69A74MET00.0210.03118.5810.0120.0120.0000.0000.0000.000
70A75GLY0-0.0090.01016.852-0.005-0.0050.0000.0000.0000.000
71A76VAL0-0.001-0.00415.6400.0000.0000.0000.0000.0000.000
72A77ARG10.8560.9167.5801.5781.5780.0000.0000.0000.000
73A78MET0-0.0370.00013.2190.0070.0070.0000.0000.0000.000
74A79ILE0-0.012-0.0028.137-0.052-0.0520.0000.0000.0000.000
75A80SER0-0.0120.01911.6050.0740.0740.0000.0000.0000.000
76A81PRO0-0.0050.00412.687-0.028-0.0280.0000.0000.0000.000
77A82THR0-0.072-0.0748.105-0.150-0.1500.0000.0000.0000.000
78A83GLY00.0250.0308.086-0.091-0.0910.0000.0000.0000.000
79A84GLU-1-0.923-0.9719.6960.4040.4040.0000.0000.0000.000
80A85ILE0-0.034-0.0315.735-0.183-0.1830.0000.0000.0000.000
81A86GLY0-0.0210.0105.8190.8090.8090.0000.0000.0000.000
82A87GLU-1-0.937-0.9818.2450.8460.8460.0000.0000.0000.000
83A88PRO0-0.046-0.0167.6960.4310.4310.0000.0000.0000.000
84A89GLY00.0440.0197.1310.0370.0370.0000.0000.0000.000
85A90ASP-1-0.943-0.9788.0420.4070.4070.0000.0000.0000.000
86A91GLY00.0180.0189.173-0.160-0.1600.0000.0000.0000.000
87A92ASP-1-0.850-0.9256.4750.9140.9140.0000.0000.0000.000
88A93LEU0-0.0090.0009.7710.0120.0120.0000.0000.0000.000
89A94VAL00.0400.01310.369-0.057-0.0570.0000.0000.0000.000
90A95SER0-0.019-0.00613.0810.0050.0050.0000.0000.0000.000
91A96ASP-1-0.826-0.93616.3670.1800.1800.0000.0000.0000.000
92A97ALA0-0.078-0.04418.8440.0060.0060.0000.0000.0000.000
93A98PHE00.007-0.0039.744-0.004-0.0040.0000.0000.0000.000
94A99LYS10.9320.95915.137-0.281-0.2810.0000.0000.0000.000
95A100ALA0-0.050-0.01916.2100.0110.0110.0000.0000.0000.000
96A101ALA0-0.0370.01816.380-0.011-0.0110.0000.0000.0000.000
97A102THR00.041-0.01417.0570.0380.0380.0000.0000.0000.000
98A103PRO00.0320.00814.595-0.040-0.0400.0000.0000.0000.000
99A104GLU-1-0.919-0.94215.189-0.048-0.0480.0000.0000.0000.000
100A105GLU-1-0.779-0.84517.525-0.020-0.0200.0000.0000.0000.000
101A106LYS10.7580.88712.379-0.256-0.2560.0000.0000.0000.000
102A107SER00.017-0.01613.105-0.085-0.0850.0000.0000.0000.000
103A108MET0-0.0260.01614.437-0.045-0.0450.0000.0000.0000.000
104A109PRO0-0.019-0.01116.327-0.019-0.0190.0000.0000.0000.000
105A110HIS00.0360.00917.3380.0430.0430.0000.0000.0000.000
106A111TRP0-0.059-0.05416.7460.0280.0280.0000.0000.0000.000
107A112PHE00.0530.01817.451-0.030-0.0300.0000.0000.0000.000
108A113ASP-1-0.807-0.86317.874-0.387-0.3870.0000.0000.0000.000
109A114THR00.0330.03717.5470.0480.0480.0000.0000.0000.000
110A115TRP0-0.077-0.03320.203-0.007-0.0070.0000.0000.0000.000
111A116ILE0-0.002-0.02017.9720.0100.0100.0000.0000.0000.000
112A117ARG10.8210.90522.5230.1550.1550.0000.0000.0000.000
113A118VAL00.0160.01021.988-0.001-0.0010.0000.0000.0000.000
114A119GLU-1-0.830-0.90924.912-0.119-0.1190.0000.0000.0000.000
115A120ARG10.8910.96327.5070.0880.0880.0000.0000.0000.000
116A121MET0-0.044-0.01628.4800.0000.0000.0000.0000.0000.000
117A122SER0-0.009-0.01930.9490.0000.0000.0000.0000.0000.000
118A123ALA0-0.044-0.01230.6930.0060.0060.0000.0000.0000.000
