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: VQ8G1

Calculation Name: 2PJQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PJQ

Chain ID: A

ChEMBL ID:

UniProt ID: F9URF4

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2344792.42306
FMO2-HF: Nuclear repulsion 2264228.196444
FMO2-HF: Total energy -80564.226616
FMO2-MP2: Total energy -80801.621638


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.186-12.4243.281-5.419-6.622-0.045
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.013
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].
3A3THR00.002-0.0043.8600.8182.840-0.014-1.004-1.0040.005
4A4GLU-1-0.893-0.9616.5000.1720.1720.0000.0000.0000.000
5A5THR0-0.0170.0009.3110.2380.2380.0000.0000.0000.000
6A6GLN00.0250.0066.479-0.694-0.6940.0000.0000.0000.000
7A7LEU00.0310.0329.3520.2560.2560.0000.0000.0000.000
8A8THR0-0.014-0.02210.7830.1010.1010.0000.0000.0000.000
9A9ALA0-0.0120.00713.0140.1180.1180.0000.0000.0000.000
10A10ILE0-0.014-0.0159.3060.1150.1150.0000.0000.0000.000
11A11GLN0-0.083-0.05413.7020.1360.1360.0000.0000.0000.000
12A12THR0-0.0030.00616.2510.0660.0660.0000.0000.0000.000
13A13TYR00.0140.00816.7000.0510.0510.0000.0000.0000.000
14A14ALA00.0610.02717.5230.0470.0470.0000.0000.0000.000
15A15LEU0-0.027-0.02119.3180.0490.0490.0000.0000.0000.000
16A16GLN0-0.100-0.04821.6980.0110.0110.0000.0000.0000.000
17A17LYS10.8520.93220.9490.3310.3310.0000.0000.0000.000
18A18LEU00.0340.02621.1890.0130.0130.0000.0000.0000.000
19A19ALA0-0.077-0.02024.8600.0260.0260.0000.0000.0000.000
20A20HIS0-0.024-0.03027.5890.0020.0020.0000.0000.0000.000
21A21ASP-1-0.803-0.89128.102-0.076-0.0760.0000.0000.0000.000
22A22HIS0-0.042-0.03029.9980.0090.0090.0000.0000.0000.000
23A23SER00.0500.03730.3000.0090.0090.0000.0000.0000.000
24A24GLY00.0430.01730.6880.0090.0090.0000.0000.0000.000
25A25HIS0-0.080-0.02925.5800.0360.0360.0000.0000.0000.000
26A26GLY00.1200.06625.996-0.018-0.0180.0000.0000.0000.000
27A27ARG10.9530.95924.2840.1790.1790.0000.0000.0000.000
28A28ASP-1-0.871-0.94023.963-0.027-0.0270.0000.0000.0000.000
29A29HIS10.7520.89922.713-0.012-0.0120.0000.0000.0000.000
30A30LEU00.0660.04019.4850.0290.0290.0000.0000.0000.000
31A31GLN0-0.008-0.00619.9970.0200.0200.0000.0000.0000.000
32A32ARG10.8220.89320.849-0.011-0.0110.0000.0000.0000.000
33A33VAL00.0690.03317.8820.0440.0440.0000.0000.0000.000
34A34ASN00.0070.00815.6650.0610.0610.0000.0000.0000.000
35A35ARG10.9020.95016.792-0.052-0.0520.0000.0000.0000.000
36A36LEU0-0.005-0.00219.0020.0420.0420.0000.0000.0000.000
37A37ALA00.0690.03814.5280.0570.0570.0000.0000.0000.000
38A38ARG10.9100.94912.893-0.083-0.0830.0000.0000.0000.000
39A39ARG10.8790.94715.324-0.283-0.2830.0000.0000.0000.000
40A40LEU00.0340.00917.1320.0350.0350.0000.0000.0000.000
41A41ALA00.003-0.00411.8330.0520.0520.0000.0000.0000.000
42A42LYS10.8650.92713.114-0.306-0.3060.0000.0000.0000.000
43A43ASP-1-0.888-0.93914.8100.5700.5700.0000.0000.0000.000
44A44GLU-1-0.897-0.95014.1930.8360.8360.0000.0000.0000.000
45A45GLY0-0.0490.00012.4750.0770.0770.0000.0000.0000.000
46A46ALA00.0090.0129.4250.3630.3630.0000.0000.0000.000
47A47ASN00.0490.0172.748-1.808-0.9530.119-0.272-0.7030.001
