FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YVJ62

Calculation Name: 2W6R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W6R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0C6

Base Structure: X-ray

Registration Date: 2023-09-23

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2828762.432102
FMO2-HF: Nuclear repulsion 2739622.508123
FMO2-HF: Total energy -89139.923979
FMO2-MP2: Total energy -89400.475106


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.997-1.8376.06-4.453-5.768-0.016
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.001
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].
3A3ARG10.7630.8631.947-1.083-0.2764.921-2.312-3.4170.009
4A4VAL00.0240.0184.4360.5250.643-0.001-0.022-0.0950.000
5A5VAL00.003-0.0027.3800.0530.0530.0000.0000.0000.000
6A6VAL00.0130.0019.6710.0610.0610.0000.0000.0000.000
7A7ALA0-0.024-0.01113.4230.0210.0210.0000.0000.0000.000
8A8ILE0-0.014-0.01015.9250.0020.0020.0000.0000.0000.000
9A9ASP-1-0.861-0.91518.869-0.031-0.0310.0000.0000.0000.000
10A10ALA00.009-0.01321.878-0.003-0.0030.0000.0000.0000.000
11A11LYS10.8390.91124.7260.0080.0080.0000.0000.0000.000
12A12ARG10.7360.81128.044-0.014-0.0140.0000.0000.0000.000
13A13VAL0-0.074-0.05131.2220.0000.0000.0000.0000.0000.000
14A14ASP-1-0.887-0.93933.805-0.007-0.0070.0000.0000.0000.000
15A15GLY0-0.038-0.01735.0000.0000.0000.0000.0000.0000.000
16A16GLU-1-0.905-0.93931.817-0.013-0.0130.0000.0000.0000.000
17A17PHE0-0.009-0.00626.5720.0000.0000.0000.0000.0000.000
18A18MET00.0150.03528.027-0.004-0.0040.0000.0000.0000.000
19A19VAL00.0420.02022.9360.0020.0020.0000.0000.0000.000
20A20PHE0-0.027-0.00324.9120.0020.0020.0000.0000.0000.000
21A21THR00.0360.01023.661-0.006-0.0060.0000.0000.0000.000
22A22HIS0-0.021-0.02225.1250.0060.0060.0000.0000.0000.000
23A23SER00.0430.00924.2800.0030.0030.0000.0000.0000.000
24A24GLY00.0850.03525.2140.0060.0060.0000.0000.0000.000
25A25LYS10.9020.95726.5340.0190.0190.0000.0000.0000.000
26A26LYS10.8760.95028.7520.0370.0370.0000.0000.0000.000
27A27ASN00.0870.04528.663-0.006-0.0060.0000.0000.0000.000
28A28THR0-0.065-0.06125.8400.0000.0000.0000.0000.0000.000
29A29GLY00.0190.01229.244-0.001-0.0010.0000.0000.0000.000
30A30ILE0-0.017-0.00125.5910.0010.0010.0000.0000.0000.000
31A31LEU00.0380.02227.5510.0000.0000.0000.0000.0000.000
32A32LEU0-0.023-0.02721.456-0.007-0.0070.0000.0000.0000.000
33A33ARG10.8530.88823.2190.0180.0180.0000.0000.0000.000
34A34ASP-1-0.797-0.87523.723-0.036-0.0360.0000.0000.0000.000
35A35TRP0-0.014-0.01919.532-0.005-0.0050.0000.0000.0000.000
36A36VAL00.0370.01718.262-0.014-0.0140.0000.0000.0000.000
37A37VAL00.0370.02618.287-0.014-0.0140.0000.0000.0000.000
