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: JQR19

Calculation Name: 2F20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F20

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A8E9

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 -3180394.013256
FMO2-HF: Nuclear repulsion 3084773.260147
FMO2-HF: Total energy -95620.753109
FMO2-MP2: Total energy -95900.119807


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-39.993-31.33121.12-13.044-16.738-0.102
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / 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].
3A4HIS00.0140.0133.209-2.7430.6250.000-1.857-1.5110.008
4A5ASN00.0660.0514.3731.5361.8900.001-0.038-0.3170.000
5A6SER00.006-0.0096.021-0.996-0.9960.0000.0000.0000.000
6A7MET0-0.004-0.0109.3890.1440.1440.0000.0000.0000.000
7A8SER00.0060.00512.437-0.101-0.1010.0000.0000.0000.000
8A9ALA00.0120.02115.359-0.076-0.0760.0000.0000.0000.000
9A10LYS10.8060.89217.824-0.198-0.1980.0000.0000.0000.000
10A11ALA00.0890.02319.2730.0270.0270.0000.0000.0000.000
11A12ILE00.0190.00020.3160.0180.0180.0000.0000.0000.000
12A13LYS10.9050.95720.378-0.237-0.2370.0000.0000.0000.000
13A14VAL00.0360.02116.3640.0110.0110.0000.0000.0000.000
14A15ALA0-0.004-0.00718.9140.0090.0090.0000.0000.0000.000
15A16ALA0-0.029-0.01421.767-0.008-0.0080.0000.0000.0000.000
16A17ARG10.7120.83416.017-0.489-0.4890.0000.0000.0000.000
17A18TYR0-0.030-0.03314.4300.0180.0180.0000.0000.0000.000
18A19GLY0-0.024-0.00420.889-0.014-0.0140.0000.0000.0000.000
19A20ARG10.7640.86021.061-0.331-0.3310.0000.0000.0000.000
20A21GLN0-0.038-0.02424.433-0.003-0.0030.0000.0000.0000.000
21A22SER00.046-0.00624.0900.0190.0190.0000.0000.0000.000
22A23ASP-1-0.834-0.87025.1560.1730.1730.0000.0000.0000.000
23A24VAL00.0140.00422.595-0.007-0.0070.0000.0000.0000.000
24A25VAL0-0.008-0.01819.248-0.001-0.0010.0000.0000.0000.000
25A26GLU-1-0.857-0.91222.0800.1900.1900.0000.0000.0000.000
26A27ILE0-0.033-0.00325.139-0.012-0.0120.0000.0000.0000.000
27A28TYR0-0.033-0.02221.347-0.021-0.0210.0000.0000.0000.000
28A29GLN00.017-0.00921.4420.0130.0130.0000.0000.0000.000
29A30SER0-0.023-0.01121.5990.0100.0100.0000.0000.0000.000
30A31ILE0-0.063-0.02918.438-0.009-0.0090.0000.0000.0000.000
31A32LEU0-0.020-0.01416.6250.0350.0350.0000.0000.0000.000
32A33ASP-1-0.805-0.89616.8140.3130.3130.0000.0000.0000.000
33A34GLU-1-0.928-0.94817.0240.1930.1930.0000.0000.0000.000
34A35GLN00.0050.00713.747-0.063-0.0630.0000.0000.0000.000
35A36TYR00.0040.00212.6290.1610.1610.0000.0000.0000.000
36A37HIS0-0.028-0.0068.4660.0550.0550.0000.0000.0000.000
37A38VAL0-0.0260.0008.777-0.149-0.1490.0000.0000.0000.000
38A39ASN00.0450.0098.0290.2250.2250.0000.0000.0000.000
39A40ALA00.0970.0486.281-0.040-0.0400.0000.0000.0000.000
40A41PHE0-0.020-0.0127.306-0.016-0.0160.0000.0000.0000.000
41A42THR0-0.073-0.03111.1100.0270.0270.0000.0000.0000.000
