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: YQK82

Calculation Name: 2FPN-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FPN

Chain ID: A

ChEMBL ID:

UniProt ID: O32277

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2210029.464847
FMO2-HF: Nuclear repulsion 2121816.485879
FMO2-HF: Total energy -88212.978968
FMO2-MP2: Total energy -88468.621422


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:LEU )


Summations of interaction energy for fragment #1(A:1:LEU )
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.
-107.983-101.5920.733-3.679-3.444-0.03
Interaction energy analysis for fragmet #1(A:1:LEU )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.908
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].
3A3PRO 00.0300.0043.819-2.877-1.641-0.006-0.594-0.6360.001
4A4LEU 00.0400.0286.6003.2133.2130.0000.0000.0000.000
5A5ALA 0-0.0010.0093.3962.2092.4770.008-0.078-0.1970.000
6A6GLN 00.007-0.0032.764-12.302-10.0400.620-1.459-1.424-0.016
7A7MET 0-0.067-0.0325.7015.3715.3710.0000.0000.0000.000
8A8ALA 00.0230.0248.6862.9302.9300.0000.0000.0000.000
9A9GLU -1-0.878-0.9475.635-45.625-45.6250.0000.0000.0000.000
10A10GLY 0-0.101-0.0489.1262.2862.2860.0000.0000.0000.000
11A11MET 0-0.038-0.02410.8142.0492.0490.0000.0000.0000.000
12A12GLU -1-0.848-0.92312.092-22.635-22.6350.0000.0000.0000.000
13A13ARG 10.9200.9638.45429.68329.6830.0000.0000.0000.000
14A14GLN 0-0.095-0.02914.7510.6910.6910.0000.0000.0000.000
15A15ASP -1-0.919-0.96816.958-14.023-14.0230.0000.0000.0000.000
16A16VAL 0-0.115-0.05216.8040.8770.8770.0000.0000.0000.000
17A17SER 00.0180.01317.102-1.244-1.2440.0000.0000.0000.000
18A18ILE 0-0.054-0.01013.2700.2310.2310.0000.0000.0000.000
19A19ASP -1-0.843-0.91317.687-13.688-13.6880.0000.0000.0000.000
20A20LYS 10.8970.93918.81214.45314.4530.0000.0000.0000.000
21A21TRP 0-0.022-0.01214.165-1.251-1.2510.0000.0000.0000.000
22A22THR 0-0.054-0.04416.1780.9530.9530.0000.0000.0000.000
23A23LEU 00.0260.02411.455-1.251-1.2510.0000.0000.0000.000
24A24HIS 00.0070.00115.4171.0911.0910.0000.0000.0000.000
25A25ALA 00.0610.04316.230-0.838-0.8380.0000.0000.0000.000
26A26LYS 10.9290.95318.01013.33313.3330.0000.0000.0000.000
27A27GLN 0-0.026-0.02321.0800.0540.0540.0000.0000.0000.000
28A28ASN 0-0.037-0.02923.2160.5290.5290.0000.0000.0000.000
29A29LEU 00.0250.00326.5210.0050.0050.0000.0000.0000.000
30A30SER 0-0.049-0.02429.2170.2440.2440.0000.0000.0000.000
31A31LEU 00.0010.00331.1780.0920.0920.0000.0000.0000.000
32A32THR 00.001-0.00234.9760.2050.2050.0000.0000.0000.000
33A33GLU -1-0.832-0.92737.661-7.538-7.5380.0000.0000.0000.000
34A34LYS 10.9860.97638.9497.1287.1280.0000.0000.0000.000
35A35GLU -1-0.825-0.90935.237-8.540-8.5400.0000.0000.0000.000
