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: J3NQ9

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 OptAll
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 -2742283.315211
FMO2-HF: Nuclear repulsion 2654326.608505
FMO2-HF: Total energy -87956.706705
FMO2-MP2: Total energy -88216.176176


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.
4.4315.906-0.004-0.828-0.6420.004
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 : 0.084 / q_NPA : 0.045
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].
3A8PRO00.0170.0083.855-0.1381.337-0.004-0.828-0.6420.004
4A9SER00.0200.0116.6100.5330.5330.0000.0000.0000.000
5A10LEU00.0150.0208.4380.0230.0230.0000.0000.0000.000
6A11LYS10.8490.93011.0630.6700.6700.0000.0000.0000.000
7A12SER00.0480.01814.3310.0100.0100.0000.0000.0000.000
8A13SER0-0.086-0.08817.869-0.023-0.0230.0000.0000.0000.000
9A14PHE00.0550.02920.7830.0140.0140.0000.0000.0000.000
10A15VAL0-0.038-0.02420.611-0.024-0.0240.0000.0000.0000.000
11A16LEU0-0.037-0.00818.8330.0200.0200.0000.0000.0000.000
12A17SER0-0.016-0.03322.0060.0290.0290.0000.0000.0000.000
13A18GLU-1-0.796-0.88623.007-0.212-0.2120.0000.0000.0000.000
14A19ASP-1-0.817-0.87823.075-0.141-0.1410.0000.0000.0000.000
15A20THR0-0.006-0.01225.183-0.013-0.0130.0000.0000.0000.000
16A21ILE00.0190.00624.2700.0050.0050.0000.0000.0000.000
17A22PRO00.023-0.00325.8230.0100.0100.0000.0000.0000.000
18A23GLY0-0.018-0.00328.815-0.005-0.0050.0000.0000.0000.000
19A24THR0-0.037-0.00329.3520.0020.0020.0000.0000.0000.000
20A25ASN0-0.053-0.03731.4840.0030.0030.0000.0000.0000.000
21A26GLU-1-0.905-0.94227.136-0.194-0.1940.0000.0000.0000.000
22A27THR0-0.039-0.02926.4850.0050.0050.0000.0000.0000.000
23A28VAL00.0030.01019.670-0.021-0.0210.0000.0000.0000.000
24A29LYS10.8410.90521.7880.2240.2240.0000.0000.0000.000
25A30THR00.0120.01517.763-0.060-0.0600.0000.0000.0000.000
26A31LEU0-0.024-0.01216.8730.0240.0240.0000.0000.0000.000
27A32LEU00.0510.03916.539-0.033-0.0330.0000.0000.0000.000
28A33PRO0-0.004-0.00812.657-0.056-0.0560.0000.0000.0000.000
29A34TYR0-0.041-0.04813.7980.0380.0380.0000.0000.0000.000
30A35GLY00.0250.01914.0650.0090.0090.0000.0000.0000.000
31A36SER0-0.017-0.01515.0890.0560.0560.0000.0000.0000.000
32A37VAL0-0.030-0.01810.044-0.068-0.0680.0000.0000.0000.000
33A38ILE00.0150.01911.9020.0870.0870.0000.0000.0000.000
34A39ASN0-0.033-0.0117.139-0.472-0.4720.0000.0000.0000.000
35A40TYR00.0420.02010.1740.1400.1400.0000.0000.0000.000
36A41TYR00.019-0.0055.502-0.351-0.3510.0000.0000.0000.000
37A42GLY00.0070.01411.7110.0950.0950.0000.0000.0000.000
38A43TYR0-0.072-0.08814.754-0.048-0.0480.0000.0000.0000.000
