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: ZVQ6N

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 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 368
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6300877.010191
FMO2-HF: Nuclear repulsion 6152977.301673
FMO2-HF: Total energy -147899.708518
FMO2-MP2: Total energy -148332.718564


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.
-14.498-3.28410.747-5.958-15.999-0.036
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 : -0.004 / q_NPA : -0.007
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-9THR0-0.003-0.0102.883-2.876-0.6760.324-1.155-1.368-0.004
4A-8THR00.0390.0155.0930.2290.341-0.001-0.003-0.1080.000
5A-7GLU-1-0.836-0.8856.842-0.238-0.2380.0000.0000.0000.000
6A-6ASN0-0.013-0.0199.1580.0160.0160.0000.0000.0000.000
7A-5LEU00.0400.0089.7530.0750.0750.0000.0000.0000.000
8A-4TYR0-0.0470.01711.9290.0430.0430.0000.0000.0000.000
9A-3PHE0-0.028-0.02613.3840.0450.0450.0000.0000.0000.000
10A-2GLN0-0.027-0.01916.1500.0030.0030.0000.0000.0000.000
11A-1GLY00.0560.04217.0030.0050.0050.0000.0000.0000.000
12A0SER0-0.001-0.00617.6110.0180.0180.0000.0000.0000.000
13A1MET0-0.0070.00119.7900.0020.0020.0000.0000.0000.000
14A2ARG10.8600.93615.3220.1820.1820.0000.0000.0000.000
15A3ARG10.9020.94522.2060.0780.0780.0000.0000.0000.000
16A4SER00.0410.00123.172-0.006-0.0060.0000.0000.0000.000
17A5VAL0-0.0090.00622.4530.0060.0060.0000.0000.0000.000
18A6TYR0-0.021-0.00824.335-0.006-0.0060.0000.0000.0000.000
19A7LEU00.0540.02422.9020.0040.0040.0000.0000.0000.000
20A8ASP-1-0.881-0.93426.437-0.035-0.0350.0000.0000.0000.000
21A9ASN0-0.052-0.01826.237-0.001-0.0010.0000.0000.0000.000
22A10THR0-0.014-0.00621.1870.0000.0000.0000.0000.0000.000
23A11ILE0-0.0160.00620.0540.0010.0010.0000.0000.0000.000
24A12GLU-1-0.806-0.89319.864-0.109-0.1090.0000.0000.0000.000
25A13PHE00.001-0.01814.6680.0000.0000.0000.0000.0000.000
26A14LEU0-0.016-0.01514.045-0.008-0.0080.0000.0000.0000.000
27A15ARG10.8640.94617.0930.1160.1160.0000.0000.0000.000
28A16GLY0-0.003-0.00919.460-0.008-0.0080.0000.0000.0000.000
29A17ARG10.6930.81913.0230.1960.1960.0000.0000.0000.000
30A18VAL00.0310.02212.073-0.010-0.0100.0000.0000.0000.000
31A19TYR0-0.011-0.03015.0680.0080.0080.0000.0000.0000.000
32A20LEU00.0050.01115.752-0.007-0.0070.0000.0000.0000.000
33A21GLY00.0290.00918.0020.0040.0040.0000.0000.0000.000
34A22ALA0-0.055-0.02620.4490.0010.0010.0000.0000.0000.000
35A23TYR00.001-0.02920.9970.0000.0000.0000.0000.0000.000
36A24ASP-1-0.885-0.92824.085-0.002-0.0020.0000.0000.0000.000
37A25TYR0-0.053-0.03425.7870.0040.0040.0000.0000.0000.000
