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: LZRZ9

Calculation Name: 1PQZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PQZ

Chain ID: A

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2663480.128412
FMO2-HF: Nuclear repulsion 2569981.277471
FMO2-HF: Total energy -93498.850941
FMO2-MP2: Total energy -93770.159014


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:GLY)


Summations of interaction energy for fragment #1(A:5: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.
-12.342-7.6115.317-5.295-4.754-0.055
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.016
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].
3A7GLU-1-0.850-0.9303.843-2.490-1.0850.001-0.800-0.6060.003
4A8SER0-0.071-0.0324.7060.1830.340-0.001-0.037-0.1190.000
5A9GLY00.022-0.0075.7470.5060.5060.0000.0000.0000.000
6A10LEU0-0.061-0.0108.521-0.113-0.1130.0000.0000.0000.000
7A11ARG10.7540.8539.6530.4780.4780.0000.0000.0000.000
8A12TYR0-0.074-0.07012.423-0.027-0.0270.0000.0000.0000.000
9A13ALA00.0200.02614.7450.0230.0230.0000.0000.0000.000
10A14TYR00.023-0.00116.4840.0110.0110.0000.0000.0000.000
11A15THR0-0.056-0.02920.3050.0100.0100.0000.0000.0000.000
12A16LEU00.0060.01323.029-0.003-0.0030.0000.0000.0000.000
13A17VAL0-0.0060.00126.8220.0050.0050.0000.0000.0000.000
14A18VAL00.0340.00629.2600.0000.0000.0000.0000.0000.000
15A19ASP-1-0.806-0.86432.805-0.031-0.0310.0000.0000.0000.000
16A20GLY00.018-0.00235.2390.0000.0000.0000.0000.0000.000
17A21THR0-0.089-0.06737.9130.0020.0020.0000.0000.0000.000
18A22ALA0-0.032-0.00739.1830.0010.0010.0000.0000.0000.000
19A23ASN0-0.035-0.01837.430-0.002-0.0020.0000.0000.0000.000
20A24THR0-0.066-0.05433.029-0.003-0.0030.0000.0000.0000.000
21A25ALA00.0470.01932.527-0.003-0.0030.0000.0000.0000.000
22A26ARG10.9340.98229.6570.0490.0490.0000.0000.0000.000
23A27CYS0-0.0030.00425.0550.0020.0020.0000.0000.0000.000
24A28PHE0-0.054-0.03021.8760.0000.0000.0000.0000.0000.000
25A29GLY00.0580.02119.7540.0020.0020.0000.0000.0000.000
26A30THR0-0.035-0.01115.297-0.009-0.0090.0000.0000.0000.000
27A31GLY00.0210.01614.329-0.003-0.0030.0000.0000.0000.000
28A32HIS10.8210.8888.9160.5030.5030.0000.0000.0000.000
29A33VAL00.0340.0048.0410.0480.0480.0000.0000.0000.000
30A34ASP-1-0.778-0.8483.373-1.704-1.5550.012-0.051-0.1100.000
31A35GLY00.0480.0523.637-0.763-0.2470.012-0.186-0.342-0.001
32A36GLU-1-0.815-0.8765.864-0.141-0.1410.0000.0000.0000.000
33A37ALA0-0.0040.0038.0050.0000.0000.0000.0000.0000.000
34A38PHE0-0.009-0.01911.6660.0170.0170.0000.0000.0000.000
35A39VAL0-0.0040.00113.9890.0410.0410.0000.0000.0000.000
36A40GLY00.0300.01716.536-0.018-0.0180.0000.0000.0000.000
37A41TYR00.0030.00719.2470.0140.0140.0000.0000.0000.000
