FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 14KKZ

Calculation Name: 2X9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P9WPF9

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 236
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2969887.311804
FMO2-HF: Nuclear repulsion 2876733.554963
FMO2-HF: Total energy -93153.756841
FMO2-MP2: Total energy -93422.863051


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:49:DPN)


Summations of interaction energy for fragment #1(A:49:DPN)
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.
-5.829-1.9620.359-1.524-2.703-0.006
Interaction energy analysis for fragmet #1(A:49:DPN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.014
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].
3A51LEU00.0560.0412.847-4.324-1.0910.331-1.417-2.147-0.006
4A52GLY0-0.004-0.0094.6570.3090.482-0.001-0.009-0.1640.000
5A53ARG10.9050.9366.0790.3140.3140.0000.0000.0000.000
6A54ARG10.8860.9327.668-0.006-0.0060.0000.0000.0000.000
7A55ILE00.0100.0153.137-0.4400.0210.029-0.098-0.3920.000
8A56PRO00.0080.0227.7610.0600.0600.0000.0000.0000.000
9A57GLU-1-0.921-0.9589.5570.9330.9330.0000.0000.0000.000
10A58ALA0-0.044-0.03311.341-0.056-0.0560.0000.0000.0000.000
11A59THR0-0.021-0.00413.807-0.045-0.0450.0000.0000.0000.000
12A60ALA00.0290.01817.5790.0050.0050.0000.0000.0000.000
13A61GLN00.0360.01820.361-0.012-0.0120.0000.0000.0000.000
14A62GLU-1-0.844-0.93022.5210.1680.1680.0000.0000.0000.000
15A63GLY00.0010.00923.824-0.011-0.0110.0000.0000.0000.000
16A64PHE0-0.079-0.04318.835-0.003-0.0030.0000.0000.0000.000
17A65LEU00.0010.01315.1580.0080.0080.0000.0000.0000.000
18A66VAL0-0.0020.00615.4790.0350.0350.0000.0000.0000.000
19A67ARG10.8550.9056.030-2.068-2.0680.0000.0000.0000.000
20A68PRO00.0290.02011.7220.0430.0430.0000.0000.0000.000
21A69PHE00.007-0.0026.3500.2210.2210.0000.0000.0000.000
22A70THR0-0.056-0.1199.397-0.027-0.0270.0000.0000.0000.000
23A71GLN00.0740.01811.6320.0510.0510.0000.0000.0000.000
24A72GLN00.0380.03213.815-0.028-0.0280.0000.0000.0000.000
25A73CYM-1-0.778-0.75713.9430.1280.1280.0000.0000.0000.000
26A74GLN0-0.005-0.00414.8450.0330.0330.0000.0000.0000.000
27A75ILE0-0.032-0.00616.853-0.008-0.0080.0000.0000.0000.000
28A76ILE00.0180.00918.8710.0010.0010.0000.0000.0000.000
29A77HIS0-0.082-0.05518.2340.0180.0180.0000.0000.0000.000
30A78THR0-0.068-0.03820.3280.0030.0030.0000.0000.0000.000
31A79GLU-1-0.962-0.97522.9510.0530.0530.0000.0000.0000.000
32A80GLY00.0280.03024.225-0.006-0.0060.0000.0000.0000.000
33A81ASP-1-0.841-0.88525.8220.0460.0460.0000.0000.0000.000
34A82HIS0-0.018-0.03425.064-0.002-0.0020.0000.0000.0000.000
35A83ALA00.0350.02821.7910.0090.0090.0000.0000.0000.000
36A84VAL00.0000.01620.918-0.009-0.0090.0000.0000.0000.000
