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: Q16GY

Calculation Name: 2W1T-A-Xray372

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: 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708392.423769
FMO2-HF: Nuclear repulsion 1640129.406901
FMO2-HF: Total energy -68263.016868
FMO2-MP2: Total energy -68461.204986


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:3:ALA)


Summations of interaction energy for fragment #1(A:3: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.
-0.4561.8740.152-1.115-1.3670.004
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / 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].
3A5GLY00.0200.0092.843-1.7900.3780.148-1.078-1.2380.004
4A6ILE0-0.0190.0024.0060.0440.2060.004-0.037-0.1290.000
5A7VAL00.0090.0007.3080.2190.2190.0000.0000.0000.000
6A8ARG10.8850.9499.704-0.167-0.1670.0000.0000.0000.000
7A9ARG10.9610.97312.708-0.025-0.0250.0000.0000.0000.000
8A10ILE0-0.0040.02015.7420.0130.0130.0000.0000.0000.000
9A11ASP-1-0.850-0.91717.5840.1210.1210.0000.0000.0000.000
10A12ASP-1-0.905-0.95821.1320.0970.0970.0000.0000.0000.000
11A13LEU00.000-0.02524.4000.0010.0010.0000.0000.0000.000
12A14GLY0-0.026-0.00620.7880.0090.0090.0000.0000.0000.000
13A15ARG10.9110.96319.531-0.104-0.1040.0000.0000.0000.000
14A16VAL00.0250.01513.055-0.017-0.0170.0000.0000.0000.000
15A17VAL0-0.033-0.01414.8970.0050.0050.0000.0000.0000.000
16A18ILE00.0850.03311.6060.0120.0120.0000.0000.0000.000
17A19PRO0-0.0020.0019.632-0.081-0.0810.0000.0000.0000.000
18A20LYS10.9530.94712.743-0.054-0.0540.0000.0000.0000.000
19A21GLU-1-0.886-0.93410.164-0.086-0.0860.0000.0000.0000.000
20A22ILE00.0660.0257.553-0.006-0.0060.0000.0000.0000.000
21A23ARG10.9280.95411.434-0.239-0.2390.0000.0000.0000.000
22A24ARG10.9480.98614.765-0.202-0.2020.0000.0000.0000.000
23A25THR0-0.040-0.00810.8130.0290.0290.0000.0000.0000.000
24A26LEU00.0240.01710.9460.0340.0340.0000.0000.0000.000
25A27ARG10.9120.96214.928-0.244-0.2440.0000.0000.0000.000
26A28ILE0-0.0320.00114.238-0.006-0.0060.0000.0000.0000.000
27A29ARG10.7730.86618.513-0.189-0.1890.0000.0000.0000.000
28A30GLU-1-0.955-0.98621.6520.1370.1370.0000.0000.0000.000
29A31GLY00.0070.00523.306-0.010-0.0100.0000.0000.0000.000
30A32ASP-1-0.821-0.88620.9370.2320.2320.0000.0000.0000.000
31A33PRO00.0280.02921.7980.0130.0130.0000.0000.0000.000
32A34LEU0-0.047-0.04915.9920.0320.0320.0000.0000.0000.000
33A35GLU-1-0.887-0.94319.0230.2550.2550.0000.0000.0000.000
34A36ILE0-0.047-0.03816.6010.0590.0590.0000.0000.0000.000
35A37PHE00.0020.00216.246-0.030-0.0300.0000.0000.0000.000
36A38VAL0-0.002-0.00715.9590.0370.0370.0000.0000.0000.000
37A39ASP-1-0.868-0.92812.7230.4310.4310.0000.0000.0000.000
38A40ARG10.8820.93115.692-0.233-0.2330.0000.0000.0000.000