38A42SER00.0600.01622.5170.0070.0070.0000.0000.0000.000
39A43ASN0-0.035-0.02425.5590.0060.0060.0000.0000.0000.000
40A44ASN0-0.017-0.01028.6310.0050.0050.0000.0000.0000.000
41A45LYS10.9510.99227.4550.0800.0800.0000.0000.0000.000
42A46THR00.026-0.00621.544-0.006-0.0060.0000.0000.0000.000
43A47HIS0-0.073-0.03619.9310.0140.0140.0000.0000.0000.000
44A48GLY00.0680.02019.151-0.015-0.0150.0000.0000.0000.000
45A49ILE0-0.062-0.02114.8430.0210.0210.0000.0000.0000.000
46A50GLY00.0650.03114.199-0.023-0.0230.0000.0000.0000.000
47A51ARG10.8730.93314.4800.2480.2480.0000.0000.0000.000
48A52TRP00.0240.01411.8390.0280.0280.0000.0000.0000.000
49A53VAL0-0.0450.01916.5270.0170.0170.0000.0000.0000.000
50A54ASN00.0290.00118.0390.0290.0290.0000.0000.0000.000
51A55ALA00.0480.00521.854-0.004-0.0040.0000.0000.0000.000
52A56SER00.0230.01524.3500.0040.0040.0000.0000.0000.000
53A57HIS00.000-0.00119.2100.0010.0010.0000.0000.0000.000
54A58VAL0-0.012-0.00520.723-0.004-0.0040.0000.0000.0000.000
55A59GLU-1-0.876-0.93422.153-0.112-0.1120.0000.0000.0000.000
56A60GLU-1-0.859-0.91822.352-0.135-0.1350.0000.0000.0000.000
57A61GLU-1-0.722-0.80617.813-0.258-0.2580.0000.0000.0000.000
58A62ASN00.0000.02021.4510.0050.0050.0000.0000.0000.000
59A63LYS10.7700.87524.5510.1320.1320.0000.0000.0000.000
60A64GLU-1-0.728-0.81920.974-0.131-0.1310.0000.0000.0000.000
61A65PHE00.0290.00617.9910.0040.0040.0000.0000.0000.000
62A66VAL0-0.013-0.00523.4480.0100.0100.0000.0000.0000.000
63A67ARG10.7270.83823.8180.1260.1260.0000.0000.0000.000
64A68GLN0-0.006-0.01521.7240.0020.0020.0000.0000.0000.000
65A70LYS10.9750.99426.5600.0830.0830.0000.0000.0000.000
66A71GLU-1-0.813-0.87426.048-0.092-0.0920.0000.0000.0000.000
67A72LEU0-0.002-0.00424.0970.0050.0050.0000.0000.0000.000
68A73GLN0-0.043-0.03327.6710.0040.0040.0000.0000.0000.000
69A74ALA0-0.0060.00430.9620.0050.0050.0000.0000.0000.000
70A75GLU-1-0.816-0.89929.613-0.050-0.0500.0000.0000.0000.000
71A76LEU00.0090.02130.4130.0040.0040.0000.0000.0000.000
72A77ASP-1-0.819-0.91132.172-0.036-0.0360.0000.0000.0000.000
73A78LYS10.7670.86733.4310.0540.0540.0000.0000.0000.000
74A79MET00.0180.02431.4190.0030.0030.0000.0000.0000.000
75A80GLN0-0.015-0.01435.0890.0060.0060.0000.0000.0000.000
76A81ASN0-0.123-0.07537.4650.0040.0040.0000.0000.0000.000
77A82ASN0-0.065-0.03137.7220.0030.0030.0000.0000.0000.000
78A83SER0-0.050-0.02038.3040.0040.0040.0000.0000.0000.000
79A84ALA00.0240.01633.887-0.002-0.0020.0000.0000.0000.000
80A85VAL0-0.031-0.01530.9450.0000.0000.0000.0000.0000.000
81A86ILE00.0330.00833.855-0.001-0.0010.0000.0000.0000.000
82A87GLY0-0.043-0.01835.6600.0020.0020.0000.0000.0000.000
83A88VAL0-0.016-0.00529.7500.0000.0000.0000.0000.0000.000