48A48LEU00.0430.0276.632-0.527-0.5270.0000.0000.0000.000
49A49ASN00.004-0.0244.639-0.922-0.918-0.001-0.0040.0010.000
50A50LEU00.0570.0484.750-1.174-0.932-0.001-0.025-0.2160.000
51A51THR00.005-0.0176.598-0.588-0.5880.0000.0000.0000.000
52A52LEU0-0.059-0.0419.840-0.273-0.2730.0000.0000.0000.000
53A53ALA0-0.0030.0198.593-0.154-0.1540.0000.0000.0000.000
54A54ALA00.0250.00810.424-0.095-0.0950.0000.0000.0000.000
55A55ALA0-0.034-0.04112.122-0.055-0.0550.0000.0000.0000.000
56A56TRP0-0.071-0.02913.077-0.025-0.0250.0000.0000.0000.000
57A57LEU00.0650.00612.125-0.005-0.0050.0000.0000.0000.000
58A58HIS10.8720.94215.9600.0090.0090.0000.0000.0000.000
59A59ASP-1-0.859-0.94117.790-0.016-0.0160.0000.0000.0000.000
60A60VAL0-0.080-0.02718.409-0.012-0.0120.0000.0000.0000.000
61A61ILE0-0.057-0.04118.811-0.018-0.0180.0000.0000.0000.000
62A62ASP-1-0.891-0.92921.674-0.031-0.0310.0000.0000.0000.000
63A72ALA00.0350.02921.6950.0060.0060.0000.0000.0000.000
64A73HIS0-0.020-0.02918.534-0.044-0.0440.0000.0000.0000.000
65A74GLN0-0.011-0.00819.197-0.050-0.0500.0000.0000.0000.000
66A75ASP-1-0.867-0.94220.015-0.413-0.4130.0000.0000.0000.000
67A76LEU00.0300.02413.939-0.065-0.0650.0000.0000.0000.000
68A77ILE00.0130.01915.135-0.130-0.1300.0000.0000.0000.000
69A78VAL00.004-0.01115.116-0.126-0.1260.0000.0000.0000.000
70A79GLN0-0.042-0.01615.215-0.115-0.1150.0000.0000.0000.000
71A80LEU00.026-0.01010.037-0.085-0.0850.0000.0000.0000.000
72A81ASN00.0660.03311.263-0.377-0.3770.0000.0000.0000.000
73A82ALA0-0.076-0.00812.576-0.139-0.1390.0000.0000.0000.000
74A83GLN0-0.056-0.04711.4750.0160.0160.0000.0000.0000.000
75A84ASN00.0070.0208.867-0.289-0.2890.0000.0000.0000.000
76A85VAL0-0.0180.0197.140-0.805-0.8050.0000.0000.0000.000
77A86THR00.020-0.0023.2890.2910.5660.007-0.063-0.2180.000
78A87ALA00.0720.0386.6090.1530.1530.0000.0000.0000.000
79A88ASP-1-0.851-0.9154.455-1.285-1.175-0.001-0.004-0.1050.000
80A89ASP-1-0.803-0.9172.499-19.435-14.2213.173-4.043-4.343-0.051
81A90GLN0-0.040-0.0395.1440.9590.999-0.001-0.004-0.0340.000
82A91THR0-0.007-0.0108.2010.4980.4980.0000.0000.0000.000
83A92ALA0-0.037-0.0245.0400.4070.4070.0000.0000.0000.000
84A93ILE0-0.020-0.0197.1280.4430.4430.0000.0000.0000.000
85A94PHE0-0.027-0.0299.6670.1730.1730.0000.0000.0000.000
86A95ALA00.0220.02410.0220.0970.0970.0000.0000.0000.000
87A96ILE0-0.0270.0099.5640.0840.0840.0000.0000.0000.000
88A97ILE0-0.052-0.01412.962-0.005-0.0050.0000.0000.0000.000
89A98ASP-1-0.770-0.87614.997-0.209-0.2090.0000.0000.0000.000
90A99HIS0-0.186-0.10814.9780.0040.0040.0000.0000.0000.000
91A100MET00.0420.03816.7500.0480.0480.0000.0000.0000.000
92A101SER00.0070.00818.6810.0030.0030.0000.0000.0000.000
93A102PHE00.0760.01722.2280.0160.0160.0000.0000.0000.000
94A103SER00.0380.03125.3330.0010.0010.0000.0000.0000.000
95A104LYS10.8360.91920.390-0.008-0.0080.0000.0000.0000.000
96A105SER00.0130.01124.3840.0050.0050.0000.0000.0000.000
97A106PHE00.0170.00325.5610.0050.0050.0000.0000.0000.000
98A107ASN0-0.097-0.04425.249-0.007-0.0070.0000.0000.0000.000
99A108GLY00.0430.03326.398-0.001-0.0010.0000.0000.0000.000
100A109PRO0-0.034-0.02223.139-0.001-0.0010.0000.0000.0000.000
101A110GLN00.002-0.00318.7570.0070.0070.0000.0000.0000.000