39A41ASP-1-0.963-0.99111.9160.2020.2020.0000.0000.0000.000
40A42GLY0-0.0230.00014.527-0.018-0.0180.0000.0000.0000.000
41A43ASP-1-0.945-0.95710.3210.6530.6530.0000.0000.0000.000
42A44VAL0-0.024-0.01711.764-0.072-0.0720.0000.0000.0000.000
43A45ILE0-0.026-0.00711.3160.1590.1590.0000.0000.0000.000
44A46LEU0-0.017-0.01912.241-0.110-0.1100.0000.0000.0000.000
45A47LYS10.9300.97513.159-0.297-0.2970.0000.0000.0000.000
46A48LYS10.8300.91715.742-0.338-0.3380.0000.0000.0000.000
47A49TYR0-0.0030.00418.5080.0010.0010.0000.0000.0000.000
48A50SER0-0.056-0.03821.833-0.020-0.0200.0000.0000.0000.000
49A51PRO00.0620.01224.470-0.007-0.0070.0000.0000.0000.000
50A52ILE00.0720.00827.899-0.005-0.0050.0000.0000.0000.000
51A53SER0-0.060-0.03025.036-0.004-0.0040.0000.0000.0000.000
52A54GLU-1-0.909-0.93624.7620.2090.2090.0000.0000.0000.000
53A55LEU0-0.023-0.01927.555-0.011-0.0110.0000.0000.0000.000
54A56GLY0-0.055-0.03729.661-0.010-0.0100.0000.0000.0000.000
55A57ASP-1-0.932-0.96130.7480.1020.1020.0000.0000.0000.000
56A58PHE0-0.0080.00534.406-0.007-0.0070.0000.0000.0000.000
57A59ALA0-0.016-0.00433.072-0.006-0.0060.0000.0000.0000.000
58A60LYS10.8530.91134.570-0.081-0.0810.0000.0000.0000.000
59A61GLU-1-0.822-0.92436.0860.0780.0780.0000.0000.0000.000
60A62TYR0-0.036-0.02738.527-0.005-0.0050.0000.0000.0000.000
61A63ALA0-0.022-0.02637.324-0.004-0.0040.0000.0000.0000.000
62A64ASP-1-0.811-0.89439.3780.0650.0650.0000.0000.0000.000
63A65ALA00.0260.02641.595-0.004-0.0040.0000.0000.0000.000
64A66LEU0-0.032-0.02540.953-0.003-0.0030.0000.0000.0000.000
65A67TYR0-0.050-0.01042.706-0.003-0.0030.0000.0000.0000.000
66A68ASP-1-0.904-0.95444.6120.0480.0480.0000.0000.0000.000
67A69SER0-0.073-0.04447.271-0.003-0.0030.0000.0000.0000.000
68A70LEU0-0.111-0.05745.783-0.002-0.0020.0000.0000.0000.000
69A71GLY00.0010.02247.399-0.002-0.0020.0000.0000.0000.000
70A72HIS0-0.023-0.00844.5950.0000.0000.0000.0000.0000.000
71A73SER0-0.050-0.01939.8440.0020.0020.0000.0000.0000.000
72A74VAL00.007-0.00338.3820.0000.0000.0000.0000.0000.000
73A75LEU0-0.058-0.03233.7350.0030.0030.0000.0000.0000.000
74A76ILE00.0360.02932.417-0.002-0.0020.0000.0000.0000.000
75A77CYS0-0.053-0.00529.0190.0010.0010.0000.0000.0000.000
76A78ASP-1-0.678-0.79324.9280.1900.1900.0000.0000.0000.000
77A79ARG10.8870.89924.753-0.151-0.1510.0000.0000.0000.000
78A80ASP-1-0.947-0.97921.4300.2520.2520.0000.0000.0000.000
79A81VAL0-0.004-0.00523.032-0.013-0.0130.0000.0000.0000.000
80A82TYR0-0.049-0.06425.799-0.005-0.0050.0000.0000.0000.000
81A83ILE00.006-0.00226.9200.0050.0050.0000.0000.0000.000
82A84ALA00.0070.01129.388-0.003-0.0030.0000.0000.0000.000
83A85VAL0-0.049-0.02632.711-0.002-0.0020.0000.0000.0000.000
84A86SER00.007-0.00535.3970.0010.0010.0000.0000.0000.000