84A89LYS10.9060.95331.3300.0240.0240.0000.0000.0000.000
85A90THR0-0.039-0.02025.025-0.006-0.0060.0000.0000.0000.000
86A91VAL00.0280.01825.9920.0050.0050.0000.0000.0000.000
87A92GLN0-0.064-0.04720.3260.0010.0010.0000.0000.0000.000
88A93LEU00.0080.01020.5500.0100.0100.0000.0000.0000.000
89A94ASP-1-0.830-0.87814.327-0.297-0.2970.0000.0000.0000.000
90A95VAL00.0230.00616.9200.0190.0190.0000.0000.0000.000
91A96GLY00.0510.01213.845-0.046-0.0460.0000.0000.0000.000
92A97CYS0-0.059-0.02312.9790.0580.0580.0000.0000.0000.000
93A98THR00.0820.0289.502-0.058-0.0580.0000.0000.0000.000
94A99SER0-0.056-0.01411.8260.0600.0600.0000.0000.0000.000
95A100LYS10.8490.92213.7220.1200.1200.0000.0000.0000.000
96A101ILE00.011-0.00315.246-0.045-0.0450.0000.0000.0000.000
97A102GLU-1-0.798-0.86814.928-0.080-0.0800.0000.0000.0000.000
98A103LYS10.8300.90317.3700.0610.0610.0000.0000.0000.000
99A104HIS10.8140.89816.2830.0870.0870.0000.0000.0000.000
100A105TYR00.0510.02920.035-0.018-0.0180.0000.0000.0000.000
101A106ALA00.0200.01421.6180.0110.0110.0000.0000.0000.000
102A107TYR00.014-0.00423.555-0.009-0.0090.0000.0000.0000.000
103A108ASP-1-0.790-0.89826.822-0.024-0.0240.0000.0000.0000.000
104A109GLY0-0.0170.00222.9290.0060.0060.0000.0000.0000.000
105A110ASN0-0.066-0.03122.8390.0090.0090.0000.0000.0000.000
106A111GLU-1-0.898-0.95619.081-0.042-0.0420.0000.0000.0000.000
107A112THR0-0.069-0.04423.1190.0060.0060.0000.0000.0000.000
108A113GLU-1-0.948-0.97025.340-0.015-0.0150.0000.0000.0000.000
109A114ASP-1-0.840-0.90221.351-0.046-0.0460.0000.0000.0000.000
110A115ASP-1-0.784-0.87324.071-0.058-0.0580.0000.0000.0000.000
111A116THR0-0.006-0.02024.363-0.007-0.0070.0000.0000.0000.000
112A117ALA0-0.0170.00326.5470.0010.0010.0000.0000.0000.000
113A118THR0-0.063-0.04226.772-0.010-0.0100.0000.0000.0000.000
114A119SER0-0.034-0.02626.8660.0030.0030.0000.0000.0000.000
115A120ALA0-0.023-0.02125.770-0.007-0.0070.0000.0000.0000.000
116A121SER00.0760.03225.458-0.007-0.0070.0000.0000.0000.000
117A122GLU-1-0.845-0.89924.433-0.103-0.1030.0000.0000.0000.000
118A123ARG10.8570.91122.3700.1310.1310.0000.0000.0000.000
119A124ALA00.0350.00519.511-0.018-0.0180.0000.0000.0000.000
120A125ARG10.8110.85618.6880.0930.0930.0000.0000.0000.000
121A126ASP-1-0.807-0.88419.983-0.148-0.1480.0000.0000.0000.000
122A128GLN00.0210.00614.098-0.084-0.0840.0000.0000.0000.000
123A129LYS10.8560.92215.4970.1250.1250.0000.0000.0000.000
124A130LYS10.8610.92816.4650.2420.2420.0000.0000.0000.000
125A131LEU00.0020.0109.197-0.024-0.0240.0000.0000.0000.000
126A132THR0-0.056-0.03712.174-0.059-0.0590.0000.0000.0000.000
127A133GLU-1-0.908-0.95714.253-0.234-0.2340.0000.0000.0000.000