37A85ILE00.0100.00320.4230.0180.0180.0000.0000.0000.000
38A86GLY00.0520.03419.685-0.015-0.0150.0000.0000.0000.000
39A87VAL0-0.041-0.04020.5680.0130.0130.0000.0000.0000.000
40A88SER00.0660.04020.282-0.007-0.0070.0000.0000.0000.000
41A89PRO00.0220.00922.6990.0070.0070.0000.0000.0000.000
42A90GLY0-0.038-0.02824.907-0.005-0.0050.0000.0000.0000.000
43A91ASN0-0.0310.00218.8750.0060.0060.0000.0000.0000.000
44A92SER0-0.010-0.01623.1370.0050.0050.0000.0000.0000.000
45A93TYR00.0450.02918.3320.0020.0020.0000.0000.0000.000
46A94PHE00.0750.04219.5470.0060.0060.0000.0000.0000.000
47A95SER00.0010.00424.291-0.013-0.0130.0000.0000.0000.000
48A96ARG10.8380.87627.438-0.054-0.0540.0000.0000.0000.000
49A97GLN0-0.017-0.00828.296-0.007-0.0070.0000.0000.0000.000
50A98ARG10.9000.96721.585-0.140-0.1400.0000.0000.0000.000
51A99LEU00.008-0.00724.8800.0070.0070.0000.0000.0000.000
52A100ARG10.8730.91526.653-0.068-0.0680.0000.0000.0000.000
53A101ASP-1-0.798-0.88824.9290.1220.1220.0000.0000.0000.000
54A102LEU0-0.002-0.00820.3140.0040.0040.0000.0000.0000.000
55A103GLY00.0240.01624.3310.0000.0000.0000.0000.0000.000
56A104LEU0-0.028-0.01227.601-0.003-0.0030.0000.0000.0000.000
57A105TRP00.0040.00419.444-0.004-0.0040.0000.0000.0000.000
58A106GLY00.0490.01824.6900.0010.0010.0000.0000.0000.000
59A107LEU0-0.016-0.02125.538-0.004-0.0040.0000.0000.0000.000
60A108THR0-0.063-0.03027.200-0.009-0.0090.0000.0000.0000.000
61A109ASN0-0.085-0.04823.8350.0070.0070.0000.0000.0000.000
62A110PHE00.0030.00520.8040.0050.0050.0000.0000.0000.000
63A111ASP-1-0.871-0.90526.8560.0570.0570.0000.0000.0000.000
64A112ARG10.7920.88728.902-0.038-0.0380.0000.0000.0000.000
65A113VAL0-0.001-0.00225.1770.0070.0070.0000.0000.0000.000
66A114ASP-1-0.747-0.84925.9250.0290.0290.0000.0000.0000.000
67A115PHE0-0.006-0.00724.4620.0040.0040.0000.0000.0000.000
68A116VAL00.0110.00223.667-0.008-0.0080.0000.0000.0000.000
69A117TYR0-0.0200.00223.7630.0020.0020.0000.0000.0000.000
70A118THR0-0.018-0.03621.863-0.002-0.0020.0000.0000.0000.000
71A119ASP-1-0.845-0.91924.960-0.003-0.0030.0000.0000.0000.000
72A120VAL00.0210.00925.956-0.001-0.0010.0000.0000.0000.000
73A121HIS00.0870.04824.951-0.001-0.0010.0000.0000.0000.000
74A122VAL00.0010.02125.741-0.002-0.0020.0000.0000.0000.000
75A123ALA0-0.045-0.02827.1930.0000.0000.0000.0000.0000.000
76A124GLU-1-0.791-0.90528.003-0.034-0.0340.0000.0000.0000.000
77A125SER00.011-0.01224.133-0.007-0.0070.0000.0000.0000.000
78A126TYR0-0.090-0.03525.3610.0010.0010.0000.0000.0000.000
79A127GLU-1-0.852-0.94828.182-0.035-0.0350.0000.0000.0000.000
80A128ALA0-0.0180.00525.782-0.002-0.0020.0000.0000.0000.000
81A129LEU0-0.052-0.02622.668-0.006-0.0060.0000.0000.0000.000
82A130GLY0-0.0020.01026.7800.0010.0010.0000.0000.0000.000
