Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Z6RMN

Calculation Name: 5D6H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D6H

Chain ID: A

ChEMBL ID:

UniProt ID: Q6XBY4

Base Structure: X-ray

Registration Date: 2023-06-21

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2662042.275912
FMO2-HF: Nuclear repulsion 2573810.222089
FMO2-HF: Total energy -88232.053823
FMO2-MP2: Total energy -88493.16763


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-18.99-15.05911.598-6.96-8.564-0.061
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.003
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].
3A3PHE00.0200.0052.349-0.6490.9421.835-1.336-2.090-0.002
4A4LEU00.0000.0255.492-0.096-0.0960.0000.0000.0000.000
5A5ILE0-0.006-0.0127.4720.0440.0440.0000.0000.0000.000
6A6TRP0-0.0110.01710.7060.0030.0030.0000.0000.0000.000
7A7PRO00.0460.01714.4390.0140.0140.0000.0000.0000.000
8A8ILE00.0410.00313.051-0.019-0.0190.0000.0000.0000.000
9A9TYR0-0.010-0.01915.948-0.025-0.0250.0000.0000.0000.000
10A10PRO00.0100.02516.9820.0230.0230.0000.0000.0000.000
11A11LYS10.7740.85719.7700.0770.0770.0000.0000.0000.000
12A12ILE00.001-0.01022.7000.0060.0060.0000.0000.0000.000
13A13GLU-1-0.731-0.83525.886-0.080-0.0800.0000.0000.0000.000
14A14ALA0-0.019-0.00329.4620.0000.0000.0000.0000.0000.000
15A15ASN0-0.040-0.03232.225-0.004-0.0040.0000.0000.0000.000
16A16GLU-1-0.750-0.83026.800-0.073-0.0730.0000.0000.0000.000
17A17LYS10.9740.97428.6170.0570.0570.0000.0000.0000.000
18A18ALA0-0.023-0.01823.439-0.005-0.0050.0000.0000.0000.000
19A19THR00.0240.02720.1480.0040.0040.0000.0000.0000.000
20A20ALA0-0.016-0.00718.081-0.001-0.0010.0000.0000.0000.000
21A21VAL0-0.0060.00312.578-0.007-0.0070.0000.0000.0000.000
22A22TRP0-0.003-0.00713.2310.0000.0000.0000.0000.0000.000
23A23LEU0-0.009-0.0047.752-0.043-0.0430.0000.0000.0000.000
24A24GLN0-0.017-0.0228.8550.0080.0080.0000.0000.0000.000
25A25ASN0-0.0020.0004.4450.0570.139-0.001-0.019-0.0620.000
26A26THR0-0.012-0.0125.9620.0060.0060.0000.0000.0000.000
27A27GLY00.0360.0364.339-0.038-0.001-0.001-0.008-0.0270.000
28A28LYS10.9180.9465.379-1.019-0.983-0.0010.000-0.0340.000
29A29THR00.0280.0124.176-0.199-0.118-0.001-0.007-0.0730.000
30A30ASP-1-0.773-0.8745.5700.5770.5770.0000.0000.0000.000
31A31ALA00.0230.0232.872-0.2850.1420.204-0.163-0.4680.001
32A32MET0-0.028-0.0224.6080.1600.172-0.001-0.008-0.0030.000
33A33VAL00.0110.0095.406-0.412-0.4120.0000.0000.0000.000
34A34GLN00.0180.0127.5510.2060.2060.0000.0000.0000.000
35A35ILE0-0.043-0.01710.405-0.077-0.0770.0000.0000.0000.000
36A36ARG10.9080.94012.6650.4520.4520.0000.0000.0000.000
37A37VAL00.0260.00915.443-0.019-0.0190.0000.0000.0000.000
