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: N2N1Q

Calculation Name: 1P2F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P2F

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXY0

Base Structure: X-ray

Registration Date: 2023-09-27

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655332.484719
FMO2-HF: Nuclear repulsion 2568008.77747
FMO2-HF: Total energy -87323.707249
FMO2-MP2: Total energy -87581.258217


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.
-9.544-5.757.22-4.006-7.008-0.013
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 : 0.019 / q_NPA : 0.021
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].
3A3TRP00.0580.0312.618-6.617-2.3421.389-2.616-3.048-0.017
4A4LYS10.8450.9152.7420.3841.2880.202-0.172-0.9340.001
5A5ILE0-0.008-0.0145.2590.3950.449-0.001-0.001-0.0520.000
6A6ALA00.0410.0379.035-0.005-0.0050.0000.0000.0000.000
7A7VAL0-0.031-0.02511.8240.0070.0070.0000.0000.0000.000
8A8VAL00.0160.00515.4230.0120.0120.0000.0000.0000.000
9A9ASP-1-0.814-0.93818.236-0.208-0.2080.0000.0000.0000.000
10A10ASP-1-0.851-0.92121.673-0.151-0.1510.0000.0000.0000.000
11A11ASP-1-0.828-0.90524.669-0.195-0.1950.0000.0000.0000.000
12A12LYS10.9870.96723.3210.1340.1340.0000.0000.0000.000
13A13ASN0-0.072-0.03223.601-0.026-0.0260.0000.0000.0000.000
14A14ILE00.0130.00621.370-0.026-0.0260.0000.0000.0000.000
15A15LEU00.0080.02218.359-0.045-0.0450.0000.0000.0000.000
16A16LYS10.8980.98418.9350.2530.2530.0000.0000.0000.000
17A17LYS10.8960.94420.2000.2150.2150.0000.0000.0000.000
18A18VAL0-0.001-0.00316.584-0.037-0.0370.0000.0000.0000.000
19A19SER0-0.005-0.02315.482-0.070-0.0700.0000.0000.0000.000
20A20GLU-1-0.900-0.96715.663-0.466-0.4660.0000.0000.0000.000
21A21LYS10.8060.90317.7290.4450.4450.0000.0000.0000.000
22A22LEU00.0690.01413.026-0.063-0.0630.0000.0000.0000.000
23A23GLN00.0020.00712.193-0.167-0.1670.0000.0000.0000.000
24A24GLN0-0.104-0.03812.284-0.118-0.1180.0000.0000.0000.000
25A25LEU0-0.033-0.0179.969-0.068-0.0680.0000.0000.0000.000
26A26GLY00.002-0.0047.412-0.711-0.7110.0000.0000.0000.000
27A27ARG10.8470.9115.8751.8101.8100.0000.0000.0000.000
28A28VAL00.0150.0117.978-0.030-0.0300.0000.0000.0000.000
29A29LYS10.8260.9139.3060.6230.6230.0000.0000.0000.000
30A30THR0-0.015-0.01312.212-0.002-0.0020.0000.0000.0000.000
31A31PHE00.0180.01012.5030.0050.0050.0000.0000.0000.000
32A32LEU0-0.016-0.01218.136-0.006-0.0060.0000.0000.0000.000
33A33THR0-0.0020.00121.0720.0060.0060.0000.0000.0000.000
34A34GLY00.039-0.00120.175-0.012-0.0120.0000.0000.0000.000
35A35GLU-1-0.963-0.99119.731-0.025-0.0250.0000.0000.0000.000
36A36ASP-1-0.925-0.95618.662-0.143-0.1430.0000.0000.0000.000
37A37PHE0-0.043-0.03412.5710.0000.0000.0000.0000.0000.000
