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: 6NLJZ

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657810.985469
FMO2-HF: Nuclear repulsion 2569579.731466
FMO2-HF: Total energy -88231.254003
FMO2-MP2: Total energy -88492.345725


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.
-15.355-9.9356.488-4.903-7.004-0.041
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 : -0.001 / q_NPA : 0.002
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].
3A3PHE00.0310.0062.371-0.7211.0621.603-1.301-2.084-0.001
4A4LEU0-0.0120.0145.676-0.046-0.0460.0000.0000.0000.000
5A5ILE0-0.002-0.0148.2040.0360.0360.0000.0000.0000.000
6A6TRP0-0.0250.02111.1650.0170.0170.0000.0000.0000.000
7A7PRO00.0470.01914.8210.0130.0130.0000.0000.0000.000
8A8ILE00.0750.01213.213-0.025-0.0250.0000.0000.0000.000
9A9TYR0-0.022-0.03016.252-0.025-0.0250.0000.0000.0000.000
10A10PRO00.0020.02517.4200.0270.0270.0000.0000.0000.000
11A11LYS10.8220.90020.2680.0930.0930.0000.0000.0000.000
12A12ILE0-0.021-0.02122.6670.0070.0070.0000.0000.0000.000
13A13GLU-1-0.748-0.85325.898-0.093-0.0930.0000.0000.0000.000
14A14ALA00.0040.00129.4820.0000.0000.0000.0000.0000.000
15A15ASN0-0.045-0.01732.536-0.004-0.0040.0000.0000.0000.000
16A16GLU-1-0.746-0.85426.981-0.085-0.0850.0000.0000.0000.000
17A17LYS10.9680.96728.6940.0640.0640.0000.0000.0000.000
18A18ALA0-0.005-0.00923.855-0.007-0.0070.0000.0000.0000.000
19A19THR00.0290.03820.3490.0060.0060.0000.0000.0000.000
20A20ALA0-0.009-0.00718.428-0.004-0.0040.0000.0000.0000.000
21A21VAL0-0.0160.00113.170-0.006-0.0060.0000.0000.0000.000
22A22TRP0-0.010-0.01613.5590.0060.0060.0000.0000.0000.000
23A23LEU00.0080.0048.073-0.053-0.0530.0000.0000.0000.000
24A24GLN0-0.023-0.0198.9760.0040.0040.0000.0000.0000.000
25A25ASN00.0050.0054.5050.0960.187-0.001-0.015-0.0760.000
26A26THR0-0.042-0.0236.0610.0210.0210.0000.0000.0000.000
27A27GLY00.0490.0374.3670.0240.057-0.001-0.008-0.0230.000
28A28LYS10.9380.9535.429-1.281-1.2810.0000.0000.0000.000
29A29THR00.0100.0063.672-0.175-0.0340.000-0.021-0.1200.000
30A30ASP-1-0.812-0.8934.9330.8390.872-0.001-0.002-0.0290.000
31A31ALA00.0390.0253.050-0.4020.0120.196-0.152-0.4580.000
32A32MET0-0.032-0.0174.7070.1250.127-0.001-0.0070.0070.000
33A33VAL00.0210.0135.459-0.305-0.3050.0000.0000.0000.000
34A34GLN0-0.0010.0037.9290.2000.2000.0000.0000.0000.000
35A35ILE0-0.039-0.01810.704-0.091-0.0910.0000.0000.0000.000
36A36ARG10.9080.94112.9130.5160.5160.0000.0000.0000.000
37A37VAL00.0060.00415.804-0.029-0.0290.0000.0000.0000.000
38A38PHE0-0.0220.00416.0430.0090.0090.0000.0000.0000.000
39A39LYS10.8170.88820.5910.1480.1480.0000.0000.0000.000
40A40TRP0-0.076-0.05922.103-0.020-0.0200.0000.0000.0000.000
