Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 851NY

Calculation Name: 4PN7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PN7

Chain ID: A

ChEMBL ID:

UniProt ID: G0RXV8

Base Structure: X-ray

Registration Date: 2023-09-20

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2308553.173784
FMO2-HF: Nuclear repulsion 2231220.975365
FMO2-HF: Total energy -77332.198419
FMO2-MP2: Total energy -77561.849892


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:17:ASN)


Summations of interaction energy for fragment #1(A:17:ASN)
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.
-2.2962.090.055-2.135-2.3080.002
Interaction energy analysis for fragmet #1(A:17:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.029
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].
3A19ASP-1-0.783-0.8752.971-4.698-1.4890.030-1.574-1.6660.005
4A20ASP-1-0.891-0.9473.5541.0552.2320.025-0.561-0.642-0.003
5A21ILE0-0.032-0.0215.5370.6910.6910.0000.0000.0000.000
6A22PRO0-0.022-0.0098.017-0.335-0.3350.0000.0000.0000.000
7A23SER00.0030.01910.2160.3260.3260.0000.0000.0000.000
8A24LEU0-0.010-0.00412.207-0.153-0.1530.0000.0000.0000.000
9A25ARG10.9510.97212.9620.6090.6090.0000.0000.0000.000
10A26THR0-0.020-0.02017.136-0.039-0.0390.0000.0000.0000.000
11A27ILE00.0130.00819.6960.0170.0170.0000.0000.0000.000
12A28ILE0-0.019-0.01422.4820.0180.0180.0000.0000.0000.000
13A29ILE00.0060.00225.998-0.011-0.0110.0000.0000.0000.000
14A30ASP-1-0.700-0.81728.234-0.113-0.1130.0000.0000.0000.000
15A31THR0-0.007-0.02731.307-0.011-0.0110.0000.0000.0000.000
16A32ASN0-0.007-0.00534.1030.0010.0010.0000.0000.0000.000
17A33PRO00.0470.02037.172-0.007-0.0070.0000.0000.0000.000
18A34ARG10.8710.91839.8290.0810.0810.0000.0000.0000.000
19A35ALA0-0.028-0.01236.214-0.001-0.0010.0000.0000.0000.000
20A36TRP0-0.016-0.04330.176-0.013-0.0130.0000.0000.0000.000
21A37ALA0-0.0110.00036.922-0.005-0.0050.0000.0000.0000.000
22A38ALA0-0.063-0.02939.224-0.001-0.0010.0000.0000.0000.000
23A39LEU00.0050.00333.098-0.003-0.0030.0000.0000.0000.000
24A40ALA0-0.023-0.00736.421-0.012-0.0120.0000.0000.0000.000
25A41ASP-1-0.865-0.92238.657-0.158-0.1580.0000.0000.0000.000
26A42VAL0-0.0260.00233.374-0.011-0.0110.0000.0000.0000.000
27A43LEU0-0.058-0.04629.345-0.020-0.0200.0000.0000.0000.000
28A44PRO00.0740.04133.4410.0030.0030.0000.0000.0000.000
29A45LEU00.0600.03731.816-0.018-0.0180.0000.0000.0000.000
30A46SER00.0070.00031.825-0.014-0.0140.0000.0000.0000.000
31A47LYS10.9270.95427.3350.3270.3270.0000.0000.0000.000
32A48ALA00.0080.01028.511-0.028-0.0280.0000.0000.0000.000
33A49ILE00.0330.00827.056-0.028-0.0280.0000.0000.0000.000
