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: 5J89Z

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2826093.774995
FMO2-HF: Nuclear repulsion 2736954.764898
FMO2-HF: Total energy -89139.010097
FMO2-MP2: Total energy -89399.541761


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.
-3.7920.0490000000000064.136-3.125-4.8510
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 : -0.034 / q_NPA : -0.022
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].
3A3ARG10.8200.8912.216-7.400-5.5953.551-2.033-3.3240.007
4A4VAL00.0230.0184.7500.0570.152-0.001-0.014-0.0800.000
5A5VAL00.000-0.0018.184-0.033-0.0330.0000.0000.0000.000
6A6VAL00.0280.00310.319-0.105-0.1050.0000.0000.0000.000
7A7ALA0-0.037-0.01313.9900.0160.0160.0000.0000.0000.000
8A8ILE0-0.015-0.00816.667-0.046-0.0460.0000.0000.0000.000
9A9ASP-1-0.855-0.91619.4070.2610.2610.0000.0000.0000.000
10A10ALA0-0.004-0.02122.527-0.017-0.0170.0000.0000.0000.000
11A11LYS10.8860.95125.214-0.120-0.1200.0000.0000.0000.000
12A12ARG10.8390.90828.620-0.125-0.1250.0000.0000.0000.000
13A13VAL0-0.093-0.05731.581-0.002-0.0020.0000.0000.0000.000
14A14ASP-1-0.867-0.92634.1720.0710.0710.0000.0000.0000.000
15A15GLY0-0.047-0.02235.168-0.002-0.0020.0000.0000.0000.000
16A16GLU-1-0.902-0.93931.8620.0840.0840.0000.0000.0000.000
17A17PHE0-0.001-0.00226.7150.0050.0050.0000.0000.0000.000
18A18MET0-0.0020.03228.1670.0010.0010.0000.0000.0000.000
19A19VAL00.0510.02123.4720.0100.0100.0000.0000.0000.000
20A20PHE0-0.0500.00225.457-0.017-0.0170.0000.0000.0000.000
21A21THR00.0410.00324.4910.0130.0130.0000.0000.0000.000
22A22HIS0-0.027-0.02026.037-0.003-0.0030.0000.0000.0000.000
23A23SER00.0420.01125.239-0.008-0.0080.0000.0000.0000.000
24A24GLY00.0900.04326.112-0.006-0.0060.0000.0000.0000.000
25A25LYS10.9160.95427.405-0.111-0.1110.0000.0000.0000.000
26A26LYS10.8720.95629.595-0.103-0.1030.0000.0000.0000.000
27A27ASN00.0870.04929.3430.0120.0120.0000.0000.0000.000
28A28THR0-0.060-0.07726.384-0.009-0.0090.0000.0000.0000.000
29A29GLY00.0210.01029.732-0.005-0.0050.0000.0000.0000.000
30A30ILE0-0.0090.00225.752-0.005-0.0050.0000.0000.0000.000
31A31LEU00.0310.01727.7760.0090.0090.0000.0000.0000.000
32A32LEU0-0.013-0.02021.5680.0060.0060.0000.0000.0000.000
33A33ARG10.8830.93323.262-0.084-0.0840.0000.0000.0000.000
34A34ASP-1-0.823-0.91423.7640.1010.1010.0000.0000.0000.000
35A35TRP0-0.024-0.02419.929-0.008-0.0080.0000.0000.0000.000
36A36VAL00.0350.01718.2870.0130.0130.0000.0000.0000.000
37A37VAL00.0320.02318.3290.0100.0100.0000.0000.0000.000
38A38GLU-1-0.906-0.95819.2800.1130.1130.0000.0000.0000.000
39A39VAL0-0.007-0.00915.3790.0000.0000.0000.0000.0000.000