128A134TYR00.005-0.04212.355-0.001-0.0010.0000.0000.0000.000
129A135ARG10.8370.8857.0540.9320.9320.0000.0000.0000.000
130A136LYS10.8870.94910.7430.2780.2780.0000.0000.0000.000
131A137LEU00.0040.00813.8000.0230.0230.0000.0000.0000.000
132A138VAL0-0.0060.0027.9550.0250.0250.0000.0000.0000.000
133A139LEU0-0.014-0.0179.7430.0280.0280.0000.0000.0000.000
134A140ALA0-0.021-0.00111.9290.0390.0390.0000.0000.0000.000
135A141SER0-0.041-0.02213.2740.0320.0320.0000.0000.0000.000
136A142ALA0-0.0160.00412.3800.0120.0120.0000.0000.0000.000
137A143VAL0-0.058-0.02813.5350.0420.0420.0000.0000.0000.000
138A144SER00.0350.00814.187-0.006-0.0060.0000.0000.0000.000
139A145PRO0-0.029-0.01713.3200.0120.0120.0000.0000.0000.000
140A146GLN00.0110.01515.9220.0230.0230.0000.0000.0000.000
141A147LEU0-0.018-0.01515.2510.0070.0070.0000.0000.0000.000
142A148GLU-1-0.793-0.88719.2780.0050.0050.0000.0000.0000.000
143A149VAL0-0.035-0.01620.7280.0120.0120.0000.0000.0000.000
144A150GLU-1-0.865-0.91823.1490.0230.0230.0000.0000.0000.000
145A151ARG10.9050.93325.262-0.030-0.0300.0000.0000.0000.000
146A152ARG10.8900.95228.024-0.041-0.0410.0000.0000.0000.000
147A153SER00.0440.01329.8300.0050.0050.0000.0000.0000.000
148A154SER0-0.049-0.05029.2690.0010.0010.0000.0000.0000.000
149A155GLY00.0250.02031.4390.0060.0060.0000.0000.0000.000
150A156ARG10.9030.94234.361-0.048-0.0480.0000.0000.0000.000
151A157GLU-1-0.856-0.91536.3140.0500.0500.0000.0000.0000.000
152A158GLY00.0120.00837.0470.0010.0010.0000.0000.0000.000
153A159GLY0-0.0060.01233.0100.0000.0000.0000.0000.0000.000
154A160MET0-0.042-0.00529.984-0.006-0.0060.0000.0000.0000.000
155A161ARG10.8490.91223.266-0.066-0.0660.0000.0000.0000.000
156A162LEU00.0050.00923.740-0.011-0.0110.0000.0000.0000.000
157A163ARG10.8150.88820.093-0.058-0.0580.0000.0000.0000.000
158A164CYS0-0.066-0.00416.6680.0070.0070.0000.0000.0000.000
159A165PHE0-0.008-0.03217.5070.0170.0170.0000.0000.0000.000
160A166ALA00.0350.03713.886-0.010-0.0100.0000.0000.0000.000
161A167ARG10.8760.91115.6980.0100.0100.0000.0000.0000.000
162A168ASP-1-0.820-0.90417.163-0.090-0.0900.0000.0000.0000.000
163A169TYR0-0.032-0.0088.9920.0380.0380.0000.0000.0000.000
164A170TYR00.0440.02511.478-0.004-0.0040.0000.0000.0000.000
165A171PRO00.0210.0007.2560.0220.0220.0000.0000.0000.000
166A172ALA00.0400.0007.2270.0180.0180.0000.0000.0000.000
167A173ASP-1-0.896-0.9422.089-10.245-7.7425.294-4.216-3.581-0.057
168A174LEU0-0.026-0.0285.001-0.192-0.191-0.001-0.0050.0040.000
169A175GLU-1-0.804-0.8686.7040.7370.7370.0000.0000.0000.000
170A176ILE00.002-0.0197.846-0.135-0.1350.0000.0000.0000.000
171A177ARG10.8370.89711.419-0.423-0.4230.0000.0000.0000.000
172A178TRP00.0230.00314.024-0.050-0.0500.0000.0000.0000.000