119A124ILE0-0.009-0.00631.752-0.005-0.0050.0000.0000.0000.000
120A125MET00.0210.03232.0770.0020.0020.0000.0000.0000.000
121A126PRO00.1140.05128.840-0.005-0.0050.0000.0000.0000.000
122A127ASP-1-0.861-0.93030.4280.0020.0020.0000.0000.0000.000
123A128GLN00.013-0.00333.026-0.003-0.0030.0000.0000.0000.000
124A129ILE00.0100.01326.751-0.007-0.0070.0000.0000.0000.000
125A130ALA0-0.0070.00130.541-0.007-0.0070.0000.0000.0000.000
126A131LYS10.8240.89231.456-0.003-0.0030.0000.0000.0000.000
127A132ALA00.0180.01931.803-0.004-0.0040.0000.0000.0000.000
128A133ALA0-0.023-0.01129.118-0.007-0.0070.0000.0000.0000.000
129A134LYS10.8340.91430.8320.0090.0090.0000.0000.0000.000
130A135ALA0-0.0420.00133.8770.0000.0000.0000.0000.0000.000
131A136LYS10.8920.93334.0610.0540.0540.0000.0000.0000.000
132A137PRO00.0460.00631.3870.0030.0030.0000.0000.0000.000
133A138VAL0-0.036-0.01133.0350.0050.0050.0000.0000.0000.000
134A139GLN00.0200.02334.426-0.002-0.0020.0000.0000.0000.000
135A147GLY00.0570.02532.2600.0030.0030.0000.0000.0000.000
136A148ASP-1-0.823-0.92026.622-0.184-0.1840.0000.0000.0000.000
137A149ASP-1-0.823-0.89427.458-0.105-0.1050.0000.0000.0000.000
138A150THR0-0.056-0.02528.4760.0150.0150.0000.0000.0000.000
139A151TYR00.002-0.01529.4260.0020.0020.0000.0000.0000.000
140A152LYS10.9170.97724.7720.2260.2260.0000.0000.0000.000
141A153GLU-1-0.780-0.87126.151-0.169-0.1690.0000.0000.0000.000
142A154GLU-1-0.847-0.90222.729-0.267-0.2670.0000.0000.0000.000
143A155ARG10.8680.92723.8520.1520.1520.0000.0000.0000.000
144A156HIS10.8440.91223.1430.2780.2780.0000.0000.0000.000
145A157ASN00.0320.03717.947-0.023-0.0230.0000.0000.0000.000
146A158LYS10.9340.95717.5260.3450.3450.0000.0000.0000.000
147A159TYR00.0260.00115.1610.0160.0160.0000.0000.0000.000
148A160ASN00.0030.00610.592-0.038-0.0380.0000.0000.0000.000
149A161SER00.0290.02513.241-0.028-0.0280.0000.0000.0000.000
150A162LEU0-0.052-0.03113.376-0.022-0.0220.0000.0000.0000.000
151A163THR00.0130.00517.0370.0530.0530.0000.0000.0000.000
152A164ARG10.7980.88616.9200.4460.4460.0000.0000.0000.000
153A165ILE0-0.0080.00321.0900.0160.0160.0000.0000.0000.000
154A166LYS10.9340.94123.3430.2420.2420.0000.0000.0000.000
155A167ILE00.0220.01625.6880.0120.0120.0000.0000.0000.000
156A168PRO00.000-0.01728.815-0.007-0.0070.0000.0000.0000.000
157A169ASN0-0.034-0.01731.990-0.006-0.0060.0000.0000.0000.000
158A170PRO0-0.034-0.00227.3840.0070.0070.0000.0000.0000.000
159A171PRO00.0250.03228.773-0.001-0.0010.0000.0000.0000.000
160A172LYS10.8820.92626.8370.1840.1840.0000.0000.0000.000
161A173SER0-0.021-0.03426.970-0.018-0.0180.0000.0000.0000.000
162A174PHE00.0590.01122.9350.0020.0020.0000.0000.0000.000
163A175ASP-1-0.774-0.88125.704-0.068-0.0680.0000.0000.0000.000
164A176ASP-1-0.831-0.90128.117-0.100-0.1000.0000.0000.0000.000
165A177LEU0-0.095-0.04825.3470.0040.0040.0000.0000.0000.000
166A178LYS10.8340.90629.1490.0720.0720.0000.0000.0000.000
