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: K35L3

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708523.40081
FMO2-HF: Nuclear repulsion 1640258.690417
FMO2-HF: Total energy -68264.710392
FMO2-MP2: Total energy -68462.77682


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.
-0.4891.830.133-1.102-1.3510.005
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 : 0.012 / q_NPA : -0.006
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].
3A5GLY00.0210.0142.857-1.8020.3580.131-1.066-1.2260.005
4A6ILE0-0.042-0.0114.1030.0560.2150.002-0.036-0.1250.000
5A7VAL00.0200.0087.3240.1930.1930.0000.0000.0000.000
6A8ARG10.8930.9519.720-0.158-0.1580.0000.0000.0000.000
7A9ARG10.9620.97612.722-0.018-0.0180.0000.0000.0000.000
8A10ILE0-0.0030.01515.7540.0120.0120.0000.0000.0000.000
9A11ASP-1-0.858-0.93117.5930.1120.1120.0000.0000.0000.000
10A12ASP-1-0.897-0.95121.1420.0860.0860.0000.0000.0000.000
11A13LEU0-0.013-0.01924.5390.0020.0020.0000.0000.0000.000
12A14GLY0-0.020-0.00720.7830.0080.0080.0000.0000.0000.000
13A15ARG10.9120.96019.503-0.095-0.0950.0000.0000.0000.000
14A16VAL00.0180.01413.108-0.014-0.0140.0000.0000.0000.000
15A17VAL0-0.031-0.01314.8900.0090.0090.0000.0000.0000.000
16A18ILE00.0750.03011.6670.0170.0170.0000.0000.0000.000
17A19PRO0-0.0090.0019.653-0.061-0.0610.0000.0000.0000.000
18A20LYS10.9850.97412.754-0.054-0.0540.0000.0000.0000.000
19A21GLU-1-0.863-0.93710.9660.1250.1250.0000.0000.0000.000
20A22ILE00.0470.0167.5740.0120.0120.0000.0000.0000.000
21A23ARG10.9290.95911.439-0.245-0.2450.0000.0000.0000.000
22A24ARG10.8900.96414.776-0.235-0.2350.0000.0000.0000.000
23A25THR0-0.009-0.00310.523-0.014-0.0140.0000.0000.0000.000
24A26LEU00.0020.00911.1180.0400.0400.0000.0000.0000.000
25A27ARG10.8350.90414.928-0.230-0.2300.0000.0000.0000.000
26A28ILE0-0.0060.01114.421-0.010-0.0100.0000.0000.0000.000
27A29ARG10.6840.82018.513-0.201-0.2010.0000.0000.0000.000
28A30GLU-1-0.958-0.99021.6540.1360.1360.0000.0000.0000.000
29A31GLY00.0190.01123.310-0.010-0.0100.0000.0000.0000.000
30A32ASP-1-0.791-0.89720.9550.2340.2340.0000.0000.0000.000
31A33PRO0-0.0080.01921.7980.0120.0120.0000.0000.0000.000
32A34LEU0-0.033-0.03515.8250.0310.0310.0000.0000.0000.000
33A35GLU-1-0.823-0.90719.0190.2450.2450.0000.0000.0000.000
34A36ILE0-0.036-0.03216.7420.0520.0520.0000.0000.0000.000
35A37PHE0-0.012-0.00316.338-0.033-0.0330.0000.0000.0000.000
36A38VAL0-0.013-0.00815.9510.0320.0320.0000.0000.0000.000
37A39ASP-1-0.851-0.91413.2370.3340.3340.0000.0000.0000.000
38A40ARG10.8970.93415.605-0.193-0.1930.0000.0000.0000.000
39A41ASP-1-0.944-0.98412.2220.0980.0980.0000.0000.0000.000
40A42GLY0-0.060-0.02114.519-0.016-0.0160.0000.0000.0000.000
