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: JLKL9

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 OptH
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 -2660717.47596
FMO2-HF: Nuclear repulsion 2567221.859903
FMO2-HF: Total energy -93495.616057
FMO2-MP2: Total energy -93767.192356


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.
-2.598-5.28416.699-9.53-4.481-0.035
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 : 0.063 / q_NPA : 0.019
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-1-0.878-0.9203.792-4.417-3.088-0.010-0.939-0.3800.006
4A8SER0-0.066-0.0374.4670.5170.660-0.001-0.025-0.1160.000
5A9GLY0-0.036-0.0185.7100.7430.7430.0000.0000.0000.000
6A10LEU0-0.043-0.0188.589-0.285-0.2850.0000.0000.0000.000
7A11ARG10.8810.9649.9831.0351.0350.0000.0000.0000.000
8A12TYR0-0.061-0.06812.561-0.066-0.0660.0000.0000.0000.000
9A13ALA0-0.026-0.00515.0120.0300.0300.0000.0000.0000.000
10A14TYR0-0.001-0.01716.7940.0190.0190.0000.0000.0000.000
11A15THR00.0100.00620.5970.0110.0110.0000.0000.0000.000
12A16LEU0-0.021-0.02023.0230.0020.0020.0000.0000.0000.000
13A17VAL0-0.0140.00026.7850.0070.0070.0000.0000.0000.000
14A18VAL00.017-0.00629.0750.0040.0040.0000.0000.0000.000
15A19ASP-1-0.905-0.95532.605-0.099-0.0990.0000.0000.0000.000
16A20GLY00.0590.00835.2850.0050.0050.0000.0000.0000.000
17A21THR0-0.048-0.00937.9150.0030.0030.0000.0000.0000.000
18A22ALA0-0.066-0.01939.2430.0040.0040.0000.0000.0000.000
19A23ASN00.015-0.00938.510-0.001-0.0010.0000.0000.0000.000
20A24THR0-0.070-0.04033.069-0.005-0.0050.0000.0000.0000.000
21A25ALA00.0470.03532.323-0.006-0.0060.0000.0000.0000.000
22A26ARG10.9500.98729.7340.1310.1310.0000.0000.0000.000
23A27CYS0-0.009-0.00525.647-0.005-0.0050.0000.0000.0000.000
24A28PHE0-0.045-0.02621.3090.0050.0050.0000.0000.0000.000
25A29GLY00.0640.03320.0250.0000.0000.0000.0000.0000.000
26A30THR0-0.044-0.01915.463-0.015-0.0150.0000.0000.0000.000
27A31GLY00.0300.01815.026-0.005-0.0050.0000.0000.0000.000
28A32HIS10.8490.9219.5481.0341.0340.0000.0000.0000.000
29A33VAL00.0480.0228.5230.1480.1480.0000.0000.0000.000
30A34ASP-1-0.786-0.9004.253-2.658-2.499-0.001-0.015-0.1420.000
31A35GLY00.0450.0244.436-1.156-1.129-0.001-0.014-0.0120.000
32A36GLU-1-0.816-0.8566.436-0.637-0.6370.0000.0000.0000.000
33A37ALA0-0.053-0.0318.6240.1230.1230.0000.0000.0000.000
34A38PHE0-0.021-0.01512.2810.0450.0450.0000.0000.0000.000
35A39VAL00.007-0.00614.7470.0920.0920.0000.0000.0000.000
36A40GLY00.0330.01917.309-0.044-0.0440.0000.0000.0000.000
37A41TYR0-0.0070.01219.7540.0420.0420.0000.0000.0000.000
38A42SER00.0660.01522.7930.0060.0060.0000.0000.0000.000