173A179TRP0-0.035-0.02514.1860.0360.0360.0000.0000.0000.000
174A180LYS10.8600.93119.995-0.115-0.1150.0000.0000.0000.000
175A181ASP-1-0.776-0.87323.8440.0960.0960.0000.0000.0000.000
176A182ASP-1-0.828-0.92225.7570.0930.0930.0000.0000.0000.000
177A183GLY0-0.020-0.00328.332-0.004-0.0040.0000.0000.0000.000
178A184GLY0-0.037-0.02030.164-0.006-0.0060.0000.0000.0000.000
179A185GLY0-0.039-0.02028.131-0.005-0.0050.0000.0000.0000.000
180A186GLY0-0.0120.00924.8130.0040.0040.0000.0000.0000.000
181A187ALA0-0.027-0.02621.126-0.007-0.0070.0000.0000.0000.000
182A188LEU00.0230.01821.1020.0210.0210.0000.0000.0000.000
183A189PRO00.0120.00016.902-0.005-0.0050.0000.0000.0000.000
184A190GLN0-0.057-0.02918.393-0.031-0.0310.0000.0000.0000.000
185A191THR00.004-0.00217.6600.0240.0240.0000.0000.0000.000
186A192SER00.0080.01616.128-0.024-0.0240.0000.0000.0000.000
187A193LYS10.9370.96318.053-0.131-0.1310.0000.0000.0000.000
188A194GLN0-0.032-0.01517.875-0.015-0.0150.0000.0000.0000.000
189A195HIS00.005-0.0158.8340.0150.0150.0000.0000.0000.000
190A196HIS00.014-0.00513.2240.0040.0040.0000.0000.0000.000
191A197ASP-1-0.816-0.8928.2330.3700.3700.0000.0000.0000.000
192A198PRO0-0.038-0.0037.698-0.020-0.0200.0000.0000.0000.000
193A199LEU00.0140.00610.889-0.023-0.0230.0000.0000.0000.000
194A200PRO00.003-0.00113.975-0.010-0.0100.0000.0000.0000.000
195A201SER0-0.059-0.05315.3850.0210.0210.0000.0000.0000.000
196A202GLY0-0.028-0.00718.3370.0080.0080.0000.0000.0000.000
197A203GLN0-0.018-0.02419.141-0.011-0.0110.0000.0000.0000.000
198A204GLY0-0.0130.00217.002-0.004-0.0040.0000.0000.0000.000
199A205LEU0-0.058-0.01014.933-0.031-0.0310.0000.0000.0000.000
200A206TYR0-0.062-0.05011.1160.0330.0330.0000.0000.0000.000
201A207GLN00.0130.00813.8620.0120.0120.0000.0000.0000.000
202A208LYS10.8730.9529.440-0.272-0.2720.0000.0000.0000.000
203A209HIS0-0.022-0.00713.723-0.018-0.0180.0000.0000.0000.000
204A210ILE00.0120.02014.0510.0290.0290.0000.0000.0000.000
205A211ASP-1-0.789-0.86816.8580.0720.0720.0000.0000.0000.000
206A212VAL00.0060.01020.2270.0220.0220.0000.0000.0000.000
207A213TYR0-0.013-0.02022.592-0.011-0.0110.0000.0000.0000.000
208A214VAL0-0.027-0.01025.8410.0070.0070.0000.0000.0000.000
209A215ASP-1-0.788-0.90528.4240.0760.0760.0000.0000.0000.000
210A216GLY0-0.023-0.00531.842-0.001-0.0010.0000.0000.0000.000
211A217GLY0-0.007-0.01033.360-0.002-0.0020.0000.0000.0000.000
212A218LEU0-0.014-0.00530.729-0.001-0.0010.0000.0000.0000.000
213A219GLU-1-0.795-0.89028.1660.0550.0550.0000.0000.0000.000
214A220HIS00.0130.00027.0400.0070.0070.0000.0000.0000.000
215A221VAL00.0160.02427.4760.0000.0000.0000.0000.0000.000
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