102A111LYS10.9540.96816.685-0.428-0.4280.0000.0000.0000.000
103A112LEU0-0.028-0.00813.856-0.022-0.0220.0000.0000.0000.000
104A113SER0-0.0190.0038.480-0.071-0.0710.0000.0000.0000.000
105A114LEU00.0570.04610.213-0.139-0.1390.0000.0000.0000.000
106A115GLU-1-0.775-0.9227.5242.9632.9630.0000.0000.0000.000
107A116GLY00.013-0.02410.717-0.281-0.2810.0000.0000.0000.000
108A117GLN0-0.016-0.00812.770-0.129-0.1290.0000.0000.0000.000
109A118VAL00.0510.04613.542-0.119-0.1190.0000.0000.0000.000
110A119VAL00.026-0.00612.880-0.120-0.1200.0000.0000.0000.000
111A120GLN0-0.021-0.00315.851-0.058-0.0580.0000.0000.0000.000
112A121ASP-1-0.745-0.85218.4790.4110.4110.0000.0000.0000.000
113A122ALA0-0.034-0.02717.831-0.052-0.0520.0000.0000.0000.000
114A123ASP-1-0.926-0.97519.7160.0480.0480.0000.0000.0000.000
115A124ARG10.9060.95421.436-0.233-0.2330.0000.0000.0000.000
116A125LEU00.0320.01621.755-0.028-0.0280.0000.0000.0000.000
117A126ASP-1-0.812-0.86323.8790.0600.0600.0000.0000.0000.000
118A127ALA0-0.047-0.01725.752-0.027-0.0270.0000.0000.0000.000
119A128ILE00.038-0.01128.217-0.007-0.0070.0000.0000.0000.000
120A129GLY00.0170.01030.1790.0010.0010.0000.0000.0000.000
121A130ALA00.0240.00032.395-0.009-0.0090.0000.0000.0000.000
122A131ILE00.011-0.00928.870-0.009-0.0090.0000.0000.0000.000
123A132GLY00.0190.01131.062-0.010-0.0100.0000.0000.0000.000
124A133ILE00.0080.00831.852-0.008-0.0080.0000.0000.0000.000
125A134ALA0-0.014-0.00734.066-0.008-0.0080.0000.0000.0000.000
126A135ARG10.8050.86726.708-0.044-0.0440.0000.0000.0000.000
127A136ALA00.0140.02133.055-0.009-0.0090.0000.0000.0000.000
128A137LEU00.0290.01334.783-0.006-0.0060.0000.0000.0000.000
129A138TYR0-0.045-0.01334.622-0.008-0.0080.0000.0000.0000.000
130A139TYR0-0.012-0.00432.706-0.010-0.0100.0000.0000.0000.000
131A140SER00.020-0.00335.403-0.003-0.0030.0000.0000.0000.000
132A141GLY0-0.023-0.01238.615-0.003-0.0030.0000.0000.0000.000
133A142HIS0-0.062-0.02635.197-0.001-0.0010.0000.0000.0000.000
134A143VAL0-0.026-0.00836.544-0.007-0.0070.0000.0000.0000.000
135A144GLY0-0.0190.00539.073-0.002-0.0020.0000.0000.0000.000
136A145GLU-1-0.918-0.95637.7490.0030.0030.0000.0000.0000.000
137A146LYS10.8380.91041.651-0.004-0.0040.0000.0000.0000.000
138A147ILE00.0750.03542.6350.0030.0030.0000.0000.0000.000
139A148TYR0-0.002-0.00943.1540.0060.0060.0000.0000.0000.000
140A149ASP-1-0.769-0.87945.7630.0090.0090.0000.0000.0000.000
141A150PRO0-0.0170.00647.4000.0030.0030.0000.0000.0000.000
142A151ALA0-0.037-0.01049.8600.0020.0020.0000.0000.0000.000
143A152ILE0-0.033-0.02143.837-0.003-0.0030.0000.0000.0000.000
144A153ALA00.0290.03844.8730.0020.0020.0000.0000.0000.000
145A154PRO0-0.038-0.01640.220-0.002-0.0020.0000.0000.0000.000
146A155ARG10.8200.88237.080-0.023-0.0230.0000.0000.0000.000
147A156GLU-1-0.914-0.95938.0350.0780.0780.0000.0000.0000.000
148A157HIS0-0.061-0.02336.2830.0110.0110.0000.0000.0000.000
149A158MET0-0.0300.01034.024-0.003-0.0030.0000.0000.0000.000
150A159THR00.0650.02832.9570.0050.0050.0000.0000.0000.000
151A160ARG10.9480.98824.7390.0090.0090.0000.0000.0000.000
152A161GLU-1-0.949-0.96930.627-0.027-0.0270.0000.0000.0000.000
153A162GLN00.0500.03333.2970.0000.0000.0000.0000.0000.000
