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: VQJ81

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 OptAll
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 -2829654.944909
FMO2-HF: Nuclear repulsion 2740514.133863
FMO2-HF: Total energy -89140.811047
FMO2-MP2: Total energy -89401.153673


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.
-9.183-6.1118.922-5.268-6.726-0.035
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 : -0.006 / q_NPA : -0.005
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].
3A3ARG10.7570.8542.159-1.7130.4172.550-1.795-2.8850.010
4A4VAL00.0340.0174.6680.5150.629-0.001-0.013-0.0990.000
5A5VAL00.0100.0097.1610.0550.0550.0000.0000.0000.000
6A6VAL00.0190.0049.5340.0840.0840.0000.0000.0000.000
7A7ALA0-0.023-0.01613.3810.0220.0220.0000.0000.0000.000
8A8ILE0-0.014-0.00215.9680.0090.0090.0000.0000.0000.000
9A9ASP-1-0.857-0.92318.869-0.029-0.0290.0000.0000.0000.000
10A10ALA00.007-0.01721.698-0.004-0.0040.0000.0000.0000.000
11A11LYS10.7960.88224.5010.0090.0090.0000.0000.0000.000
12A12ARG10.7280.81327.748-0.009-0.0090.0000.0000.0000.000
13A13VAL0-0.053-0.03931.0180.0010.0010.0000.0000.0000.000
14A14ASP-1-0.910-0.95633.791-0.009-0.0090.0000.0000.0000.000
15A15GLY0-0.0080.00335.1680.0010.0010.0000.0000.0000.000
16A16GLU-1-0.928-0.96231.574-0.017-0.0170.0000.0000.0000.000
17A17PHE0-0.013-0.01226.5670.0000.0000.0000.0000.0000.000
18A18MET0-0.0110.01827.991-0.005-0.0050.0000.0000.0000.000
19A19VAL00.0430.02222.7570.0010.0010.0000.0000.0000.000
20A20PHE0-0.029-0.01424.4800.0050.0050.0000.0000.0000.000
21A21THR00.0300.00123.587-0.007-0.0070.0000.0000.0000.000
22A22HIS0-0.021-0.01625.0330.0060.0060.0000.0000.0000.000
23A23SER00.0360.00924.0070.0050.0050.0000.0000.0000.000
24A24GLY00.0800.03524.9290.0060.0060.0000.0000.0000.000
25A25LYS10.9060.95926.3960.0140.0140.0000.0000.0000.000
26A26LYS10.8870.96028.6290.0340.0340.0000.0000.0000.000
27A27ASN00.0800.04528.505-0.006-0.0060.0000.0000.0000.000
28A28THR0-0.039-0.05525.4920.0000.0000.0000.0000.0000.000
29A29GLY0-0.0030.00528.951-0.001-0.0010.0000.0000.0000.000
30A30ILE0-0.028-0.01125.7720.0010.0010.0000.0000.0000.000
31A31LEU00.0380.02327.6300.0000.0000.0000.0000.0000.000
32A32LEU0-0.024-0.02521.408-0.007-0.0070.0000.0000.0000.000
33A33ARG10.8610.89423.1920.0230.0230.0000.0000.0000.000
34A34ASP-1-0.797-0.86623.987-0.042-0.0420.0000.0000.0000.000
35A35TRP0-0.010-0.02819.959-0.005-0.0050.0000.0000.0000.000
36A36VAL00.0120.01218.144-0.015-0.0150.0000.0000.0000.000
37A37VAL00.0520.03118.397-0.017-0.0170.0000.0000.0000.000
38A38GLU-1-0.849-0.89219.776-0.104-0.1040.0000.0000.0000.000