38A38LEU0-0.055-0.03315.1770.0170.0170.0000.0000.0000.000
39A39ASN0-0.044-0.01717.2820.0440.0440.0000.0000.0000.000
40A40ASH0-0.068-0.04010.9750.0350.0350.0000.0000.0000.000
41A41GLU-1-0.875-0.93112.0390.1940.1940.0000.0000.0000.000
42A42GLU-1-0.908-0.9086.963-0.518-0.5180.0000.0000.0000.000
43A43ALA0-0.003-0.0016.153-0.032-0.0320.0000.0000.0000.000
44A44PHE0-0.008-0.0255.587-0.257-0.2570.0000.0000.0000.000
45A45HIS00.0610.0322.275-4.126-5.5655.630-1.217-2.9740.003
46A46VAL0-0.010-0.0087.573-0.043-0.0430.0000.0000.0000.000
47A47VAL00.0080.01010.558-0.073-0.0730.0000.0000.0000.000
48A48VAL0-0.034-0.02213.2100.0260.0260.0000.0000.0000.000
49A49LEU00.0300.02016.1030.0040.0040.0000.0000.0000.000
50A50ASP-1-0.780-0.86619.007-0.172-0.1720.0000.0000.0000.000
51A51VAL0-0.006-0.01222.6250.0160.0160.0000.0000.0000.000
52A52MET0-0.062-0.02525.2490.0220.0220.0000.0000.0000.000
53A53LEU00.0040.00721.302-0.014-0.0140.0000.0000.0000.000
54A54PRO0-0.025-0.02125.3710.0100.0100.0000.0000.0000.000
55A55ASP-1-0.759-0.87624.316-0.072-0.0720.0000.0000.0000.000
56A56TYR0-0.0030.01023.7130.0170.0170.0000.0000.0000.000
57A57SER00.0230.02025.912-0.015-0.0150.0000.0000.0000.000
58A58GLY00.059-0.00922.6090.0050.0050.0000.0000.0000.000
59A59TYR0-0.034-0.03422.2090.0010.0010.0000.0000.0000.000
60A60GLU-1-0.898-0.95523.621-0.002-0.0020.0000.0000.0000.000
61A61ILE00.0210.01918.1650.0140.0140.0000.0000.0000.000
62A62CYS0-0.065-0.02818.8370.0090.0090.0000.0000.0000.000
63A63ARG10.8710.93019.237-0.017-0.0170.0000.0000.0000.000
64A64MET00.0140.00719.4540.0200.0200.0000.0000.0000.000
65A65ILE0-0.037-0.00713.8720.0330.0330.0000.0000.0000.000
66A66LYS10.8170.88815.6240.0500.0500.0000.0000.0000.000
67A67GLU-1-0.862-0.91017.9800.0960.0960.0000.0000.0000.000
68A68THR0-0.072-0.03515.3730.0260.0260.0000.0000.0000.000
69A69ARG10.8880.95110.402-0.307-0.3070.0000.0000.0000.000
70A70PRO00.0560.03813.549-0.028-0.0280.0000.0000.0000.000
71A71GLU-1-0.933-0.9719.8800.5600.5600.0000.0000.0000.000
72A72THR0-0.089-0.04210.595-0.016-0.0160.0000.0000.0000.000
73A73TRP00.0020.00910.383-0.041-0.0410.0000.0000.0000.000
74A74VAL00.0190.00313.364-0.041-0.0410.0000.0000.0000.000
75A75ILE0-0.060-0.02115.9210.0010.0010.0000.0000.0000.000
76A76LEU00.0170.00718.269-0.010-0.0100.0000.0000.0000.000
77A77LEU0-0.042-0.01920.153-0.019-0.0190.0000.0000.0000.000
78A78THR00.0720.02923.1160.0210.0210.0000.0000.0000.000
79A79LEU00.0350.01226.782-0.012-0.0120.0000.0000.0000.000
80A80LEU0-0.030-0.00330.2700.0020.0020.0000.0000.0000.000
81A81SER00.006-0.01430.365-0.005-0.0050.0000.0000.0000.000
82A82ASP-1-0.841-0.88531.508-0.088-0.0880.0000.0000.0000.000
83A83ASP-1-0.755-0.88033.130-0.084-0.0840.0000.0000.0000.000