38A38PHE0-0.0130.01815.8230.0110.0110.0000.0000.0000.000
39A39LYS10.8220.89220.2880.1290.1290.0000.0000.0000.000
40A40TRP0-0.086-0.06021.943-0.020-0.0200.0000.0000.0000.000
41A41ASN00.0260.01723.9000.0100.0100.0000.0000.0000.000
42A42GLN00.018-0.02825.909-0.001-0.0010.0000.0000.0000.000
43A43ASP-1-0.848-0.91328.497-0.108-0.1080.0000.0000.0000.000
44A44GLY0-0.017-0.01430.297-0.007-0.0070.0000.0000.0000.000
45A45LEU0-0.072-0.03031.8810.0000.0000.0000.0000.0000.000
46A46LYS10.9810.99027.0130.1420.1420.0000.0000.0000.000
47A47ASP-1-0.821-0.88322.855-0.186-0.1860.0000.0000.0000.000
48A48ASN0-0.064-0.03524.139-0.013-0.0130.0000.0000.0000.000
49A49TYR0-0.006-0.02520.073-0.010-0.0100.0000.0000.0000.000
50A50SER0-0.015-0.00722.7540.0070.0070.0000.0000.0000.000
51A51GLU-1-0.862-0.93621.113-0.236-0.2360.0000.0000.0000.000
52A52GLN0-0.043-0.03521.9010.0260.0260.0000.0000.0000.000
53A53SER00.0250.01423.904-0.005-0.0050.0000.0000.0000.000
54A54GLU-1-0.768-0.83326.066-0.111-0.1110.0000.0000.0000.000
55A55ILE0-0.010-0.01221.5890.0100.0100.0000.0000.0000.000
56A56ILE00.0310.02421.869-0.015-0.0150.0000.0000.0000.000
57A57PRO0-0.0060.00416.4700.0140.0140.0000.0000.0000.000
58A58SER0-0.0260.00717.8670.0070.0070.0000.0000.0000.000
59A59PRO0-0.006-0.00613.6280.0140.0140.0000.0000.0000.000
60A60PRO00.0650.02014.879-0.016-0.0160.0000.0000.0000.000
61A61VAL00.004-0.00511.825-0.052-0.0520.0000.0000.0000.000
62A62ALA0-0.0040.00410.3160.0540.0540.0000.0000.0000.000
63A63LYS10.8940.9488.781-0.232-0.2320.0000.0000.0000.000
64A64ILE0-0.026-0.0086.502-0.013-0.0130.0000.0000.0000.000
65A65LYS10.8530.9096.964-0.158-0.1580.0000.0000.0000.000
66A66ALA0-0.0090.0047.5320.0140.0140.0000.0000.0000.000
67A67GLY00.0250.0228.464-0.119-0.1190.0000.0000.0000.000
68A68GLU-1-0.858-0.91810.0210.1320.1320.0000.0000.0000.000
69A69LYS10.8850.9169.621-0.052-0.0520.0000.0000.0000.000
70A70HIS00.0660.04210.532-0.031-0.0310.0000.0000.0000.000
71A71MET0-0.012-0.01912.226-0.012-0.0120.0000.0000.0000.000
72A72LEU0-0.0010.01611.333-0.003-0.0030.0000.0000.0000.000
73A73ARG10.9420.96915.1590.0770.0770.0000.0000.0000.000
74A74LEU0-0.011-0.01216.355-0.015-0.0150.0000.0000.0000.000
75A75THR00.004-0.01320.1930.0160.0160.0000.0000.0000.000
76A76LYS10.8370.92723.7450.0720.0720.0000.0000.0000.000
77A77SER0-0.045-0.02726.7530.0080.0080.0000.0000.0000.000
78A78VAL0-0.004-0.00928.7010.0070.0070.0000.0000.0000.000
79A79ASN0-0.033-0.02631.225-0.005-0.0050.0000.0000.0000.000
80A80LEU00.0280.02428.2590.0000.0000.0000.0000.0000.000
81A81PRO00.015-0.00632.7970.0050.0050.0000.0000.0000.000
82A82ASP-1-0.752-0.85235.238-0.059-0.0590.0000.0000.0000.000
83A83GLY0-0.029-0.01037.7180.0000.0000.0000.0000.0000.000