38A26THR0-0.001-0.00522.016-0.004-0.0040.0000.0000.0000.000
39A27PRO0-0.0250.00621.4340.0010.0010.0000.0000.0000.000
40A28GLU-1-0.962-0.98223.0930.0120.0120.0000.0000.0000.000
41A29ASP-1-0.827-0.92719.493-0.015-0.0150.0000.0000.0000.000
42A30THR0-0.037-0.04122.3510.0030.0030.0000.0000.0000.000
43A31ASP-1-0.902-0.95522.465-0.012-0.0120.0000.0000.0000.000
44A32GLU-1-0.929-0.94222.591-0.039-0.0390.0000.0000.0000.000
45A33LEU0-0.073-0.02620.009-0.015-0.0150.0000.0000.0000.000
46A34VAL00.0270.02415.2330.0070.0070.0000.0000.0000.000
47A35PHE0-0.017-0.01416.806-0.021-0.0210.0000.0000.0000.000
48A36PHE0-0.008-0.00610.2630.0110.0110.0000.0000.0000.000
49A37THR00.017-0.01315.325-0.017-0.0170.0000.0000.0000.000
50A38VAL00.0350.00310.6250.0090.0090.0000.0000.0000.000
51A39GLU-1-0.786-0.87814.0640.0150.0150.0000.0000.0000.000
52A40ASP-1-0.898-0.94516.3150.0960.0960.0000.0000.0000.000
53A41ALA0-0.022-0.01413.6220.0180.0180.0000.0000.0000.000
54A42ILE0-0.062-0.0309.3690.0310.0310.0000.0000.0000.000
55A43PHE0-0.0200.00113.610-0.020-0.0200.0000.0000.0000.000
56A44TYR0-0.036-0.03215.908-0.001-0.0010.0000.0000.0000.000
57A45ASN0-0.038-0.02317.1850.0120.0120.0000.0000.0000.000
58A46SER0-0.038-0.00419.987-0.003-0.0030.0000.0000.0000.000
59A47PHE0-0.002-0.00920.9370.0050.0050.0000.0000.0000.000
60A48HIS0-0.050-0.02525.2790.0030.0030.0000.0000.0000.000
61A49LEU0-0.010-0.00727.1550.0010.0010.0000.0000.0000.000
62A50ASP-1-0.778-0.85722.342-0.003-0.0030.0000.0000.0000.000
63A51PHE0-0.008-0.03520.8650.0060.0060.0000.0000.0000.000
64A52GLY00.0750.05817.5680.0020.0020.0000.0000.0000.000
65A53PRO0-0.060-0.02714.5320.0010.0010.0000.0000.0000.000
66A54MET00.009-0.00211.8180.0070.0070.0000.0000.0000.000
67A55ASN0-0.0160.00011.153-0.018-0.0180.0000.0000.0000.000
68A56ILE00.008-0.0016.987-0.002-0.0020.0000.0000.0000.000
69A57GLY00.0360.0156.493-0.046-0.0460.0000.0000.0000.000
70A58HIS00.0350.0117.3310.0010.0010.0000.0000.0000.000
71A59LEU00.0130.0024.336-0.0670.007-0.001-0.007-0.0660.000
72A60TYR00.0180.0082.484-5.285-2.5374.412-1.700-5.460-0.017
73A61ARG10.8460.8933.480-0.972-0.2740.026-0.214-0.510-0.002
74A62PHE00.008-0.0016.1440.0530.0530.0000.0000.0000.000
75A63ALA00.001-0.0062.574-0.682-0.2141.318-0.425-1.360-0.001
76A64VAL0-0.030-0.0092.238-2.404-0.6141.945-1.292-2.443-0.008
77A65ILE00.0510.0353.949-0.224-0.0780.007-0.037-0.1160.000
78A66PHE0-0.010-0.0066.203-0.030-0.0300.0000.0000.0000.000
79A67HIS00.009-0.0032.547-0.7940.0522.171-0.648-2.368-0.004
80A68GLU-1-0.949-0.9745.3350.8750.917-0.001-0.001-0.0390.000
81A69ILE0-0.0020.0027.8960.0010.0010.0000.0000.0000.000