40A40GLU-1-0.739-0.83314.7470.1940.1940.0000.0000.0000.000
41A41LYS10.8320.92115.337-0.114-0.1140.0000.0000.0000.000
42A42ARG10.8420.92717.069-0.151-0.1510.0000.0000.0000.000
43A43GLY00.0050.00713.766-0.018-0.0180.0000.0000.0000.000
44A44ALA0-0.082-0.02811.6650.0260.0260.0000.0000.0000.000
45A45GLY00.0250.0097.836-0.068-0.0680.0000.0000.0000.000
46A46GLU-1-0.799-0.8907.0732.0032.0030.0000.0000.0000.000
47A47ILE00.0280.0179.837-0.049-0.0490.0000.0000.0000.000
48A48LEU0-0.0280.00213.3450.0260.0260.0000.0000.0000.000
49A49LEU00.0030.00014.867-0.049-0.0490.0000.0000.0000.000
50A50THR00.004-0.00818.1770.0010.0010.0000.0000.0000.000
51A51SER0-0.017-0.03020.991-0.024-0.0240.0000.0000.0000.000
52A52ILE0-0.004-0.01024.387-0.006-0.0060.0000.0000.0000.000
53A53ASP-1-0.848-0.92626.9790.1150.1150.0000.0000.0000.000
54A54ARG10.9020.95226.094-0.141-0.1410.0000.0000.0000.000
55A55ASP-1-0.899-0.94524.2410.2110.2110.0000.0000.0000.000
56A56GLY0-0.062-0.00526.392-0.010-0.0100.0000.0000.0000.000
57A57THR00.002-0.02728.260-0.011-0.0110.0000.0000.0000.000
58A58LYS10.8700.94028.072-0.146-0.1460.0000.0000.0000.000
59A59SER00.020-0.01129.633-0.002-0.0020.0000.0000.0000.000
60A60GLY00.0310.02926.966-0.007-0.0070.0000.0000.0000.000
61A61TYR0-0.019-0.04120.082-0.005-0.0050.0000.0000.0000.000
62A62ASP-1-0.757-0.85524.2590.1320.1320.0000.0000.0000.000
63A63THR00.003-0.01224.3500.0050.0050.0000.0000.0000.000
64A64GLU-1-0.943-0.96025.2780.1070.1070.0000.0000.0000.000
65A65MET00.0020.01623.0670.0060.0060.0000.0000.0000.000
66A66ILE0-0.025-0.01619.5910.0060.0060.0000.0000.0000.000
67A67ARG10.9580.97421.655-0.119-0.1190.0000.0000.0000.000
68A68PHE0-0.035-0.01924.105-0.006-0.0060.0000.0000.0000.000
69A69VAL00.016-0.00718.757-0.005-0.0050.0000.0000.0000.000
70A70ARG10.7810.87914.729-0.240-0.2400.0000.0000.0000.000
71A71PRO0-0.034-0.02619.647-0.002-0.0020.0000.0000.0000.000
72A72LEU0-0.082-0.02921.223-0.010-0.0100.0000.0000.0000.000
73A73THR0-0.021-0.00615.7170.0150.0150.0000.0000.0000.000
74A74THR0-0.050-0.06114.416-0.001-0.0010.0000.0000.0000.000
75A75LEU0-0.054-0.00810.6820.0130.0130.0000.0000.0000.000
76A76PRO00.0200.0157.907-0.020-0.0200.0000.0000.0000.000
77A77ILE00.0000.00611.1230.0510.0510.0000.0000.0000.000
78A78ILE0-0.051-0.03010.240-0.012-0.0120.0000.0000.0000.000
79A79ALA00.0180.00214.172-0.035-0.0350.0000.0000.0000.000
80A80SER00.007-0.00817.8580.0190.0190.0000.0000.0000.000
81A81GLY00.0930.05019.822-0.020-0.0200.0000.0000.0000.000
82A82GLY0-0.004-0.01223.469-0.004-0.0040.0000.0000.0000.000
83A83ALA0-0.0120.00522.716-0.014-0.0140.0000.0000.0000.000