85A87GLY00.0690.05239.1460.0000.0000.0000.0000.0000.000
86A88SER0-0.028-0.02237.907-0.003-0.0030.0000.0000.0000.000
87A89SER0-0.027-0.01535.8020.0020.0020.0000.0000.0000.000
88A90LYS11.0110.98232.931-0.074-0.0740.0000.0000.0000.000
89A91LYS10.9100.97331.319-0.044-0.0440.0000.0000.0000.000
90A92ASP-1-0.882-0.95030.8830.0590.0590.0000.0000.0000.000
91A93TYR0-0.043-0.06130.9510.0020.0020.0000.0000.0000.000
92A94LEU0-0.037-0.01428.7550.0070.0070.0000.0000.0000.000
93A95ASN0-0.021-0.02024.2610.0080.0080.0000.0000.0000.000
94A96LYS10.8590.95624.379-0.074-0.0740.0000.0000.0000.000
95A97SER00.003-0.00822.4260.0070.0070.0000.0000.0000.000
96A98ILE00.0380.02825.230-0.017-0.0170.0000.0000.0000.000
97A99SER0-0.028-0.03727.2970.0040.0040.0000.0000.0000.000
98A100GLU-1-0.846-0.94027.8810.0760.0760.0000.0000.0000.000
99A101MET0-0.067-0.02330.0720.0020.0020.0000.0000.0000.000
100A102LEU00.0680.02230.973-0.002-0.0020.0000.0000.0000.000
101A103GLU-1-0.856-0.91126.0360.1340.1340.0000.0000.0000.000
102A104ARG10.9470.97530.056-0.064-0.0640.0000.0000.0000.000
103A105THR0-0.0160.00332.861-0.004-0.0040.0000.0000.0000.000
104A106MET0-0.037-0.01629.1930.0000.0000.0000.0000.0000.000
105A107ASP-1-0.883-0.92729.8890.1120.1120.0000.0000.0000.000
106A108GLN0-0.091-0.06232.637-0.002-0.0020.0000.0000.0000.000
107A109ARG10.8650.93732.073-0.100-0.1000.0000.0000.0000.000
108A110SER0-0.057-0.02236.763-0.001-0.0010.0000.0000.0000.000
109A111SER0-0.045-0.03639.5840.0010.0010.0000.0000.0000.000
110A112VAL00.0040.00639.806-0.003-0.0030.0000.0000.0000.000
111A113LEU0-0.042-0.02242.4900.0020.0020.0000.0000.0000.000
112A114GLU-1-0.920-0.93142.4100.0410.0410.0000.0000.0000.000
113A115SER0-0.039-0.04845.2410.0000.0000.0000.0000.0000.000
114A116ASP-1-0.869-0.94947.4500.0280.0280.0000.0000.0000.000
115A117ALA0-0.0220.01044.8920.0010.0010.0000.0000.0000.000
116A118LYS10.9030.96743.580-0.029-0.0290.0000.0000.0000.000
117A119SER0-0.045-0.03039.735-0.002-0.0020.0000.0000.0000.000
118A120VAL00.0150.02837.0460.0010.0010.0000.0000.0000.000
119A121GLN00.0610.02431.6030.0060.0060.0000.0000.0000.000
120A122LEU0-0.0020.03733.5080.0040.0040.0000.0000.0000.000
121A123VAL00.0440.03328.1050.0100.0100.0000.0000.0000.000
122A124ASN0-0.056-0.03824.710-0.012-0.0120.0000.0000.0000.000
123A125GLY0-0.024-0.00427.7820.0000.0000.0000.0000.0000.000
124A126ILE0-0.071-0.03529.708-0.007-0.0070.0000.0000.0000.000
125A127ASP-1-0.867-0.91732.4950.0440.0440.0000.0000.0000.000
126A128GLU-1-0.833-0.91735.1160.0580.0580.0000.0000.0000.000
127A129ASP-1-0.939-0.97338.4530.0320.0320.0000.0000.0000.000
128A130MET0-0.032-0.03239.1810.0020.0020.0000.0000.0000.000
129A131ASN0-0.104-0.02343.241-0.002-0.0020.0000.0000.0000.000
130A132SER00.0570.04045.1820.0000.0000.0000.0000.0000.000
