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: 6YQNZ

Calculation Name: 5XW4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XW4

Chain ID: A

ChEMBL ID:

UniProt ID: Q00684

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptHSide
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 368
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6285440.147776
FMO2-HF: Nuclear repulsion 6137540.650098
FMO2-HF: Total energy -147899.497678
FMO2-MP2: Total energy -148332.585028


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:-11:ILE)


Summations of interaction energy for fragment #1(A:-11:ILE)
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.
-14.824-4.17810.999-5.96-15.682-0.035
Interaction energy analysis for fragmet #1(A:-11:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.018
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].
3A-9THR00.0060.0002.625-3.403-0.9870.842-1.391-1.867-0.005
4A-8THR00.0180.0034.9290.2780.404-0.001-0.004-0.1200.000
5A-7GLU-1-0.855-0.8866.652-0.199-0.1990.0000.0000.0000.000
6A-6ASN0-0.002-0.0188.9090.0080.0080.0000.0000.0000.000
7A-5LEU00.0240.0009.8980.0630.0630.0000.0000.0000.000
8A-4TYR0-0.0340.01611.9790.0370.0370.0000.0000.0000.000
9A-3PHE0-0.024-0.02413.5940.0380.0380.0000.0000.0000.000
10A-2GLN0-0.012-0.00616.4140.0060.0060.0000.0000.0000.000
11A-1GLY00.0280.03117.1940.0060.0060.0000.0000.0000.000
12A0SER0-0.014-0.01717.8560.0130.0130.0000.0000.0000.000
13A1MET0-0.023-0.02020.0760.0030.0030.0000.0000.0000.000
14A2ARG10.9290.97316.3250.1120.1120.0000.0000.0000.000
15A3ARG10.9170.95522.5760.0540.0540.0000.0000.0000.000
16A4SER00.0440.01223.558-0.003-0.0030.0000.0000.0000.000
17A5VAL0-0.0180.00422.2990.0050.0050.0000.0000.0000.000
18A6TYR0-0.018-0.01724.763-0.005-0.0050.0000.0000.0000.000
19A7LEU00.0400.02223.0310.0040.0040.0000.0000.0000.000
20A8ASP-1-0.888-0.93826.522-0.022-0.0220.0000.0000.0000.000
21A9ASN0-0.052-0.03026.2750.0010.0010.0000.0000.0000.000
22A10THR0-0.008-0.00421.2650.0020.0020.0000.0000.0000.000
23A11ILE0-0.0160.00520.341-0.001-0.0010.0000.0000.0000.000
24A12GLU-1-0.796-0.88520.117-0.077-0.0770.0000.0000.0000.000
25A13PHE0-0.003-0.01715.133-0.003-0.0030.0000.0000.0000.000
26A14LEU0-0.008-0.00214.167-0.008-0.0080.0000.0000.0000.000
27A15ARG10.8880.95717.3730.0930.0930.0000.0000.0000.000
28A16GLY0-0.016-0.01619.728-0.007-0.0070.0000.0000.0000.000
29A17ARG10.7040.81313.0100.1260.1260.0000.0000.0000.000
30A18VAL00.0250.02312.408-0.001-0.0010.0000.0000.0000.000
31A19TYR0-0.002-0.03115.3790.0000.0000.0000.0000.0000.000
32A20LEU00.0020.00815.903-0.001-0.0010.0000.0000.0000.000
33A21GLY00.0250.01318.2600.0010.0010.0000.0000.0000.000