39A39VAL0-0.007-0.01315.063-0.014-0.0140.0000.0000.0000.000
40A40GLU-1-0.731-0.81514.689-0.153-0.1530.0000.0000.0000.000
41A41LYS10.8420.90715.7680.0770.0770.0000.0000.0000.000
42A42ARG10.7520.87416.8100.1220.1220.0000.0000.0000.000
43A43GLY00.0050.01013.9280.0050.0050.0000.0000.0000.000
44A44ALA0-0.064-0.02211.567-0.055-0.0550.0000.0000.0000.000
45A45GLY00.0280.0037.6350.0220.0220.0000.0000.0000.000
46A46GLU-1-0.773-0.8707.150-0.341-0.3410.0000.0000.0000.000
47A47ILE00.0150.0149.5260.0030.0030.0000.0000.0000.000
48A48LEU0-0.033-0.00212.8080.0460.0460.0000.0000.0000.000
49A49LEU00.0150.00414.139-0.007-0.0070.0000.0000.0000.000
50A50THR0-0.038-0.02617.7750.0220.0220.0000.0000.0000.000
51A51SER00.025-0.01920.271-0.005-0.0050.0000.0000.0000.000
52A52ILE0-0.0100.00523.7030.0070.0070.0000.0000.0000.000
53A53ASP-1-0.788-0.85426.2950.0010.0010.0000.0000.0000.000
54A54ARG10.8850.93125.373-0.029-0.0290.0000.0000.0000.000
55A55ASP-1-0.813-0.89823.5330.0320.0320.0000.0000.0000.000
56A56GLY0-0.075-0.01525.360-0.003-0.0030.0000.0000.0000.000
57A57THR0-0.071-0.06827.4920.0050.0050.0000.0000.0000.000
58A58LYS10.8690.94926.305-0.060-0.0600.0000.0000.0000.000
59A59SER0-0.0020.00328.8200.0030.0030.0000.0000.0000.000
60A60GLY00.0280.02226.163-0.002-0.0020.0000.0000.0000.000
61A61TYR0-0.022-0.04719.165-0.001-0.0010.0000.0000.0000.000
62A62ASP-1-0.699-0.79823.6380.0100.0100.0000.0000.0000.000
63A63THR0-0.048-0.03123.883-0.006-0.0060.0000.0000.0000.000
64A64GLU-1-0.861-0.89625.1690.0100.0100.0000.0000.0000.000
65A65MET00.0030.00622.878-0.004-0.0040.0000.0000.0000.000
66A66ILE0-0.022-0.01719.278-0.007-0.0070.0000.0000.0000.000
67A67ARG10.8930.95221.375-0.047-0.0470.0000.0000.0000.000
68A68PHE0-0.027-0.01023.931-0.003-0.0030.0000.0000.0000.000
69A69VAL00.014-0.00118.534-0.005-0.0050.0000.0000.0000.000
70A70ARG10.8070.87614.680-0.002-0.0020.0000.0000.0000.000
71A71PRO0-0.051-0.02919.618-0.004-0.0040.0000.0000.0000.000
72A72LEU0-0.065-0.01821.084-0.003-0.0030.0000.0000.0000.000
73A73THR0-0.042-0.04315.492-0.017-0.0170.0000.0000.0000.000
74A74THR0-0.049-0.05014.6750.0140.0140.0000.0000.0000.000
75A75LEU0-0.0400.00610.405-0.006-0.0060.0000.0000.0000.000
76A76PRO00.0090.0037.7990.0640.0640.0000.0000.0000.000
77A77ILE0-0.018-0.00711.041-0.060-0.0600.0000.0000.0000.000
78A78ILE0-0.041-0.0179.4210.0620.0620.0000.0000.0000.000
79A79ALA00.0350.01113.670-0.027-0.0270.0000.0000.0000.000
80A80SER0-0.002-0.00616.9520.0260.0260.0000.0000.0000.000
81A81GLY00.0740.03818.774-0.009-0.0090.0000.0000.0000.000
82A82GLY00.0310.00122.3930.0010.0010.0000.0000.0000.000
83A83ALA0-0.054-0.01722.0210.0010.0010.0000.0000.0000.000
84A84GLY0-0.060-0.06124.088-0.005-0.0050.0000.0000.0000.000