84A84LYS10.8440.91533.5980.0840.0840.0000.0000.0000.000
85A85GLU-1-0.712-0.80528.626-0.107-0.1070.0000.0000.0000.000
86A86GLN0-0.0140.00528.042-0.005-0.0050.0000.0000.0000.000
87A87SER00.0510.01724.863-0.002-0.0020.0000.0000.0000.000
88A88TYR0-0.035-0.06121.2620.0030.0030.0000.0000.0000.000
89A89ARG10.8650.94515.8030.3020.3020.0000.0000.0000.000
90A90LEU00.0110.01813.4440.0070.0070.0000.0000.0000.000
91A91ILE0-0.042-0.02711.707-0.034-0.0340.0000.0000.0000.000
92A92VAL00.009-0.0017.0070.0650.0650.0000.0000.0000.000
93A93ASP-1-0.789-0.8557.609-0.879-0.8790.0000.0000.0000.000
94A94GLU-1-0.788-0.8991.973-18.372-17.8259.431-5.089-4.889-0.060
95A95LEU0-0.044-0.0225.3960.2270.231-0.001-0.001-0.0010.000
96A96PRO00.0100.0116.529-0.132-0.1320.0000.0000.0000.000
97A97ILE0-0.022-0.0086.6200.3000.3000.0000.0000.0000.000
98A108SER00.0360.00619.316-0.005-0.0050.0000.0000.0000.000
99A109LYS10.8740.94110.522-0.335-0.3350.0000.0000.0000.000
100A110VAL00.0710.04413.071-0.016-0.0160.0000.0000.0000.000
101A111SER0-0.038-0.0278.6260.1000.1000.0000.0000.0000.000
102A112PHE00.008-0.0075.6490.0140.0140.0000.0000.0000.000
103A113GLN0-0.0040.0025.1060.0610.0610.0000.0000.0000.000
104A114MET0-0.042-0.0202.9840.6001.3070.117-0.185-0.6380.000
105A115ARG10.8910.9135.2200.9531.017-0.0010.000-0.0620.000
106A116TYR00.0180.0143.631-0.2710.0720.018-0.144-0.2170.000
107A117SER00.0280.0018.7980.1040.1040.0000.0000.0000.000
108A118ILE0-0.030-0.00212.5320.0150.0150.0000.0000.0000.000
109A119PRO0-0.043-0.00915.0860.0070.0070.0000.0000.0000.000
110A120LEU00.0030.00118.6280.0030.0030.0000.0000.0000.000
111A121PHE00.0150.00820.5910.0000.0000.0000.0000.0000.000
112A122ALA0-0.012-0.00324.3950.0040.0040.0000.0000.0000.000
113A123TYR0-0.012-0.03826.986-0.001-0.0010.0000.0000.0000.000
114A124GLY00.0430.04030.7640.0010.0010.0000.0000.0000.000
115A125LYS10.8310.86834.1690.0560.0560.0000.0000.0000.000
116A126GLY00.0310.01137.199-0.001-0.0010.0000.0000.0000.000
117A127ILE0-0.053-0.01133.3160.0010.0010.0000.0000.0000.000
118A128GLY00.0290.00631.5720.0000.0000.0000.0000.0000.000
119A129SER0-0.016-0.04727.2960.0000.0000.0000.0000.0000.000
120A130GLY00.0150.00529.300-0.002-0.0020.0000.0000.0000.000
121A131LEU0-0.0030.00124.6460.0040.0040.0000.0000.0000.000
122A132THR00.0340.02628.7240.0030.0030.0000.0000.0000.000
123A133GLU-1-0.764-0.88531.085-0.033-0.0330.0000.0000.0000.000
124A134GLU-1-0.887-0.93033.755-0.044-0.0440.0000.0000.0000.000
125A135SER0-0.014-0.01831.437-0.001-0.0010.0000.0000.0000.000
126A136GLN0-0.041-0.02531.9590.0020.0020.0000.0000.0000.000
127A137LYS10.8940.94335.5930.0330.0330.0000.0000.0000.000
128A138LEU0-0.062-0.00235.3850.0020.0020.0000.0000.0000.000