84A84GLY0-0.093-0.05624.787-0.003-0.0030.0000.0000.0000.000
85A85LYS10.8990.96926.561-0.114-0.1140.0000.0000.0000.000
86A86MET00.0510.02923.0060.0180.0180.0000.0000.0000.000
87A87GLU-1-0.817-0.93223.8200.1150.1150.0000.0000.0000.000
88A88HIS00.0210.03224.7260.0120.0120.0000.0000.0000.000
89A89PHE00.0430.01619.4350.0080.0080.0000.0000.0000.000
90A90LEU00.0260.01620.6810.0080.0080.0000.0000.0000.000
91A91GLU-1-0.937-0.98622.8730.1270.1270.0000.0000.0000.000
92A92ALA0-0.040-0.01520.240-0.004-0.0040.0000.0000.0000.000
93A93PHE0-0.021-0.00615.7610.0010.0010.0000.0000.0000.000
94A94LEU0-0.036-0.01419.770-0.008-0.0080.0000.0000.0000.000
95A95ALA0-0.112-0.06222.537-0.010-0.0100.0000.0000.0000.000
96A96GLY00.0400.02019.330-0.006-0.0060.0000.0000.0000.000
97A97ALA0-0.0350.00316.5880.0130.0130.0000.0000.0000.000
98A98ASP-1-0.743-0.85111.9160.2960.2960.0000.0000.0000.000
99A99LYS10.7830.8826.906-1.406-1.4060.0000.0000.0000.000
100A100ALA00.0280.02213.806-0.034-0.0340.0000.0000.0000.000
101A101LEU0-0.0170.00915.5010.0270.0270.0000.0000.0000.000
102A102ALA0-0.0230.00817.180-0.050-0.0500.0000.0000.0000.000
103A103ALA0-0.005-0.00319.8560.0070.0070.0000.0000.0000.000
104A104SER00.006-0.01522.6870.0100.0100.0000.0000.0000.000
105A105VAL00.0040.02222.343-0.022-0.0220.0000.0000.0000.000
106A106PHE0-0.045-0.03824.5940.0060.0060.0000.0000.0000.000
107A107HIS00.017-0.00227.0960.0010.0010.0000.0000.0000.000
108A108PHE0-0.030-0.01126.643-0.004-0.0040.0000.0000.0000.000
109A109ARG10.8950.95325.718-0.076-0.0760.0000.0000.0000.000
110A110GLU-1-0.857-0.92026.5260.0670.0670.0000.0000.0000.000
111A111ILE0-0.083-0.05026.0960.0070.0070.0000.0000.0000.000
112A112ASP-1-0.743-0.86624.9870.1400.1400.0000.0000.0000.000
113A113MET0-0.0010.02719.9040.0100.0100.0000.0000.0000.000
114A114ARG10.9150.95020.671-0.074-0.0740.0000.0000.0000.000
115A115GLU-1-0.923-0.94321.8340.0750.0750.0000.0000.0000.000
116A116LEU00.0110.00819.019-0.005-0.0050.0000.0000.0000.000
117A117LYS10.9250.97213.817-0.185-0.1850.0000.0000.0000.000
118A118GLU-1-0.912-0.94717.8890.0490.0490.0000.0000.0000.000
119A119TYR00.005-0.00120.399-0.007-0.0070.0000.0000.0000.000
120A120LEU0-0.048-0.00515.611-0.009-0.0090.0000.0000.0000.000
121A121LYS10.8260.87916.241-0.086-0.0860.0000.0000.0000.000
122A122LYS10.8610.95918.699-0.029-0.0290.0000.0000.0000.000
123A123HIS0-0.001-0.01921.006-0.004-0.0040.0000.0000.0000.000
124A124GLY00.0610.04019.2880.0050.0050.0000.0000.0000.000
125A125GLY0-0.026-0.00717.1290.0140.0140.0000.0000.0000.000
126A126SER00.029-0.00712.275-0.009-0.0090.0000.0000.0000.000
127A127GLY00.0000.01310.033-0.023-0.0230.0000.0000.0000.000