85A85LYS10.8270.93026.034-0.076-0.0760.0000.0000.0000.000
86A86MET00.0470.04623.0910.0100.0100.0000.0000.0000.000
87A87GLU-1-0.786-0.91323.6590.0950.0950.0000.0000.0000.000
88A88HIS00.0460.03224.0790.0020.0020.0000.0000.0000.000
89A89PHE00.021-0.00419.260-0.002-0.0020.0000.0000.0000.000
90A90LEU00.0330.02020.4930.0030.0030.0000.0000.0000.000
91A91GLU-1-0.890-0.95022.6010.0630.0630.0000.0000.0000.000
92A92ALA0-0.013-0.01019.598-0.010-0.0100.0000.0000.0000.000
93A93PHE00.0260.01316.128-0.003-0.0030.0000.0000.0000.000
94A94LEU0-0.0140.00119.473-0.009-0.0090.0000.0000.0000.000
95A95ALA0-0.065-0.03821.985-0.011-0.0110.0000.0000.0000.000
96A96GLY00.0150.01419.261-0.013-0.0130.0000.0000.0000.000
97A97ALA0-0.027-0.01216.438-0.014-0.0140.0000.0000.0000.000
98A98ASP-1-0.777-0.87411.9560.0860.0860.0000.0000.0000.000
99A99LYS10.7620.8536.595-0.485-0.4850.0000.0000.0000.000
100A100ALA00.0030.01013.626-0.054-0.0540.0000.0000.0000.000
101A101LEU0-0.0070.00914.1970.0390.0390.0000.0000.0000.000
102A102ALA0-0.0050.01516.111-0.020-0.0200.0000.0000.0000.000
103A103ALA0-0.017-0.00518.956-0.011-0.0110.0000.0000.0000.000
104A104SER0-0.027-0.02621.9520.0070.0070.0000.0000.0000.000
105A105VAL00.0220.02621.592-0.005-0.0050.0000.0000.0000.000
106A106PHE0-0.019-0.02623.3820.0010.0010.0000.0000.0000.000
107A107HIS00.0170.00526.1220.0000.0000.0000.0000.0000.000
108A108PHE00.0000.00426.0190.0040.0040.0000.0000.0000.000
109A109ARG10.8940.94225.042-0.089-0.0890.0000.0000.0000.000
110A110GLU-1-0.862-0.92025.5610.0880.0880.0000.0000.0000.000
111A111ILE0-0.053-0.04325.3410.0150.0150.0000.0000.0000.000
112A112ASP-1-0.726-0.86524.6540.1450.1450.0000.0000.0000.000
113A113MET0-0.0330.00219.4910.0210.0210.0000.0000.0000.000
114A114ARG10.8520.92520.853-0.164-0.1640.0000.0000.0000.000
115A115GLU-1-0.935-0.95221.8490.1410.1410.0000.0000.0000.000
116A116LEU00.0140.00919.3170.0050.0050.0000.0000.0000.000
117A117LYS10.8790.93314.960-0.435-0.4350.0000.0000.0000.000
118A118GLU-1-0.856-0.91818.1050.3000.3000.0000.0000.0000.000
119A119TYR0-0.007-0.01620.756-0.002-0.0020.0000.0000.0000.000
120A120LEU0-0.032-0.02015.786-0.014-0.0140.0000.0000.0000.000
121A121LYS10.8020.91316.634-0.266-0.2660.0000.0000.0000.000
122A122LYS10.8700.93818.836-0.164-0.1640.0000.0000.0000.000
123A123HIS00.007-0.01420.972-0.015-0.0150.0000.0000.0000.000
124A124GLY00.0450.04018.947-0.016-0.0160.0000.0000.0000.000
125A125GLY0-0.0020.01217.1400.0200.0200.0000.0000.0000.000
126A126SER00.0480.01113.0340.0350.0350.0000.0000.0000.000
127A127GLY0-0.0240.00510.000-0.052-0.0520.0000.0000.0000.000
128A128GLN0-0.003-0.00810.2890.0230.0230.0000.0000.0000.000