82A70LEU0-0.049-0.0207.3060.0150.0150.0000.0000.0000.000
83A71ASN0-0.022-0.0226.704-0.043-0.0430.0000.0000.0000.000
84A72ASP-1-0.877-0.91810.4360.0640.0640.0000.0000.0000.000
85A73PRO0-0.038-0.02213.350-0.028-0.0280.0000.0000.0000.000
86A74GLU-1-0.934-0.96316.5880.0060.0060.0000.0000.0000.000
87A75ASN00.016-0.00713.5210.0000.0000.0000.0000.0000.000
88A76ALA0-0.0130.01115.659-0.025-0.0250.0000.0000.0000.000
89A77ASN0-0.117-0.07816.679-0.028-0.0280.0000.0000.0000.000
90A78LYS10.8800.97917.3500.0270.0270.0000.0000.0000.000
91A79ALA0-0.049-0.02016.940-0.024-0.0240.0000.0000.0000.000
92A80VAL00.0150.00511.8700.0130.0130.0000.0000.0000.000
93A81VAL0-0.042-0.02415.179-0.016-0.0160.0000.0000.0000.000
94A82PHE00.0050.02112.9590.0120.0120.0000.0000.0000.000
95A83TYR0-0.009-0.01614.9420.0020.0020.0000.0000.0000.000
96A84SER0-0.0020.00017.3400.0040.0040.0000.0000.0000.000
97A85SER00.005-0.01019.747-0.003-0.0030.0000.0000.0000.000
98A86ALA00.001-0.00822.990-0.007-0.0070.0000.0000.0000.000
99A87SER0-0.023-0.01123.888-0.003-0.0030.0000.0000.0000.000
100A88THR00.0380.00323.724-0.002-0.0020.0000.0000.0000.000
101A89ARG10.9130.97322.6800.0090.0090.0000.0000.0000.000
102A90GLN00.0260.01419.514-0.010-0.0100.0000.0000.0000.000
103A91ARG10.9020.96218.7020.0340.0340.0000.0000.0000.000
104A92ALA0-0.020-0.00718.952-0.010-0.0100.0000.0000.0000.000
105A93ASN0-0.014-0.03616.031-0.016-0.0160.0000.0000.0000.000
106A94ALA00.0260.02314.481-0.011-0.0110.0000.0000.0000.000
107A95ALA00.0340.01714.001-0.020-0.0200.0000.0000.0000.000
108A96CYS0-0.011-0.00714.023-0.017-0.0170.0000.0000.0000.000
109A97MET0-0.0080.0249.279-0.011-0.0110.0000.0000.0000.000
110A98LEU00.0480.0339.673-0.029-0.0290.0000.0000.0000.000
111A99CYS0-0.046-0.02810.618-0.031-0.0310.0000.0000.0000.000
112A100CYS0-0.035-0.0299.959-0.019-0.0190.0000.0000.0000.000
113A101TYR00.029-0.0104.219-0.0740.098-0.001-0.015-0.1560.000
114A102MET00.0030.0097.055-0.083-0.0830.0000.0000.0000.000
115A103ILE0-0.086-0.0319.676-0.020-0.0200.0000.0000.0000.000
116A104LEU0-0.059-0.0366.535-0.021-0.0210.0000.0000.0000.000
117A105VAL0-0.041-0.0072.957-0.879-0.0670.209-0.180-0.841-0.001
118A106GLN00.0170.0115.620-0.085-0.0850.0000.0000.0000.000
119A107ALA0-0.046-0.0178.7680.0520.0520.0000.0000.0000.000
120A108TRP0-0.026-0.03011.4300.0450.0450.0000.0000.0000.000
121A109THR0-0.015-0.03913.8240.0040.0040.0000.0000.0000.000
122A110PRO00.0590.00816.4540.0000.0000.0000.0000.0000.000
123A111HIS00.0160.02117.7520.0020.0020.0000.0000.0000.000
124A112GLN0-0.0110.00816.8990.0000.0000.0000.0000.0000.000
125A113VAL00.0100.00613.1520.0040.0040.0000.0000.0000.000