131A133TYR00.019-0.01239.4040.0010.0010.0000.0000.0000.000
132A134THR0-0.036-0.03742.029-0.001-0.0010.0000.0000.0000.000
133A135VAL00.016-0.00336.1800.0030.0030.0000.0000.0000.000
134A136GLY00.0440.01638.607-0.003-0.0030.0000.0000.0000.000
135A137PRO0-0.024-0.00835.0600.0050.0050.0000.0000.0000.000
136A138ILE00.0010.01133.320-0.005-0.0050.0000.0000.0000.000
137A139VAL0-0.052-0.02333.2480.0080.0080.0000.0000.0000.000
138A140ALA00.0340.03732.534-0.006-0.0060.0000.0000.0000.000
139A141ASN0-0.009-0.00332.0860.0010.0010.0000.0000.0000.000
140A142GLY0-0.040-0.01933.3100.0030.0030.0000.0000.0000.000
141A143ASP-1-0.880-0.95728.2380.1450.1450.0000.0000.0000.000
142A144PRO0-0.072-0.02630.479-0.001-0.0010.0000.0000.0000.000
143A145ILE00.0270.01828.4860.0100.0100.0000.0000.0000.000
144A146GLY00.017-0.01928.9830.0100.0100.0000.0000.0000.000
145A147ALA0-0.045-0.02830.760-0.008-0.0080.0000.0000.0000.000
146A148VAL00.0200.02533.8750.0030.0030.0000.0000.0000.000
147A149VAL0-0.017-0.00935.159-0.004-0.0040.0000.0000.0000.000
148A150ILE00.0160.02937.9750.0000.0000.0000.0000.0000.000
149A151PHE00.015-0.01937.901-0.002-0.0020.0000.0000.0000.000
150A152SER00.0700.03242.212-0.001-0.0010.0000.0000.0000.000
151A153LYS10.8510.91538.860-0.047-0.0470.0000.0000.0000.000
152A154ASP-1-0.966-0.99445.1600.0320.0320.0000.0000.0000.000
153A155GLN00.0090.01948.293-0.001-0.0010.0000.0000.0000.000
154A156THR0-0.025-0.01048.4820.0010.0010.0000.0000.0000.000
155A157MET0-0.0520.00745.3010.0010.0010.0000.0000.0000.000
156A158GLY00.0550.00148.680-0.002-0.0020.0000.0000.0000.000
157A159GLU-1-0.869-0.95649.3890.0440.0440.0000.0000.0000.000
158A160VAL0-0.0330.00649.8960.0020.0020.0000.0000.0000.000
159A161GLU-1-0.734-0.87645.9490.0440.0440.0000.0000.0000.000
160A162HIS10.8520.92044.557-0.048-0.0480.0000.0000.0000.000
161A163LYS10.9170.94245.562-0.044-0.0440.0000.0000.0000.000
162A164ALA00.0130.01945.7020.0030.0030.0000.0000.0000.000
163A165VAL00.0070.00840.8590.0030.0030.0000.0000.0000.000
164A166GLU-1-0.851-0.89741.3120.0590.0590.0000.0000.0000.000
165A167THR0-0.072-0.03642.7770.0020.0020.0000.0000.0000.000
166A168ALA0-0.022-0.00140.1300.0020.0020.0000.0000.0000.000
167A169ALA00.0190.00238.0260.0040.0040.0000.0000.0000.000
168A170GLY00.0180.00838.3760.0040.0040.0000.0000.0000.000
169A171PHE0-0.055-0.03140.2940.0020.0020.0000.0000.0000.000
170A172LEU00.038-0.00435.6170.0030.0030.0000.0000.0000.000
171A173ALA00.0170.00635.4020.0060.0060.0000.0000.0000.000
172A174ARG10.9120.95835.969-0.067-0.0670.0000.0000.0000.000
173A175GLN0-0.072-0.02135.8030.0010.0010.0000.0000.0000.000
174A176MET0-0.0790.00529.9220.0040.0040.0000.0000.0000.000
175A177GLU-1-0.921-0.96633.2970.0950.0950.0000.0000.0000.000