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: 3QRVL

Calculation Name: 2W8M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W8M

Chain ID: A

ChEMBL ID:

UniProt ID: Q6TRV5

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 OptH
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2000030.051341
FMO2-HF: Nuclear repulsion 1928580.317942
FMO2-HF: Total energy -71449.733399
FMO2-MP2: Total energy -71664.495405


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:19:ILE)


Summations of interaction energy for fragment #1(A:19: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.
-1.7830.7430.056-0.852-1.730.003
Interaction energy analysis for fragmet #1(A:19:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.013
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].
3A21PRO00.0070.0023.818-1.5270.298-0.013-0.733-1.0790.003
4A22THR00.0290.0135.3770.4100.468-0.001-0.003-0.0550.000
5A23VAL00.0340.0058.025-0.133-0.1330.0000.0000.0000.000
6A24GLY00.0210.01710.509-0.030-0.0300.0000.0000.0000.000
7A25LEU00.0740.0412.990-0.557-0.0940.070-0.090-0.4420.000
8A26GLY0-0.011-0.0087.686-0.076-0.0760.0000.0000.0000.000
9A27ARG10.9260.9659.0200.1360.1360.0000.0000.0000.000
10A28GLU-1-0.862-0.9379.153-0.080-0.0800.0000.0000.0000.000
11A29TYR00.007-0.0023.671-0.1000.0800.000-0.026-0.1540.000
12A30LEU0-0.050-0.0029.8440.0230.0230.0000.0000.0000.000
13A31VAL00.002-0.00713.1500.0240.0240.0000.0000.0000.000
14A32LEU00.0160.01110.4830.0190.0190.0000.0000.0000.000
15A33GLY00.0390.01213.3150.0140.0140.0000.0000.0000.000
16A34LYS10.9420.96614.8140.1980.1980.0000.0000.0000.000
17A35LEU00.0090.00817.1340.0200.0200.0000.0000.0000.000
18A36LEU00.0430.01814.5210.0170.0170.0000.0000.0000.000
19A37ILE00.0050.02118.5540.0170.0170.0000.0000.0000.000
20A38SER0-0.072-0.03820.8560.0170.0170.0000.0000.0000.000
21A39LEU00.0210.01020.0830.0110.0110.0000.0000.0000.000
22A40SER00.015-0.00121.5000.0070.0070.0000.0000.0000.000
23A41LYS10.9100.94724.1960.1300.1300.0000.0000.0000.000
24A42TRP00.005-0.01225.2000.0090.0090.0000.0000.0000.000
25A43ARG10.9300.98927.2830.0930.0930.0000.0000.0000.000
26A44ALA0-0.009-0.00528.4740.0050.0050.0000.0000.0000.000
27A45LYS10.8880.93829.2260.0960.0960.0000.0000.0000.000
28A46GLY00.0620.05132.2530.0040.0040.0000.0000.0000.000
29A47LEU0-0.090-0.03230.3360.0040.0040.0000.0000.0000.000
30A48ILE0-0.053-0.03628.2840.0050.0050.0000.0000.0000.000
31A49ASP-1-0.854-0.92531.414-0.063-0.0630.0000.0000.0000.000
32A50PHE0-0.057-0.02728.4300.0010.0010.0000.0000.0000.000
33A51ASP-1-0.874-0.94326.895-0.100-0.1000.0000.0000.0000.000
34A52VAL0-0.018-0.01922.7680.0070.0070.0000.0000.0000.000
35A53TYR0-0.022-0.02321.954-0.010-0.0100.0000.0000.0000.000
36A54LEU00.0540.03716.1600.0090.0090.0000.0000.0000.000