34A22ALA0-0.057-0.02920.3770.0010.0010.0000.0000.0000.000
35A23TYR0-0.021-0.02721.236-0.001-0.0010.0000.0000.0000.000
36A24ASP-1-0.849-0.92724.5760.0090.0090.0000.0000.0000.000
37A25TYR0-0.061-0.02826.5500.0030.0030.0000.0000.0000.000
38A26THR0-0.002-0.01022.320-0.003-0.0030.0000.0000.0000.000
39A27PRO0-0.050-0.01321.6590.0010.0010.0000.0000.0000.000
40A28GLU-1-0.950-0.96923.1080.0320.0320.0000.0000.0000.000
41A29ASP-1-0.836-0.92019.4150.0340.0340.0000.0000.0000.000
42A30THR0-0.033-0.04422.4390.0010.0010.0000.0000.0000.000
43A31ASP-1-0.901-0.95022.9880.0200.0200.0000.0000.0000.000
44A32GLU-1-0.937-0.95222.688-0.011-0.0110.0000.0000.0000.000
45A33LEU0-0.064-0.02220.102-0.012-0.0120.0000.0000.0000.000
46A34VAL00.0170.02415.5450.0060.0060.0000.0000.0000.000
47A35PHE0-0.020-0.02316.924-0.019-0.0190.0000.0000.0000.000
48A36PHE00.0070.00110.2830.0140.0140.0000.0000.0000.000
49A37THR00.008-0.01715.583-0.019-0.0190.0000.0000.0000.000
50A38VAL00.0450.01110.7510.0150.0150.0000.0000.0000.000
51A39GLU-1-0.781-0.86914.1350.0210.0210.0000.0000.0000.000
52A40ASP-1-0.938-0.96116.3700.1210.1210.0000.0000.0000.000
53A41ALA0-0.013-0.01013.8250.0170.0170.0000.0000.0000.000
54A42ILE0-0.086-0.0419.5730.0150.0150.0000.0000.0000.000
55A43PHE0-0.017-0.00113.851-0.018-0.0180.0000.0000.0000.000
56A44TYR0-0.058-0.04916.180-0.006-0.0060.0000.0000.0000.000
57A45ASN0-0.030-0.01717.4190.0090.0090.0000.0000.0000.000
58A46SER0-0.0170.00520.002-0.005-0.0050.0000.0000.0000.000
59A47PHE0-0.025-0.01720.7810.0050.0050.0000.0000.0000.000
60A48HIS0-0.031-0.03225.0910.0050.0050.0000.0000.0000.000
61A49LEU0-0.029-0.01627.4780.0020.0020.0000.0000.0000.000
62A50ASP-1-0.800-0.86622.442-0.015-0.0150.0000.0000.0000.000
63A51PHE0-0.001-0.03121.0510.0050.0050.0000.0000.0000.000
64A52GLY00.0620.05617.9420.0030.0030.0000.0000.0000.000
65A53PRO0-0.083-0.03714.9930.0010.0010.0000.0000.0000.000
66A54MET00.0160.00112.1380.0040.0040.0000.0000.0000.000
67A55ASN00.0060.01011.201-0.024-0.0240.0000.0000.0000.000
68A56ILE00.0220.0076.911-0.001-0.0010.0000.0000.0000.000
69A57GLY00.0370.0176.510-0.082-0.0820.0000.0000.0000.000
70A58HIS00.0330.0127.389-0.006-0.0060.0000.0000.0000.000
71A59LEU0-0.0010.0004.361-0.0640.017-0.001-0.006-0.0730.000
72A60TYR00.0230.0062.454-6.185-3.3404.647-1.796-5.695-0.019
73A61ARG10.8760.9193.504-0.908-0.2320.023-0.218-0.480-0.002
74A62PHE00.0090.0036.0590.1050.1050.0000.0000.0000.000
75A63ALA0-0.001-0.0022.717-0.746-0.1000.893-0.348-1.191-0.001
76A64VAL0-0.024-0.0072.228-1.741-0.3802.000-1.106-2.256-0.007
77A65ILE00.0400.0284.125-0.1140.0300.004-0.052-0.0960.000
78A66PHE0-0.018-0.0136.162-0.036-0.0360.0000.0000.0000.000
79A67HIS00.009-0.0092.499-0.6000.0012.364-0.667-2.298-0.002