41A43ASP-1-0.944-0.9639.7730.5740.5740.0000.0000.0000.000
42A44VAL0-0.032-0.01311.779-0.056-0.0560.0000.0000.0000.000
43A45ILE0-0.025-0.00811.0880.1400.1400.0000.0000.0000.000
44A46LEU0-0.022-0.01412.229-0.098-0.0980.0000.0000.0000.000
45A47LYS10.8660.93313.151-0.221-0.2210.0000.0000.0000.000
46A48LYS10.7790.87515.735-0.333-0.3330.0000.0000.0000.000
47A49TYR0-0.086-0.05418.5020.0020.0020.0000.0000.0000.000
48A50SER0-0.034-0.05521.826-0.019-0.0190.0000.0000.0000.000
49A51PRO00.0730.03124.470-0.007-0.0070.0000.0000.0000.000
50A52ILE00.0450.00227.892-0.006-0.0060.0000.0000.0000.000
51A53SER0-0.042-0.02225.066-0.004-0.0040.0000.0000.0000.000
52A54GLU-1-0.879-0.90325.0010.1860.1860.0000.0000.0000.000
53A55LEU0-0.018-0.01727.498-0.011-0.0110.0000.0000.0000.000
54A56GLY0-0.034-0.02629.646-0.010-0.0100.0000.0000.0000.000
55A57ASP-1-0.909-0.95330.6920.0960.0960.0000.0000.0000.000
56A58PHE0-0.017-0.00934.344-0.006-0.0060.0000.0000.0000.000
57A59ALA00.0020.01033.029-0.006-0.0060.0000.0000.0000.000
58A60LYS10.8300.90534.478-0.077-0.0770.0000.0000.0000.000
59A61GLU-1-0.855-0.93736.0860.0700.0700.0000.0000.0000.000
60A62TYR0-0.053-0.03238.531-0.005-0.0050.0000.0000.0000.000
61A63ALA0-0.014-0.02237.299-0.004-0.0040.0000.0000.0000.000
62A64ASP-1-0.775-0.87039.3780.0620.0620.0000.0000.0000.000
63A65ALA00.0320.03041.595-0.004-0.0040.0000.0000.0000.000
64A66LEU0-0.036-0.02540.796-0.003-0.0030.0000.0000.0000.000
65A67TYR0-0.028-0.00642.704-0.003-0.0030.0000.0000.0000.000
66A68ASP-1-0.904-0.95144.6120.0460.0460.0000.0000.0000.000
67A69SER0-0.126-0.05347.265-0.002-0.0020.0000.0000.0000.000
68A70LEU0-0.067-0.04945.769-0.002-0.0020.0000.0000.0000.000
69A71GLY00.0050.02147.373-0.002-0.0020.0000.0000.0000.000
70A72HIS0-0.040-0.02544.6460.0000.0000.0000.0000.0000.000
71A73SER0-0.039-0.01139.8650.0020.0020.0000.0000.0000.000
72A74VAL00.006-0.00638.5300.0000.0000.0000.0000.0000.000
73A75LEU0-0.059-0.02933.7030.0030.0030.0000.0000.0000.000
74A76ILE00.0190.02032.594-0.002-0.0020.0000.0000.0000.000
75A77CYS0-0.061-0.01229.0510.0010.0010.0000.0000.0000.000
76A78ASP-1-0.681-0.78224.7810.1890.1890.0000.0000.0000.000
77A79ARG10.8660.90324.600-0.149-0.1490.0000.0000.0000.000
78A80ASP-1-0.829-0.91021.6000.2470.2470.0000.0000.0000.000
79A81VAL00.0050.00822.960-0.010-0.0100.0000.0000.0000.000
80A82TYR0-0.027-0.04125.799-0.006-0.0060.0000.0000.0000.000
81A83ILE0-0.004-0.00726.9250.0050.0050.0000.0000.0000.000
82A84ALA00.0060.01029.388-0.004-0.0040.0000.0000.0000.000
83A85VAL0-0.044-0.02232.659-0.001-0.0010.0000.0000.0000.000
84A86SER00.012-0.00335.3970.0000.0000.0000.0000.0000.000
85A87GLY00.0680.05139.1460.0000.0000.0000.0000.0000.000
86A88SER0-0.033-0.02837.842-0.003-0.0030.0000.0000.0000.000