38A38GLU-1-0.836-0.90219.238-0.105-0.1050.0000.0000.0000.000
39A39VAL0-0.007-0.00815.256-0.015-0.0150.0000.0000.0000.000
40A40GLU-1-0.727-0.80614.412-0.122-0.1220.0000.0000.0000.000
41A41LYS10.8290.91515.2960.0690.0690.0000.0000.0000.000
42A42ARG10.7560.87117.2070.1180.1180.0000.0000.0000.000
43A43GLY00.0100.00913.7220.0020.0020.0000.0000.0000.000
44A44ALA0-0.088-0.02911.615-0.069-0.0690.0000.0000.0000.000
45A45GLY00.0370.0117.7880.0170.0170.0000.0000.0000.000
46A46GLU-1-0.779-0.8756.879-0.260-0.2600.0000.0000.0000.000
47A47ILE00.0250.0179.793-0.001-0.0010.0000.0000.0000.000
48A48LEU0-0.0210.00612.8910.0430.0430.0000.0000.0000.000
49A49LEU00.0100.00314.255-0.007-0.0070.0000.0000.0000.000
50A50THR0-0.029-0.03117.7170.0240.0240.0000.0000.0000.000
51A51SER0-0.018-0.04420.318-0.006-0.0060.0000.0000.0000.000
52A52ILE00.001-0.00323.7940.0050.0050.0000.0000.0000.000
53A53ASP-1-0.819-0.87626.2420.0040.0040.0000.0000.0000.000
54A54ARG10.9050.95125.469-0.031-0.0310.0000.0000.0000.000
55A55ASP-1-0.882-0.93223.5520.0240.0240.0000.0000.0000.000
56A56GLY0-0.056-0.00125.520-0.002-0.0020.0000.0000.0000.000
57A57THR0-0.005-0.03627.406-0.001-0.0010.0000.0000.0000.000
58A58LYS10.8510.94327.129-0.053-0.0530.0000.0000.0000.000
59A59SER00.025-0.00428.9780.0030.0030.0000.0000.0000.000
60A60GLY00.0410.02926.4580.0000.0000.0000.0000.0000.000
61A61TYR0-0.025-0.03719.366-0.001-0.0010.0000.0000.0000.000
62A62ASP-1-0.731-0.82023.8150.0160.0160.0000.0000.0000.000
63A63THR0-0.004-0.01524.219-0.006-0.0060.0000.0000.0000.000
64A64GLU-1-0.888-0.91325.2580.0150.0150.0000.0000.0000.000
65A65MET00.0010.01422.948-0.004-0.0040.0000.0000.0000.000
66A66ILE0-0.028-0.01919.661-0.005-0.0050.0000.0000.0000.000
67A67ARG10.9520.97421.633-0.055-0.0550.0000.0000.0000.000
68A68PHE0-0.034-0.01824.086-0.003-0.0030.0000.0000.0000.000
69A69VAL00.016-0.00718.726-0.005-0.0050.0000.0000.0000.000
70A70ARG10.8040.89014.758-0.037-0.0370.0000.0000.0000.000
71A71PRO0-0.042-0.02419.630-0.003-0.0030.0000.0000.0000.000
72A72LEU0-0.083-0.02621.167-0.004-0.0040.0000.0000.0000.000
73A73THR0-0.030-0.03415.715-0.017-0.0170.0000.0000.0000.000
74A74THR0-0.042-0.05214.2110.0160.0160.0000.0000.0000.000
75A75LEU0-0.065-0.00910.5060.0010.0010.0000.0000.0000.000
76A76PRO00.0260.0127.8360.0590.0590.0000.0000.0000.000
77A77ILE0-0.011-0.00111.104-0.062-0.0620.0000.0000.0000.000
78A78ILE0-0.045-0.0299.5620.0590.0590.0000.0000.0000.000
79A79ALA00.0170.00613.761-0.030-0.0300.0000.0000.0000.000
80A80SER00.0320.00417.2040.0240.0240.0000.0000.0000.000
81A81GLY00.0890.04919.088-0.010-0.0100.0000.0000.0000.000
82A82GLY0-0.003-0.01322.6710.0020.0020.0000.0000.0000.000