39A44VAL0-0.0280.01517.4330.0300.0300.0000.0000.0000.000
40A45LYS10.9180.96720.6950.0350.0350.0000.0000.0000.000
41A46PRO00.033-0.00122.869-0.005-0.0050.0000.0000.0000.000
42A47GLY0-0.0020.00625.8720.0110.0110.0000.0000.0000.000
43A48GLN0-0.0070.00523.1350.0060.0060.0000.0000.0000.000
44A49ALA00.0230.01427.322-0.013-0.0130.0000.0000.0000.000
45A50PRO0-0.046-0.01927.361-0.004-0.0040.0000.0000.0000.000
46A51ASP-1-0.791-0.89325.214-0.112-0.1120.0000.0000.0000.000
47A52GLY0-0.0040.00328.5450.0080.0080.0000.0000.0000.000
48A53LEU0-0.020-0.00529.850-0.007-0.0070.0000.0000.0000.000
49A54VAL00.0220.00628.1720.0030.0030.0000.0000.0000.000
50A55ASP-1-0.798-0.90031.186-0.156-0.1560.0000.0000.0000.000
51A56GLY00.0070.01733.3810.0040.0040.0000.0000.0000.000
52A57ASN0-0.072-0.03132.739-0.004-0.0040.0000.0000.0000.000
53A58LYS10.7750.88628.1830.1750.1750.0000.0000.0000.000
54A59LYS10.9020.94726.1710.1610.1610.0000.0000.0000.000
55A60ALA0-0.0240.01125.685-0.020-0.0200.0000.0000.0000.000
56A61TYR0-0.003-0.01022.5960.0110.0110.0000.0000.0000.000
57A62TYR0-0.051-0.04623.575-0.017-0.0170.0000.0000.0000.000
58A63LEU0-0.024-0.01216.4630.0000.0000.0000.0000.0000.000
59A64TYR0-0.037-0.02621.021-0.013-0.0130.0000.0000.0000.000
60A65VAL00.019-0.00519.3150.0020.0020.0000.0000.0000.000
61A66TRP0-0.036-0.02021.875-0.006-0.0060.0000.0000.0000.000
62A67ILE00.0200.00122.0900.0000.0000.0000.0000.0000.000
63A68PRO00.0610.02222.863-0.001-0.0010.0000.0000.0000.000
64A69ALA0-0.010-0.00725.2360.0070.0070.0000.0000.0000.000
65A70VAL0-0.0060.00325.677-0.010-0.0100.0000.0000.0000.000
66A71ILE0-0.036-0.00821.9190.0020.0020.0000.0000.0000.000
67A72ALA00.0270.00324.2310.0000.0000.0000.0000.0000.000
68A73GLU-1-0.766-0.84820.171-0.289-0.2890.0000.0000.0000.000
69A74MET00.0030.01218.8080.0160.0160.0000.0000.0000.000
70A75GLY0-0.0050.00316.972-0.004-0.0040.0000.0000.0000.000
71A76VAL0-0.006-0.01115.9790.0070.0070.0000.0000.0000.000
72A77ARG10.8600.9107.7731.5621.5620.0000.0000.0000.000
73A78MET0-0.041-0.00113.4130.0050.0050.0000.0000.0000.000
74A79ILE0-0.005-0.0068.222-0.076-0.0760.0000.0000.0000.000
75A80SER00.0140.01711.9470.0510.0510.0000.0000.0000.000
76A81PRO0-0.0360.00113.207-0.010-0.0100.0000.0000.0000.000
77A82THR0-0.061-0.0639.020-0.134-0.1340.0000.0000.0000.000
78A83GLY00.0150.0268.545-0.183-0.1830.0000.0000.0000.000
79A84GLU-1-0.857-0.93510.3700.2130.2130.0000.0000.0000.000
80A85ILE0-0.034-0.0246.129-0.163-0.1630.0000.0000.0000.000
81A86GLY0-0.0170.0076.0240.6510.6510.0000.0000.0000.000
82A87GLU-1-0.927-0.9718.5820.6240.6240.0000.0000.0000.000
83A88PRO0-0.047-0.0247.5390.4150.4150.0000.0000.0000.000
84A89GLY00.0280.0167.2080.1640.1640.0000.0000.0000.000