41A41ASN00.0040.00424.0790.0130.0130.0000.0000.0000.000
42A42GLN00.044-0.00825.7140.0030.0030.0000.0000.0000.000
43A43ASP-1-0.874-0.91828.814-0.123-0.1230.0000.0000.0000.000
44A44GLY0-0.013-0.01130.540-0.008-0.0080.0000.0000.0000.000
45A45LEU0-0.075-0.04231.8880.0000.0000.0000.0000.0000.000
46A46LYS10.9540.97527.1420.1650.1650.0000.0000.0000.000
47A47ASP-1-0.832-0.88623.002-0.220-0.2200.0000.0000.0000.000
48A48ASN0-0.065-0.03224.471-0.014-0.0140.0000.0000.0000.000
49A49TYR0-0.004-0.02920.139-0.014-0.0140.0000.0000.0000.000
50A50SER00.0010.00322.8850.0070.0070.0000.0000.0000.000
51A51GLU-1-0.877-0.93421.798-0.247-0.2470.0000.0000.0000.000
52A52GLN0-0.014-0.03222.6770.0210.0210.0000.0000.0000.000
53A53SER00.0300.01524.205-0.008-0.0080.0000.0000.0000.000
54A54GLU-1-0.799-0.85026.479-0.131-0.1310.0000.0000.0000.000
55A55ILE00.0070.00021.6420.0110.0110.0000.0000.0000.000
56A56ILE00.0200.01921.853-0.017-0.0170.0000.0000.0000.000
57A57PRO0-0.0050.00016.5430.0150.0150.0000.0000.0000.000
58A58SER0-0.0550.00518.1420.0060.0060.0000.0000.0000.000
59A59PRO00.000-0.00713.8920.0120.0120.0000.0000.0000.000
60A60PRO00.0890.02615.016-0.021-0.0210.0000.0000.0000.000
61A61VAL00.001-0.00311.895-0.057-0.0570.0000.0000.0000.000
62A62ALA00.0170.01010.4210.0540.0540.0000.0000.0000.000
63A63LYS10.9490.9799.226-0.145-0.1450.0000.0000.0000.000
64A64ILE0-0.0240.0006.5960.0010.0010.0000.0000.0000.000
65A65LYS10.8490.9076.971-0.219-0.2190.0000.0000.0000.000
66A66ALA00.0130.0137.3900.0090.0090.0000.0000.0000.000
67A67GLY0-0.007-0.0018.361-0.150-0.1500.0000.0000.0000.000
68A68GLU-1-0.848-0.9159.9300.1300.1300.0000.0000.0000.000
69A69LYS10.8860.9239.584-0.078-0.0780.0000.0000.0000.000
70A70HIS00.0340.01410.653-0.026-0.0260.0000.0000.0000.000
71A71MET0-0.021-0.01512.418-0.028-0.0280.0000.0000.0000.000
72A72LEU00.0070.01611.470-0.004-0.0040.0000.0000.0000.000
73A73ARG10.9440.97215.3230.0970.0970.0000.0000.0000.000
74A74LEU0-0.008-0.00516.658-0.018-0.0180.0000.0000.0000.000
75A75THR0-0.014-0.02220.4660.0170.0170.0000.0000.0000.000
76A76LYS10.8640.93024.0240.0860.0860.0000.0000.0000.000
77A77SER0-0.046-0.02526.8610.0090.0090.0000.0000.0000.000
78A78VAL00.002-0.00628.8740.0090.0090.0000.0000.0000.000
79A79ASN0-0.045-0.02931.451-0.007-0.0070.0000.0000.0000.000
80A80LEU00.0250.02328.485-0.001-0.0010.0000.0000.0000.000
81A81PRO00.014-0.00633.0970.0050.0050.0000.0000.0000.000
82A82ASP-1-0.764-0.87635.581-0.068-0.0680.0000.0000.0000.000
83A83GLY0-0.025-0.01337.619-0.001-0.0010.0000.0000.0000.000
84A84LYS10.8470.92333.9700.0920.0920.0000.0000.0000.000
85A85GLU-1-0.719-0.82028.751-0.124-0.1240.0000.0000.0000.000