36A36PHE 00.0120.00033.406-0.237-0.2370.0000.0000.0000.000
37A37TYR 00.0410.00234.655-0.242-0.2420.0000.0000.0000.000
38A38GLN 0-0.0370.00235.240-0.095-0.0950.0000.0000.0000.000
39A39LYS 10.9650.98026.89310.74410.7440.0000.0000.0000.000
40A40VAL 00.0180.01031.416-0.240-0.2400.0000.0000.0000.000
41A41GLN 0-0.023-0.00532.8050.0140.0140.0000.0000.0000.000
42A42ARG 10.9480.96530.4459.4179.4170.0000.0000.0000.000
43A43LEU 00.0020.01326.689-0.189-0.1890.0000.0000.0000.000
44A44LYS 10.9270.97029.2528.5438.5430.0000.0000.0000.000
45A45GLN 0-0.043-0.02031.9520.2440.2440.0000.0000.0000.000
46A46GLU -1-0.946-0.97425.453-11.198-11.1980.0000.0000.0000.000
47A47TYR 0-0.044-0.02322.600-0.195-0.1950.0000.0000.0000.000
48A48ARG 10.9440.95627.35210.03910.0390.0000.0000.0000.000
49A49GLN 00.0310.02823.6920.7490.7490.0000.0000.0000.000
50A50TYR 0-0.060-0.02122.868-0.099-0.0990.0000.0000.0000.000
51A51ASP -1-0.883-0.92129.259-9.322-9.3220.0000.0000.0000.000
52A52TRP 0-0.036-0.03928.311-0.130-0.1300.0000.0000.0000.000
53A53VAL 00.0210.02033.6960.3270.3270.0000.0000.0000.000
54A54ILE 0-0.053-0.03134.896-0.226-0.2260.0000.0000.0000.000
55A55ALA 00.0020.00136.4070.2040.2040.0000.0000.0000.000
56A56ARG 10.8920.93837.5557.2537.2530.0000.0000.0000.000
57A57GLU -1-0.886-0.94037.314-8.427-8.4270.0000.0000.0000.000
58A58ASP -1-0.872-0.92939.934-7.450-7.4500.0000.0000.0000.000
59A59LYS 10.8530.92741.6087.1387.1380.0000.0000.0000.000
60A60MET 0-0.017-0.01034.693-0.229-0.2290.0000.0000.0000.000
61A61ILE 0-0.010-0.00436.6340.1730.1730.0000.0000.0000.000
62A62LYS 10.9930.99331.5929.5339.5330.0000.0000.0000.000
63A63ALA 0-0.0130.00832.2320.2560.2560.0000.0000.0000.000
64A64ILE 0-0.016-0.02629.383-0.381-0.3810.0000.0000.0000.000
65A65GLY 00.0280.01728.9400.3390.3390.0000.0000.0000.000
66A66THR 00.003-0.01527.543-0.701-0.7010.0000.0000.0000.000
67A67TYR 00.0760.03623.6070.2280.2280.0000.0000.0000.000
68A68THR 0-0.047-0.00824.750-0.514-0.5140.0000.0000.0000.000
69A69ASP -1-0.776-0.87621.501-13.880-13.8800.0000.0000.0000.000
70A70LYS 10.9760.95523.07810.20310.2030.0000.0000.0000.000
71A71LYS 10.9220.98221.62013.66113.6610.0000.0000.0000.000
72A72ASN 0-0.054-0.04218.462-0.639-0.6390.0000.0000.0000.000
73A73ARG 10.8670.96717.18815.61115.6110.0000.0000.0000.000
74A74THR 00.0030.04718.136-0.840-0.8400.0000.0000.0000.000
75A75SER 00.010-0.01120.2381.0801.0800.0000.0000.0000.000
76A76PHE 00.0270.00917.934-0.467-0.4670.0000.0000.0000.000
77A77ARG 10.8980.95722.77413.50513.5050.0000.0000.0000.000
78A78LEU 00.0100.01123.372-0.475-0.4750.0000.0000.0000.000
79A79GLN 0-0.038-0.01725.3070.4780.4780.0000.0000.0000.000
80A80LEU 00.0050.00727.130-0.258-0.2580.0000.0000.0000.000
81A81VAL 0-0.035-0.01229.6770.3780.3780.0000.0000.0000.000