85A90ASP-1-0.918-0.9668.0520.4570.4570.0000.0000.0000.000
86A91GLY00.0010.0119.708-0.144-0.1440.0000.0000.0000.000
87A92ASP-1-0.820-0.8986.4750.5110.5110.0000.0000.0000.000
88A93LEU00.0010.00410.0140.0340.0340.0000.0000.0000.000
89A94VAL00.0280.01510.300-0.099-0.0990.0000.0000.0000.000
90A95SER0-0.012-0.01712.9580.0240.0240.0000.0000.0000.000
91A96ASP-1-0.821-0.92416.3960.1010.1010.0000.0000.0000.000
92A97ALA0-0.031-0.01519.0650.0030.0030.0000.0000.0000.000
93A98PHE00.0290.00510.416-0.010-0.0100.0000.0000.0000.000
94A99LYS10.8390.90415.124-0.150-0.1500.0000.0000.0000.000
95A100ALA0-0.030-0.00816.5910.0140.0140.0000.0000.0000.000
96A101ALA0-0.0580.00316.551-0.013-0.0130.0000.0000.0000.000
97A102THR00.023-0.03517.2560.0260.0260.0000.0000.0000.000
98A103PRO00.0330.00215.258-0.038-0.0380.0000.0000.0000.000
99A104GLU-1-0.929-0.93915.516-0.123-0.1230.0000.0000.0000.000
100A105GLU-1-0.781-0.84117.657-0.100-0.1000.0000.0000.0000.000
101A106LYS10.8150.90912.805-0.140-0.1400.0000.0000.0000.000
102A107SER00.001-0.00513.403-0.114-0.1140.0000.0000.0000.000
103A108MET0-0.0060.01614.589-0.049-0.0490.0000.0000.0000.000
104A109PRO0-0.016-0.00616.757-0.023-0.0230.0000.0000.0000.000
105A110HIS00.0370.01017.8710.0560.0560.0000.0000.0000.000
106A111TRP0-0.074-0.05917.3100.0330.0330.0000.0000.0000.000
107A112PHE00.0590.03017.650-0.030-0.0300.0000.0000.0000.000
108A113ASP-1-0.808-0.87418.322-0.399-0.3990.0000.0000.0000.000
109A114THR00.0210.03218.0290.0440.0440.0000.0000.0000.000
110A115TRP0-0.059-0.02820.622-0.006-0.0060.0000.0000.0000.000
111A116ILE00.000-0.01017.9870.0060.0060.0000.0000.0000.000
112A117ARG10.7890.88222.4930.1700.1700.0000.0000.0000.000
113A118VAL00.0140.01522.299-0.008-0.0080.0000.0000.0000.000
114A119GLU-1-0.786-0.86425.040-0.135-0.1350.0000.0000.0000.000
115A120ARG10.8870.94127.6950.0920.0920.0000.0000.0000.000
116A121MET0-0.040-0.01328.3860.0000.0000.0000.0000.0000.000
117A122SER0-0.004-0.00530.9450.0030.0030.0000.0000.0000.000
118A123ALA0-0.052-0.02831.0320.0060.0060.0000.0000.0000.000
119A124ILE00.0080.00631.796-0.005-0.0050.0000.0000.0000.000
120A125MET00.0070.02832.5450.0030.0030.0000.0000.0000.000
121A126PRO00.1040.04829.242-0.006-0.0060.0000.0000.0000.000
122A127ASP-1-0.836-0.92430.680-0.010-0.0100.0000.0000.0000.000
123A128GLN00.0250.00833.347-0.005-0.0050.0000.0000.0000.000
124A129ILE00.0130.02026.928-0.006-0.0060.0000.0000.0000.000
125A130ALA0-0.003-0.00530.675-0.008-0.0080.0000.0000.0000.000
126A131LYS10.8010.89331.5890.0130.0130.0000.0000.0000.000
127A132ALA00.0210.00431.915-0.004-0.0040.0000.0000.0000.000
128A133ALA0-0.009-0.00829.031-0.007-0.0070.0000.0000.0000.000