42A43PHE0-0.035-0.02511.7990.0270.0270.0000.0000.0000.000
43A44PRO00.0120.02411.1120.0100.0100.0000.0000.0000.000
44A45ARG10.9340.97013.424-0.160-0.1600.0000.0000.0000.000
45A46TYR0-0.060-0.06110.4350.0720.0720.0000.0000.0000.000
46A47PRO00.0460.01913.591-0.061-0.0610.0000.0000.0000.000
47A48ILE0-0.031-0.01411.5270.1160.1160.0000.0000.0000.000
48A49ILE0-0.0050.01514.954-0.085-0.0850.0000.0000.0000.000
49A50THR00.0460.00616.3980.0450.0450.0000.0000.0000.000
50A51SER00.008-0.00419.020-0.004-0.0040.0000.0000.0000.000
51A52SER0-0.026-0.00722.173-0.023-0.0230.0000.0000.0000.000
52A53ASP-1-0.815-0.90823.1950.2190.2190.0000.0000.0000.000
53A54GLH0-0.096-0.08224.3550.0070.0070.0000.0000.0000.000
54A55VAL00.0000.01618.3210.0170.0170.0000.0000.0000.000
55A56GLN0-0.060-0.03618.413-0.043-0.0430.0000.0000.0000.000
56A57VAL0-0.011-0.01117.3480.0420.0420.0000.0000.0000.000
57A58PHE0-0.0070.01214.787-0.034-0.0340.0000.0000.0000.000
58A59ASN0-0.007-0.01814.5550.0500.0500.0000.0000.0000.000
59A60TRP0-0.046-0.0224.261-0.2450.032-0.001-0.101-0.1760.000
60A61GLY00.016-0.01210.733-0.110-0.1100.0000.0000.0000.000
61A62LEU0-0.048-0.02211.4890.0120.0120.0000.0000.0000.000
62A63ILE00.0440.03613.515-0.055-0.0550.0000.0000.0000.000
63A64PRO0-0.028-0.00916.4730.0200.0200.0000.0000.0000.000
64A65PHE0-0.015-0.01118.981-0.018-0.0180.0000.0000.0000.000
65A66TRP0-0.071-0.04419.108-0.016-0.0160.0000.0000.0000.000
66A67VAL0-0.020-0.00319.927-0.012-0.0120.0000.0000.0000.000
67A68ARG10.9170.95823.255-0.023-0.0230.0000.0000.0000.000
68A69SER00.017-0.01525.1180.0010.0010.0000.0000.0000.000
69A70GLU-1-0.852-0.93723.4760.0030.0030.0000.0000.0000.000
70A71GLU-1-0.940-0.96422.524-0.060-0.0600.0000.0000.0000.000
71A72ASP-1-0.868-0.90821.783-0.053-0.0530.0000.0000.0000.000
72A73ALA0-0.037-0.02219.434-0.014-0.0140.0000.0000.0000.000
73A74THR0-0.064-0.03317.802-0.007-0.0070.0000.0000.0000.000
74A75GLU-1-0.782-0.87516.841-0.218-0.2180.0000.0000.0000.000
75A76ILE0-0.013-0.01815.206-0.041-0.0410.0000.0000.0000.000
76A77ARG10.9180.99413.5400.0070.0070.0000.0000.0000.000
77A78LYS10.7690.86311.4420.1810.1810.0000.0000.0000.000
78A79MET0-0.091-0.03810.093-0.151-0.1510.0000.0000.0000.000
79A80THR0-0.054-0.04010.1100.0210.0210.0000.0000.0000.000
80A81LEU00.0550.0506.7070.1340.1340.0000.0000.0000.000
81A82ASN0-0.071-0.0452.354-3.436-2.0682.151-1.463-2.056-0.016
82A83ALA00.0340.0186.042-0.055-0.0550.0000.0000.0000.000
83A84ARG10.8460.9138.6290.0030.0030.0000.0000.0000.000
84A85ALA00.0700.0309.607-0.131-0.1310.0000.0000.0000.000
85A86ASP-1-0.841-0.89811.6670.2790.2790.0000.0000.0000.000
86A87THR00.009-0.00513.773-0.062-0.0620.0000.0000.0000.000
87A88ILE0-0.0420.00111.514-0.053-0.0530.0000.0000.0000.000
88A89PHE00.006-0.02014.923-0.024-0.0240.0000.0000.0000.000
89A90GLU-1-0.833-0.93118.0210.1580.1580.0000.0000.0000.000
90A91LYS10.9030.94612.204-0.143-0.1430.0000.0000.0000.000