126A114LEU00.0110.00616.2650.0090.0090.0000.0000.0000.000
127A115GLN0-0.031-0.00519.4480.0160.0160.0000.0000.0000.000
128A116PRO0-0.019-0.00218.0150.0090.0090.0000.0000.0000.000
129A117LEU0-0.018-0.01017.5530.0070.0070.0000.0000.0000.000
130A118ALA0-0.015-0.00521.8900.0070.0070.0000.0000.0000.000
131A119GLN0-0.064-0.04725.1410.0000.0000.0000.0000.0000.000
132A120VAL00.0030.02823.5270.0030.0030.0000.0000.0000.000
133A121ASP-1-0.900-0.94726.793-0.031-0.0310.0000.0000.0000.000
134A122PRO00.021-0.00128.8350.0000.0000.0000.0000.0000.000
135A123PRO0-0.0050.01027.120-0.003-0.0030.0000.0000.0000.000
136A124PHE00.006-0.00120.9210.0030.0030.0000.0000.0000.000
137A125MET0-0.077-0.03124.0100.0010.0010.0000.0000.0000.000
138A126PRO00.0200.01123.119-0.004-0.0040.0000.0000.0000.000
139A127PHE00.0070.00117.7860.0030.0030.0000.0000.0000.000
140A128ARG10.8360.90322.7750.0100.0100.0000.0000.0000.000
141A129ASP-1-0.798-0.88523.662-0.017-0.0170.0000.0000.0000.000
142A130ALA00.0250.00724.0030.0020.0020.0000.0000.0000.000
143A131GLY0-0.028-0.00625.8740.0030.0030.0000.0000.0000.000
144A132TYR0-0.032-0.03929.147-0.001-0.0010.0000.0000.0000.000
145A133SER0-0.037-0.00632.5290.0010.0010.0000.0000.0000.000
146A134ASN00.001-0.00432.7100.0010.0010.0000.0000.0000.000
147A135ALA00.0130.01130.2040.0000.0000.0000.0000.0000.000
148A136ASP-1-0.874-0.94831.774-0.019-0.0190.0000.0000.0000.000
149A137PHE0-0.038-0.01926.379-0.002-0.0020.0000.0000.0000.000
150A138GLU-1-0.932-0.96426.435-0.027-0.0270.0000.0000.0000.000
151A139ILE0-0.046-0.00520.334-0.003-0.0030.0000.0000.0000.000
152A140THR00.008-0.03322.4540.0000.0000.0000.0000.0000.000
153A141ILE00.0730.01617.017-0.003-0.0030.0000.0000.0000.000
154A142GLN00.0190.01418.242-0.011-0.0110.0000.0000.0000.000
155A143ASP-1-0.807-0.87219.790-0.069-0.0690.0000.0000.0000.000
156A144VAL00.0360.01214.781-0.004-0.0040.0000.0000.0000.000
157A145VAL00.0150.02314.536-0.009-0.0090.0000.0000.0000.000
158A146TYR0-0.019-0.01915.792-0.014-0.0140.0000.0000.0000.000
159A147GLY00.0080.00817.723-0.004-0.0040.0000.0000.0000.000
160A148VAL00.0250.00210.946-0.006-0.0060.0000.0000.0000.000
161A149TRP0-0.019-0.01513.435-0.005-0.0050.0000.0000.0000.000
162A150ARG10.7990.87614.9270.0830.0830.0000.0000.0000.000
163A151ALA00.0310.00314.3940.0000.0000.0000.0000.0000.000
164A152LYS10.9000.96710.3050.2520.2520.0000.0000.0000.000
165A153GLU-1-0.878-0.92313.156-0.222-0.2220.0000.0000.0000.000
166A154LYS10.8040.88716.0670.1460.1460.0000.0000.0000.000
167A155GLY00.0000.01213.9890.0110.0110.0000.0000.0000.000
168A156LEU0-0.069-0.03314.3280.0000.0000.0000.0000.0000.000
169A157ILE0-0.014-0.0088.5960.0130.0130.0000.0000.0000.000