83A83ALA0-0.0280.00222.0810.0010.0010.0000.0000.0000.000
84A84GLY0-0.069-0.06524.214-0.005-0.0050.0000.0000.0000.000
85A85LYS10.8260.91926.219-0.075-0.0750.0000.0000.0000.000
86A86MET00.0540.03823.0170.0100.0100.0000.0000.0000.000
87A87GLU-1-0.755-0.88423.8010.0970.0970.0000.0000.0000.000
88A88HIS00.0520.04924.3350.0070.0070.0000.0000.0000.000
89A89PHE00.0380.00619.541-0.002-0.0020.0000.0000.0000.000
90A90LEU00.0360.02020.5920.0080.0080.0000.0000.0000.000
91A91GLU-1-0.959-0.99622.9160.0670.0670.0000.0000.0000.000
92A92ALA0-0.037-0.01820.001-0.009-0.0090.0000.0000.0000.000
93A93PHE0-0.001-0.00315.8090.0000.0000.0000.0000.0000.000
94A94LEU0-0.035-0.01219.770-0.005-0.0050.0000.0000.0000.000
95A95ALA0-0.114-0.06222.430-0.007-0.0070.0000.0000.0000.000
96A96GLY00.0420.01919.327-0.013-0.0130.0000.0000.0000.000
97A97ALA0-0.037-0.00416.574-0.008-0.0080.0000.0000.0000.000
98A98ASP-1-0.759-0.86311.8590.1350.1350.0000.0000.0000.000
99A99LYS10.7370.8486.524-0.548-0.5480.0000.0000.0000.000
100A100ALA00.0020.01313.521-0.055-0.0550.0000.0000.0000.000
101A101LEU0-0.0040.01314.4350.0350.0350.0000.0000.0000.000
102A102ALA0-0.0140.01216.480-0.017-0.0170.0000.0000.0000.000
103A103ALA0-0.001-0.00219.293-0.012-0.0120.0000.0000.0000.000
104A104SER00.002-0.01122.0260.0050.0050.0000.0000.0000.000
105A105VAL00.0090.02222.320-0.003-0.0030.0000.0000.0000.000
106A106PHE0-0.042-0.04023.937-0.001-0.0010.0000.0000.0000.000
107A107HIS00.0190.00326.329-0.002-0.0020.0000.0000.0000.000
108A108PHE0-0.009-0.00126.3120.0030.0030.0000.0000.0000.000
109A109ARG10.8770.93625.514-0.074-0.0740.0000.0000.0000.000
110A110GLU-1-0.873-0.92826.2930.0790.0790.0000.0000.0000.000
111A111ILE0-0.061-0.04326.0570.0120.0120.0000.0000.0000.000
112A112ASP-1-0.731-0.85825.2490.1340.1340.0000.0000.0000.000
113A113MET0-0.0140.01919.8210.0130.0130.0000.0000.0000.000
114A114ARG10.8980.94621.032-0.148-0.1480.0000.0000.0000.000
115A115GLU-1-0.942-0.95322.4520.1360.1360.0000.0000.0000.000
116A116LEU00.0120.00619.4050.0050.0050.0000.0000.0000.000
117A117LYS10.9020.95014.834-0.406-0.4060.0000.0000.0000.000
118A118GLU-1-0.868-0.93118.6550.2940.2940.0000.0000.0000.000
119A119TYR0-0.014-0.00921.211-0.001-0.0010.0000.0000.0000.000
120A120LEU0-0.048-0.00116.227-0.011-0.0110.0000.0000.0000.000
121A121LYS10.8190.88516.949-0.260-0.2600.0000.0000.0000.000
122A122LYS10.8580.95219.394-0.173-0.1730.0000.0000.0000.000
123A123HIS00.020-0.01221.522-0.014-0.0140.0000.0000.0000.000
124A124GLY00.0620.04319.411-0.015-0.0150.0000.0000.0000.000
125A125GLY0-0.031-0.00417.3370.0240.0240.0000.0000.0000.000
126A126SER00.041-0.00312.9130.0300.0300.0000.0000.0000.000
127A127GLY0-0.0060.00910.337-0.035-0.0350.0000.0000.0000.000