91A92PRO00.0350.00617.6030.0210.0210.0000.0000.0000.000
92A93SER00.0000.00815.0370.0060.0060.0000.0000.0000.000
93A94PHE00.026-0.00411.0080.0280.0280.0000.0000.0000.000
94A95ARG10.8700.94216.105-0.071-0.0710.0000.0000.0000.000
95A96GLU-1-0.810-0.90519.2220.1170.1170.0000.0000.0000.000
96A97PRO00.0030.00216.1440.0060.0060.0000.0000.0000.000
97A98ILE00.0470.03914.6690.0230.0230.0000.0000.0000.000
98A99MET0-0.035-0.00517.1570.0090.0090.0000.0000.0000.000
99A100LYS10.9010.92820.704-0.168-0.1680.0000.0000.0000.000
100A101LYS10.8030.91118.347-0.208-0.2080.0000.0000.0000.000
101A102ARG10.8580.92715.486-0.301-0.3010.0000.0000.0000.000
102A103CYS0-0.061-0.02313.386-0.021-0.0210.0000.0000.0000.000
103A104ILE00.0230.02312.5700.0630.0630.0000.0000.0000.000
104A105VAL00.0320.0087.802-0.081-0.0810.0000.0000.0000.000
105A106PRO00.0060.0199.9380.1870.1870.0000.0000.0000.000
106A107SER00.0340.0107.3260.0740.0740.0000.0000.0000.000
107A108THR00.0330.0329.984-0.233-0.2330.0000.0000.0000.000
108A109GLY0-0.009-0.0048.340-0.323-0.3230.0000.0000.0000.000
109A110TYR0-0.044-0.0282.311-0.2271.2332.060-1.226-2.294-0.004
110A111PHE0-0.021-0.0164.555-1.200-1.082-0.001-0.012-0.1040.000
111A112GLU-1-0.806-0.9011.892-30.106-30.95114.207-7.307-6.055-0.091
112A113TRP0-0.052-0.0325.7251.0331.0330.0000.0000.0000.000
113A114ARG10.8780.9538.8990.4410.4410.0000.0000.0000.000
114A115HIS0-0.041-0.0389.4820.3570.3570.0000.0000.0000.000
115A116GLU-1-0.806-0.88413.705-0.426-0.4260.0000.0000.0000.000
116A117GLY00.0100.01817.3250.0360.0360.0000.0000.0000.000
117A118ALA0-0.015-0.02218.448-0.032-0.0320.0000.0000.0000.000
118A119ASN0-0.061-0.02317.845-0.010-0.0100.0000.0000.0000.000
119A120LYS10.9200.96311.8100.7140.7140.0000.0000.0000.000
120A121ILE00.0260.01013.3980.0680.0680.0000.0000.0000.000
121A122PRO0-0.0130.01510.365-0.205-0.2050.0000.0000.0000.000
122A123TYR00.042-0.0029.2550.2310.2310.0000.0000.0000.000
123A124TYR0-0.045-0.0288.295-0.212-0.2120.0000.0000.0000.000
124A125ILE0-0.006-0.0155.743-0.024-0.0240.0000.0000.0000.000
125A126TYR0-0.059-0.0588.2310.3820.3820.0000.0000.0000.000
126A127VAL0-0.015-0.00310.370-0.104-0.1040.0000.0000.0000.000
127A128LYS10.8500.90812.691-0.025-0.0250.0000.0000.0000.000
128A129ASP-1-0.940-0.97216.3530.1640.1640.0000.0000.0000.000
129A130GLU-1-0.795-0.90214.8510.5030.5030.0000.0000.0000.000
130A131PRO0-0.065-0.03314.6750.0550.0550.0000.0000.0000.000
131A132ILE0-0.031-0.01213.6960.0500.0500.0000.0000.0000.000
132A133PHE00.0710.0477.349-0.051-0.0510.0000.0000.0000.000
133A134SER00.030-0.02611.6310.1290.1290.0000.0000.0000.000
134A135MET0-0.048-0.0085.5920.1450.252-0.001-0.009-0.0960.000
135A136ALA00.0290.0169.140-0.150-0.1500.0000.0000.0000.000
136A137GLY00.0310.0068.7930.2060.2060.0000.0000.0000.000
137A138ILE0-0.049-0.01910.542-0.105-0.1050.0000.0000.0000.000
138A139TYR00.0460.00412.4460.0140.0140.0000.0000.0000.000