83A131ASP-1-0.850-0.89330.531-0.018-0.0180.0000.0000.0000.000
84A132SER00.0520.02132.682-0.002-0.0020.0000.0000.0000.000
85A133ALA00.0490.03035.0490.0030.0030.0000.0000.0000.000
86A134ILE0-0.062-0.04336.0480.0020.0020.0000.0000.0000.000
87A135GLU-1-0.752-0.84034.751-0.006-0.0060.0000.0000.0000.000
88A136ALA00.0230.01831.7030.0030.0030.0000.0000.0000.000
89A137ARG11.0121.00232.4340.0170.0170.0000.0000.0000.000
90A138ARG10.7980.86934.6790.0070.0070.0000.0000.0000.000
91A139LYS10.7770.86130.4550.0200.0200.0000.0000.0000.000
92A140ALA00.0590.03630.2340.0040.0040.0000.0000.0000.000
93A141VAL00.003-0.00231.2370.0040.0040.0000.0000.0000.000
94A142LYS10.8900.94732.237-0.005-0.0050.0000.0000.0000.000
95A143ASN0-0.005-0.01328.2130.0070.0070.0000.0000.0000.000
96A144ILE00.0310.02429.2220.0060.0060.0000.0000.0000.000
97A145ARG10.9140.95530.838-0.002-0.0020.0000.0000.0000.000
98A146GLY00.0130.00832.1190.0030.0030.0000.0000.0000.000
99A147VAL0-0.005-0.00826.0830.0040.0040.0000.0000.0000.000
100A148ARG10.9910.99429.485-0.006-0.0060.0000.0000.0000.000
101A149ALA00.0040.01631.9070.0020.0020.0000.0000.0000.000
102A150LYS10.8450.92527.480-0.047-0.0470.0000.0000.0000.000
103A151ILE00.0350.03526.8860.0040.0040.0000.0000.0000.000
104A152THR0-0.001-0.01230.4470.0010.0010.0000.0000.0000.000
105A153THR0-0.065-0.04033.939-0.001-0.0010.0000.0000.0000.000
106A154THR0-0.018-0.03029.6510.0020.0020.0000.0000.0000.000
107A155VAL00.0360.02031.1900.0030.0030.0000.0000.0000.000
108A156ASN00.0160.00433.4340.0000.0000.0000.0000.0000.000
109A157GLU-1-0.832-0.86534.6830.0560.0560.0000.0000.0000.000
110A158LEU0-0.060-0.02730.6840.0040.0040.0000.0000.0000.000
111A159ASP-1-0.738-0.86434.4150.0470.0470.0000.0000.0000.000
112A160PRO0-0.040-0.02536.233-0.003-0.0030.0000.0000.0000.000
113A161ALA0-0.044-0.01538.976-0.003-0.0030.0000.0000.0000.000
114A162GLY0-0.0220.00735.950-0.002-0.0020.0000.0000.0000.000
115A163ALA0-0.045-0.01936.359-0.002-0.0020.0000.0000.0000.000
116A164ARG10.7570.85430.479-0.070-0.0700.0000.0000.0000.000
117A165LEU0-0.027-0.00428.7480.0030.0030.0000.0000.0000.000
118A166CYS0-0.016-0.00830.238-0.007-0.0070.0000.0000.0000.000
119A167VAL0-0.038-0.03129.0750.0050.0050.0000.0000.0000.000
120A168ARG10.8000.90028.852-0.025-0.0250.0000.0000.0000.000
121A169PRO0-0.052-0.02128.5010.0030.0030.0000.0000.0000.000
122A170MET00.0460.02322.423-0.001-0.0010.0000.0000.0000.000
123A171SER0-0.088-0.07927.316-0.003-0.0030.0000.0000.0000.000
124A172GLU-1-0.827-0.90130.5890.0080.0080.0000.0000.0000.000
125A173PHE00.0630.02326.911-0.001-0.0010.0000.0000.0000.000
126A174GLN0-0.0210.00230.264-0.006-0.0060.0000.0000.0000.000
127A175SER0-0.081-0.03931.850-0.002-0.0020.0000.0000.0000.000
128A176ASN0-0.024-0.01430.692-0.003-0.0030.0000.0000.0000.000