129A134LYS10.8220.91730.6870.0270.0270.0000.0000.0000.000
130A135ALA0-0.0090.01233.7070.0000.0000.0000.0000.0000.000
131A136LYS10.9020.94334.0250.0620.0620.0000.0000.0000.000
132A137PRO00.0430.00231.2920.0040.0040.0000.0000.0000.000
133A138VAL0-0.031-0.00833.0640.0070.0070.0000.0000.0000.000
134A139GLN00.0230.02434.274-0.001-0.0010.0000.0000.0000.000
135A147GLY00.0650.02732.3180.0030.0030.0000.0000.0000.000
136A148ASP-1-0.845-0.93426.658-0.179-0.1790.0000.0000.0000.000
137A149ASP-1-0.820-0.89727.697-0.104-0.1040.0000.0000.0000.000
138A150THR0-0.070-0.02528.7410.0110.0110.0000.0000.0000.000
139A151TYR0-0.008-0.01929.5660.0010.0010.0000.0000.0000.000
140A152LYS10.8740.94524.9110.2300.2300.0000.0000.0000.000
141A153GLU-1-0.775-0.86826.341-0.179-0.1790.0000.0000.0000.000
142A154GLU-1-0.809-0.88422.659-0.272-0.2720.0000.0000.0000.000
143A155ARG10.8530.92023.8940.1560.1560.0000.0000.0000.000
144A156HIS10.8570.90923.2080.2990.2990.0000.0000.0000.000
145A157ASN00.0360.04617.888-0.024-0.0240.0000.0000.0000.000
146A158LYS10.9390.96517.1220.3720.3720.0000.0000.0000.000
147A159TYR00.019-0.00415.0390.0170.0170.0000.0000.0000.000
148A160ASN00.0150.01310.726-0.118-0.1180.0000.0000.0000.000
149A161SER00.0130.01113.010-0.023-0.0230.0000.0000.0000.000
150A162LEU0-0.042-0.02213.030-0.038-0.0380.0000.0000.0000.000
151A163THR00.0200.00916.8450.0620.0620.0000.0000.0000.000
152A164ARG10.8000.89416.9620.4160.4160.0000.0000.0000.000
153A165ILE0-0.006-0.00121.2080.0150.0150.0000.0000.0000.000
154A166LYS10.9200.94523.4350.2300.2300.0000.0000.0000.000
155A167ILE00.0340.02825.9680.0100.0100.0000.0000.0000.000
156A168PRO0-0.025-0.02729.058-0.007-0.0070.0000.0000.0000.000
157A169ASN0-0.026-0.01331.872-0.004-0.0040.0000.0000.0000.000
158A170PRO0-0.025-0.00127.1100.0070.0070.0000.0000.0000.000
159A171PRO0-0.0040.02128.678-0.001-0.0010.0000.0000.0000.000
160A172LYS10.8710.93026.5290.1570.1570.0000.0000.0000.000
161A173SER0-0.031-0.05526.459-0.015-0.0150.0000.0000.0000.000
162A174PHE00.047-0.00422.768-0.001-0.0010.0000.0000.0000.000
163A175ASP-1-0.782-0.88925.172-0.043-0.0430.0000.0000.0000.000
164A176ASP-1-0.814-0.87827.899-0.087-0.0870.0000.0000.0000.000
165A177LEU0-0.060-0.02625.3840.0020.0020.0000.0000.0000.000
166A178LYS10.8250.90228.9200.0470.0470.0000.0000.0000.000
167A179ASN0-0.043-0.02531.4170.0010.0010.0000.0000.0000.000
168A180ILE0-0.0030.01730.225-0.001-0.0010.0000.0000.0000.000
169A181ASP-1-0.816-0.91133.555-0.052-0.0520.0000.0000.0000.000
170A182THR00.0510.01332.567-0.007-0.0070.0000.0000.0000.000
171A183LYS10.9190.97233.3810.0500.0500.0000.0000.0000.000
172A184LYS10.8450.90233.0110.0650.0650.0000.0000.0000.000