86A86GLN0-0.0080.00528.063-0.008-0.0080.0000.0000.0000.000
87A87SER00.0480.01825.014-0.003-0.0030.0000.0000.0000.000
88A88TYR0-0.026-0.05621.4270.0020.0020.0000.0000.0000.000
89A89ARG10.8530.94216.0310.3530.3530.0000.0000.0000.000
90A90LEU00.0150.01613.8260.0100.0100.0000.0000.0000.000
91A91ILE0-0.047-0.03212.029-0.046-0.0460.0000.0000.0000.000
92A92VAL00.0320.0177.1080.0610.0610.0000.0000.0000.000
93A93ASP-1-0.806-0.8687.989-0.981-0.9810.0000.0000.0000.000
94A94GLU-1-0.801-0.9072.329-14.857-12.5734.673-3.204-3.754-0.040
95A95LEU0-0.056-0.0385.3450.1190.118-0.001-0.0010.0030.000
96A96PRO00.0230.0176.573-0.142-0.1420.0000.0000.0000.000
97A97ILE0-0.025-0.0106.3540.2750.2750.0000.0000.0000.000
98A108SER00.0130.00019.347-0.007-0.0070.0000.0000.0000.000
99A109LYS10.9080.94810.573-0.201-0.2010.0000.0000.0000.000
100A110VAL00.0650.04813.029-0.031-0.0310.0000.0000.0000.000
101A111SER0-0.034-0.0238.3330.1070.1070.0000.0000.0000.000
102A112PHE0-0.005-0.0205.7380.0310.0310.0000.0000.0000.000
103A113GLN0-0.0060.0055.589-0.237-0.2370.0000.0000.0000.000
104A114MET0-0.031-0.0053.5170.8851.2810.014-0.086-0.3240.000
105A115ARG10.8870.9115.6491.0191.0190.0000.0000.0000.000
106A116TYR00.0020.0063.781-0.247-0.0030.007-0.106-0.1460.000
107A117SER00.0180.0049.2730.1220.1220.0000.0000.0000.000
108A118ILE0-0.044-0.01612.6640.0160.0160.0000.0000.0000.000
109A119PRO0-0.049-0.00515.2890.0100.0100.0000.0000.0000.000
110A120LEU00.0160.00419.0570.0040.0040.0000.0000.0000.000
111A121PHE00.0250.01720.9430.0010.0010.0000.0000.0000.000
112A122ALA00.0000.00824.7230.0060.0060.0000.0000.0000.000
113A123TYR0-0.034-0.04027.124-0.001-0.0010.0000.0000.0000.000
114A124GLY00.0230.03230.8350.0020.0020.0000.0000.0000.000
115A125LYS10.8430.87434.1490.0640.0640.0000.0000.0000.000
116A126GLY00.0380.01837.128-0.001-0.0010.0000.0000.0000.000
117A127ILE0-0.041-0.00733.6740.0020.0020.0000.0000.0000.000
118A128GLY00.0340.00931.954-0.001-0.0010.0000.0000.0000.000
119A129SER0-0.023-0.04027.7100.0000.0000.0000.0000.0000.000
120A130GLY00.006-0.00229.713-0.002-0.0020.0000.0000.0000.000
121A131LEU00.0090.00525.2280.0030.0030.0000.0000.0000.000
122A132THR00.0270.02329.2220.0040.0040.0000.0000.0000.000
123A133GLU-1-0.776-0.89131.583-0.039-0.0390.0000.0000.0000.000
124A134GLU-1-0.933-0.95934.106-0.052-0.0520.0000.0000.0000.000
125A135SER0-0.016-0.02031.952-0.001-0.0010.0000.0000.0000.000
126A136GLN0-0.019-0.01332.5330.0020.0020.0000.0000.0000.000
127A137LYS10.8850.93536.0760.0380.0380.0000.0000.0000.000
128A138LEU0-0.083-0.02635.3990.0020.0020.0000.0000.0000.000
129A139ASN00.025-0.02633.4430.0010.0010.0000.0000.0000.000
130A140ALA0-0.0060.00937.8940.0000.0000.0000.0000.0000.000