82A82THR 00.0120.01131.622-0.159-0.1590.0000.0000.0000.000
83A83THR 0-0.006-0.00434.3380.1250.1250.0000.0000.0000.000
84A84LEU 00.0190.01136.9230.0600.0600.0000.0000.0000.000
85A85LYS 10.9470.97040.1897.0497.0490.0000.0000.0000.000
86A86LYS 10.8910.93436.5178.4488.4480.0000.0000.0000.000
87A87HIS 00.0380.03241.438-0.149-0.1490.0000.0000.0000.000
88A88ASN 0-0.001-0.01236.850-0.150-0.1500.0000.0000.0000.000
89A89PRO 00.0310.04736.559-0.093-0.0930.0000.0000.0000.000
90A90THR 00.009-0.00132.337-0.124-0.1240.0000.0000.0000.000
91A91SER 0-0.007-0.02531.4800.1550.1550.0000.0000.0000.000
92A92TYR 0-0.013-0.01326.133-0.125-0.1250.0000.0000.0000.000
93A93LEU 00.0110.01724.0730.4580.4580.0000.0000.0000.000
94A94LEU 0-0.056-0.02721.428-0.339-0.3390.0000.0000.0000.000
95A95TYR 0-0.044-0.03116.7631.0631.0630.0000.0000.0000.000
96A96GLU -1-0.918-0.97719.356-14.834-14.8340.0000.0000.0000.000
97A97GLN 00.0360.00515.624-0.292-0.2920.0000.0000.0000.000
98A98MET 0-0.028-0.00717.815-0.621-0.6210.0000.0000.0000.000
99A99SER 00.000-0.03617.4210.4610.4610.0000.0000.0000.000
100A100LEU 0-0.015-0.00518.919-0.321-0.3210.0000.0000.0000.000
101A101GLU -1-0.836-0.91718.911-14.089-14.0890.0000.0000.0000.000
102A102THR 00.0130.03214.261-0.601-0.6010.0000.0000.0000.000
103A103PRO 0-0.025-0.01011.4851.1301.1300.0000.0000.0000.000
104A104ASP -1-0.897-0.94813.125-19.555-19.5550.0000.0000.0000.000
105A105SER 0-0.021-0.0288.395-2.829-2.8290.0000.0000.0000.000
106A106TRP 00.0740.0196.926-0.290-0.2900.0000.0000.0000.000
107A107ASN 00.0060.0092.916-16.189-13.8530.110-1.479-0.966-0.015
108A108ASP -1-0.802-0.8815.886-29.826-29.8260.0000.0000.0000.000
109A109THR 0-0.062-0.0288.9401.8831.8830.0000.0000.0000.000
110A110TYR 00.0380.0077.0140.9060.9060.0000.0000.0000.000
111A111GLU -1-0.917-0.9724.069-42.940-42.6510.001-0.069-0.2210.000
112A112GLN 0-0.063-0.0457.9773.0143.0140.0000.0000.0000.000
113A113PHE 00.0310.04311.6661.6441.6440.0000.0000.0000.000
114A114GLU -1-0.962-0.9967.603-28.406-28.4060.0000.0000.0000.000
115A115ARG 10.9190.9668.82826.00226.0020.0000.0000.0000.000
116A116GLU -1-0.838-0.92012.717-16.684-16.6840.0000.0000.0000.000
117A117THR 0-0.025-0.00514.2631.4781.4780.0000.0000.0000.000
118A118LEU 0-0.032-0.01112.6131.0841.0840.0000.0000.0000.000
119A119GLY 0-0.0150.00316.7380.8910.8910.0000.0000.0000.000
120A120ILE 0-0.065-0.01819.1470.8970.8970.0000.0000.0000.000
121A121PHE 0-0.082-0.06618.3340.7860.7860.0000.0000.0000.000
122A122GLN 0-0.040-0.01220.3450.6820.6820.0000.0000.0000.000
123A123GLU -1-0.864-0.91619.340-13.028-13.0280.0000.0000.0000.000
124A124LYS 10.9470.98611.71021.03321.0330.0000.0000.0000.000
125A125VAL 00.0120.01115.5970.5090.5090.0000.0000.0000.000
126A126VAL 0-0.023-0.01914.317-1.247-1.2470.0000.0000.0000.000