87A89SER0-0.076-0.06736.1360.0020.0020.0000.0000.0000.000
88A90LYS10.9940.96432.990-0.071-0.0710.0000.0000.0000.000
89A91LYS10.8640.92631.367-0.049-0.0490.0000.0000.0000.000
90A92ASP-1-0.804-0.86730.9440.0630.0630.0000.0000.0000.000
91A93TYR00.003-0.02631.0100.0020.0020.0000.0000.0000.000
92A94LEU0-0.022-0.00528.6700.0070.0070.0000.0000.0000.000
93A95ASN0-0.027-0.02224.2620.0060.0060.0000.0000.0000.000
94A96LYS10.8260.94024.448-0.077-0.0770.0000.0000.0000.000
95A97SER00.000-0.00822.7940.0010.0010.0000.0000.0000.000
96A98ILE00.0280.02425.311-0.015-0.0150.0000.0000.0000.000
97A99SER0-0.023-0.03127.3850.0050.0050.0000.0000.0000.000
98A100GLU-1-0.868-0.94928.2160.0850.0850.0000.0000.0000.000
99A101MET0-0.055-0.01230.1610.0020.0020.0000.0000.0000.000
100A102LEU00.0640.02830.845-0.002-0.0020.0000.0000.0000.000
101A103GLU-1-0.776-0.85725.6310.1530.1530.0000.0000.0000.000
102A104ARG10.9610.98330.056-0.069-0.0690.0000.0000.0000.000
103A105THR0-0.011-0.00632.861-0.004-0.0040.0000.0000.0000.000
104A106MET0-0.028-0.00729.065-0.001-0.0010.0000.0000.0000.000
105A107ASP-1-0.858-0.91229.7710.1150.1150.0000.0000.0000.000
106A108GLN0-0.085-0.06232.638-0.003-0.0030.0000.0000.0000.000
107A109ARG10.8380.93131.537-0.101-0.1010.0000.0000.0000.000
108A110SER0-0.047-0.01536.762-0.002-0.0020.0000.0000.0000.000
109A111SER0-0.067-0.04939.5840.0010.0010.0000.0000.0000.000
110A112VAL00.0100.00239.867-0.003-0.0030.0000.0000.0000.000
111A113LEU0-0.034-0.01642.4900.0010.0010.0000.0000.0000.000
112A114GLU-1-0.915-0.92642.4650.0440.0440.0000.0000.0000.000
113A115SER0-0.035-0.04145.2650.0000.0000.0000.0000.0000.000
114A116ASP-1-0.876-0.94147.5590.0300.0300.0000.0000.0000.000
115A117ALA0-0.042-0.01245.1650.0020.0020.0000.0000.0000.000
116A118LYS10.8180.91543.945-0.031-0.0310.0000.0000.0000.000
117A119SER0-0.047-0.02339.756-0.002-0.0020.0000.0000.0000.000
118A120VAL00.0120.02037.1810.0010.0010.0000.0000.0000.000
119A121GLN00.0460.01131.7420.0060.0060.0000.0000.0000.000
120A122LEU0-0.0130.02933.5930.0040.0040.0000.0000.0000.000
121A123VAL00.0330.01728.2220.0090.0090.0000.0000.0000.000
122A124ASN0-0.043-0.03624.713-0.012-0.0120.0000.0000.0000.000
123A125GLY0-0.0170.00227.8660.0010.0010.0000.0000.0000.000
124A126ILE0-0.072-0.03229.793-0.007-0.0070.0000.0000.0000.000
125A127ASP-1-0.860-0.91032.5760.0510.0510.0000.0000.0000.000
126A128GLU-1-0.814-0.90435.3160.0620.0620.0000.0000.0000.000
127A129ASP-1-0.830-0.90638.5340.0330.0330.0000.0000.0000.000
128A130MET0-0.030-0.03238.9760.0020.0020.0000.0000.0000.000
129A131ASN0-0.054-0.01043.324-0.001-0.0010.0000.0000.0000.000
130A132SER00.0330.02145.3200.0000.0000.0000.0000.0000.000