129A177GLU-1-0.906-0.95531.869-0.023-0.0230.0000.0000.0000.000
130A178ALA00.1060.05328.926-0.004-0.0040.0000.0000.0000.000
131A179TYR0-0.053-0.05425.182-0.006-0.0060.0000.0000.0000.000
132A180ARG10.8630.91727.6480.0180.0180.0000.0000.0000.000
133A181GLU-1-0.925-0.95329.629-0.039-0.0390.0000.0000.0000.000
134A182LEU0-0.007-0.00623.595-0.008-0.0080.0000.0000.0000.000
135A183HIS00.006-0.00224.818-0.009-0.0090.0000.0000.0000.000
136A184ALA0-0.016-0.00626.041-0.006-0.0060.0000.0000.0000.000
137A185ASP-1-0.819-0.86024.223-0.098-0.0980.0000.0000.0000.000
138A186LEU00.0220.01420.000-0.010-0.0100.0000.0000.0000.000
139A187LEU00.003-0.01323.503-0.010-0.0100.0000.0000.0000.000
140A188THR0-0.055-0.02425.791-0.001-0.0010.0000.0000.0000.000
141A189ARG10.8080.86522.2680.1060.1060.0000.0000.0000.000
142A190LEU00.002-0.00319.755-0.008-0.0080.0000.0000.0000.000
143A191LYS10.8120.90923.5660.0780.0780.0000.0000.0000.000
144A192ASP-1-0.868-0.94127.137-0.087-0.0870.0000.0000.0000.000
145A193ASP-1-0.872-0.92222.086-0.170-0.1700.0000.0000.0000.000
146A194GLU-1-0.889-0.95922.675-0.136-0.1360.0000.0000.0000.000
147A195ASP-1-0.889-0.92819.410-0.199-0.1990.0000.0000.0000.000
148A196MET0-0.043-0.02517.995-0.025-0.0250.0000.0000.0000.000
149A197ARG10.8790.93617.9680.1150.1150.0000.0000.0000.000
150A198ALA0-0.0060.00418.619-0.009-0.0090.0000.0000.0000.000
151A199VAL0-0.005-0.00712.635-0.023-0.0230.0000.0000.0000.000
152A200CYS0-0.044-0.02114.028-0.036-0.0360.0000.0000.0000.000
153A201GLN0-0.007-0.02115.4500.0020.0020.0000.0000.0000.000
154A202ASP-1-0.821-0.87912.507-0.404-0.4040.0000.0000.0000.000
155A203LEU00.0230.0139.057-0.034-0.0340.0000.0000.0000.000
156A204VAL00.0030.00411.8430.0040.0040.0000.0000.0000.000
157A205ARG10.8150.87814.6320.2360.2360.0000.0000.0000.000
158A206ARG10.7820.8658.8430.4760.4760.0000.0000.0000.000
159A207PHE00.0850.05011.2280.0340.0340.0000.0000.0000.000
160A208LEU00.0400.02112.1160.0440.0440.0000.0000.0000.000
161A209SER0-0.093-0.03812.2530.0200.0200.0000.0000.0000.000
162A210THR0-0.055-0.04010.3370.0290.0290.0000.0000.0000.000
163A211LYS10.8040.91913.0840.1000.1000.0000.0000.0000.000
164A212VAL00.019-0.00317.077-0.010-0.0100.0000.0000.0000.000
165A213GLY00.0220.00220.1910.0130.0130.0000.0000.0000.000
166A214PRO0-0.0110.00821.327-0.005-0.0050.0000.0000.0000.000
167A215ARG10.9120.95313.9160.1850.1850.0000.0000.0000.000
168A216GLN0-0.017-0.01720.258-0.005-0.0050.0000.0000.0000.000
169A217GLY0-0.033-0.00620.078-0.001-0.0010.0000.0000.0000.000
170A218ALA00.0160.00719.5920.0130.0130.0000.0000.0000.000
171A219THR00.0160.00121.348-0.003-0.0030.0000.0000.0000.000
172A220ALA00.0630.02123.100-0.005-0.0050.0000.0000.0000.000
173A221THR00.0180.00724.518-0.003-0.0030.0000.0000.0000.000