34A50ALA00.0250.01226.490-0.028-0.0280.0000.0000.0000.000
35A51ASN00.0160.00524.464-0.048-0.0480.0000.0000.0000.000
36A52ILE00.0240.00922.641-0.050-0.0500.0000.0000.0000.000
37A53LEU0-0.0080.00521.846-0.041-0.0410.0000.0000.0000.000
38A54ILE0-0.003-0.00120.147-0.049-0.0490.0000.0000.0000.000
39A55PHE0-0.002-0.00115.707-0.068-0.0680.0000.0000.0000.000
40A56VAL0-0.004-0.00517.072-0.085-0.0850.0000.0000.0000.000
41A57ASN0-0.026-0.01417.296-0.131-0.1310.0000.0000.0000.000
42A58ALA00.0190.01014.690-0.095-0.0950.0000.0000.0000.000
43A59HIS0-0.017-0.02012.879-0.258-0.2580.0000.0000.0000.000
44A60LEU0-0.063-0.03212.381-0.164-0.1640.0000.0000.0000.000
45A61ALA0-0.013-0.00712.102-0.093-0.0930.0000.0000.0000.000
46A62PHE0-0.056-0.0188.255-0.115-0.1150.0000.0000.0000.000
47A63SER0-0.006-0.0046.454-0.684-0.6840.0000.0000.0000.000
48A64ASN0-0.022-0.0217.4310.7570.7570.0000.0000.0000.000
49A65SER0-0.037-0.0087.2270.2810.2810.0000.0000.0000.000
50A66ASN00.0150.0139.5470.5260.5260.0000.0000.0000.000
51A67GLN0-0.063-0.04611.6520.0820.0820.0000.0000.0000.000
52A68VAL0-0.031-0.00415.4580.0030.0030.0000.0000.0000.000
53A69ALA0-0.038-0.01618.6970.0370.0370.0000.0000.0000.000
54A70ILE0-0.010-0.00522.286-0.014-0.0140.0000.0000.0000.000
55A71ILE00.0030.00725.1230.0180.0180.0000.0000.0000.000
56A72ALA00.0490.03428.187-0.012-0.0120.0000.0000.0000.000
57A73SER0-0.047-0.05330.9240.0180.0180.0000.0000.0000.000
58A74HIS00.0900.06632.570-0.011-0.0110.0000.0000.0000.000
59A75THR0-0.033-0.04936.1590.0040.0040.0000.0000.0000.000
60A76ASN0-0.019-0.01739.3760.0060.0060.0000.0000.0000.000
61A77ARG10.7920.87237.2490.1030.1030.0000.0000.0000.000
62A78ALA00.0040.01132.523-0.007-0.0070.0000.0000.0000.000
63A79VAL00.002-0.00932.8820.0080.0080.0000.0000.0000.000
64A80TRP0-0.022-0.01025.050-0.015-0.0150.0000.0000.0000.000
65A81LEU0-0.0060.00728.2450.0010.0010.0000.0000.0000.000
66A82TYR00.0500.02721.952-0.018-0.0180.0000.0000.0000.000
67A83PRO00.010-0.01023.848-0.012-0.0120.0000.0000.0000.000
68A84GLN0-0.031-0.02126.4640.0130.0130.0000.0000.0000.000
69A85PRO00.0190.02729.604-0.004-0.0040.0000.0000.0000.000
70A106ILE0-0.017-0.02019.529-0.008-0.0080.0000.0000.0000.000
71A107GLY00.0350.01418.978-0.005-0.0050.0000.0000.0000.000
72A108LYS10.9320.95912.0360.6200.6200.0000.0000.0000.000
73A109TYR00.0710.04813.8840.0770.0770.0000.0000.0000.000
74A110PRO00.015-0.00215.4410.0600.0600.0000.0000.0000.000
75A111GLN0-0.003-0.00318.3780.0480.0480.0000.0000.0000.000
76A112PHE00.0620.03919.0920.0390.0390.0000.0000.0000.000
77A113ALA00.0590.02320.9590.0360.0360.0000.0000.0000.000
78A114GLN00.0010.01223.8650.0320.0320.0000.0000.0000.000