80A68GLU-1-0.940-0.9675.5611.0221.0220.0000.0000.0000.000
81A69ILE0-0.0080.0018.062-0.029-0.0290.0000.0000.0000.000
82A70LEU0-0.071-0.0357.360-0.009-0.0090.0000.0000.0000.000
83A71ASN0-0.038-0.0296.642-0.079-0.0790.0000.0000.0000.000
84A72ASP-1-0.880-0.91110.4950.1270.1270.0000.0000.0000.000
85A73PRO0-0.020-0.01913.419-0.033-0.0330.0000.0000.0000.000
86A74GLU-1-0.953-0.97116.6070.0450.0450.0000.0000.0000.000
87A75ASN00.010-0.00613.985-0.012-0.0120.0000.0000.0000.000
88A76ALA0-0.0120.00416.208-0.023-0.0230.0000.0000.0000.000
89A77ASN0-0.116-0.07617.216-0.026-0.0260.0000.0000.0000.000
90A78LYS10.9050.98417.729-0.016-0.0160.0000.0000.0000.000
91A79ALA0-0.063-0.02417.451-0.018-0.0180.0000.0000.0000.000
92A80VAL00.0270.00812.1830.0120.0120.0000.0000.0000.000
93A81VAL0-0.037-0.01915.424-0.017-0.0170.0000.0000.0000.000
94A82PHE0-0.0010.00813.1730.0100.0100.0000.0000.0000.000
95A83TYR00.001-0.00415.183-0.004-0.0040.0000.0000.0000.000
96A84SER00.0010.00817.5180.0050.0050.0000.0000.0000.000
97A85SER0-0.044-0.04919.748-0.003-0.0030.0000.0000.0000.000
98A86ALA00.0250.00923.002-0.007-0.0070.0000.0000.0000.000
99A87SER0-0.021-0.00624.307-0.004-0.0040.0000.0000.0000.000
100A88THR00.0500.00224.293-0.002-0.0020.0000.0000.0000.000
101A89ARG10.9310.97323.0880.0090.0090.0000.0000.0000.000
102A90GLN00.0670.03119.670-0.008-0.0080.0000.0000.0000.000
103A91ARG10.9190.97819.2360.0240.0240.0000.0000.0000.000
104A92ALA0-0.041-0.01419.239-0.008-0.0080.0000.0000.0000.000
105A93ASN0-0.009-0.02816.326-0.018-0.0180.0000.0000.0000.000
106A94ALA00.0290.02814.874-0.011-0.0110.0000.0000.0000.000
107A95ALA00.0390.01814.331-0.015-0.0150.0000.0000.0000.000
108A96CYS0-0.014-0.00814.361-0.015-0.0150.0000.0000.0000.000
109A97MET00.0090.0289.694-0.019-0.0190.0000.0000.0000.000
110A98LEU00.0510.0369.995-0.024-0.0240.0000.0000.0000.000
111A99CYS0-0.041-0.02410.900-0.024-0.0240.0000.0000.0000.000
112A100CYS0-0.045-0.03410.016-0.018-0.0180.0000.0000.0000.000
113A101TYR00.025-0.0134.408-0.1120.031-0.001-0.010-0.1320.000
114A102MET00.0030.0097.363-0.061-0.0610.0000.0000.0000.000
115A103ILE0-0.080-0.0299.957-0.024-0.0240.0000.0000.0000.000
116A104LEU0-0.065-0.0416.747-0.027-0.0270.0000.0000.0000.000
117A105VAL0-0.040-0.0103.369-0.638-0.0630.050-0.126-0.5000.000
118A106GLN00.0190.0095.957-0.097-0.0970.0000.0000.0000.000
119A107ALA0-0.054-0.0148.9340.0360.0360.0000.0000.0000.000
120A108TRP0-0.021-0.02411.8260.0430.0430.0000.0000.0000.000
121A109THR0-0.012-0.02714.003-0.003-0.0030.0000.0000.0000.000
122A110PRO00.0540.00816.7790.0050.0050.0000.0000.0000.000
123A111HIS00.0140.01118.0970.0030.0030.0000.0000.0000.000
124A112GLN0-0.0040.01017.167-0.002-0.0020.0000.0000.0000.000