167A179ASN0-0.048-0.02831.4560.0010.0010.0000.0000.0000.000
168A180ILE00.0020.02030.1570.0000.0000.0000.0000.0000.000
169A181ASP-1-0.816-0.91533.504-0.059-0.0590.0000.0000.0000.000
170A182THR00.0500.01532.563-0.006-0.0060.0000.0000.0000.000
171A183LYS10.9310.98133.0130.0500.0500.0000.0000.0000.000
172A184LYS10.8320.89232.7080.0720.0720.0000.0000.0000.000
173A185LEU0-0.050-0.01127.742-0.009-0.0090.0000.0000.0000.000
174A186LEU0-0.0170.00624.5450.0030.0030.0000.0000.0000.000
175A187VAL0-0.028-0.02127.9670.0080.0080.0000.0000.0000.000
176A188ARG10.8180.90527.0930.0060.0060.0000.0000.0000.000
177A189GLY00.0290.00426.8300.0010.0010.0000.0000.0000.000
178A190LEU0-0.0160.00525.430-0.003-0.0030.0000.0000.0000.000
179A191TYR0-0.043-0.04523.548-0.009-0.0090.0000.0000.0000.000
180A192ARG10.8730.92623.9740.1070.1070.0000.0000.0000.000
181A193ILE00.000-0.00218.634-0.013-0.0130.0000.0000.0000.000
182A194SER0-0.030-0.01422.5060.0150.0150.0000.0000.0000.000
183A195PHE00.0050.00018.656-0.028-0.0280.0000.0000.0000.000
184A196THR00.023-0.02621.8940.0230.0230.0000.0000.0000.000
185A197THR0-0.027-0.02021.836-0.028-0.0280.0000.0000.0000.000
186A198TYR0-0.064-0.05423.8160.0350.0350.0000.0000.0000.000
187A199LYS10.8820.95525.7790.1440.1440.0000.0000.0000.000
188A200PRO00.012-0.00426.468-0.004-0.0040.0000.0000.0000.000
189A201GLY00.0660.03923.4520.0030.0030.0000.0000.0000.000
190A202GLU-1-0.878-0.95322.770-0.101-0.1010.0000.0000.0000.000
191A203VAL0-0.0040.01719.702-0.017-0.0170.0000.0000.0000.000
192A204LYS10.8750.92019.9500.1430.1430.0000.0000.0000.000
193A205GLY00.0590.04117.794-0.033-0.0330.0000.0000.0000.000
194A206SER0-0.006-0.00612.418-0.018-0.0180.0000.0000.0000.000
195A207PHE00.000-0.01612.322-0.046-0.0460.0000.0000.0000.000
196A208VAL00.0120.0047.0910.1070.1070.0000.0000.0000.000
197A209ALA0-0.026-0.00710.522-0.128-0.1280.0000.0000.0000.000
198A210SER0-0.030-0.0188.725-0.031-0.0310.0000.0000.0000.000
199A211VAL00.002-0.00511.478-0.012-0.0120.0000.0000.0000.000
200A212GLY00.006-0.00113.7940.0270.0270.0000.0000.0000.000
201A213LEU0-0.005-0.00314.9000.0040.0040.0000.0000.0000.000
202A214LEU0-0.026-0.01617.721-0.002-0.0020.0000.0000.0000.000
203A215PHE00.0510.02819.5970.0070.0070.0000.0000.0000.000
204A216PRO00.007-0.00222.913-0.009-0.0090.0000.0000.0000.000
205A217PRO00.0160.01025.0920.0090.0090.0000.0000.0000.000
206A218GLY0-0.011-0.00125.3190.0060.0060.0000.0000.0000.000
207A219ILE0-0.039-0.01125.1860.0110.0110.0000.0000.0000.000
208A220PRO0-0.012-0.00322.738-0.009-0.0090.0000.0000.0000.000
209A221GLY00.0060.00319.511-0.008-0.0080.0000.0000.0000.000
210A222VAL00.0080.00320.5850.0220.0220.0000.0000.0000.000
211A223SER0-0.012-0.00716.267-0.033-0.0330.0000.0000.0000.000
212A224PRO00.0080.01416.0720.0050.0050.0000.0000.0000.000
213A225LEU00.0160.01817.6440.0200.0200.0000.0000.0000.000
214A226ILE00.011-0.01214.855-0.031-0.0310.0000.0000.0000.000
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