79A115ILE0-0.0040.01520.2150.0320.0320.0000.0000.0000.000
80A116GLU-1-0.886-0.94624.469-0.373-0.3730.0000.0000.0000.000
81A117LYS10.8610.90726.1980.3030.3030.0000.0000.0000.000
82A118SER0-0.034-0.02527.3880.0250.0250.0000.0000.0000.000
83A119LEU00.0170.02525.9480.0220.0220.0000.0000.0000.000
84A120LEU0-0.013-0.01329.0700.0190.0190.0000.0000.0000.000
85A121SER0-0.031-0.00431.6600.0180.0180.0000.0000.0000.000
86A122SER00.007-0.02731.4350.0160.0160.0000.0000.0000.000
87A123ILE0-0.015-0.01230.8080.0110.0110.0000.0000.0000.000
88A124ARG10.9080.96634.1960.1860.1860.0000.0000.0000.000
89A125ALA00.0900.04737.2050.0080.0080.0000.0000.0000.000
90A126LEU0-0.012-0.01134.6370.0080.0080.0000.0000.0000.000
91A127MET0-0.062-0.02736.8850.0060.0060.0000.0000.0000.000
92A128ASP-1-0.919-0.96239.572-0.128-0.1280.0000.0000.0000.000
93A129ASP-1-0.846-0.90041.270-0.093-0.0930.0000.0000.0000.000
94A130THR0-0.131-0.05841.4400.0060.0060.0000.0000.0000.000
95A131THR0-0.005-0.02643.6220.0050.0050.0000.0000.0000.000
96A132PRO00.043-0.01246.208-0.002-0.0020.0000.0000.0000.000
97A133SER00.0420.02146.7980.0000.0000.0000.0000.0000.000
98A134ASP-1-0.775-0.80342.193-0.085-0.0850.0000.0000.0000.000
99A135LEU0-0.0150.00042.787-0.006-0.0060.0000.0000.0000.000
100A136ASP-1-0.849-0.90245.077-0.075-0.0750.0000.0000.0000.000
101A137THR0-0.055-0.01841.0250.0050.0050.0000.0000.0000.000
102A138THR00.001-0.00241.288-0.006-0.0060.0000.0000.0000.000
103A139THR0-0.0060.00938.116-0.005-0.0050.0000.0000.0000.000
104A140THR00.0500.02033.172-0.004-0.0040.0000.0000.0000.000
105A141GLN0-0.0040.02135.7140.0110.0110.0000.0000.0000.000
106A142ILE00.0410.01128.1870.0000.0000.0000.0000.0000.000
107A143SER00.0220.01630.898-0.001-0.0010.0000.0000.0000.000
108A144GLY00.0300.03232.3010.0070.0070.0000.0000.0000.000
109A145ALA00.0240.00029.4550.0010.0010.0000.0000.0000.000
110A146LEU00.0250.00425.991-0.006-0.0060.0000.0000.0000.000
111A147THR0-0.021-0.01627.7470.0120.0120.0000.0000.0000.000
112A148LEU0-0.038-0.01429.3410.0070.0070.0000.0000.0000.000
113A149ALA00.0170.00324.335-0.003-0.0030.0000.0000.0000.000
114A150LEU0-0.007-0.00523.8210.0030.0030.0000.0000.0000.000
115A151ALA0-0.0020.01125.3330.0160.0160.0000.0000.0000.000
116A152HIS00.0590.02521.2280.0300.0300.0000.0000.0000.000
117A153ILE00.0240.02419.842-0.005-0.0050.0000.0000.0000.000
118A154ASN00.0110.00821.5060.0350.0350.0000.0000.0000.000
119A155LYS10.9050.95523.3770.1150.1150.0000.0000.0000.000
120A156THR0-0.051-0.04118.256-0.008-0.0080.0000.0000.0000.000
121A157ALA00.0270.01018.6990.0030.0030.0000.0000.0000.000
122A158LEU00.0070.01019.7840.0250.0250.0000.0000.0000.000