131A141LYS10.9040.96441.0570.0440.0440.0000.0000.0000.000
132A142ASN0-0.004-0.00338.9490.0000.0000.0000.0000.0000.000
133A143ALA00.0510.01940.692-0.002-0.0020.0000.0000.0000.000
134A144LEU00.0220.00139.327-0.001-0.0010.0000.0000.0000.000
135A145ALA0-0.0320.01536.313-0.006-0.0060.0000.0000.0000.000
136A146LYS10.9010.92234.6720.0650.0650.0000.0000.0000.000
137A147PRO00.0400.04532.4110.0010.0010.0000.0000.0000.000
138A148VAL0-0.008-0.00734.7210.0060.0060.0000.0000.0000.000
139A149LEU00.0230.01933.154-0.002-0.0020.0000.0000.0000.000
140A150GLN00.0520.02037.3440.0030.0030.0000.0000.0000.000
141A151TRP0-0.017-0.01737.898-0.007-0.0070.0000.0000.0000.000
142A152SER00.019-0.00338.6720.0070.0070.0000.0000.0000.000
143A153VAL00.0050.01338.583-0.005-0.0050.0000.0000.0000.000
144A154ARG10.9390.97739.6480.0770.0770.0000.0000.0000.000
145A155ASN00.0290.02539.404-0.004-0.0040.0000.0000.0000.000
146A156ASN00.0220.01539.1780.0050.0050.0000.0000.0000.000
147A157GLN0-0.002-0.00141.568-0.002-0.0020.0000.0000.0000.000
148A158GLN00.0030.01041.6590.0010.0010.0000.0000.0000.000
149A159GLY00.0330.00637.885-0.006-0.0060.0000.0000.0000.000
150A160GLN0-0.021-0.00634.8660.0000.0000.0000.0000.0000.000
151A161SER0-0.034-0.06137.9770.0010.0010.0000.0000.0000.000
152A162GLU-1-0.817-0.87834.988-0.114-0.1140.0000.0000.0000.000
153A163LEU0-0.012-0.00933.9390.0080.0080.0000.0000.0000.000
154A164TYR0-0.052-0.04634.192-0.007-0.0070.0000.0000.0000.000
155A165LEU00.015-0.01031.8050.0060.0060.0000.0000.0000.000
156A166LYS10.8520.93434.1240.0720.0720.0000.0000.0000.000
157A167ASN0-0.007-0.01531.9090.0130.0130.0000.0000.0000.000
158A168ASN0-0.040-0.03035.404-0.001-0.0010.0000.0000.0000.000
159A169GLY00.0040.01736.3730.0040.0040.0000.0000.0000.000
160A170GLN0-0.001-0.01135.074-0.008-0.0080.0000.0000.0000.000
161A171LYS10.8160.91529.0100.1070.1070.0000.0000.0000.000
162A172PHE0-0.053-0.02425.6450.0010.0010.0000.0000.0000.000
163A173ALA00.0140.01529.6150.0070.0070.0000.0000.0000.000
164A174ARG10.7890.86622.1970.1590.1590.0000.0000.0000.000
165A175LEU0-0.007-0.02226.7140.0090.0090.0000.0000.0000.000
166A176SER00.0080.00525.931-0.009-0.0090.0000.0000.0000.000
167A177ALA00.0050.00827.2530.0010.0010.0000.0000.0000.000
168A178LEU00.0270.01230.7390.0010.0010.0000.0000.0000.000
169A179LYS10.8750.95234.2480.0650.0650.0000.0000.0000.000
170A180THR00.0450.01737.562-0.001-0.0010.0000.0000.0000.000
171A181SER00.002-0.01640.8330.0020.0020.0000.0000.0000.000
172A182LYN00.0490.02140.586-0.002-0.0020.0000.0000.0000.000
173A183THR0-0.0030.00340.343-0.001-0.0010.0000.0000.0000.000
174A184GLY00.0100.02840.9870.0020.0020.0000.0000.0000.000