39A43ASN0-0.042-0.02525.6680.0140.0140.0000.0000.0000.000
40A44ASN0-0.014-0.01728.3110.0140.0140.0000.0000.0000.000
41A45LYS10.9780.99627.6990.1760.1760.0000.0000.0000.000
42A46THR00.0020.00121.869-0.017-0.0170.0000.0000.0000.000
43A47HIS0-0.049-0.01920.8230.0300.0300.0000.0000.0000.000
44A48GLY00.0380.01519.869-0.030-0.0300.0000.0000.0000.000
45A49ILE0-0.037-0.01315.5790.0310.0310.0000.0000.0000.000
46A50GLY00.0680.04215.189-0.052-0.0520.0000.0000.0000.000
47A51ARG10.8840.94415.2580.4240.4240.0000.0000.0000.000
48A52TRP00.0250.01412.3460.0820.0820.0000.0000.0000.000
49A53VAL0-0.0530.01317.1570.0380.0380.0000.0000.0000.000
50A54ASN00.0640.03718.6460.0320.0320.0000.0000.0000.000
51A55ALA00.057-0.01022.430-0.012-0.0120.0000.0000.0000.000
52A56SER00.0020.00624.7050.0080.0080.0000.0000.0000.000
53A57HIS00.0460.02319.868-0.007-0.0070.0000.0000.0000.000
54A58VAL0-0.0080.00521.485-0.006-0.0060.0000.0000.0000.000
55A59GLU-1-0.949-0.97722.783-0.192-0.1920.0000.0000.0000.000
56A60GLU-1-0.834-0.92423.107-0.207-0.2070.0000.0000.0000.000
57A61GLU-1-0.806-0.88418.684-0.448-0.4480.0000.0000.0000.000
58A62ASN00.0140.01022.161-0.004-0.0040.0000.0000.0000.000
59A63LYS10.8570.94124.9870.1940.1940.0000.0000.0000.000
60A64GLU-1-0.789-0.88221.837-0.217-0.2170.0000.0000.0000.000
61A65PHE00.0570.03518.5700.0030.0030.0000.0000.0000.000
62A66VAL0-0.0160.00623.9630.0160.0160.0000.0000.0000.000
63A67ARG10.7480.84724.7130.2110.2110.0000.0000.0000.000
64A68GLN0-0.020-0.03422.3350.0040.0040.0000.0000.0000.000
65A70LYS10.9190.98726.9220.1520.1520.0000.0000.0000.000
66A71GLU-1-0.899-0.96326.916-0.155-0.1550.0000.0000.0000.000
67A72LEU0-0.0020.01424.5710.0060.0060.0000.0000.0000.000
68A73GLN0-0.043-0.04228.2160.0060.0060.0000.0000.0000.000
69A74ALA00.0100.02531.3800.0090.0090.0000.0000.0000.000
70A75GLU-1-0.992-1.00528.996-0.102-0.1020.0000.0000.0000.000
71A76LEU00.0030.02030.9360.0050.0050.0000.0000.0000.000
72A77ASP-1-0.854-0.94532.503-0.091-0.0910.0000.0000.0000.000
73A78LYS10.8930.93735.2490.0870.0870.0000.0000.0000.000
74A79MET00.0400.03230.8330.0080.0080.0000.0000.0000.000
75A80GLN00.0400.02035.3730.0070.0070.0000.0000.0000.000
76A81ASN0-0.124-0.05737.6280.0080.0080.0000.0000.0000.000
77A82ASN0-0.040-0.01438.0810.0080.0080.0000.0000.0000.000
78A83SER0-0.061-0.01238.3010.0040.0040.0000.0000.0000.000
79A84ALA00.0290.02134.136-0.004-0.0040.0000.0000.0000.000
80A85VAL0-0.020-0.02930.898-0.003-0.0030.0000.0000.0000.000
81A86ILE00.0210.01134.130-0.001-0.0010.0000.0000.0000.000
82A87GLY0-0.056-0.02435.8960.0010.0010.0000.0000.0000.000
83A88VAL00.0090.01729.783-0.002-0.0020.0000.0000.0000.000
84A89LYS10.9020.94431.3120.0910.0910.0000.0000.0000.000