174A222GLN00.005-0.00821.811-0.006-0.0060.0000.0000.0000.000
175A223GLU-1-0.802-0.86819.111-0.180-0.1800.0000.0000.0000.000
176A224GLN0-0.055-0.02720.872-0.010-0.0100.0000.0000.0000.000
177A225VAL00.0400.01523.2460.0020.0020.0000.0000.0000.000
178A226CYS0-0.057-0.02617.6270.0020.0020.0000.0000.0000.000
179A227MET00.0130.01917.492-0.002-0.0020.0000.0000.0000.000
180A228ASP-1-0.827-0.89520.328-0.077-0.0770.0000.0000.0000.000
181A229TYR0-0.103-0.08318.8830.0100.0100.0000.0000.0000.000
182A230ILE0-0.003-0.01115.1390.0080.0080.0000.0000.0000.000
183A231CYS0-0.074-0.04019.0380.0030.0030.0000.0000.0000.000
184A232ALA00.0240.01921.5970.0070.0070.0000.0000.0000.000
185A233GLU-1-0.794-0.86318.400-0.001-0.0010.0000.0000.0000.000
186A234ALA0-0.008-0.00118.6210.0090.0090.0000.0000.0000.000
187A235PRO00.0340.01619.6220.0030.0030.0000.0000.0000.000
188A236LEU00.0490.02521.1850.0030.0030.0000.0000.0000.000
189A237PHE0-0.047-0.00615.1080.0160.0160.0000.0000.0000.000
190A238LEU0-0.0230.00817.486-0.010-0.0100.0000.0000.0000.000
191A239ASP-1-0.778-0.90720.037-0.016-0.0160.0000.0000.0000.000
192A240THR00.0270.01521.7910.0000.0000.0000.0000.0000.000
193A241PRO0-0.053-0.01423.3620.0010.0010.0000.0000.0000.000
194A242ALA00.0100.00526.4790.0010.0010.0000.0000.0000.000
195A243ILE0-0.072-0.01924.7100.0000.0000.0000.0000.0000.000
196A244LEU0-0.037-0.02726.4690.0010.0010.0000.0000.0000.000
197A245GLY0-0.0040.02629.5560.0030.0030.0000.0000.0000.000
198A246VAL0-0.061-0.02226.5870.0030.0030.0000.0000.0000.000
199A247PRO00.0150.01028.196-0.005-0.0050.0000.0000.0000.000
200A248SER0-0.042-0.04923.392-0.003-0.0030.0000.0000.0000.000
201A249SER0-0.004-0.02422.5220.0030.0030.0000.0000.0000.000
202A250LEU00.0220.01516.310-0.003-0.0030.0000.0000.0000.000
203A251ASN0-0.034-0.02316.9930.0170.0170.0000.0000.0000.000
204A252CYS0-0.0050.01215.9340.0410.0410.0000.0000.0000.000
205A253TYR0-0.002-0.03114.201-0.036-0.0360.0000.0000.0000.000
206A254HIS0-0.0050.01814.2560.0620.0620.0000.0000.0000.000
207A255GLN0-0.025-0.02010.864-0.007-0.0070.0000.0000.0000.000
208A256SER00.0360.0207.2730.0250.0250.0000.0000.0000.000
209A257LEU0-0.0020.0099.436-0.104-0.1040.0000.0000.0000.000
210A258PRO0-0.013-0.0159.841-0.052-0.0520.0000.0000.0000.000
211A259LEU00.0890.03610.104-0.091-0.0910.0000.0000.0000.000
212A260ALA0-0.0110.0048.763-0.012-0.0120.0000.0000.0000.000
213A261GLU-1-0.964-0.9905.671-1.589-1.5890.0000.0000.0000.000
214A262MET0-0.0180.0008.5680.0110.0110.0000.0000.0000.000
215A263LEU0-0.017-0.01612.3070.0290.0290.0000.0000.0000.000
216A264TYR00.009-0.01611.2090.0500.0500.0000.0000.0000.000
217A265ALA00.0030.02810.942-0.005-0.0050.0000.0000.0000.000
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