129A139ASN00.040-0.02033.1050.0010.0010.0000.0000.0000.000
130A140ALA0-0.018-0.00437.5850.0000.0000.0000.0000.0000.000
131A141LYS10.8770.94140.6340.0400.0400.0000.0000.0000.000
132A142ASN0-0.019-0.01238.6290.0000.0000.0000.0000.0000.000
133A143ALA00.0560.01940.180-0.002-0.0020.0000.0000.0000.000
134A144LEU00.0510.02438.941-0.001-0.0010.0000.0000.0000.000
135A145ALA0-0.0260.01335.860-0.005-0.0050.0000.0000.0000.000
136A146LYS10.8390.90334.2440.0580.0580.0000.0000.0000.000
137A147PRO00.0500.04132.1770.0000.0000.0000.0000.0000.000
138A148VAL0-0.017-0.01834.3310.0050.0050.0000.0000.0000.000
139A149LEU00.0130.01832.924-0.002-0.0020.0000.0000.0000.000
140A150GLN00.0590.02537.0140.0030.0030.0000.0000.0000.000
141A151TRP00.0080.00537.295-0.006-0.0060.0000.0000.0000.000
142A152SER0-0.011-0.00638.3700.0050.0050.0000.0000.0000.000
143A153VAL00.0250.01238.219-0.004-0.0040.0000.0000.0000.000
144A154ARG10.9410.98339.4130.0660.0660.0000.0000.0000.000
145A155ASN00.0390.01839.194-0.003-0.0030.0000.0000.0000.000
146A156ASN00.0120.01238.6510.0050.0050.0000.0000.0000.000
147A157GLN00.0150.01441.179-0.001-0.0010.0000.0000.0000.000
148A158GLN0-0.013-0.00841.0540.0000.0000.0000.0000.0000.000
149A159GLY00.009-0.00637.567-0.005-0.0050.0000.0000.0000.000
150A160GLN00.0030.01734.6560.0000.0000.0000.0000.0000.000
151A161SER0-0.015-0.04837.7900.0010.0010.0000.0000.0000.000
152A162GLU-1-0.799-0.87034.783-0.097-0.0970.0000.0000.0000.000
153A163LEU0-0.018-0.00433.4510.0070.0070.0000.0000.0000.000
154A164TYR0-0.046-0.03833.762-0.006-0.0060.0000.0000.0000.000
155A165LEU00.0300.00431.3180.0060.0060.0000.0000.0000.000
156A166LYS10.8700.93934.0550.0640.0640.0000.0000.0000.000
157A167ASN0-0.005-0.01331.6160.0110.0110.0000.0000.0000.000
158A168ASN0-0.020-0.02235.132-0.002-0.0020.0000.0000.0000.000
159A169GLY00.0020.01836.3080.0030.0030.0000.0000.0000.000
160A170GLN0-0.005-0.01734.704-0.009-0.0090.0000.0000.0000.000
161A171LYS10.8140.91028.6780.0920.0920.0000.0000.0000.000
162A172PHE0-0.051-0.01425.4700.0020.0020.0000.0000.0000.000
163A173ALA00.0080.01529.2750.0060.0060.0000.0000.0000.000
164A174ARG10.8030.87321.7370.1330.1330.0000.0000.0000.000
165A175LEU0-0.0030.00526.3530.0060.0060.0000.0000.0000.000
166A176SER00.001-0.00425.909-0.009-0.0090.0000.0000.0000.000
167A177ALA00.0030.01126.998-0.001-0.0010.0000.0000.0000.000
168A178LEU00.010-0.00130.3470.0000.0000.0000.0000.0000.000
169A179LYS10.8620.93333.9180.0580.0580.0000.0000.0000.000
170A180THR00.0420.00637.436-0.001-0.0010.0000.0000.0000.000
171A181SER0-0.010-0.01640.7390.0020.0020.0000.0000.0000.000
172A182LYN00.0530.01540.356-0.002-0.0020.0000.0000.0000.000
173A183THR0-0.011-0.00440.166-0.001-0.0010.0000.0000.0000.000