128A128GLN0-0.0140.00810.838-0.010-0.0100.0000.0000.0000.000
129A129ALA00.005-0.00411.1690.0410.0410.0000.0000.0000.000
130A130VAL00.0270.00913.176-0.064-0.0640.0000.0000.0000.000
131A131VAL0-0.007-0.01110.9800.0510.0510.0000.0000.0000.000
132A132VAL00.024-0.00113.535-0.047-0.0470.0000.0000.0000.000
133A133ALA00.0250.02614.8240.0090.0090.0000.0000.0000.000
134A134ILE0-0.057-0.02816.1790.0020.0020.0000.0000.0000.000
135A135ASP-1-0.846-0.90617.2100.0040.0040.0000.0000.0000.000
136A136ALA00.006-0.01919.6850.0070.0070.0000.0000.0000.000
137A137LYS10.8370.91321.2740.0010.0010.0000.0000.0000.000
138A138ARG10.7400.81920.6610.0370.0370.0000.0000.0000.000
139A139VAL0-0.061-0.05126.043-0.002-0.0020.0000.0000.0000.000
140A140ASP-1-0.893-0.93929.4280.0030.0030.0000.0000.0000.000
141A141GLY0-0.056-0.02828.0820.0010.0010.0000.0000.0000.000
142A142GLU-1-0.864-0.92926.7320.0220.0220.0000.0000.0000.000
143A143PHE0-0.014-0.00421.043-0.002-0.0020.0000.0000.0000.000
144A144MET0-0.0180.01224.0330.0110.0110.0000.0000.0000.000
145A145VAL00.0580.02821.641-0.003-0.0030.0000.0000.0000.000
146A146PHE0-0.033-0.01623.389-0.004-0.0040.0000.0000.0000.000
147A147THR00.0480.02523.7020.0030.0030.0000.0000.0000.000
148A148HIS0-0.027-0.03425.747-0.005-0.0050.0000.0000.0000.000
149A149SER00.0830.04424.256-0.003-0.0030.0000.0000.0000.000
150A150GLY00.0700.01924.910-0.006-0.0060.0000.0000.0000.000
151A151LYS10.8170.90925.6020.0080.0080.0000.0000.0000.000
152A152LYS10.9030.96228.536-0.026-0.0260.0000.0000.0000.000
153A153ASN00.0980.06428.2390.0070.0070.0000.0000.0000.000
154A154THR0-0.055-0.04926.4230.0010.0010.0000.0000.0000.000
155A155GLY0-0.0050.00129.1920.0020.0020.0000.0000.0000.000
156A156ILE0-0.034-0.00425.6360.0010.0010.0000.0000.0000.000
157A157LEU00.0560.01725.430-0.001-0.0010.0000.0000.0000.000
158A158LEU0-0.027-0.02618.1050.0090.0090.0000.0000.0000.000
159A159ARG10.8940.91920.956-0.035-0.0350.0000.0000.0000.000
160A160ASP-1-0.827-0.89521.6330.0740.0740.0000.0000.0000.000
161A161TRP00.0120.00120.4570.0130.0130.0000.0000.0000.000
162A162VAL00.0110.00816.0440.0130.0130.0000.0000.0000.000
163A163VAL00.0480.02718.2430.0260.0260.0000.0000.0000.000
164A164GLU-1-0.830-0.88020.3470.1200.1200.0000.0000.0000.000
165A165VAL00.0460.00116.6750.0090.0090.0000.0000.0000.000
166A166GLU-1-0.760-0.81115.4120.3680.3680.0000.0000.0000.000
167A167LYS10.8280.90617.686-0.109-0.1090.0000.0000.0000.000
168A168ARG10.7190.82120.815-0.144-0.1440.0000.0000.0000.000
169A169GLY00.013-0.00118.726-0.006-0.0060.0000.0000.0000.000
170A170ALA00.0100.01315.4770.0160.0160.0000.0000.0000.000
171A171GLY0-0.012-0.00913.0000.0190.0190.0000.0000.0000.000