37A68TYR0-0.008-0.02131.9420.0000.0000.0000.0000.0000.000
38A69GLU-1-0.894-0.93925.867-0.035-0.0350.0000.0000.0000.000
39A70TYR00.017-0.00828.9840.0060.0060.0000.0000.0000.000
40A71TYR0-0.036-0.02526.101-0.005-0.0050.0000.0000.0000.000
41A72LYS11.0101.02024.3020.0160.0160.0000.0000.0000.000
42A73GLY0-0.051-0.02023.5990.0030.0030.0000.0000.0000.000
43A74LEU0-0.061-0.04322.8240.0100.0100.0000.0000.0000.000
44A75GLU-1-0.933-0.95818.842-0.036-0.0360.0000.0000.0000.000
45A76ASP-1-0.887-0.93915.940-0.001-0.0010.0000.0000.0000.000
46A77LYS10.8530.95016.854-0.038-0.0380.0000.0000.0000.000
47A78TYR0-0.082-0.05617.4030.0160.0160.0000.0000.0000.000
48A79ASP-1-0.786-0.85913.095-0.039-0.0390.0000.0000.0000.000
49A80LEU0-0.021-0.01213.699-0.031-0.0310.0000.0000.0000.000
50A81THR00.0080.00916.1250.0250.0250.0000.0000.0000.000
51A82LEU0-0.058-0.02119.361-0.015-0.0150.0000.0000.0000.000
52A83TYR00.0640.01219.4980.0120.0120.0000.0000.0000.000
53A84ILE0-0.025-0.00223.970-0.006-0.0060.0000.0000.0000.000
54A85ARG10.9570.97426.5630.0970.0970.0000.0000.0000.000
55A86ALA0-0.0270.00929.3980.0030.0030.0000.0000.0000.000
56A87LYS10.9620.95531.9820.0450.0450.0000.0000.0000.000
57A88ASP-1-0.887-0.92131.156-0.063-0.0630.0000.0000.0000.000
58A89SER0-0.057-0.02428.9090.0000.0000.0000.0000.0000.000
59A90TYR00.011-0.00624.968-0.005-0.0050.0000.0000.0000.000
60A91TYR00.0500.02026.9510.0050.0050.0000.0000.0000.000
61A92PRO00.0010.01623.521-0.007-0.0070.0000.0000.0000.000
62A93LEU0-0.038-0.01725.1820.0070.0070.0000.0000.0000.000
63A94LEU0-0.038-0.02723.9620.0070.0070.0000.0000.0000.000
64A95TRP00.0380.02320.663-0.006-0.0060.0000.0000.0000.000
65A96ILE0-0.030-0.03417.6980.0060.0060.0000.0000.0000.000
66A97ASP-1-0.796-0.90416.6960.0040.0040.0000.0000.0000.000
67A98ILE0-0.084-0.05112.643-0.005-0.0050.0000.0000.0000.000
68A99THR0-0.006-0.00714.5970.0250.0250.0000.0000.0000.000
69A100GLY00.015-0.00313.253-0.018-0.0180.0000.0000.0000.000
70A101SER0-0.031-0.02214.238-0.023-0.0230.0000.0000.0000.000
71A102SER0-0.035-0.02315.9390.0210.0210.0000.0000.0000.000
72A103TRP00.019-0.00619.1410.0050.0050.0000.0000.0000.000
73A104THR00.0210.02421.3440.0070.0070.0000.0000.0000.000
74A105GLU-1-0.870-0.92818.679-0.045-0.0450.0000.0000.0000.000
75A106GLU-1-0.980-0.97617.6080.1010.1010.0000.0000.0000.000
76A107GLN0-0.007-0.02319.8260.0210.0210.0000.0000.0000.000
77A108SER00.0040.02321.3260.0040.0040.0000.0000.0000.000
78A109LYS10.8660.92223.397-0.059-0.0590.0000.0000.0000.000
79A110GLU-1-0.877-0.92226.2710.0370.0370.0000.0000.0000.000
80A111ARG10.8650.92327.155-0.026-0.0260.0000.0000.0000.000
81A112TYR0-0.015-0.01929.2710.0000.0000.0000.0000.0000.000
82A113GLY00.0400.01429.6790.0040.0040.0000.0000.0000.000
83A114GLU-1-0.808-0.87229.149-0.010-0.0100.0000.0000.0000.000
