Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 63JQZ

Calculation Name: 2W1T-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W1T

Chain ID: A

ChEMBL ID:

UniProt ID: P37554

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1714800.042217
FMO2-HF: Nuclear repulsion 1646366.909271
FMO2-HF: Total energy -68433.132947
FMO2-MP2: Total energy -68631.848534


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:2:ACE )


Summations of interaction energy for fragment #1(A:2:ACE )
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.
1.2072.046-0.006-0.388-0.445-0.001
Interaction energy analysis for fragmet #1(A:2:ACE )
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 : 0.003
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].
3A4THR 0-0.0030.0113.8200.9641.803-0.006-0.388-0.445-0.001
4A5GLY 00.0260.0136.6860.2730.2730.0000.0000.0000.000
5A6ILE 0-0.0210.0018.7740.2520.2520.0000.0000.0000.000
6A7VAL 00.0100.00011.190-0.056-0.0560.0000.0000.0000.000
7A8ARG 10.8840.94913.7680.2980.2980.0000.0000.0000.000
8A9ARG 10.9600.97216.4030.1860.1860.0000.0000.0000.000
9A10ILE 0-0.0010.02019.4140.0020.0020.0000.0000.0000.000
10A11ASP -1-0.852-0.91820.777-0.112-0.1120.0000.0000.0000.000
11A12ASP -1-0.907-0.95924.309-0.094-0.0940.0000.0000.0000.000
12A13LEU 00.001-0.02426.9640.0050.0050.0000.0000.0000.000
13A14GLY 0-0.027-0.00623.3860.0030.0030.0000.0000.0000.000
14A15ARG 10.9120.96321.7700.0890.0890.0000.0000.0000.000
15A16VAL 00.0270.01515.927-0.011-0.0110.0000.0000.0000.000
16A17VAL 0-0.032-0.01317.5330.0160.0160.0000.0000.0000.000
17A18ILE 00.0850.03212.917-0.040-0.0400.0000.0000.0000.000
18A19PRO 0-0.0020.00012.2570.0510.0510.0000.0000.0000.000
19A20LYS 10.9530.94814.4350.0930.0930.0000.0000.0000.000
20A21GLU -1-0.886-0.93511.935-0.141-0.1410.0000.0000.0000.000
21A22ILE 00.0640.0249.0230.0420.0420.0000.0000.0000.000
22A23ARG 10.9280.95511.9320.1180.1180.0000.0000.0000.000
23A24ARG 10.9520.98814.9850.0040.0040.0000.0000.0000.000
24A25THR 0-0.041-0.00910.6410.0260.0260.0000.0000.0000.000
25A26LEU 00.0190.0159.9220.0420.0420.0000.0000.0000.000
26A27ARG 10.9150.96313.894-0.112-0.1120.0000.0000.0000.000
27A28ILE 0-0.0320.00113.841-0.004-0.0040.0000.0000.0000.000
28A29ARG 10.7750.86518.170-0.052-0.0520.0000.0000.0000.000
29A30GLU -1-0.958-0.98621.679-0.033-0.0330.0000.0000.0000.000
30A31GLY 00.0090.00523.8710.0060.0060.0000.0000.0000.000
31A32ASP -1-0.818-0.88420.7310.0170.0170.0000.0000.0000.000
32A33PRO 00.0280.02921.877-0.012-0.0120.0000.0000.0000.000
33A34LEU 0-0.047-0.04916.2710.0070.0070.0000.0000.0000.000
34A35GLU -1-0.888-0.94318.2680.0000.0000.0000.0000.0000.000
35A36ILE 0-0.046-0.03816.993-0.009-0.0090.0000.0000.0000.000
36A37PHE 00.0000.00115.2780.0180.0180.0000.0000.0000.000
37A38VAL 0-0.002-0.00715.807-0.029-0.0290.0000.0000.0000.000