131A133TYR00.007-0.02038.8460.0030.0030.0000.0000.0000.000
132A134THR0-0.048-0.04142.030-0.002-0.0020.0000.0000.0000.000
133A135VAL00.0270.00336.1000.0030.0030.0000.0000.0000.000
134A136GLY00.0440.01538.609-0.003-0.0030.0000.0000.0000.000
135A137PRO0-0.023-0.00734.9830.0050.0050.0000.0000.0000.000
136A138ILE0-0.0160.00733.130-0.005-0.0050.0000.0000.0000.000
137A139VAL0-0.052-0.02433.2440.0080.0080.0000.0000.0000.000
138A140ALA00.0370.03432.551-0.006-0.0060.0000.0000.0000.000
139A141ASN0-0.024-0.01332.3920.0020.0020.0000.0000.0000.000
140A142GLY0-0.040-0.01533.3090.0020.0020.0000.0000.0000.000
141A143ASP-1-0.858-0.94628.1430.1400.1400.0000.0000.0000.000
142A144PRO0-0.071-0.02730.6290.0000.0000.0000.0000.0000.000
143A145ILE00.0180.01227.9500.0110.0110.0000.0000.0000.000
144A146GLY00.021-0.01828.9830.0090.0090.0000.0000.0000.000
145A147ALA0-0.039-0.02330.760-0.007-0.0070.0000.0000.0000.000
146A148VAL00.0170.01933.8750.0030.0030.0000.0000.0000.000
147A149VAL0-0.014-0.01235.155-0.003-0.0030.0000.0000.0000.000
148A150ILE00.0130.02837.9750.0000.0000.0000.0000.0000.000
149A151PHE00.033-0.01237.448-0.002-0.0020.0000.0000.0000.000
150A152SER00.0870.04042.249-0.001-0.0010.0000.0000.0000.000
151A153LYS10.8080.87939.054-0.051-0.0510.0000.0000.0000.000
152A154ASP-1-0.939-0.96945.2380.0350.0350.0000.0000.0000.000
153A155GLN0-0.035-0.01048.367-0.002-0.0020.0000.0000.0000.000
154A156THR0-0.026-0.00348.5640.0010.0010.0000.0000.0000.000
155A157MET0-0.0330.01545.1490.0010.0010.0000.0000.0000.000
156A158GLY00.0560.00648.680-0.002-0.0020.0000.0000.0000.000
157A159GLU-1-0.790-0.89649.3890.0450.0450.0000.0000.0000.000
158A160VAL0-0.0210.01349.8960.0020.0020.0000.0000.0000.000
159A161GLU-1-0.726-0.86845.9320.0440.0440.0000.0000.0000.000
160A162HIS10.8110.88544.651-0.047-0.0470.0000.0000.0000.000
161A163LYS10.7860.87045.562-0.044-0.0440.0000.0000.0000.000
162A164ALA00.0110.02145.7300.0020.0020.0000.0000.0000.000
163A165VAL00.0170.01140.8060.0030.0030.0000.0000.0000.000
164A166GLU-1-0.787-0.86341.3120.0570.0570.0000.0000.0000.000
165A167THR0-0.070-0.04142.7770.0010.0010.0000.0000.0000.000
166A168ALA0-0.0170.00240.1660.0020.0020.0000.0000.0000.000
167A169ALA00.0150.00138.0100.0040.0040.0000.0000.0000.000
168A170GLY00.0170.00938.3710.0040.0040.0000.0000.0000.000
169A171PHE0-0.032-0.02039.9250.0010.0010.0000.0000.0000.000
170A172LEU00.0370.00135.6760.0020.0020.0000.0000.0000.000
171A173ALA00.0120.00335.3950.0050.0050.0000.0000.0000.000
172A174ARG10.9030.95735.963-0.065-0.0650.0000.0000.0000.000
173A175GLN0-0.091-0.03935.7300.0000.0000.0000.0000.0000.000
174A176MET0-0.071-0.00530.1950.0020.0020.0000.0000.0000.000
175A177GLU-1-0.901-0.95733.2920.0900.0900.0000.0000.0000.000