139A140ASP-1-0.805-0.90115.0790.1380.1380.0000.0000.0000.000
140A141ARG10.9560.98518.070-0.126-0.1260.0000.0000.0000.000
141A142TRP0-0.052-0.03820.898-0.009-0.0090.0000.0000.0000.000
142A143LEU00.0470.03922.5010.0010.0010.0000.0000.0000.000
143A144ASP-1-0.835-0.90625.2330.0190.0190.0000.0000.0000.000
144A145LYS10.8270.90126.673-0.025-0.0250.0000.0000.0000.000
145A146ASP-1-0.898-0.95429.6540.0130.0130.0000.0000.0000.000
146A147THR0-0.011-0.00127.723-0.003-0.0030.0000.0000.0000.000
147A148GLY0-0.074-0.03329.8410.0020.0020.0000.0000.0000.000
148A149GLU-1-0.928-0.98023.8580.0810.0810.0000.0000.0000.000
149A150GLU-1-0.913-0.96324.2470.1080.1080.0000.0000.0000.000
150A151HIS10.8530.93319.937-0.068-0.0680.0000.0000.0000.000
151A152GLU-1-0.863-0.93218.8370.2190.2190.0000.0000.0000.000
152A153THR0-0.048-0.01614.2600.0030.0030.0000.0000.0000.000
153A154PHE00.0170.0028.254-0.020-0.0200.0000.0000.0000.000
154A155SER0-0.020-0.0308.639-0.040-0.0400.0000.0000.0000.000
155A156ILE00.0080.0143.868-0.1130.1190.001-0.038-0.1950.000
156A157ILE0-0.018-0.0096.100-0.242-0.2420.0000.0000.0000.000
157A158THR0-0.008-0.0043.583-0.3730.1780.195-0.137-0.6090.000
158A159THR0-0.027-0.0336.072-0.744-0.7440.0000.0000.0000.000
159A160ASP-1-0.878-0.9486.8630.6600.6600.0000.0000.0000.000
160A161THR0-0.009-0.0196.6940.1770.1770.0000.0000.0000.000
161A162ASN0-0.018-0.0118.897-0.074-0.0740.0000.0000.0000.000
162A163SER00.030-0.01011.266-0.094-0.0940.0000.0000.0000.000
163A164LEU00.0140.02310.473-0.075-0.0750.0000.0000.0000.000
164A165THR00.023-0.0326.311-0.067-0.0670.0000.0000.0000.000
165A166ASP-1-0.824-0.8687.727-0.687-0.6870.0000.0000.0000.000
166A167TYR0-0.026-0.00110.070-0.027-0.0270.0000.0000.0000.000
167A168ILE0-0.025-0.0247.480-0.006-0.0060.0000.0000.0000.000
168A169ASP-1-0.698-0.8585.009-1.801-1.8010.0000.0000.0000.000
169A170ASN0-0.011-0.0067.1360.2030.2030.0000.0000.0000.000
170A171THR0-0.050-0.0219.1050.1560.1560.0000.0000.0000.000
171A172LYS10.7660.8706.2701.2731.2730.0000.0000.0000.000
172A173HIS0-0.053-0.0167.7000.3210.3210.0000.0000.0000.000
173A174ARG10.7870.9083.901-0.786-0.4060.110-0.130-0.3600.001
174A175MET0-0.0130.0153.167-2.835-2.0570.619-0.501-0.897-0.003
175A176PRO00.0310.0052.7330.7641.2541.770-0.216-2.0440.003
176A177ALA0-0.014-0.0204.740-1.027-1.0030.009-0.009-0.0240.000
177A178ILE0-0.029-0.0057.2140.0080.0080.0000.0000.0000.000
178A179LEU0-0.0110.0029.864-0.136-0.1360.0000.0000.0000.000
179A180THR0-0.052-0.05613.487-0.009-0.0090.0000.0000.0000.000
180A181GLN00.017-0.00416.116-0.021-0.0210.0000.0000.0000.000
181A182GLU-1-0.937-0.97118.2910.2730.2730.0000.0000.0000.000
182A183GLU-1-0.917-0.93417.0350.3830.3830.0000.0000.0000.000
183A184GLU-1-0.760-0.81116.1710.5250.5250.0000.0000.0000.000
184A185GLU-1-0.741-0.86118.4200.3330.3330.0000.0000.0000.000
185A186LYS10.8990.96721.129-0.286-0.2860.0000.0000.0000.000