38A39ASP -1-0.870-0.92911.191-0.069-0.0690.0000.0000.0000.000
39A40ARG 10.8830.93114.4710.0130.0130.0000.0000.0000.000
40A41ASP -1-0.965-0.99111.217-0.332-0.3320.0000.0000.0000.000
41A42GLY 0-0.023-0.00113.848-0.024-0.0240.0000.0000.0000.000
42A43ASP -1-0.946-0.9579.394-0.499-0.4990.0000.0000.0000.000
43A44VAL 0-0.022-0.01612.5070.0710.0710.0000.0000.0000.000
44A45ILE 0-0.029-0.00810.595-0.051-0.0510.0000.0000.0000.000
45A46LEU 0-0.015-0.01811.9640.0200.0200.0000.0000.0000.000
46A47LYS 10.9290.97312.339-0.064-0.0640.0000.0000.0000.000
47A48LYS 10.8300.91714.577-0.066-0.0660.0000.0000.0000.000
48A49TYR 0-0.0040.00417.2800.0080.0080.0000.0000.0000.000
49A50SER 0-0.055-0.03920.549-0.006-0.0060.0000.0000.0000.000
50A51PRO 00.0630.01222.7910.0050.0050.0000.0000.0000.000
51A52ILE 00.0700.00926.2830.0030.0030.0000.0000.0000.000
52A53SER 0-0.058-0.03023.0210.0060.0060.0000.0000.0000.000
53A54GLU -1-0.909-0.93722.8790.0450.0450.0000.0000.0000.000
54A55LEU 0-0.023-0.01825.474-0.004-0.0040.0000.0000.0000.000
55A56GLY 0-0.057-0.03827.521-0.002-0.0020.0000.0000.0000.000
56A57ASP -1-0.936-0.96428.5080.0590.0590.0000.0000.0000.000
57A58PHE 0-0.0060.00532.127-0.003-0.0030.0000.0000.0000.000
58A59ALA 0-0.013-0.00330.907-0.001-0.0010.0000.0000.0000.000
59A60LYS 10.8500.91032.217-0.053-0.0530.0000.0000.0000.000
60A61GLU -1-0.824-0.92533.7950.0420.0420.0000.0000.0000.000
61A62TYR 0-0.034-0.02636.345-0.003-0.0030.0000.0000.0000.000
62A63ALA 0-0.024-0.02535.182-0.002-0.0020.0000.0000.0000.000
63A64ASP -1-0.808-0.89437.2140.0460.0460.0000.0000.0000.000
64A65ALA 00.0210.02439.308-0.002-0.0020.0000.0000.0000.000
65A66LEU 0-0.026-0.02238.943-0.002-0.0020.0000.0000.0000.000
66A67TYR 0-0.055-0.01240.497-0.001-0.0010.0000.0000.0000.000
67A68ASP -1-0.904-0.95542.4170.0330.0330.0000.0000.0000.000
68A69SER 0-0.075-0.04545.081-0.002-0.0020.0000.0000.0000.000
69A70LEU 0-0.107-0.05543.806-0.001-0.0010.0000.0000.0000.000
70A71GLY 0-0.0010.02045.2110.0000.0000.0000.0000.0000.000
71A72HIS 0-0.020-0.00742.6280.0020.0020.0000.0000.0000.000
72A73SER 0-0.053-0.02237.8190.0020.0020.0000.0000.0000.000
73A74VAL 00.0110.00036.331-0.002-0.0020.0000.0000.0000.000
74A75LEU 0-0.064-0.03631.8510.0040.0040.0000.0000.0000.000
75A76ILE 00.0390.03130.485-0.004-0.0040.0000.0000.0000.000
76A77CYS 0-0.054-0.00627.2550.0050.0050.0000.0000.0000.000
77A78ASP -1-0.680-0.79423.0530.0710.0710.0000.0000.0000.000
78A79ARG 10.8880.90023.454-0.028-0.0280.0000.0000.0000.000
79A80ASP -1-0.949-0.98019.8740.0800.0800.0000.0000.0000.000
80A81VAL 0-0.007-0.00621.1250.0060.0060.0000.0000.0000.000
81A82TYR 0-0.046-0.06223.906-0.011-0.0110.0000.0000.0000.000
82A83ILE 00.007-0.00124.7990.0090.0090.0000.0000.0000.000
83A84ALA 00.0050.01027.2230.0000.0000.0000.0000.0000.000
84A85VAL 0-0.047-0.02630.4720.0000.0000.0000.0000.0000.000
85A86SER 00.005-0.00633.1590.0020.0020.0000.0000.0000.000