154A163TYR0-0.001-0.01128.6610.0010.0010.0000.0000.0000.000
155A164ARG10.9290.94027.8010.0430.0430.0000.0000.0000.000
156A165HIS0-0.021-0.02431.972-0.004-0.0040.0000.0000.0000.000
157A166GLN00.0170.02335.2810.0010.0010.0000.0000.0000.000
158A167PRO00.0040.00737.3370.0060.0060.0000.0000.0000.000
159A168GLY0-0.0030.00738.8100.0020.0020.0000.0000.0000.000
160A169THR0-0.024-0.01640.232-0.001-0.0010.0000.0000.0000.000
161A170ALA00.0730.02338.8700.0050.0050.0000.0000.0000.000
162A171ILE0-0.048-0.03338.8410.0070.0070.0000.0000.0000.000
163A172ASN0-0.039-0.04439.7950.0100.0100.0000.0000.0000.000
164A173HIS00.0610.04331.8650.0070.0070.0000.0000.0000.000
165A174PHE00.003-0.02234.8010.0090.0090.0000.0000.0000.000
166A175TYR00.0190.01535.6300.0080.0080.0000.0000.0000.000
167A176GLU-1-0.791-0.88434.8400.0490.0490.0000.0000.0000.000
168A177LYS10.8900.94826.956-0.069-0.0690.0000.0000.0000.000
169A178LEU00.001-0.00230.9950.0160.0160.0000.0000.0000.000
170A179PHE00.009-0.00632.0170.0120.0120.0000.0000.0000.000
171A180LYS10.8760.93730.570-0.086-0.0860.0000.0000.0000.000
172A181LEU0-0.038-0.01126.7750.0180.0180.0000.0000.0000.000
173A182ALA00.0270.00827.3400.0210.0210.0000.0000.0000.000
174A183ALA0-0.0060.00027.8110.0190.0190.0000.0000.0000.000
175A184LEU0-0.070-0.04424.7820.0120.0120.0000.0000.0000.000
176A185MET0-0.092-0.01622.7740.0210.0210.0000.0000.0000.000
177A186ASN0-0.028-0.02418.909-0.017-0.0170.0000.0000.0000.000
178A187THR0-0.072-0.05218.6620.0400.0400.0000.0000.0000.000
179A188ASP-1-0.899-0.95720.2480.3320.3320.0000.0000.0000.000
180A189THR00.025-0.00121.217-0.053-0.0530.0000.0000.0000.000
181A190ALA0-0.013-0.01121.510-0.044-0.0440.0000.0000.0000.000
182A191LYS10.9380.97823.452-0.388-0.3880.0000.0000.0000.000
183A192ALA00.0120.02026.128-0.031-0.0310.0000.0000.0000.000
184A193LEU0-0.068-0.03524.298-0.028-0.0280.0000.0000.0000.000
185A194ALA0-0.013-0.02727.253-0.027-0.0270.0000.0000.0000.000
186A195ALA00.0430.03428.960-0.020-0.0200.0000.0000.0000.000
187A196HIS00.0440.01732.128-0.015-0.0150.0000.0000.0000.000
188A197ARG10.8560.93126.011-0.180-0.1800.0000.0000.0000.000
189A198THR00.0400.01331.534-0.011-0.0110.0000.0000.0000.000
190A199ALA00.0350.02933.981-0.009-0.0090.0000.0000.0000.000
191A200VAL00.0170.00335.522-0.008-0.0080.0000.0000.0000.000
192A201MET0-0.0940.00332.926-0.005-0.0050.0000.0000.0000.000
193A202HIS00.0240.01136.777-0.003-0.0030.0000.0000.0000.000
194A203GLU-1-0.910-0.93839.9740.0860.0860.0000.0000.0000.000
195A204PHE0-0.044-0.03139.825-0.007-0.0070.0000.0000.0000.000
196A205VAL0-0.015-0.02240.129-0.006-0.0060.0000.0000.0000.000
197A206ASP-1-0.927-0.96042.8790.0700.0700.0000.0000.0000.000
198A207GLN00.013-0.01045.487-0.003-0.0030.0000.0000.0000.000
199A208PHE00.0360.04144.851-0.005-0.0050.0000.0000.0000.000
200A209LYS10.9350.96044.613-0.056-0.0560.0000.0000.0000.000
201A210ALA0-0.024-0.00148.710-0.002-0.0020.0000.0000.0000.000
202A211GLU-1-0.926-0.99248.7540.0330.0330.0000.0000.0000.000
203A212TRP0-0.084-0.03748.772-0.003-0.0030.0000.0000.0000.000
204A213THR0-0.012-0.00651.992-0.002-0.0020.0000.0000.0000.000
205A214ALA0-0.101-0.03154.773-0.001-0.0010.0000.0000.0000.000
206A215ASP-1-1.013-0.99954.6730.0200.0200.0000.0000.0000.000