85A90THR0-0.042-0.00625.076-0.011-0.0110.0000.0000.0000.000
86A91VAL00.0350.02725.6220.0060.0060.0000.0000.0000.000
87A92GLN0-0.035-0.01919.7240.0050.0050.0000.0000.0000.000
88A93LEU00.0030.00120.4980.0210.0210.0000.0000.0000.000
89A94ASP-1-0.882-0.94414.433-0.589-0.5890.0000.0000.0000.000
90A95VAL0-0.028-0.02017.3390.0370.0370.0000.0000.0000.000
91A96GLY00.0950.05113.912-0.063-0.0630.0000.0000.0000.000
92A97CYS0-0.006-0.03513.0440.0770.0770.0000.0000.0000.000
93A98THR00.0220.0079.188-0.067-0.0670.0000.0000.0000.000
94A99SER0-0.064-0.01411.5320.0930.0930.0000.0000.0000.000
95A100LYS10.9530.97313.1730.0280.0280.0000.0000.0000.000
96A101ILE00.013-0.00415.126-0.054-0.0540.0000.0000.0000.000
97A102GLU-1-0.947-0.98313.961-0.322-0.3220.0000.0000.0000.000
98A103LYS10.9230.97917.4490.1460.1460.0000.0000.0000.000
99A104HIS10.9280.99816.3880.2250.2250.0000.0000.0000.000
100A105TYR00.0900.03220.109-0.037-0.0370.0000.0000.0000.000
101A106ALA00.0420.01421.7240.0090.0090.0000.0000.0000.000
102A107TYR00.0010.00723.685-0.016-0.0160.0000.0000.0000.000
103A108ASP-1-0.805-0.93326.997-0.102-0.1020.0000.0000.0000.000
104A109GLY0-0.041-0.01623.1070.0080.0080.0000.0000.0000.000
105A110ASN0-0.049-0.01923.2090.0060.0060.0000.0000.0000.000
106A111GLU-1-0.908-0.95519.581-0.153-0.1530.0000.0000.0000.000
107A112THR0-0.068-0.05423.1980.0130.0130.0000.0000.0000.000
108A113GLU-1-0.954-0.95425.800-0.051-0.0510.0000.0000.0000.000
109A114ASP-1-0.936-0.96221.817-0.106-0.1060.0000.0000.0000.000
110A115ASP-1-0.900-0.94824.521-0.077-0.0770.0000.0000.0000.000
111A116THR0-0.050-0.04923.754-0.010-0.0100.0000.0000.0000.000
112A117ALA00.0310.03026.3590.0060.0060.0000.0000.0000.000
113A118THR0-0.054-0.03526.775-0.011-0.0110.0000.0000.0000.000
114A119SER0-0.004-0.00826.9630.0030.0030.0000.0000.0000.000
115A120ALA0-0.016-0.00325.217-0.010-0.0100.0000.0000.0000.000
116A121SER00.0840.03624.977-0.009-0.0090.0000.0000.0000.000
117A122GLU-1-0.919-0.96723.366-0.076-0.0760.0000.0000.0000.000
118A123ARG10.9770.99522.2410.1910.1910.0000.0000.0000.000
119A124ALA0-0.002-0.01518.795-0.029-0.0290.0000.0000.0000.000
120A125ARG10.9430.96118.2510.0820.0820.0000.0000.0000.000
121A126ASP-1-0.886-0.95119.989-0.174-0.1740.0000.0000.0000.000
122A128GLN00.0550.03113.820-0.111-0.1110.0000.0000.0000.000
123A129LYS10.8720.95514.9870.1620.1620.0000.0000.0000.000
124A130LYS10.9100.95516.3920.3870.3870.0000.0000.0000.000
125A131LEU00.0010.0119.174-0.066-0.0660.0000.0000.0000.000
126A132THR0-0.051-0.02212.075-0.059-0.0590.0000.0000.0000.000
127A133GLU-1-0.948-0.97613.678-0.322-0.3220.0000.0000.0000.000