86A87GLY 00.0730.05436.877-0.001-0.0010.0000.0000.0000.000
87A88SER 0-0.029-0.02235.8600.0010.0010.0000.0000.0000.000
88A89SER 0-0.032-0.01833.7270.0020.0020.0000.0000.0000.000
89A90LYS 11.0130.98330.570-0.061-0.0610.0000.0000.0000.000
90A91LYS 10.9060.97229.136-0.071-0.0710.0000.0000.0000.000
91A92ASP -1-0.882-0.95028.8600.0820.0820.0000.0000.0000.000
92A93TYR 0-0.045-0.06129.0130.0030.0030.0000.0000.0000.000
93A94LEU 0-0.031-0.01226.3830.0030.0030.0000.0000.0000.000
94A95ASN 0-0.027-0.02322.0070.0050.0050.0000.0000.0000.000
95A96LYS 10.8590.95622.316-0.093-0.0930.0000.0000.0000.000
96A97SER 0-0.002-0.01120.951-0.005-0.0050.0000.0000.0000.000
97A98ILE 00.0390.02923.592-0.004-0.0040.0000.0000.0000.000
98A99SER 0-0.020-0.03425.9560.0020.0020.0000.0000.0000.000
99A100GLU -1-0.852-0.94427.2220.0450.0450.0000.0000.0000.000
100A101MET 0-0.064-0.02129.085-0.006-0.0060.0000.0000.0000.000
101A102LEU 00.0660.02229.554-0.005-0.0050.0000.0000.0000.000
102A103GLU -1-0.857-0.91125.0680.0480.0480.0000.0000.0000.000
103A104ARG 10.9440.97328.945-0.032-0.0320.0000.0000.0000.000
104A105THR 00.0020.01131.951-0.004-0.0040.0000.0000.0000.000
105A106MET 0-0.044-0.01727.837-0.001-0.0010.0000.0000.0000.000
106A107ASP -1-0.890-0.93129.3480.0140.0140.0000.0000.0000.000
107A108GLN 0-0.092-0.06231.981-0.002-0.0020.0000.0000.0000.000
108A109ARG 10.8520.93232.072-0.005-0.0050.0000.0000.0000.000
109A110SER 0-0.047-0.01835.965-0.001-0.0010.0000.0000.0000.000
110A111SER 0-0.075-0.05738.4250.0020.0020.0000.0000.0000.000
111A112VAL 00.0020.00538.562-0.001-0.0010.0000.0000.0000.000
112A113LEU 00.0010.00041.1910.0020.0020.0000.0000.0000.000
113A114GLU -1-0.936-0.94141.1630.0220.0220.0000.0000.0000.000
114A115SER 0-0.034-0.04643.8740.0010.0010.0000.0000.0000.000
115A116ASP -1-0.873-0.95146.1350.0230.0230.0000.0000.0000.000
116A117ALA 0-0.0220.00943.7750.0000.0000.0000.0000.0000.000
117A118LYS 10.9000.96642.286-0.031-0.0310.0000.0000.0000.000
118A119SER 0-0.049-0.03238.7690.0000.0000.0000.0000.0000.000
119A120VAL 00.0220.03235.7660.0000.0000.0000.0000.0000.000
120A121GLN 00.0580.02230.5900.0060.0060.0000.0000.0000.000
121A122LEU 0-0.0030.03831.994-0.002-0.0020.0000.0000.0000.000
122A123VAL 00.0440.03226.5380.0030.0030.0000.0000.0000.000
123A124ASN 0-0.057-0.03823.639-0.010-0.0100.0000.0000.0000.000
124A125GLY 0-0.026-0.00526.5960.0080.0080.0000.0000.0000.000
125A126ILE 0-0.073-0.03728.6980.0000.0000.0000.0000.0000.000
126A127ASP -1-0.867-0.91731.2770.0480.0480.0000.0000.0000.000
127A128GLU -1-0.834-0.91833.5590.0600.0600.0000.0000.0000.000
128A129ASP -1-0.942-0.97537.0990.0410.0410.0000.0000.0000.000
129A130MET 0-0.029-0.03037.5630.0010.0010.0000.0000.0000.000
130A131ASN 0-0.111-0.02641.770-0.002-0.0020.0000.0000.0000.000
131A132SER 00.0590.04243.699-0.002-0.0020.0000.0000.0000.000