127A127ILE 00.0020.01010.6751.0361.0360.0000.0000.0000.000
128A128PHE 0-0.068-0.03612.796-0.888-0.8880.0000.0000.0000.000
129A129THR 00.0270.00310.659-0.939-0.9390.0000.0000.0000.000
130A130CYS 0-0.052-0.02113.5570.5480.5480.0000.0000.0000.000
131A131LEU 00.0480.01911.3930.0590.0590.0000.0000.0000.000
132A132ASN 0-0.061-0.03715.8070.8550.8550.0000.0000.0000.000
133A133GLY 00.0650.02018.624-0.606-0.6060.0000.0000.0000.000
134A134HIS 0-0.086-0.04319.8560.7070.7070.0000.0000.0000.000
135A135LEU 00.007-0.01121.658-0.491-0.4910.0000.0000.0000.000
136A136ASP -1-0.818-0.92323.725-11.539-11.5390.0000.0000.0000.000
137A137ASP -1-0.936-0.95925.415-10.381-10.3810.0000.0000.0000.000
138A138ASN 00.0310.01528.5010.8590.8590.0000.0000.0000.000
139A139MET 0-0.025-0.00830.2490.0670.0670.0000.0000.0000.000
140A140ASN 00.023-0.00332.4590.2160.2160.0000.0000.0000.000
141A141ILE 0-0.0070.01626.4260.2020.2020.0000.0000.0000.000
142A142VAL 00.0100.00329.130-0.005-0.0050.0000.0000.0000.000
143A143LEU 0-0.057-0.03031.0760.2150.2150.0000.0000.0000.000
144A144GLN 00.0750.02431.2500.3750.3750.0000.0000.0000.000
145A145LYS 10.9461.00027.87210.90110.9010.0000.0000.0000.000
146A146LYS 10.9950.98131.3819.3579.3570.0000.0000.0000.000
147A147ALA 00.0220.02134.2020.2000.2000.0000.0000.0000.000
148A148ASN 00.0060.00532.7640.3160.3160.0000.0000.0000.000
149A149GLN 0-0.077-0.04031.2450.0870.0870.0000.0000.0000.000
150A150LEU 00.0490.02234.4870.1250.1250.0000.0000.0000.000
151A151LEU 00.0040.01237.1110.2070.2070.0000.0000.0000.000
152A152ASN 0-0.037-0.02833.6520.3020.3020.0000.0000.0000.000
153A153GLU -1-1.015-0.99637.393-8.238-8.2380.0000.0000.0000.000
154A154PHE 0-0.0050.00538.9880.1970.1970.0000.0000.0000.000
155A155GLN 0-0.021-0.01940.4140.2240.2240.0000.0000.0000.000
156A156ALA 00.104-0.05641.350-0.063-0.0630.0000.0000.0000.000
157A157ARG 10.8790.90541.1987.2157.2150.0000.0000.0000.000
158A158SER 0-0.087-0.05341.960-0.068-0.0680.0000.0000.0000.000
159A159VAL 0-0.020-0.03939.2140.1620.1620.0000.0000.0000.000
160A160GLU -1-0.926-0.97241.714-6.772-6.7720.0000.0000.0000.000
161A161HIS 00.0440.03739.0010.0430.0430.0000.0000.0000.000
162A162VAL 0-0.0550.00939.6300.1230.1230.0000.0000.0000.000
163A163VAL 0-0.011-0.02635.422-0.252-0.2520.0000.0000.0000.000
164A164GLU -1-0.930-0.96438.779-7.160-7.1600.0000.0000.0000.000
165A165PRO 0-0.055-0.03138.243-0.155-0.1550.0000.0000.0000.000
166A166ASN 00.0690.04136.557-0.396-0.3960.0000.0000.0000.000
167A167PHE 0-0.023-0.03038.5820.1890.1890.0000.0000.0000.000
168A168VAL 00.0500.02536.713-0.168-0.1680.0000.0000.0000.000
169A169SER 00.007-0.00139.4650.1730.1730.0000.0000.0000.000
170A170ILE 0-0.028-0.01438.219-0.135-0.1350.0000.0000.0000.000