84A115SER00.0110.00723.1060.0090.0090.0000.0000.0000.000
85A116ILE00.028-0.00324.824-0.002-0.0020.0000.0000.0000.000
86A117TYR00.0470.01919.2070.0030.0030.0000.0000.0000.000
87A118ALA00.0080.01320.6490.0010.0010.0000.0000.0000.000
88A119ILE00.0030.00720.3570.0010.0010.0000.0000.0000.000
89A120LEU00.0020.00717.7980.0040.0040.0000.0000.0000.000
90A121SER00.0460.01221.980-0.015-0.0150.0000.0000.0000.000
91A122VAL00.0500.02222.431-0.008-0.0080.0000.0000.0000.000
92A123LYS10.8340.91016.296-0.050-0.0500.0000.0000.0000.000
93A124VAL00.0090.00622.815-0.012-0.0120.0000.0000.0000.000
94A125GLU-1-0.937-0.97326.3200.0600.0600.0000.0000.0000.000
95A126THR0-0.056-0.02823.474-0.001-0.0010.0000.0000.0000.000
96A127ALA00.0460.02225.915-0.005-0.0050.0000.0000.0000.000
97A128LYS10.9350.96827.299-0.033-0.0330.0000.0000.0000.000
98A129LYS10.9110.96928.036-0.044-0.0440.0000.0000.0000.000
99A130TYR0-0.038-0.03126.7770.0020.0020.0000.0000.0000.000
100A131ASP-1-0.923-0.94530.021-0.005-0.0050.0000.0000.0000.000
101A132VAL00.017-0.00526.704-0.005-0.0050.0000.0000.0000.000
102A133LEU00.0060.00528.329-0.003-0.0030.0000.0000.0000.000
103A134GLY0-0.007-0.01328.926-0.001-0.0010.0000.0000.0000.000
104A135ARG10.8400.92927.3720.0250.0250.0000.0000.0000.000
105A136VAL00.0240.03322.869-0.006-0.0060.0000.0000.0000.000
106A137PHE0-0.026-0.03222.9020.0050.0050.0000.0000.0000.000
107A138PHE00.0310.02220.107-0.002-0.0020.0000.0000.0000.000
108A139ILE0-0.026-0.03218.343-0.002-0.0020.0000.0000.0000.000
109A140HIS00.0710.04218.083-0.003-0.0030.0000.0000.0000.000
110A141TYR0-0.083-0.06417.826-0.004-0.0040.0000.0000.0000.000
111A142ASN00.0110.01019.6640.0050.0050.0000.0000.0000.000
112A143ASP-1-0.833-0.93219.905-0.116-0.1160.0000.0000.0000.000
113A144THR0-0.063-0.03522.6020.0000.0000.0000.0000.0000.000
114A145GLU-1-0.950-0.98326.197-0.045-0.0450.0000.0000.0000.000
115A146ASP-1-0.890-0.89423.484-0.120-0.1200.0000.0000.0000.000
116A147LYS10.8910.94023.8530.0630.0630.0000.0000.0000.000
117A148LEU0-0.029-0.00918.5440.0030.0030.0000.0000.0000.000
118A149LYS10.8330.91722.1360.0460.0460.0000.0000.0000.000
119A150CYS0-0.067-0.03122.443-0.003-0.0030.0000.0000.0000.000
120A151ILE00.0270.01624.3750.0050.0050.0000.0000.0000.000
121A152SER00.0530.04225.0200.0010.0010.0000.0000.0000.000
122A153ALA00.0790.02726.2460.0050.0050.0000.0000.0000.000
123A154LEU0-0.033-0.01527.7030.0050.0050.0000.0000.0000.000
124A155GLN00.0450.01130.0350.0020.0020.0000.0000.0000.000
125A156ILE00.0230.02525.3820.0020.0020.0000.0000.0000.000
126A157LEU00.0280.00930.0220.0030.0030.0000.0000.0000.000
127A158ASN0-0.074-0.03932.7220.0030.0030.0000.0000.0000.000
128A159LEU0-0.008-0.01030.8270.0000.0000.0000.0000.0000.000
129A160GLU-1-0.850-0.92132.8840.0380.0380.0000.0000.0000.000
130A161ARG10.9050.95234.754-0.011-0.0110.0000.0000.0000.000