132A133TYR 00.012-0.01738.0000.0030.0030.0000.0000.0000.000
133A134THR 0-0.023-0.02640.356-0.002-0.0020.0000.0000.0000.000
134A135VAL 00.013-0.00634.7250.0030.0030.0000.0000.0000.000
135A136GLY 00.0580.02337.020-0.003-0.0030.0000.0000.0000.000
136A137PRO 0-0.032-0.01233.8210.0030.0030.0000.0000.0000.000
137A138ILE 00.0020.01231.628-0.002-0.0020.0000.0000.0000.000
138A139VAL 0-0.053-0.02331.9990.0000.0000.0000.0000.0000.000
139A140ALA 00.0350.03731.559-0.001-0.0010.0000.0000.0000.000
140A141ASN 0-0.016-0.00831.555-0.003-0.0030.0000.0000.0000.000
141A142GLY 0-0.042-0.01933.120-0.002-0.0020.0000.0000.0000.000
142A143ASP -1-0.879-0.95727.7570.0040.0040.0000.0000.0000.000
143A144PRO 0-0.068-0.02429.6840.0020.0020.0000.0000.0000.000
144A145ILE 00.0250.01727.2850.0020.0020.0000.0000.0000.000
145A146GLY 00.013-0.02327.4430.0060.0060.0000.0000.0000.000
146A147ALA 0-0.045-0.02729.207-0.005-0.0050.0000.0000.0000.000
147A148VAL 00.0170.02332.1410.0040.0040.0000.0000.0000.000
148A149VAL 0-0.010-0.00633.452-0.002-0.0020.0000.0000.0000.000
149A150ILE 00.0190.03136.1970.0020.0020.0000.0000.0000.000
150A151PHE 00.012-0.02035.958-0.001-0.0010.0000.0000.0000.000
151A152SER 00.0720.03340.4090.0010.0010.0000.0000.0000.000
152A153LYS 10.8430.91137.245-0.050-0.0500.0000.0000.0000.000
153A154ASP -1-0.972-0.99743.4770.0320.0320.0000.0000.0000.000
154A155GLN 00.0080.01646.553-0.003-0.0030.0000.0000.0000.000
155A156THR 0-0.026-0.01146.7960.0010.0010.0000.0000.0000.000
156A157MET 0-0.0580.00543.6210.0000.0000.0000.0000.0000.000
157A158GLY 00.053-0.00146.982-0.001-0.0010.0000.0000.0000.000
158A159GLU -1-0.863-0.94847.7460.0160.0160.0000.0000.0000.000
159A160VAL 0-0.058-0.00348.2430.0000.0000.0000.0000.0000.000
160A161GLU -1-0.755-0.89144.1550.0240.0240.0000.0000.0000.000
161A162HIS 0-0.018-0.01943.1720.0010.0010.0000.0000.0000.000
162A163LYS 10.9210.94143.973-0.014-0.0140.0000.0000.0000.000
163A164ALA 0-0.0020.01243.8290.0000.0000.0000.0000.0000.000
164A165VAL 00.0050.00739.2080.0010.0010.0000.0000.0000.000
165A166GLU -1-0.840-0.88739.6630.0150.0150.0000.0000.0000.000
166A167THR 0-0.083-0.04241.205-0.001-0.0010.0000.0000.0000.000
167A168ALA 0-0.026-0.00538.2700.0000.0000.0000.0000.0000.000
168A169ALA 00.0160.00136.3800.0000.0000.0000.0000.0000.000
169A170GLY 00.0230.01036.825-0.001-0.0010.0000.0000.0000.000
170A171PHE 0-0.056-0.03238.723-0.002-0.0020.0000.0000.0000.000
171A172LEU 00.034-0.00733.742-0.001-0.0010.0000.0000.0000.000
172A173ALA 00.0130.00434.0280.0000.0000.0000.0000.0000.000
173A174ARG 10.9110.95834.717-0.011-0.0110.0000.0000.0000.000
174A175GLN 0-0.071-0.02034.087-0.001-0.0010.0000.0000.0000.000
175A176MET 0-0.0840.00328.3530.0010.0010.0000.0000.0000.000
176A177GLU -1-0.882-0.95932.3170.0020.0020.0000.0000.0000.000
177A178NME 0-0.041-0.00934.3990.0000.0000.0000.0000.0000.000