171A171SER 0-0.012-0.01042.3170.1930.1930.0000.0000.0000.000
172A172ALA 0-0.0090.06343.047-0.163-0.1630.0000.0000.0000.000
173A173PHE 00.0000.01144.8130.2270.2270.0000.0000.0000.000
174A174THR 0-0.0040.04144.396-0.212-0.2120.0000.0000.0000.000
175A175ASP -1-0.895-0.93446.884-6.618-6.6180.0000.0000.0000.000
176A176GLU -1-0.890-0.95545.615-6.860-6.8600.0000.0000.0000.000
177A177TRP 0-0.060-0.01547.1920.0330.0330.0000.0000.0000.000
178A178GLU -1-0.909-0.94452.544-5.711-5.7110.0000.0000.0000.000
179A179GLU -1-0.936-0.96554.268-5.783-5.7830.0000.0000.0000.000
180A180TYR 0-0.052-0.04353.426-0.154-0.1540.0000.0000.0000.000
181A181ILE 00.0010.00553.1460.1330.1330.0000.0000.0000.000
182A182MET 00.0050.00553.827-0.137-0.1370.0000.0000.0000.000
183A183THR 00.0030.00454.7820.1030.1030.0000.0000.0000.000
184A184SER 00.0520.03254.219-0.060-0.0600.0000.0000.0000.000
185A185LYS 10.9180.95448.2596.4476.4470.0000.0000.0000.000
186A186HIS 10.8820.93647.8716.4566.4560.0000.0000.0000.000
187A187LYS 10.8950.96050.1906.2736.2730.0000.0000.0000.000
188A188MET 0-0.0430.01848.068-0.115-0.1150.0000.0000.0000.000
189A189ASN 0-0.037-0.05348.8220.0310.0310.0000.0000.0000.000
190A190LEU 00.1180.06143.674-0.009-0.0090.0000.0000.0000.000
191A191GLN 00.0620.04045.752-0.025-0.0250.0000.0000.0000.000
192A192ILE 0-0.0200.01040.1780.0360.0360.0000.0000.0000.000
193A193ALA 0-0.002-0.01742.401-0.052-0.0520.0000.0000.0000.000
194A194LEU 0-0.039-0.01037.5520.0600.0600.0000.0000.0000.000
195A195ARG 10.9370.97040.6267.1587.1580.0000.0000.0000.000
196A196SER 00.0420.00236.9330.0040.0040.0000.0000.0000.000
197A197ALA 0-0.032-0.03938.5890.2570.2570.0000.0000.0000.000
198A198GLY 0-0.0290.01639.024-0.089-0.0890.0000.0000.0000.000
199A199MET 00.003-0.01932.653-0.022-0.0220.0000.0000.0000.000
200A200GLY 00.0660.02333.364-0.343-0.3430.0000.0000.0000.000
201A201GLY 0-0.049-0.00634.8940.1190.1190.0000.0000.0000.000
202A202LYS 10.9050.93537.8097.6397.6390.0000.0000.0000.000
203A203HIS 00.0390.03535.2230.0430.0430.0000.0000.0000.000
204A204THR 0-0.0270.00040.1070.0810.0810.0000.0000.0000.000
205A205VAL 00.0350.01240.243-0.173-0.1730.0000.0000.0000.000
206A206THR 0-0.057-0.02242.8820.2230.2230.0000.0000.0000.000
207A207VAL 00.0300.01043.664-0.130-0.1300.0000.0000.0000.000
208A208GLY 0-0.0110.00946.3380.1330.1330.0000.0000.0000.000
209A209THR 00.0390.04649.099-0.124-0.1240.0000.0000.0000.000
210A210PRO 0-0.024-0.02251.6580.0990.0990.0000.0000.0000.000
211A211ILE 00.001-0.02350.648-0.119-0.1190.0000.0000.0000.000
212A212VAL 00.0000.00048.2170.0760.0760.0000.0000.0000.000
213A213THR 0-0.005-0.00351.369-0.022-0.0220.0000.0000.0000.000
214A214THR 0-0.001-0.01353.945-0.043-0.0430.0000.0000.0000.000
215A215NME 0-0.0270.00356.4780.0880.0880.0000.0000.0000.000