128A134TYR00.006-0.02512.8060.0080.0080.0000.0000.0000.000
129A135ARG10.8550.9226.6881.1321.1320.0000.0000.0000.000
130A136LYS10.8800.95010.8240.2450.2450.0000.0000.0000.000
131A137LEU00.001-0.00213.7160.0260.0260.0000.0000.0000.000
132A138VAL0-0.0080.0158.9690.0320.0320.0000.0000.0000.000
133A139LEU0-0.0050.0069.1350.0420.0420.0000.0000.0000.000
134A140ALA0-0.0010.01012.2160.0610.0610.0000.0000.0000.000
135A141SER0-0.097-0.06513.5140.0190.0190.0000.0000.0000.000
136A142ALA0-0.030-0.00612.812-0.013-0.0130.0000.0000.0000.000
137A143VAL0-0.038-0.01813.9080.0600.0600.0000.0000.0000.000
138A144SER00.0520.02014.699-0.017-0.0170.0000.0000.0000.000
139A145PRO0-0.015-0.01714.0580.0010.0010.0000.0000.0000.000
140A146GLN0-0.0250.00616.5570.0470.0470.0000.0000.0000.000
141A147LEU0-0.029-0.02416.0920.0010.0010.0000.0000.0000.000
142A148GLU-1-0.910-0.94820.058-0.025-0.0250.0000.0000.0000.000
143A149VAL0-0.025-0.00821.5200.0080.0080.0000.0000.0000.000
144A150GLU-1-0.913-0.97123.661-0.038-0.0380.0000.0000.0000.000
145A151ARG10.9230.97625.594-0.018-0.0180.0000.0000.0000.000
146A152ARG10.9000.95328.135-0.002-0.0020.0000.0000.0000.000
147A153SER00.0490.02429.7430.0080.0080.0000.0000.0000.000
148A154SER0-0.050-0.03128.917-0.006-0.0060.0000.0000.0000.000
149A155GLY00.0410.02831.5310.0050.0050.0000.0000.0000.000
150A156ARG10.9180.94833.850-0.034-0.0340.0000.0000.0000.000
151A157GLU-1-0.871-0.94035.9960.0430.0430.0000.0000.0000.000
152A158GLY0-0.0210.00036.4900.0030.0030.0000.0000.0000.000
153A159GLY00.0030.01032.3310.0010.0010.0000.0000.0000.000
154A160MET0-0.032-0.00829.893-0.010-0.0100.0000.0000.0000.000
155A161ARG10.9260.96623.743-0.008-0.0080.0000.0000.0000.000
156A162LEU0-0.019-0.00423.952-0.012-0.0120.0000.0000.0000.000
157A163ARG10.8070.88020.4590.0170.0170.0000.0000.0000.000
158A164CYS0-0.088-0.02517.3760.0150.0150.0000.0000.0000.000
159A165PHE00.015-0.01417.8410.0000.0000.0000.0000.0000.000
160A166ALA00.0480.03414.5920.0100.0100.0000.0000.0000.000
161A167ARG10.8930.92616.0210.0670.0670.0000.0000.0000.000
162A168ASP-1-0.847-0.92817.756-0.192-0.1920.0000.0000.0000.000
163A169TYR0-0.068-0.0189.7560.0770.0770.0000.0000.0000.000
164A170TYR00.0410.01711.809-0.053-0.0530.0000.0000.0000.000
165A171PRO0-0.008-0.0147.8890.1150.1150.0000.0000.0000.000
166A172ALA00.0600.0137.4930.1220.1220.0000.0000.0000.000
167A173ASP-1-0.899-0.9382.0551.831-2.51516.713-8.535-3.832-0.041
168A174LEU0-0.030-0.0085.3660.0420.044-0.001-0.0020.0010.000
169A175GLU-1-0.949-0.9627.4750.8730.8730.0000.0000.0000.000
170A176ILE00.019-0.0068.700-0.112-0.1120.0000.0000.0000.000
171A177ARG10.9610.95711.918-0.536-0.5360.0000.0000.0000.000