186A187TRP00.005-0.01713.428-0.021-0.0210.0000.0000.0000.000
187A188LEU0-0.0170.00916.885-0.001-0.0010.0000.0000.0000.000
188A189ASN00.0430.03720.002-0.036-0.0360.0000.0000.0000.000
189A190PRO00.001-0.01523.0580.0040.0040.0000.0000.0000.000
190A191SER0-0.057-0.03924.490-0.013-0.0130.0000.0000.0000.000
191A192LEU0-0.073-0.00420.385-0.009-0.0090.0000.0000.0000.000
192A193SER0-0.029-0.04023.971-0.005-0.0050.0000.0000.0000.000
193A194LYS10.9040.94520.449-0.172-0.1720.0000.0000.0000.000
194A195ALA00.001-0.00221.0520.0220.0220.0000.0000.0000.000
195A196GLU-1-0.820-0.88121.2720.2180.2180.0000.0000.0000.000
196A197ILE00.0010.00716.8710.0240.0240.0000.0000.0000.000
197A198ALA00.0130.00016.8060.0480.0480.0000.0000.0000.000
198A199SER0-0.077-0.04916.5890.0220.0220.0000.0000.0000.000
199A200LEU0-0.020-0.00516.372-0.018-0.0180.0000.0000.0000.000
200A201LEU0-0.0390.00211.3840.0750.0750.0000.0000.0000.000
201A202LYS10.8810.94512.738-0.385-0.3850.0000.0000.0000.000
202A203PRO00.0300.01610.2260.1060.1060.0000.0000.0000.000
203A204PHE00.0180.00710.491-0.073-0.0730.0000.0000.0000.000
204A205ASP-1-0.817-0.90812.3980.0490.0490.0000.0000.0000.000
205A206THR00.034-0.00413.364-0.023-0.0230.0000.0000.0000.000
206A207GLU-1-0.901-0.94214.386-0.042-0.0420.0000.0000.0000.000
207A208LYS10.8800.96215.184-0.243-0.2430.0000.0000.0000.000
208A209MET0-0.0160.0177.9240.0520.0520.0000.0000.0000.000
209A210ASP-1-0.829-0.89612.448-0.123-0.1230.0000.0000.0000.000
210A211ALA0-0.015-0.01210.914-0.025-0.0250.0000.0000.0000.000
211A212TYR0-0.064-0.02512.6480.0200.0200.0000.0000.0000.000
212A213VAL00.0130.01712.843-0.053-0.0530.0000.0000.0000.000
213A214ILE00.0110.00710.7960.0910.0910.0000.0000.0000.000
214A215ARG10.9020.94514.7160.0810.0810.0000.0000.0000.000
215A216ASN00.034-0.00814.177-0.056-0.0560.0000.0000.0000.000
216A217ASP-1-0.959-0.99315.241-0.165-0.1650.0000.0000.0000.000
217A218PHE00.0430.0258.7650.0190.0190.0000.0000.0000.000
218A219LEU00.0070.00710.6110.0490.0490.0000.0000.0000.000
219A220LYS10.8720.93613.8860.1910.1910.0000.0000.0000.000
220A221LYS10.8370.94716.5510.0710.0710.0000.0000.0000.000
221A222SER00.0310.01516.8120.0000.0000.0000.0000.0000.000
222A223PRO00.0640.02714.694-0.001-0.0010.0000.0000.0000.000
223A224ASN00.007-0.00115.5170.0410.0410.0000.0000.0000.000
224A225ASP-1-0.839-0.88517.8000.0320.0320.0000.0000.0000.000
225A226PRO00.1000.02717.1980.0080.0080.0000.0000.0000.000
226A227THR0-0.130-0.08217.661-0.016-0.0160.0000.0000.0000.000
227A228ILE0-0.044-0.01512.637-0.056-0.0560.0000.0000.0000.000
228A229VAL00.0380.02012.243-0.051-0.0510.0000.0000.0000.000
229A230GLN0-0.070-0.02014.642-0.031-0.0310.0000.0000.0000.000
230A231ARG11.0221.01516.8300.0180.0180.0000.0000.0000.000
231A232ALA00.0160.00117.7580.0170.0170.0000.0000.0000.000
232A233LEU0-0.130-0.04419.0290.0250.0250.0000.0000.0000.000
233A234GLU-1-0.893-0.95822.611-0.153-0.1530.0000.0000.0000.000