131A162GLN0-0.046-0.01837.6570.0000.0000.0000.0000.0000.000
132A163ASN0-0.033-0.01537.3380.0020.0020.0000.0000.0000.000
133A164LYS10.9470.98635.149-0.002-0.0020.0000.0000.0000.000
134A165ILE0-0.0130.00229.4340.0000.0000.0000.0000.0000.000
135A166LYS10.8930.93431.479-0.034-0.0340.0000.0000.0000.000
136A167LYS10.9110.98229.108-0.053-0.0530.0000.0000.0000.000
137A168ASP-1-0.815-0.90128.3850.0630.0630.0000.0000.0000.000
138A169LYS10.8910.95626.755-0.101-0.1010.0000.0000.0000.000
139A170PHE0-0.003-0.01225.4700.0130.0130.0000.0000.0000.000
140A171GLU-1-0.774-0.88322.7780.1540.1540.0000.0000.0000.000
141A172ARG10.9010.95016.404-0.221-0.2210.0000.0000.0000.000
142A173GLY00.0370.00919.500-0.018-0.0180.0000.0000.0000.000
143A174ALA0-0.006-0.00819.462-0.020-0.0200.0000.0000.0000.000
144A175LYS10.8320.92021.321-0.187-0.1870.0000.0000.0000.000
145A176SER0-0.076-0.05621.6390.0050.0050.0000.0000.0000.000
146A177GLU-1-0.884-0.93723.7040.0800.0800.0000.0000.0000.000
147A178TYR00.0290.00818.3010.0130.0130.0000.0000.0000.000
148A179TYR0-0.005-0.01424.835-0.003-0.0030.0000.0000.0000.000
149A180LEU00.0220.01424.996-0.002-0.0020.0000.0000.0000.000
150A181ILE0-0.030-0.02425.817-0.004-0.0040.0000.0000.0000.000
151A182PRO00.0370.02426.442-0.003-0.0030.0000.0000.0000.000
152A183THR00.0660.01725.261-0.005-0.0050.0000.0000.0000.000
153A184SER0-0.072-0.04927.421-0.005-0.0050.0000.0000.0000.000
154A185TYR0-0.038-0.02029.979-0.003-0.0030.0000.0000.0000.000
155A186TRP0-0.046-0.01021.405-0.004-0.0040.0000.0000.0000.000
156A187LYS10.9760.98227.5690.0200.0200.0000.0000.0000.000
157A188ASN00.0280.01226.881-0.005-0.0050.0000.0000.0000.000
158A189LEU00.0600.01222.2380.0040.0040.0000.0000.0000.000
159A190THR0-0.047-0.03126.585-0.004-0.0040.0000.0000.0000.000
160A191GLU-1-0.887-0.93928.889-0.029-0.0290.0000.0000.0000.000
161A192LEU00.0350.02222.9040.0010.0010.0000.0000.0000.000
162A193ARG10.8890.96327.4080.0690.0690.0000.0000.0000.000
163A194ILE0-0.016-0.01529.1060.0000.0000.0000.0000.0000.000
164A195ALA00.0360.02729.0260.0020.0020.0000.0000.0000.000
165A196LEU0-0.023-0.00525.8710.0010.0010.0000.0000.0000.000
166A197ARG10.9450.96029.2410.0530.0530.0000.0000.0000.000
167A198GLY00.0200.02232.6380.0020.0020.0000.0000.0000.000
168A199PHE00.042-0.00530.8340.0030.0030.0000.0000.0000.000
169A200TYR0-0.0050.00430.8490.0020.0020.0000.0000.0000.000
170A201GLN00.002-0.00632.707-0.002-0.0020.0000.0000.0000.000
171A202SER00.0050.00235.2960.0030.0030.0000.0000.0000.000
172A203PHE00.007-0.00532.1800.0020.0020.0000.0000.0000.000
173A204LYS10.9220.96035.1460.0420.0420.0000.0000.0000.000
174A205GLU-1-0.980-0.98236.684-0.024-0.0240.0000.0000.0000.000
175A206TYR0-0.065-0.02036.3130.0020.0020.0000.0000.0000.000
176A207LEU0-0.046-0.00234.2640.0010.0010.0000.0000.0000.000