172A178TRP00.0200.01114.512-0.029-0.0290.0000.0000.0000.000
173A179TRP0-0.030-0.02414.6700.0400.0400.0000.0000.0000.000
174A180LYS10.9210.96120.342-0.157-0.1570.0000.0000.0000.000
175A181ASP-1-0.841-0.90124.0740.1510.1510.0000.0000.0000.000
176A182ASP-1-0.852-0.93126.4550.1540.1540.0000.0000.0000.000
177A183GLY0-0.025-0.01128.922-0.008-0.0080.0000.0000.0000.000
178A184GLY0-0.014-0.01330.253-0.009-0.0090.0000.0000.0000.000
179A185GLY0-0.041-0.01127.9010.0020.0020.0000.0000.0000.000
180A186GLY00.0170.01525.5720.0150.0150.0000.0000.0000.000
181A187ALA0-0.033-0.03321.126-0.011-0.0110.0000.0000.0000.000
182A188LEU00.001-0.00121.2590.0350.0350.0000.0000.0000.000
183A189PRO00.005-0.00117.150-0.014-0.0140.0000.0000.0000.000
184A190GLN0-0.047-0.01418.701-0.037-0.0370.0000.0000.0000.000
185A191THR00.002-0.00116.8810.0410.0410.0000.0000.0000.000
186A192SER0-0.002-0.00315.762-0.031-0.0310.0000.0000.0000.000
187A193LYS10.9360.96917.396-0.083-0.0830.0000.0000.0000.000
188A194GLN0-0.047-0.03517.528-0.015-0.0150.0000.0000.0000.000
189A195HIS00.0550.0128.8570.0370.0370.0000.0000.0000.000
190A196HIS0-0.0290.00213.768-0.012-0.0120.0000.0000.0000.000
191A197ASP-1-0.885-0.9349.493-0.186-0.1860.0000.0000.0000.000
192A198PRO0-0.067-0.0248.6490.0550.0550.0000.0000.0000.000
193A199LEU00.009-0.00711.764-0.040-0.0400.0000.0000.0000.000
194A200PRO00.0050.00314.3210.0010.0010.0000.0000.0000.000
195A201SER00.017-0.02615.6680.0340.0340.0000.0000.0000.000
196A202GLY0-0.046-0.00618.6680.0280.0280.0000.0000.0000.000
197A203GLN00.022-0.01119.113-0.018-0.0180.0000.0000.0000.000
198A204GLY0-0.029-0.01216.9860.0030.0030.0000.0000.0000.000
199A205LEU0-0.083-0.00115.104-0.057-0.0570.0000.0000.0000.000
200A206TYR0-0.062-0.07111.3000.0110.0110.0000.0000.0000.000
201A207GLN00.0230.01914.3440.0440.0440.0000.0000.0000.000
202A208LYS10.9310.9858.513-0.009-0.0090.0000.0000.0000.000
203A209HIS0-0.009-0.01414.2900.0030.0030.0000.0000.0000.000
204A210ILE00.0080.03313.7840.0150.0150.0000.0000.0000.000
205A211ASP-1-0.835-0.90616.8120.0210.0210.0000.0000.0000.000
206A212VAL0-0.0020.01019.9570.0250.0250.0000.0000.0000.000
207A213TYR0-0.041-0.03422.379-0.024-0.0240.0000.0000.0000.000
208A214VAL0-0.0110.00225.9870.0100.0100.0000.0000.0000.000
209A215ASP-1-0.841-0.92128.4430.0720.0720.0000.0000.0000.000
210A216GLY00.0140.00132.1680.0000.0000.0000.0000.0000.000
211A217GLY0-0.025-0.01234.0010.0020.0020.0000.0000.0000.000
212A218LEU0-0.008-0.00230.9160.0030.0030.0000.0000.0000.000
213A219GLU-1-0.817-0.93528.6350.0570.0570.0000.0000.0000.000
214A220HIS0-0.003-0.01727.7070.0090.0090.0000.0000.0000.000
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