175A185ASN00.018-0.00137.116-0.002-0.0020.0000.0000.0000.000
176A186ASP-1-0.880-0.95633.157-0.072-0.0720.0000.0000.0000.000
177A187ILE0-0.026-0.01835.1050.0020.0020.0000.0000.0000.000
178A188SER0-0.031-0.03133.535-0.004-0.0040.0000.0000.0000.000
179A189LEU0-0.0110.01130.491-0.005-0.0050.0000.0000.0000.000
180A190GLY00.0590.03729.469-0.005-0.0050.0000.0000.0000.000
181A191LYS10.7820.87928.0490.0950.0950.0000.0000.0000.000
182A192ALA0-0.022-0.01028.332-0.004-0.0040.0000.0000.0000.000
183A193ALA0-0.0060.01723.975-0.007-0.0070.0000.0000.0000.000
184A194PHE00.003-0.01325.1830.0020.0020.0000.0000.0000.000
185A195GLY00.0620.02724.465-0.005-0.0050.0000.0000.0000.000
186A196TYR0-0.0120.01520.3220.0130.0130.0000.0000.0000.000
187A197VAL00.0090.03025.979-0.001-0.0010.0000.0000.0000.000
188A198LEU00.0340.00525.1910.0080.0080.0000.0000.0000.000
189A199SER00.0340.01829.1940.0070.0070.0000.0000.0000.000
190A200ASN0-0.050-0.01332.392-0.004-0.0040.0000.0000.0000.000
191A201SER00.0490.03831.302-0.004-0.0040.0000.0000.0000.000
192A202THR0-0.075-0.05833.2520.0070.0070.0000.0000.0000.000
193A203VAL00.0470.02228.162-0.004-0.0040.0000.0000.0000.000
194A204LYS10.8190.90331.0230.1260.1260.0000.0000.0000.000
195A205PHE00.0150.00829.253-0.010-0.0100.0000.0000.0000.000
196A206ALA00.0240.02330.6130.0110.0110.0000.0000.0000.000
197A207ILE00.0200.00131.503-0.003-0.0030.0000.0000.0000.000
198A208ASP-1-0.812-0.89933.436-0.091-0.0910.0000.0000.0000.000
199A209GLN00.0710.04735.791-0.002-0.0020.0000.0000.0000.000
200A210SER00.0310.01138.1440.0010.0010.0000.0000.0000.000
201A211THR00.0560.02035.3040.0020.0020.0000.0000.0000.000
202A212ALA00.0280.00738.2160.0010.0010.0000.0000.0000.000
203A213HIS00.003-0.01540.2500.0010.0010.0000.0000.0000.000
204A214GLU-1-0.887-0.92840.091-0.051-0.0510.0000.0000.0000.000
205A215LEU00.002-0.00337.4270.0020.0020.0000.0000.0000.000
206A216ALA0-0.035-0.01642.0680.0010.0010.0000.0000.0000.000
207A217LYS10.8070.91644.3660.0500.0500.0000.0000.0000.000
208A218THR00.0430.02243.3930.0020.0020.0000.0000.0000.000
209A219SER00.013-0.00445.538-0.002-0.0020.0000.0000.0000.000
210A220LYS10.8600.92443.2840.0490.0490.0000.0000.0000.000
211A221ILE0-0.0080.00537.7440.0020.0020.0000.0000.0000.000
212A222TYR0-0.001-0.01237.6920.0010.0010.0000.0000.0000.000
213A223GLY00.0360.04133.643-0.002-0.0020.0000.0000.0000.000
214A224VAL0-0.0070.00229.8080.0050.0050.0000.0000.0000.000
215A225ASP-1-0.727-0.84429.561-0.124-0.1240.0000.0000.0000.000
216A226SER00.0220.00225.5790.0020.0020.0000.0000.0000.000
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218A228GLY00.0280.02127.648-0.001-0.0010.0000.0000.0000.000
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