129A129ALA0-0.009-0.01010.9480.0610.0610.0000.0000.0000.000
130A130VAL00.0150.01112.987-0.069-0.0690.0000.0000.0000.000
131A131VAL00.0000.00310.6160.0530.0530.0000.0000.0000.000
132A132VAL00.024-0.00413.120-0.055-0.0550.0000.0000.0000.000
133A133ALA00.0190.01414.5050.0100.0100.0000.0000.0000.000
134A134ILE0-0.047-0.02815.7470.0060.0060.0000.0000.0000.000
135A135ASP-1-0.833-0.90017.0710.0180.0180.0000.0000.0000.000
136A136ALA0-0.010-0.02119.0690.0090.0090.0000.0000.0000.000
137A137LYS10.8240.90120.826-0.020-0.0200.0000.0000.0000.000
138A138ARG10.7510.82420.3430.0030.0030.0000.0000.0000.000
139A139VAL0-0.067-0.05325.496-0.004-0.0040.0000.0000.0000.000
140A140ASP-1-0.900-0.94728.9840.0200.0200.0000.0000.0000.000
141A141GLY0-0.019-0.00228.625-0.001-0.0010.0000.0000.0000.000
142A142GLU-1-0.814-0.90625.8750.0530.0530.0000.0000.0000.000
143A143PHE0-0.013-0.00520.973-0.003-0.0030.0000.0000.0000.000
144A144MET0-0.0210.00923.9260.0100.0100.0000.0000.0000.000
145A145VAL00.0420.02421.108-0.002-0.0020.0000.0000.0000.000
146A146PHE0-0.041-0.01922.740-0.008-0.0080.0000.0000.0000.000
147A147THR00.0500.02523.3090.0050.0050.0000.0000.0000.000
148A148HIS0-0.029-0.03225.393-0.006-0.0060.0000.0000.0000.000
149A149SER00.0820.03923.768-0.003-0.0030.0000.0000.0000.000
150A150GLY00.0650.03124.206-0.006-0.0060.0000.0000.0000.000
151A151LYS10.8060.89725.018-0.007-0.0070.0000.0000.0000.000
152A152LYS10.9040.96028.112-0.039-0.0390.0000.0000.0000.000
153A153ASN00.0750.04327.7190.0080.0080.0000.0000.0000.000
154A154THR0-0.029-0.03725.4560.0000.0000.0000.0000.0000.000
155A155GLY0-0.0050.00528.4130.0000.0000.0000.0000.0000.000
156A156ILE0-0.036-0.01124.9720.0010.0010.0000.0000.0000.000
157A157LEU00.0580.02225.3210.0000.0000.0000.0000.0000.000
158A158LEU0-0.032-0.02917.6360.0100.0100.0000.0000.0000.000
159A159ARG10.8050.86720.252-0.055-0.0550.0000.0000.0000.000
160A160ASP-1-0.790-0.87121.1440.0990.0990.0000.0000.0000.000
161A161TRP0-0.013-0.01619.9010.0110.0110.0000.0000.0000.000
162A162VAL00.0130.01315.4600.0130.0130.0000.0000.0000.000
163A163VAL00.0450.02817.6450.0290.0290.0000.0000.0000.000
164A164GLU-1-0.846-0.89419.7520.1370.1370.0000.0000.0000.000
165A165VAL00.0300.00316.0230.0060.0060.0000.0000.0000.000
166A166GLU-1-0.758-0.82314.8130.4480.4480.0000.0000.0000.000
167A167LYS10.8190.90217.176-0.136-0.1360.0000.0000.0000.000
168A168ARG10.7510.84920.697-0.169-0.1690.0000.0000.0000.000
169A169GLY00.0350.01118.950-0.007-0.0070.0000.0000.0000.000
170A170ALA00.0270.02614.7120.0120.0120.0000.0000.0000.000
171A171GLY0-0.011-0.01112.7410.0180.0180.0000.0000.0000.000
172A172GLU-1-0.753-0.8536.0431.0451.0450.0000.0000.0000.000