128A128GLN0-0.0120.00810.6860.1050.1050.0000.0000.0000.000
129A129ALA00.011-0.00211.094-0.029-0.0290.0000.0000.0000.000
130A130VAL00.0190.00613.0140.0000.0000.0000.0000.0000.000
131A131VAL00.009-0.00411.5350.0170.0170.0000.0000.0000.000
132A132VAL00.018-0.00413.996-0.077-0.0770.0000.0000.0000.000
133A133ALA00.0220.02615.5050.0560.0560.0000.0000.0000.000
134A134ILE0-0.056-0.03016.832-0.058-0.0580.0000.0000.0000.000
135A135ASP-1-0.841-0.91318.0290.2960.2960.0000.0000.0000.000
136A136ALA0-0.006-0.02620.014-0.027-0.0270.0000.0000.0000.000
137A137LYS10.9010.95521.674-0.088-0.0880.0000.0000.0000.000
138A138ARG10.7530.81720.509-0.083-0.0830.0000.0000.0000.000
139A139VAL0-0.076-0.05326.0400.0010.0010.0000.0000.0000.000
140A140ASP-1-0.888-0.93929.4270.0410.0410.0000.0000.0000.000
141A141GLY0-0.045-0.02328.080-0.003-0.0030.0000.0000.0000.000
142A142GLU-1-0.890-0.93026.8030.0380.0380.0000.0000.0000.000
143A143PHE00.009-0.00220.8600.0120.0120.0000.0000.0000.000
144A144MET0-0.0260.00524.0350.0010.0010.0000.0000.0000.000
145A145VAL00.0670.03622.0820.0140.0140.0000.0000.0000.000
146A146PHE0-0.045-0.02624.071-0.022-0.0220.0000.0000.0000.000
147A147THR00.0530.02324.6030.0120.0120.0000.0000.0000.000
148A148HIS0-0.031-0.03526.692-0.008-0.0080.0000.0000.0000.000
149A149SER00.0630.03625.262-0.006-0.0060.0000.0000.0000.000
150A150GLY00.0660.01125.876-0.007-0.0070.0000.0000.0000.000
151A151LYS10.8490.93026.462-0.132-0.1320.0000.0000.0000.000
152A152LYS10.9110.97329.451-0.102-0.1020.0000.0000.0000.000
153A153ASN00.0920.06229.0390.0150.0150.0000.0000.0000.000
154A154THR0-0.050-0.05227.248-0.005-0.0050.0000.0000.0000.000
155A155GLY0-0.011-0.00229.791-0.005-0.0050.0000.0000.0000.000
156A156ILE0-0.0270.00025.878-0.008-0.0080.0000.0000.0000.000
157A157LEU00.0570.01725.2870.0090.0090.0000.0000.0000.000
158A158LEU0-0.016-0.01718.1900.0060.0060.0000.0000.0000.000
159A159ARG10.9180.94920.982-0.037-0.0370.0000.0000.0000.000
160A160ASP-1-0.861-0.93021.6430.0670.0670.0000.0000.0000.000
161A161TRP00.003-0.00420.922-0.007-0.0070.0000.0000.0000.000
162A162VAL00.0160.00916.2810.0140.0140.0000.0000.0000.000
163A163VAL00.0320.01918.2930.0090.0090.0000.0000.0000.000
164A164GLU-1-0.887-0.92920.2850.0920.0920.0000.0000.0000.000
165A165VAL00.041-0.00616.723-0.003-0.0030.0000.0000.0000.000
166A166GLU-1-0.768-0.83115.1950.1360.1360.0000.0000.0000.000
167A167LYS10.9050.95817.471-0.077-0.0770.0000.0000.0000.000
168A168ARG10.7260.82820.543-0.171-0.1710.0000.0000.0000.000
169A169GLY00.0050.00018.2870.0030.0030.0000.0000.0000.000
170A170ALA00.0060.01115.5370.0100.0100.0000.0000.0000.000