123A159SER00.0090.00620.8630.0060.0060.0000.0000.0000.000
124A160LEU0-0.0280.00314.008-0.015-0.0150.0000.0000.0000.000
125A161THR0-0.046-0.03817.9770.0290.0290.0000.0000.0000.000
126A162ALA00.0110.01919.7290.0170.0170.0000.0000.0000.000
127A163SER0-0.009-0.01417.405-0.012-0.0120.0000.0000.0000.000
128A164ASN0-0.047-0.02614.252-0.049-0.0490.0000.0000.0000.000
129A165THR0-0.049-0.03917.5380.0310.0310.0000.0000.0000.000
130A166ALA0-0.0440.00121.1130.0000.0000.0000.0000.0000.000
131A167ALA0-0.011-0.00718.667-0.016-0.0160.0000.0000.0000.000
132A168ALA0-0.019-0.00320.6220.0130.0130.0000.0000.0000.000
133A198ALA00.0220.0089.9410.0290.0290.0000.0000.0000.000
134A199GLY00.002-0.00211.631-0.184-0.1840.0000.0000.0000.000
135A200LEU0-0.036-0.02412.5990.0420.0420.0000.0000.0000.000
136A201HIS0-0.0020.00511.2140.1350.1350.0000.0000.0000.000
137A202ALA0-0.008-0.01713.258-0.146-0.1460.0000.0000.0000.000
138A203ARG10.8610.92814.0170.0760.0760.0000.0000.0000.000
139A204ILE0-0.023-0.00617.442-0.048-0.0480.0000.0000.0000.000
140A205LEU0-0.0080.00318.399-0.003-0.0030.0000.0000.0000.000
141A206ILE0-0.008-0.00321.133-0.011-0.0110.0000.0000.0000.000
142A207ILE00.0160.01523.110-0.003-0.0030.0000.0000.0000.000
143A208SER0-0.071-0.05726.1030.0170.0170.0000.0000.0000.000
144A209VAL0-0.003-0.00829.493-0.008-0.0080.0000.0000.0000.000
145A210SER00.011-0.00632.8770.0080.0080.0000.0000.0000.000
146A211ASP-1-0.817-0.89334.631-0.092-0.0920.0000.0000.0000.000
147A212SER0-0.015-0.01034.9420.0030.0030.0000.0000.0000.000
148A213SER00.016-0.00537.1510.0030.0030.0000.0000.0000.000
149A214ALA00.0390.00639.7610.0020.0020.0000.0000.0000.000
150A215ALA00.0230.01441.4370.0040.0040.0000.0000.0000.000
151A216GLN00.0260.01237.3060.0020.0020.0000.0000.0000.000
152A217TYR00.0030.02335.7290.0020.0020.0000.0000.0000.000
153A218ILE00.0480.02236.1970.0020.0020.0000.0000.0000.000
154A219PRO0-0.003-0.00836.3250.0040.0040.0000.0000.0000.000
155A220THR0-0.030-0.03031.738-0.003-0.0030.0000.0000.0000.000
156A221MET00.012-0.00331.7740.0050.0050.0000.0000.0000.000
157A222ASN0-0.0060.00831.9460.0170.0170.0000.0000.0000.000
158A223ALA00.0210.01529.4560.0100.0100.0000.0000.0000.000
159A224VAL0-0.0010.00727.3420.0060.0060.0000.0000.0000.000
160A225PHE00.025-0.00127.0880.0140.0140.0000.0000.0000.000
161A226ALA0-0.0100.00727.8210.0200.0200.0000.0000.0000.000
162A227ALA0-0.002-0.00323.7300.0190.0190.0000.0000.0000.000
163A228ALA00.0190.00423.0740.0270.0270.0000.0000.0000.000
164A229HIS0-0.030-0.00623.4940.0420.0420.0000.0000.0000.000
165A230ALA0-0.031-0.02322.4200.0350.0350.0000.0000.0000.000
166A231ARG10.8610.93318.695-0.307-0.3070.0000.0000.0000.000