173A173ILE00.0040.0069.729-0.147-0.1470.0000.0000.0000.000
174A174LEU0-0.022-0.0039.941-0.009-0.0090.0000.0000.0000.000
175A175LEU00.0070.00611.8120.0000.0000.0000.0000.0000.000
176A176THR0-0.032-0.02513.761-0.039-0.0390.0000.0000.0000.000
177A177SER0-0.020-0.04416.4440.0130.0130.0000.0000.0000.000
178A178ILE00.0140.00318.488-0.013-0.0130.0000.0000.0000.000
179A179ASP-1-0.811-0.86521.7890.0040.0040.0000.0000.0000.000
180A180ARG10.9150.95818.8280.0340.0340.0000.0000.0000.000
181A181ASP-1-0.785-0.88719.491-0.063-0.0630.0000.0000.0000.000
182A182GLY0-0.082-0.01820.5970.0060.0060.0000.0000.0000.000
183A183THR0-0.067-0.05621.887-0.004-0.0040.0000.0000.0000.000
184A184LYS10.8750.95420.9470.0790.0790.0000.0000.0000.000
185A185SER00.0380.00221.508-0.005-0.0050.0000.0000.0000.000
186A186GLY00.019-0.01317.899-0.001-0.0010.0000.0000.0000.000
187A187TYR0-0.020-0.03112.3510.0000.0000.0000.0000.0000.000
188A188ASP-1-0.718-0.80315.5540.0050.0050.0000.0000.0000.000
189A189THR00.014-0.00413.9070.0190.0190.0000.0000.0000.000
190A190GLU-1-0.858-0.90015.1570.0100.0100.0000.0000.0000.000
191A191MET00.0040.01316.8680.0130.0130.0000.0000.0000.000
192A192ILE0-0.026-0.01610.4290.0180.0180.0000.0000.0000.000
193A193ARG10.9360.96813.1910.0570.0570.0000.0000.0000.000
194A194PHE0-0.033-0.01214.6840.0130.0130.0000.0000.0000.000
195A195VAL00.0330.00413.2470.0090.0090.0000.0000.0000.000
196A196ARG10.7990.8857.096-0.739-0.7390.0000.0000.0000.000
197A197PRO0-0.033-0.01012.4480.0560.0560.0000.0000.0000.000
198A198LEU0-0.060-0.02115.073-0.009-0.0090.0000.0000.0000.000
199A199THR0-0.060-0.05011.7970.0230.0230.0000.0000.0000.000
200A200THR0-0.050-0.05611.9670.0580.0580.0000.0000.0000.000
201A201LEU0-0.064-0.01610.3510.1920.1920.0000.0000.0000.000
202A202PRO00.0160.0075.030-0.015-0.0150.0000.0000.0000.000
203A203ILE0-0.021-0.0116.354-0.435-0.4350.0000.0000.0000.000
204A204ILE0-0.013-0.0056.474-0.231-0.2310.0000.0000.0000.000
205A205ALA00.0200.0037.9180.0990.0990.0000.0000.0000.000
206A206SER00.015-0.00310.408-0.083-0.0830.0000.0000.0000.000
207A207GLY00.0540.02713.5160.0280.0280.0000.0000.0000.000
208A208GLY00.0340.01116.547-0.003-0.0030.0000.0000.0000.000
209A209ALA0-0.045-0.00414.9270.0040.0040.0000.0000.0000.000
210A210GLY0-0.021-0.04316.8210.0100.0100.0000.0000.0000.000
211A211LYS10.8130.92717.8920.0990.0990.0000.0000.0000.000
212A212MET00.0440.02912.378-0.014-0.0140.0000.0000.0000.000
213A213GLU-1-0.785-0.93213.816-0.117-0.1170.0000.0000.0000.000
214A214HIS0-0.0350.02213.589-0.005-0.0050.0000.0000.0000.000
215A215PHE00.0180.00910.0060.0130.0130.0000.0000.0000.000
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