84A84GLU-1-0.888-0.91633.597-0.056-0.0560.0000.0000.0000.000
85A85SER0-0.027-0.04530.5570.0040.0040.0000.0000.0000.000
86A86VAL0-0.028-0.01428.497-0.002-0.0020.0000.0000.0000.000
87A87LEU0-0.060-0.02928.7890.0020.0020.0000.0000.0000.000
88A88LYS10.9430.97529.3690.0710.0710.0000.0000.0000.000
89A89GLY0-0.002-0.00125.6360.0040.0040.0000.0000.0000.000
90A90PHE0-0.064-0.05524.9400.0010.0010.0000.0000.0000.000
91A91GLU-1-0.960-0.97926.001-0.026-0.0260.0000.0000.0000.000
92A92ALA0-0.025-0.00323.7520.0120.0120.0000.0000.0000.000
93A93GLY00.0160.01622.0670.0110.0110.0000.0000.0000.000
94A94ALA0-0.005-0.00220.128-0.001-0.0010.0000.0000.0000.000
95A95ASP-1-0.781-0.87416.828-0.087-0.0870.0000.0000.0000.000
96A96ASP-1-0.754-0.87319.492-0.298-0.2980.0000.0000.0000.000
97A97TYR0-0.042-0.03721.0580.0060.0060.0000.0000.0000.000
98A98VAL0-0.007-0.01521.202-0.019-0.0190.0000.0000.0000.000
99A99THR0-0.0010.01624.0840.0070.0070.0000.0000.0000.000
100A100LYS10.7960.91324.7760.1790.1790.0000.0000.0000.000
101A101PRO00.014-0.00128.1220.0120.0120.0000.0000.0000.000
102A102PHE00.024-0.00121.649-0.001-0.0010.0000.0000.0000.000
103A103ASN00.0220.01425.236-0.024-0.0240.0000.0000.0000.000
104A104PRO00.0600.00820.910-0.010-0.0100.0000.0000.0000.000
105A105GLU-1-0.828-0.90320.528-0.516-0.5160.0000.0000.0000.000
106A106ILE0-0.036-0.01421.036-0.025-0.0250.0000.0000.0000.000
107A107LEU00.0290.01817.494-0.011-0.0110.0000.0000.0000.000
108A108LEU00.004-0.00115.164-0.041-0.0410.0000.0000.0000.000
109A109ALA0-0.022-0.01216.332-0.067-0.0670.0000.0000.0000.000
110A110ARG10.8730.92617.9040.2660.2660.0000.0000.0000.000
111A111VAL00.0520.03212.1900.0080.0080.0000.0000.0000.000
112A112LYS10.8500.90913.1270.8800.8800.0000.0000.0000.000
113A113ARG10.7530.87414.2030.2870.2870.0000.0000.0000.000
114A114PHE00.0150.01512.8630.0360.0360.0000.0000.0000.000
115A115LEU00.0110.0117.9210.0840.0840.0000.0000.0000.000
116A116GLU-1-0.874-0.92810.595-1.165-1.1650.0000.0000.0000.000
117A117ARG10.8600.92412.6050.5820.5820.0000.0000.0000.000
118A118GLU-1-0.916-0.93511.290-0.217-0.2170.0000.0000.0000.000
119A119LYS10.7450.86114.8040.3300.3300.0000.0000.0000.000
120A120LYS10.8470.90817.1690.0500.0500.0000.0000.0000.000
121A121GLY0-0.014-0.00219.4180.0040.0040.0000.0000.0000.000
122A122LEU0-0.0400.00122.0730.0150.0150.0000.0000.0000.000
123A123TYR0-0.032-0.03821.6490.0050.0050.0000.0000.0000.000
124A124ASP-1-0.769-0.86724.932-0.024-0.0240.0000.0000.0000.000
125A125PHE00.011-0.00625.4680.0120.0120.0000.0000.0000.000
126A126GLY00.0390.02629.1210.0060.0060.0000.0000.0000.000
127A127ASP-1-0.828-0.90431.406-0.011-0.0110.0000.0000.0000.000
128A128LEU0-0.0200.01132.283-0.006-0.0060.0000.0000.0000.000