173A185LEU0-0.037-0.00728.000-0.009-0.0090.0000.0000.0000.000
174A186LEU0-0.021-0.00224.7210.0030.0030.0000.0000.0000.000
175A187VAL0-0.004-0.00628.0930.0080.0080.0000.0000.0000.000
176A188ARG10.8080.88527.6050.0100.0100.0000.0000.0000.000
177A189GLY00.0210.00527.4900.0020.0020.0000.0000.0000.000
178A190LEU0-0.0270.00425.750-0.003-0.0030.0000.0000.0000.000
179A191TYR0-0.039-0.03524.003-0.009-0.0090.0000.0000.0000.000
180A192ARG10.8760.93124.4090.1270.1270.0000.0000.0000.000
181A193ILE00.0040.01218.272-0.010-0.0100.0000.0000.0000.000
182A194SER0-0.022-0.02922.3780.0130.0130.0000.0000.0000.000
183A195PHE0-0.037-0.02219.058-0.026-0.0260.0000.0000.0000.000
184A196THR00.023-0.03122.3450.0220.0220.0000.0000.0000.000
185A197THR0-0.033-0.02722.257-0.028-0.0280.0000.0000.0000.000
186A198TYR0-0.055-0.05224.2880.0360.0360.0000.0000.0000.000
187A199LYS10.8810.94826.2070.1720.1720.0000.0000.0000.000
188A200PRO00.0470.01226.482-0.003-0.0030.0000.0000.0000.000
189A201GLY00.0540.04223.9760.0100.0100.0000.0000.0000.000
190A202GLU-1-0.885-0.96123.372-0.138-0.1380.0000.0000.0000.000
191A203VAL00.0040.02120.301-0.020-0.0200.0000.0000.0000.000
192A204LYS10.8490.91120.6250.1890.1890.0000.0000.0000.000
193A205GLY00.0570.03718.629-0.034-0.0340.0000.0000.0000.000
194A206SER0-0.033-0.02513.173-0.008-0.0080.0000.0000.0000.000
195A207PHE0-0.008-0.02512.878-0.037-0.0370.0000.0000.0000.000
196A208VAL00.0150.0087.5950.0800.0800.0000.0000.0000.000
197A209ALA0-0.014-0.00110.918-0.077-0.0770.0000.0000.0000.000
198A210SER0-0.023-0.0048.841-0.054-0.0540.0000.0000.0000.000
199A211VAL0-0.013-0.01611.4470.0040.0040.0000.0000.0000.000
200A212GLY00.0100.00513.8530.0290.0290.0000.0000.0000.000
201A213LEU00.0030.01115.164-0.012-0.0120.0000.0000.0000.000
202A214LEU0-0.014-0.01617.8140.0010.0010.0000.0000.0000.000
203A215PHE00.0740.04119.8070.0020.0020.0000.0000.0000.000
204A216PRO00.014-0.00423.072-0.005-0.0050.0000.0000.0000.000
205A217PRO0-0.0040.00725.0900.0120.0120.0000.0000.0000.000
206A218GLY0-0.0020.00625.3220.0030.0030.0000.0000.0000.000
207A219ILE0-0.039-0.01225.4420.0100.0100.0000.0000.0000.000
208A220PRO0-0.013-0.01123.134-0.005-0.0050.0000.0000.0000.000
209A221GLY0-0.0030.01019.860-0.011-0.0110.0000.0000.0000.000
210A222VAL00.007-0.00520.7860.0230.0230.0000.0000.0000.000
211A223SER00.009-0.00316.231-0.032-0.0320.0000.0000.0000.000
212A224PRO0-0.0190.00416.6470.0040.0040.0000.0000.0000.000
213A225LEU00.0200.02018.3720.0210.0210.0000.0000.0000.000
214A226ILE0-0.002-0.01915.290-0.025-0.0250.0000.0000.0000.000
215A227HIS00.0480.03218.6550.0050.0050.0000.0000.0000.000
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