174A184GLY00.0190.03840.7580.0020.0020.0000.0000.0000.000
175A185ASN00.0230.00037.329-0.002-0.0020.0000.0000.0000.000
176A186ASP-1-0.877-0.94033.282-0.064-0.0640.0000.0000.0000.000
177A187ILE0-0.026-0.01335.1310.0020.0020.0000.0000.0000.000
178A188SER0-0.013-0.01933.688-0.004-0.0040.0000.0000.0000.000
179A189LEU00.0180.01530.599-0.004-0.0040.0000.0000.0000.000
180A190GLY00.0780.05529.354-0.008-0.0080.0000.0000.0000.000
181A191LYS10.7210.84728.8920.0870.0870.0000.0000.0000.000
182A192ALA0-0.012-0.00228.466-0.006-0.0060.0000.0000.0000.000
183A193ALA0-0.0110.00123.891-0.004-0.0040.0000.0000.0000.000
184A194PHE00.0310.01424.804-0.007-0.0070.0000.0000.0000.000
185A195GLY00.0630.02824.689-0.007-0.0070.0000.0000.0000.000
186A196TYR0-0.030-0.01519.8340.0100.0100.0000.0000.0000.000
187A197VAL00.0070.01225.6330.0010.0010.0000.0000.0000.000
188A198LEU00.0430.01724.8570.0080.0080.0000.0000.0000.000
189A199SER00.006-0.00928.8940.0060.0060.0000.0000.0000.000
190A200ASN0-0.074-0.02031.866-0.003-0.0030.0000.0000.0000.000
191A201SER00.0320.03530.968-0.002-0.0020.0000.0000.0000.000
192A202THR0-0.090-0.07732.6810.0060.0060.0000.0000.0000.000
193A203VAL00.0290.02127.829-0.004-0.0040.0000.0000.0000.000
194A204LYS10.7980.89130.9180.1070.1070.0000.0000.0000.000
195A205PHE00.0250.01828.876-0.008-0.0080.0000.0000.0000.000
196A206ALA00.0220.01730.4700.0090.0090.0000.0000.0000.000
197A207ILE0-0.009-0.01831.599-0.002-0.0020.0000.0000.0000.000
198A208ASP-1-0.784-0.87833.557-0.079-0.0790.0000.0000.0000.000
199A209GLN00.0590.04335.989-0.002-0.0020.0000.0000.0000.000
200A210SER00.0340.02137.7200.0010.0010.0000.0000.0000.000
201A211THR00.030-0.01234.7690.0030.0030.0000.0000.0000.000
202A212ALA00.0230.00737.9320.0010.0010.0000.0000.0000.000
203A213HIS00.003-0.01740.0410.0010.0010.0000.0000.0000.000
204A214GLU-1-0.882-0.91939.757-0.044-0.0440.0000.0000.0000.000
205A215LEU00.0200.00236.9630.0020.0020.0000.0000.0000.000
206A216ALA0-0.046-0.02441.5680.0010.0010.0000.0000.0000.000
207A217LYS10.8250.91444.4210.0440.0440.0000.0000.0000.000
208A218THR00.0290.02742.9890.0020.0020.0000.0000.0000.000
209A219SER00.024-0.00445.518-0.002-0.0020.0000.0000.0000.000
210A220LYS10.8090.88943.1130.0430.0430.0000.0000.0000.000
211A221ILE00.0120.01737.4220.0020.0020.0000.0000.0000.000
212A222TYR00.0040.00337.6710.0010.0010.0000.0000.0000.000
213A223GLY00.0240.01533.443-0.002-0.0020.0000.0000.0000.000
214A224VAL0-0.009-0.00129.9090.0040.0040.0000.0000.0000.000
215A225ASP-1-0.744-0.84229.441-0.106-0.1060.0000.0000.0000.000
216A226SER00.020-0.00325.4620.0010.0010.0000.0000.0000.000
217A227SER0-0.079-0.04926.192-0.006-0.0060.0000.0000.0000.000
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