172A172GLU-1-0.731-0.8486.6480.9290.9290.0000.0000.0000.000
173A173ILE00.0140.01310.398-0.113-0.1130.0000.0000.0000.000
174A174LEU0-0.027-0.00810.585-0.003-0.0030.0000.0000.0000.000
175A175LEU00.004-0.00312.0180.0010.0010.0000.0000.0000.000
176A176THR0-0.006-0.02313.995-0.042-0.0420.0000.0000.0000.000
177A177SER0-0.056-0.04716.5140.0160.0160.0000.0000.0000.000
178A178ILE00.009-0.00918.779-0.010-0.0100.0000.0000.0000.000
179A179ASP-1-0.812-0.87822.157-0.023-0.0230.0000.0000.0000.000
180A180ARG10.9230.97119.0850.0720.0720.0000.0000.0000.000
181A181ASP-1-0.839-0.91619.697-0.075-0.0750.0000.0000.0000.000
182A182GLY0-0.055-0.01220.7570.0070.0070.0000.0000.0000.000
183A183THR0-0.063-0.04021.817-0.002-0.0020.0000.0000.0000.000
184A184LYS10.8700.94520.7600.0970.0970.0000.0000.0000.000
185A185SER00.018-0.01121.717-0.003-0.0030.0000.0000.0000.000
186A186GLY00.011-0.02217.532-0.001-0.0010.0000.0000.0000.000
187A187TYR0-0.030-0.04112.4310.0000.0000.0000.0000.0000.000
188A188ASP-1-0.706-0.80215.735-0.037-0.0370.0000.0000.0000.000
189A189THR00.021-0.00113.8550.0160.0160.0000.0000.0000.000
190A190GLU-1-0.864-0.90515.376-0.030-0.0300.0000.0000.0000.000
191A191MET00.0010.02017.0380.0120.0120.0000.0000.0000.000
192A192ILE0-0.017-0.01110.5810.0180.0180.0000.0000.0000.000
193A193ARG10.9360.96413.4740.1220.1220.0000.0000.0000.000
194A194PHE0-0.030-0.01314.8220.0160.0160.0000.0000.0000.000
195A195VAL00.008-0.01213.7230.0130.0130.0000.0000.0000.000
196A196ARG10.8060.8987.506-0.518-0.5180.0000.0000.0000.000
197A197PRO0-0.041-0.01512.7420.0520.0520.0000.0000.0000.000
198A198LEU0-0.054-0.01915.3100.0040.0040.0000.0000.0000.000
199A199THR0-0.060-0.04812.4500.0260.0260.0000.0000.0000.000
200A200THR0-0.054-0.06712.3010.0370.0370.0000.0000.0000.000
201A201LEU0-0.068-0.02110.7990.1660.1660.0000.0000.0000.000
202A202PRO00.0030.0115.366-0.035-0.0350.0000.0000.0000.000
203A203ILE0-0.006-0.0026.958-0.325-0.3250.0000.0000.0000.000
204A204ILE0-0.009-0.0106.886-0.150-0.1500.0000.0000.0000.000
205A205ALA00.0210.0148.3460.0710.0710.0000.0000.0000.000
206A206SER00.0220.01010.826-0.079-0.0790.0000.0000.0000.000
207A207GLY00.0750.04213.7230.0270.0270.0000.0000.0000.000
208A208GLY00.032-0.00216.873-0.002-0.0020.0000.0000.0000.000
209A209ALA0-0.0600.00214.9190.0030.0030.0000.0000.0000.000
210A210GLY0-0.028-0.04516.8530.0160.0160.0000.0000.0000.000
211A211LYS10.8840.96718.1120.1460.1460.0000.0000.0000.000
212A212MET00.0480.03712.378-0.015-0.0150.0000.0000.0000.000
213A213GLU-1-0.808-0.94513.612-0.164-0.1640.0000.0000.0000.000
214A214HIS0-0.0490.00614.018-0.012-0.0120.0000.0000.0000.000
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