125A113VAL00.0180.00813.5310.0050.0050.0000.0000.0000.000
126A114LEU0-0.009-0.01016.7590.0090.0090.0000.0000.0000.000
127A115GLN0-0.037-0.00919.9010.0140.0140.0000.0000.0000.000
128A116PRO0-0.0100.00418.4900.0070.0070.0000.0000.0000.000
129A117LEU0-0.024-0.00717.6570.0070.0070.0000.0000.0000.000
130A118ALA0-0.023-0.00721.8310.0060.0060.0000.0000.0000.000
131A119GLN0-0.047-0.03525.0680.0010.0010.0000.0000.0000.000
132A120VAL00.0000.02023.5230.0030.0030.0000.0000.0000.000
133A121ASP-1-0.901-0.93226.864-0.025-0.0250.0000.0000.0000.000
134A122PRO0-0.009-0.02528.4160.0010.0010.0000.0000.0000.000
135A123PRO00.0250.01826.982-0.002-0.0020.0000.0000.0000.000
136A124PHE0-0.017-0.01321.2000.0030.0030.0000.0000.0000.000
137A125MET0-0.072-0.02324.4390.0010.0010.0000.0000.0000.000
138A126PRO00.0260.01423.588-0.004-0.0040.0000.0000.0000.000
139A127PHE00.0060.00018.1390.0030.0030.0000.0000.0000.000
140A128ARG10.8680.91223.1920.0170.0170.0000.0000.0000.000
141A129ASP-1-0.802-0.89723.995-0.025-0.0250.0000.0000.0000.000
142A130ALA00.0240.01723.8300.0030.0030.0000.0000.0000.000
143A131GLY0-0.027-0.00325.8950.0030.0030.0000.0000.0000.000
144A132TYR00.001-0.01229.5720.0000.0000.0000.0000.0000.000
145A133SER0-0.041-0.00832.6900.0020.0020.0000.0000.0000.000
146A134ASN0-0.022-0.01832.9330.0000.0000.0000.0000.0000.000
147A135ALA00.0120.00830.264-0.001-0.0010.0000.0000.0000.000
148A136ASP-1-0.898-0.95031.916-0.025-0.0250.0000.0000.0000.000
149A137PHE0-0.037-0.03126.422-0.002-0.0020.0000.0000.0000.000
150A138GLU-1-0.937-0.96426.744-0.031-0.0310.0000.0000.0000.000
151A139ILE0-0.044-0.00420.510-0.003-0.0030.0000.0000.0000.000
152A140THR00.004-0.04222.8350.0010.0010.0000.0000.0000.000
153A141ILE00.0840.02217.240-0.005-0.0050.0000.0000.0000.000
154A142GLN00.0090.01718.640-0.011-0.0110.0000.0000.0000.000
155A143ASP-1-0.799-0.87220.279-0.075-0.0750.0000.0000.0000.000
156A144VAL00.0290.00815.015-0.007-0.0070.0000.0000.0000.000
157A145VAL00.0120.01114.911-0.013-0.0130.0000.0000.0000.000
158A146TYR0-0.016-0.01416.014-0.015-0.0150.0000.0000.0000.000
159A147GLY00.0020.00117.972-0.006-0.0060.0000.0000.0000.000
160A148VAL00.0210.00411.225-0.010-0.0100.0000.0000.0000.000
161A149TRP0-0.015-0.00813.629-0.009-0.0090.0000.0000.0000.000
162A150ARG10.8120.88114.9690.0960.0960.0000.0000.0000.000
163A151ALA00.0330.00114.364-0.003-0.0030.0000.0000.0000.000
164A152LYS10.8750.94110.2410.2700.2700.0000.0000.0000.000
165A153GLU-1-0.895-0.93413.050-0.231-0.2310.0000.0000.0000.000
166A154LYS10.8300.91916.1550.1400.1400.0000.0000.0000.000
167A155GLY00.0010.01314.1660.0110.0110.0000.0000.0000.000
168A156LEU0-0.072-0.04214.6300.0010.0010.0000.0000.0000.000