171A171GLY0-0.029-0.02212.742-0.040-0.0400.0000.0000.0000.000
172A172GLU-1-0.781-0.8898.0931.7131.7130.0000.0000.0000.000
173A173ILE00.0250.01610.794-0.125-0.1250.0000.0000.0000.000
174A174LEU0-0.031-0.01111.3700.1810.1810.0000.0000.0000.000
175A175LEU00.004-0.00612.891-0.116-0.1160.0000.0000.0000.000
176A176THR00.009-0.00514.6050.0390.0390.0000.0000.0000.000
177A177SER0-0.049-0.04117.256-0.046-0.0460.0000.0000.0000.000
178A178ILE00.007-0.01219.137-0.006-0.0060.0000.0000.0000.000
179A179ASP-1-0.832-0.90122.3430.0920.0920.0000.0000.0000.000
180A180ARG10.9020.95519.180-0.092-0.0920.0000.0000.0000.000
181A181ASP-1-0.876-0.93420.4340.2330.2330.0000.0000.0000.000
182A182GLY0-0.050-0.01121.328-0.019-0.0190.0000.0000.0000.000
183A183THR0-0.051-0.03222.088-0.018-0.0180.0000.0000.0000.000
184A184LYS10.8660.94521.017-0.135-0.1350.0000.0000.0000.000
185A185SER00.008-0.01521.769-0.017-0.0170.0000.0000.0000.000
186A186GLY00.007-0.00317.518-0.024-0.0240.0000.0000.0000.000
187A187TYR0-0.029-0.04412.8680.0030.0030.0000.0000.0000.000
188A188ASP-1-0.706-0.79215.7230.0690.0690.0000.0000.0000.000
189A189THR00.016-0.00413.7770.0170.0170.0000.0000.0000.000
190A190GLU-1-0.896-0.93015.3660.0160.0160.0000.0000.0000.000
191A191MET00.0040.02116.7820.0050.0050.0000.0000.0000.000
192A192ILE0-0.030-0.01510.6230.0130.0130.0000.0000.0000.000
193A193ARG10.9650.97513.4740.0640.0640.0000.0000.0000.000
194A194PHE0-0.041-0.01614.818-0.017-0.0170.0000.0000.0000.000
195A195VAL00.003-0.01313.637-0.012-0.0120.0000.0000.0000.000
196A196ARG10.8150.8907.687-0.350-0.3500.0000.0000.0000.000
197A197PRO0-0.040-0.00812.747-0.012-0.0120.0000.0000.0000.000
198A198LEU0-0.064-0.02215.318-0.010-0.0100.0000.0000.0000.000
199A199THR0-0.050-0.03112.3750.0410.0410.0000.0000.0000.000
200A200THR0-0.051-0.05812.107-0.007-0.0070.0000.0000.0000.000
201A201LEU0-0.070-0.01910.280-0.030-0.0300.0000.0000.0000.000
202A202PRO00.0030.0155.4440.0550.0550.0000.0000.0000.000
203A203ILE0-0.010-0.0057.281-0.185-0.1850.0000.0000.0000.000
204A204ILE00.000-0.0097.3950.4290.4290.0000.0000.0000.000
205A205ALA00.0150.0109.273-0.320-0.3200.0000.0000.0000.000
206A206SER00.0140.00811.3300.0520.0520.0000.0000.0000.000
207A207GLY00.0830.04914.487-0.050-0.0500.0000.0000.0000.000
208A208GLY00.029-0.00517.153-0.008-0.0080.0000.0000.0000.000
209A209ALA0-0.0590.00215.309-0.037-0.0370.0000.0000.0000.000
210A210GLY0-0.030-0.04317.131-0.001-0.0010.0000.0000.0000.000
211A211LYS10.8910.95817.958-0.011-0.0110.0000.0000.0000.000
212A212MET00.0580.04312.6620.0170.0170.0000.0000.0000.000
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