167A232ILE0-0.0170.01118.4590.0190.0190.0000.0000.0000.000
168A233ALA00.0190.00717.449-0.024-0.0240.0000.0000.0000.000
169A234ILE00.002-0.01119.484-0.039-0.0390.0000.0000.0000.000
170A235ASP-1-0.774-0.86016.976-0.185-0.1850.0000.0000.0000.000
171A236THR0-0.049-0.03420.552-0.005-0.0050.0000.0000.0000.000
172A237LEU0-0.014-0.00822.550-0.009-0.0090.0000.0000.0000.000
173A238ALA0-0.0020.00824.7930.0000.0000.0000.0000.0000.000
174A239LEU0-0.013-0.01726.668-0.010-0.0100.0000.0000.0000.000
175A240ARG10.8310.89730.1620.1170.1170.0000.0000.0000.000
176A241GLY00.0060.01933.0210.0000.0000.0000.0000.0000.000
177A242SER00.002-0.01534.249-0.002-0.0020.0000.0000.0000.000
178A243ALA00.0340.02131.1920.0100.0100.0000.0000.0000.000
179A244THR00.0220.00031.4140.0000.0000.0000.0000.0000.000
180A245PHE00.003-0.00632.0590.0080.0080.0000.0000.0000.000
181A246LEU00.011-0.00127.7660.0090.0090.0000.0000.0000.000
182A247GLU-1-0.785-0.84227.094-0.079-0.0790.0000.0000.0000.000
183A248GLN0-0.014-0.01727.5470.0090.0090.0000.0000.0000.000
184A249ALA00.0290.01126.8140.0150.0150.0000.0000.0000.000
185A250SER0-0.033-0.00222.9600.0120.0120.0000.0000.0000.000
186A251PHE00.0000.00923.1180.0210.0210.0000.0000.0000.000
187A252ILE0-0.019-0.01124.6530.0230.0230.0000.0000.0000.000
188A253THR0-0.071-0.05722.2620.0210.0210.0000.0000.0000.000
189A254ARG10.9190.96719.710-0.187-0.1870.0000.0000.0000.000
190A255GLY0-0.0260.00318.5860.0170.0170.0000.0000.0000.000
191A256THR0-0.003-0.00917.5500.0340.0340.0000.0000.0000.000
192A257PHE00.0300.00220.248-0.011-0.0110.0000.0000.0000.000
193A258ILE0-0.031-0.00420.411-0.005-0.0050.0000.0000.0000.000
194A259ARG10.8090.87024.7690.1030.1030.0000.0000.0000.000
195A260ALA0-0.015-0.00726.779-0.001-0.0010.0000.0000.0000.000
196A261ALA00.0280.02028.1340.0130.0130.0000.0000.0000.000
197A262GLU-1-0.941-0.96628.951-0.230-0.2300.0000.0000.0000.000
198A263PRO00.0280.00328.868-0.025-0.0250.0000.0000.0000.000
199A264ARG10.8540.91328.8290.1870.1870.0000.0000.0000.000
200A265GLY00.0450.03526.254-0.018-0.0180.0000.0000.0000.000
201A266LEU0-0.050-0.01324.245-0.029-0.0290.0000.0000.0000.000
202A267LEU00.0140.00019.876-0.015-0.0150.0000.0000.0000.000
203A268GLN00.0140.00520.223-0.042-0.0420.0000.0000.0000.000
204A269TYR00.0340.00919.577-0.027-0.0270.0000.0000.0000.000
205A270LEU0-0.043-0.02519.295-0.002-0.0020.0000.0000.0000.000
206A271MET0-0.048-0.01813.802-0.029-0.0290.0000.0000.0000.000
207A272PHE0-0.028-0.02314.696-0.097-0.0970.0000.0000.0000.000
208A273GLY00.0230.03216.3280.0300.0300.0000.0000.0000.000
209A274PHE0-0.035-0.01213.0890.0660.0660.0000.0000.0000.000