170A158ASP-1-0.791-0.8767.840-0.629-0.6290.0000.0000.0000.000
171A159LEU0-0.010-0.0142.712-0.7850.0180.338-0.222-0.9190.001
172A160HIS0-0.043-0.0144.036-1.109-0.8060.001-0.059-0.2450.000
173A161SER0-0.079-0.0626.1610.1520.1520.0000.0000.0000.000
174A162PHE0-0.0220.0005.3530.2040.2040.0000.0000.0000.000
175A163ASN0-0.022-0.0116.593-0.121-0.1210.0000.0000.0000.000
176A164LEU00.0440.0316.4510.0020.0020.0000.0000.0000.000
177A165GLU-1-0.866-0.9328.0050.6600.6600.0000.0000.0000.000
178A166SER0-0.016-0.02311.233-0.031-0.0310.0000.0000.0000.000
179A167TYR0-0.079-0.05410.529-0.018-0.0180.0000.0000.0000.000
180A168GLU-1-0.796-0.89810.8200.1970.1970.0000.0000.0000.000
181A169LYS10.8660.96213.573-0.117-0.1170.0000.0000.0000.000
182A170TYR0-0.014-0.02416.295-0.001-0.0010.0000.0000.0000.000
183A171GLU-1-0.812-0.87214.3240.0150.0150.0000.0000.0000.000
184A172HIS0-0.045-0.01017.1990.0020.0020.0000.0000.0000.000
185A173VAL00.0350.00820.450-0.005-0.0050.0000.0000.0000.000
186A174GLU-1-0.892-0.95523.4200.0790.0790.0000.0000.0000.000
187A175PHE0-0.057-0.04620.5610.0030.0030.0000.0000.0000.000
188A176GLY00.006-0.01022.981-0.003-0.0030.0000.0000.0000.000
189A177ASP-1-0.848-0.88521.0710.0130.0130.0000.0000.0000.000
190A178PHE0-0.046-0.03519.015-0.008-0.0080.0000.0000.0000.000
191A179ASN00.0440.02014.3680.0090.0090.0000.0000.0000.000
192A180VAL0-0.037-0.02615.1710.0010.0010.0000.0000.0000.000
193A181LEU0-0.020-0.01114.847-0.011-0.0110.0000.0000.0000.000
194A182THR00.003-0.02415.475-0.012-0.0120.0000.0000.0000.000
195A183PRO00.008-0.00415.5820.0110.0110.0000.0000.0000.000
196A184ASP-1-0.788-0.87617.760-0.070-0.0700.0000.0000.0000.000
197A185PHE0-0.010-0.00519.9780.0120.0120.0000.0000.0000.000
198A186ILE0-0.013-0.00519.270-0.005-0.0050.0000.0000.0000.000
199A187ALA0-0.0070.01720.0930.0020.0020.0000.0000.0000.000
200A188PHE00.028-0.01020.8640.0030.0030.0000.0000.0000.000
201A189ALA00.0350.03423.439-0.004-0.0040.0000.0000.0000.000
202A190SER0-0.065-0.04426.0780.0000.0000.0000.0000.0000.000
203A191PRO00.0090.01228.8120.0040.0040.0000.0000.0000.000
204A192GLN0-0.003-0.01030.623-0.005-0.0050.0000.0000.0000.000
205A193GLU-1-0.777-0.88133.7810.0220.0220.0000.0000.0000.000
206A194ASP-1-0.928-0.95036.7230.0270.0270.0000.0000.0000.000
207A207LEU00.0160.01533.788-0.001-0.0010.0000.0000.0000.000
208A208ASN0-0.043-0.04631.8700.0050.0050.0000.0000.0000.000
209A209GLN0-0.017-0.02325.737-0.001-0.0010.0000.0000.0000.000
210A210PRO00.0590.04426.5160.0010.0010.0000.0000.0000.000
211A211PHE00.0170.00926.970-0.003-0.0030.0000.0000.0000.000
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