129A129LYS10.8360.91029.3520.0310.0310.0000.0000.0000.000
130A130ILE0-0.010-0.01428.179-0.003-0.0030.0000.0000.0000.000
131A131ASP-1-0.704-0.82827.124-0.155-0.1550.0000.0000.0000.000
132A132ALA0-0.047-0.04524.5950.0010.0010.0000.0000.0000.000
133A133THR0-0.086-0.05723.360-0.022-0.0220.0000.0000.0000.000
134A134GLY00.0150.01026.155-0.005-0.0050.0000.0000.0000.000
135A135PHE0-0.105-0.04328.1900.0080.0080.0000.0000.0000.000
136A136THR0-0.0020.00230.9230.0110.0110.0000.0000.0000.000
137A137VAL0-0.0060.00231.530-0.002-0.0020.0000.0000.0000.000
138A138PHE00.005-0.00731.2300.0030.0030.0000.0000.0000.000
139A139LEU00.004-0.00534.6030.0030.0030.0000.0000.0000.000
140A140LYS10.8410.90336.4700.0140.0140.0000.0000.0000.000
141A141GLY00.0350.02635.7200.0010.0010.0000.0000.0000.000
142A142LYS10.9280.97536.7530.0370.0370.0000.0000.0000.000
143A143ARG10.8630.91334.6800.0920.0920.0000.0000.0000.000
144A144ILE0-0.025-0.00537.1480.0040.0040.0000.0000.0000.000
145A145HIS0-0.015-0.01538.744-0.007-0.0070.0000.0000.0000.000
146A146LEU00.013-0.00835.6600.0040.0040.0000.0000.0000.000
147A147PRO0-0.0250.00138.166-0.006-0.0060.0000.0000.0000.000
148A148LYS11.0071.00633.9830.1360.1360.0000.0000.0000.000
149A149LYS10.8190.91235.3150.1040.1040.0000.0000.0000.000
150A150GLU-1-0.782-0.91335.673-0.072-0.0720.0000.0000.0000.000
151A151PHE00.0140.01829.7020.0020.0020.0000.0000.0000.000
152A152GLU-1-0.836-0.92431.145-0.132-0.1320.0000.0000.0000.000
153A153ILE0-0.011-0.00330.692-0.003-0.0030.0000.0000.0000.000
154A154LEU0-0.005-0.00231.5240.0040.0040.0000.0000.0000.000
155A155LEU00.0170.01525.5830.0060.0060.0000.0000.0000.000
156A156PHE00.0190.01225.650-0.001-0.0010.0000.0000.0000.000
157A157LEU0-0.032-0.03026.9440.0040.0040.0000.0000.0000.000
158A158ALA00.000-0.00127.2420.0090.0090.0000.0000.0000.000
159A159GLU-1-0.784-0.87322.846-0.195-0.1950.0000.0000.0000.000
160A160ASN0-0.091-0.03122.476-0.002-0.0020.0000.0000.0000.000
161A161ALA00.0440.02524.7180.0140.0140.0000.0000.0000.000
162A162GLY0-0.042-0.02024.9090.0080.0080.0000.0000.0000.000
163A163LYS10.9060.94820.9850.0870.0870.0000.0000.0000.000
164A164VAL0-0.037-0.02027.443-0.006-0.0060.0000.0000.0000.000
165A165VAL00.0130.01328.592-0.006-0.0060.0000.0000.0000.000
166A166THR00.0520.01331.1050.0020.0020.0000.0000.0000.000
167A167ARG10.8420.87134.0740.0270.0270.0000.0000.0000.000
168A168GLU-1-0.933-0.96535.018-0.056-0.0560.0000.0000.0000.000
169A169LYS10.9961.00527.7280.1200.1200.0000.0000.0000.000
170A170LEU0-0.019-0.00732.011-0.010-0.0100.0000.0000.0000.000
171A171LEU0-0.057-0.03134.050-0.005-0.0050.0000.0000.0000.000
172A172GLU-1-0.915-0.94633.268-0.090-0.0900.0000.0000.0000.000