169A157ILE0-0.028-0.0148.4500.0060.0060.0000.0000.0000.000
170A158ASP-1-0.793-0.8908.246-0.685-0.6850.0000.0000.0000.000
171A159LEU0-0.010-0.0122.874-0.834-0.0620.179-0.196-0.7540.001
172A160HIS0-0.031-0.0024.148-1.097-0.8370.000-0.040-0.2200.000
173A161SER0-0.070-0.0555.9130.0480.0480.0000.0000.0000.000
174A162PHE0-0.046-0.0045.3330.2510.2510.0000.0000.0000.000
175A163ASN00.0060.0066.630-0.111-0.1110.0000.0000.0000.000
176A164LEU00.0590.0316.2370.0130.0130.0000.0000.0000.000
177A165GLU-1-0.868-0.9378.0060.6000.6000.0000.0000.0000.000
178A166SER0-0.042-0.03711.089-0.014-0.0140.0000.0000.0000.000
179A167TYR0-0.075-0.05910.345-0.010-0.0100.0000.0000.0000.000
180A168GLU-1-0.793-0.89410.8910.1700.1700.0000.0000.0000.000
181A169LYS10.8750.96613.545-0.076-0.0760.0000.0000.0000.000
182A170TYR0-0.033-0.03716.3460.0090.0090.0000.0000.0000.000
183A171GLU-1-0.838-0.88914.702-0.029-0.0290.0000.0000.0000.000
184A172HIS0-0.061-0.02317.0760.0090.0090.0000.0000.0000.000
185A173VAL00.0390.01020.424-0.006-0.0060.0000.0000.0000.000
186A174GLU-1-0.889-0.95323.3240.0620.0620.0000.0000.0000.000
187A175PHE0-0.049-0.04920.6570.0030.0030.0000.0000.0000.000
188A176GLY00.004-0.01122.712-0.005-0.0050.0000.0000.0000.000
189A177ASP-1-0.861-0.89020.968-0.013-0.0130.0000.0000.0000.000
190A178PHE0-0.030-0.03118.815-0.007-0.0070.0000.0000.0000.000
191A179ASN00.0330.01614.4800.0090.0090.0000.0000.0000.000
192A180VAL0-0.033-0.02415.0620.0070.0070.0000.0000.0000.000
193A181LEU0-0.035-0.01214.800-0.017-0.0170.0000.0000.0000.000
194A182THR00.009-0.02815.316-0.015-0.0150.0000.0000.0000.000
195A183PRO00.017-0.00115.8750.0110.0110.0000.0000.0000.000
196A184ASP-1-0.840-0.90118.014-0.105-0.1050.0000.0000.0000.000
197A185PHE0-0.015-0.00620.0030.0160.0160.0000.0000.0000.000
198A186ILE0-0.010-0.00219.342-0.009-0.0090.0000.0000.0000.000
199A187ALA0-0.0080.01320.2310.0050.0050.0000.0000.0000.000
200A188PHE00.018-0.01521.0500.0010.0010.0000.0000.0000.000
201A189ALA00.0400.04123.514-0.002-0.0020.0000.0000.0000.000
202A190SER0-0.068-0.03826.1050.0000.0000.0000.0000.0000.000
203A191PRO0-0.0020.00028.7580.0040.0040.0000.0000.0000.000
204A192GLN0-0.010-0.00930.416-0.003-0.0030.0000.0000.0000.000
205A193GLU-1-0.749-0.86333.5100.0100.0100.0000.0000.0000.000
206A194ASP-1-0.950-0.95736.4880.0160.0160.0000.0000.0000.000
207A207LEU00.0150.01433.598-0.001-0.0010.0000.0000.0000.000
208A208ASN0-0.031-0.03531.4290.0040.0040.0000.0000.0000.000
209A209GLN00.005-0.00425.304-0.001-0.0010.0000.0000.0000.000
210A210PRO00.0590.03526.2980.0000.0000.0000.0000.0000.000
211A211PHE0-0.0010.00426.872-0.005-0.0050.0000.0000.0000.000
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