173A173THR0-0.084-0.04129.184-0.013-0.0130.0000.0000.0000.000
174A174PHE0-0.043-0.02929.366-0.008-0.0080.0000.0000.0000.000
175A175TRP00.003-0.01434.3850.0050.0050.0000.0000.0000.000
176A176GLU-1-0.911-0.93736.193-0.124-0.1240.0000.0000.0000.000
177A177ASP-1-0.913-0.93738.061-0.084-0.0840.0000.0000.0000.000
178A178PRO0-0.003-0.01640.9600.0010.0010.0000.0000.0000.000
179A179VAL0-0.006-0.00340.9540.0030.0030.0000.0000.0000.000
180A180SER0-0.024-0.01043.3180.0020.0020.0000.0000.0000.000
181A181PRO00.1220.03242.111-0.002-0.0020.0000.0000.0000.000
182A182ARG10.9820.99742.5620.0390.0390.0000.0000.0000.000
183A183VAL0-0.021-0.00841.8760.0020.0020.0000.0000.0000.000
184A184VAL00.0610.03737.814-0.001-0.0010.0000.0000.0000.000
185A185ASP-1-0.794-0.85940.383-0.036-0.0360.0000.0000.0000.000
186A186THR0-0.080-0.04342.5690.0030.0030.0000.0000.0000.000
187A187VAL00.0160.01337.8590.0010.0010.0000.0000.0000.000
188A188ILE00.0250.01736.0780.0000.0000.0000.0000.0000.000
189A189LYS10.9240.96739.6490.0320.0320.0000.0000.0000.000
190A190ARG10.8490.91241.8750.0590.0590.0000.0000.0000.000
191A191ILE00.0370.02635.6060.0010.0010.0000.0000.0000.000
192A192ARG10.8480.89238.7150.0250.0250.0000.0000.0000.000
193A193LYS10.9070.94640.5020.0340.0340.0000.0000.0000.000
194A194ALA0-0.0140.00839.8000.0020.0020.0000.0000.0000.000
195A195ILE00.0010.00235.192-0.001-0.0010.0000.0000.0000.000
196A196GLU-1-0.795-0.89737.901-0.014-0.0140.0000.0000.0000.000
197A197ASP-1-0.868-0.93840.655-0.013-0.0130.0000.0000.0000.000
198A198ASP-1-0.773-0.87043.405-0.007-0.0070.0000.0000.0000.000
199A199PRO0-0.026-0.00243.2810.0020.0020.0000.0000.0000.000
200A200ASN0-0.124-0.07344.367-0.002-0.0020.0000.0000.0000.000
201A201ARG10.8480.91043.1430.0020.0020.0000.0000.0000.000
202A202PRO0-0.034-0.01038.6590.0010.0010.0000.0000.0000.000
203A203ARG10.8550.92134.4830.0060.0060.0000.0000.0000.000
204A204TYR0-0.048-0.03931.9790.0040.0040.0000.0000.0000.000
205A205ILE00.0240.03333.423-0.001-0.0010.0000.0000.0000.000
206A206LYS10.9020.97034.979-0.003-0.0030.0000.0000.0000.000
207A207THR00.0260.00436.152-0.006-0.0060.0000.0000.0000.000
208A208ILE0-0.0020.00134.0860.0050.0050.0000.0000.0000.000
209A209TRP00.0480.00733.514-0.005-0.0050.0000.0000.0000.000
210A210GLY00.0140.01839.945-0.001-0.0010.0000.0000.0000.000
211A211VAL00.003-0.00136.763-0.004-0.0040.0000.0000.0000.000
212A212GLY00.0140.00535.279-0.007-0.0070.0000.0000.0000.000
213A213TYR0-0.086-0.04434.3760.0070.0070.0000.0000.0000.000
214A214MET00.0140.01930.005-0.002-0.0020.0000.0000.0000.000
215A215PHE00.0170.02128.4550.0030.0030.0000.0000.0000.000
216A216THR0-0.035-0.02229.3400.0050.0050.0000.0000.0000.000
217A217GLY00.0730.03328.348-0.004-0.0040.0000.0000.0000.000