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: G6MY1

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299278.126528
FMO2-HF: Nuclear repulsion 2221946.18534
FMO2-HF: Total energy -77331.941188
FMO2-MP2: Total energy -77561.566835


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.
-2.8521.2230.111-1.739-2.4460.007
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 : 0.063 / q_NPA : 0.026
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-1-0.803-0.8922.733-7.173-3.4800.111-1.693-2.1110.007
4A20ASP-1-0.911-0.9384.1792.8033.1850.000-0.046-0.3350.000
5A21ILE0-0.031-0.0246.1040.6520.6520.0000.0000.0000.000
6A22PRO00.0010.0048.268-0.416-0.4160.0000.0000.0000.000
7A23SER00.0160.01710.3880.3090.3090.0000.0000.0000.000
8A24LEU0-0.0030.00412.368-0.127-0.1270.0000.0000.0000.000
9A25ARG10.9550.97612.4190.8990.8990.0000.0000.0000.000
10A26THR0-0.019-0.01816.898-0.023-0.0230.0000.0000.0000.000
11A27ILE00.0100.00519.1980.0060.0060.0000.0000.0000.000
12A28ILE0-0.011-0.01222.3210.0230.0230.0000.0000.0000.000
13A29ILE00.009-0.01125.779-0.011-0.0110.0000.0000.0000.000
14A30ASP-1-0.747-0.84127.961-0.169-0.1690.0000.0000.0000.000
15A31THR0-0.009-0.01531.026-0.015-0.0150.0000.0000.0000.000
16A32ASN0-0.012-0.01233.7740.0070.0070.0000.0000.0000.000
17A33PRO00.0540.02636.671-0.007-0.0070.0000.0000.0000.000
18A34ARG10.9010.93539.1620.1120.1120.0000.0000.0000.000
19A35ALA0-0.021-0.00235.939-0.001-0.0010.0000.0000.0000.000
20A36TRP0-0.011-0.04829.596-0.014-0.0140.0000.0000.0000.000
21A37ALA0-0.036-0.01436.318-0.005-0.0050.0000.0000.0000.000
22A38ALA0-0.047-0.02738.5110.0000.0000.0000.0000.0000.000
23A39LEU0-0.0050.01132.423-0.001-0.0010.0000.0000.0000.000
24A40ALA0-0.0070.00635.715-0.013-0.0130.0000.0000.0000.000
25A41ASP-1-0.883-0.93137.578-0.199-0.1990.0000.0000.0000.000
26A42VAL0-0.020-0.00833.130-0.011-0.0110.0000.0000.0000.000
27A43LEU0-0.078-0.04928.894-0.023-0.0230.0000.0000.0000.000
28A44PRO00.0780.03732.9400.0020.0020.0000.0000.0000.000
29A45LEU00.0680.03731.365-0.021-0.0210.0000.0000.0000.000
30A46SER00.005-0.00431.265-0.019-0.0190.0000.0000.0000.000
31A47LYS10.9240.95127.0340.3890.3890.0000.0000.0000.000
32A48ALA00.0200.01027.854-0.034-0.0340.0000.0000.0000.000
33A49ILE00.0150.00426.471-0.034-0.0340.0000.0000.0000.000
34A50ALA00.0220.01425.933-0.034-0.0340.0000.0000.0000.000
35A51ASN00.0270.00623.873-0.048-0.0480.0000.0000.0000.000
36A52ILE00.0260.01322.034-0.064-0.0640.0000.0000.0000.000
37A53LEU00.0020.00521.277-0.052-0.0520.0000.0000.0000.000
38A54ILE0-0.018-0.00519.441-0.055-0.0550.0000.0000.0000.000
39A55PHE0-0.008-0.00515.271-0.080-0.0800.0000.0000.0000.000
40A56VAL00.0050.00216.349-0.118-0.1180.0000.0000.0000.000
41A57ASN0-0.008-0.00616.447-0.157-0.1570.0000.0000.0000.000
42A58ALA00.0090.01013.974-0.088-0.0880.0000.0000.0000.000
43A59HIS0-0.007-0.00212.246-0.354-0.3540.0000.0000.0000.000
44A60LEU0-0.066-0.03811.752-0.227-0.2270.0000.0000.0000.000
45A61ALA00.0000.00811.682-0.072-0.0720.0000.0000.0000.000
46A62PHE0-0.059-0.0247.811-0.122-0.1220.0000.0000.0000.000
47A63SER00.0400.0265.734-0.822-0.8220.0000.0000.0000.000
48A64ASN0-0.002-0.0047.0820.9110.9110.0000.0000.0000.000
49A65SER0-0.115-0.0717.0870.4710.4710.0000.0000.0000.000
50A66ASN00.0160.0149.2820.3960.3960.0000.0000.0000.000
51A67GLN0-0.080-0.05711.5500.1250.1250.0000.0000.0000.000
52A68VAL0-0.027-0.01315.340-0.023-0.0230.0000.0000.0000.000
53A69ALA0-0.048-0.01518.3760.0530.0530.0000.0000.0000.000
54A70ILE0-0.009-0.00221.970-0.017-0.0170.0000.0000.0000.000
55A71ILE00.000-0.00324.7310.0270.0270.0000.0000.0000.000
56A72ALA00.0650.04327.793-0.017-0.0170.0000.0000.0000.000
57A73SER0-0.068-0.05530.6780.0210.0210.0000.0000.0000.000
58A74HIS00.0930.06332.253-0.013-0.0130.0000.0000.0000.000
59A75THR0-0.027-0.04235.7570.0030.0030.0000.0000.0000.000
60A76ASN0-0.024-0.02438.8110.0030.0030.0000.0000.0000.000
61A77ARG10.8730.94437.2240.1470.1470.0000.0000.0000.000
62A78ALA0-0.0160.00332.203-0.010-0.0100.0000.0000.0000.000
63A79VAL00.014-0.00432.6950.0110.0110.0000.0000.0000.000
64A80TRP0-0.030-0.01124.943-0.020-0.0200.0000.0000.0000.000
65A81LEU0-0.0080.00727.8160.0050.0050.0000.0000.0000.000
66A82TYR00.0470.02821.673-0.012-0.0120.0000.0000.0000.000
67A83PRO00.009-0.01823.886-0.020-0.0200.0000.0000.0000.000
68A84GLN0-0.039-0.02926.3120.0170.0170.0000.0000.0000.000
69A85PRO00.0290.03229.489-0.002-0.0020.0000.0000.0000.000
70A106ILE0-0.027-0.02619.857-0.008-0.0080.0000.0000.0000.000
71A107GLY00.0450.02219.145-0.006-0.0060.0000.0000.0000.000
72A108LYS10.9590.99012.1200.7230.7230.0000.0000.0000.000
73A109TYR00.0790.04913.6410.0920.0920.0000.0000.0000.000
74A110PRO00.0170.00115.3290.0610.0610.0000.0000.0000.000
75A111GLN0-0.028-0.02118.2180.0470.0470.0000.0000.0000.000
76A112PHE00.0660.03218.8060.0380.0380.0000.0000.0000.000
77A113ALA00.0440.02020.7230.0390.0390.0000.0000.0000.000
78A114GLN0-0.030-0.02423.6780.0310.0310.0000.0000.0000.000
79A115ILE0-0.0100.00720.0270.0320.0320.0000.0000.0000.000
80A116GLU-1-0.924-0.96524.116-0.440-0.4400.0000.0000.0000.000
81A117LYS10.9410.96725.8670.3520.3520.0000.0000.0000.000
82A118SER0-0.011-0.02227.2980.0270.0270.0000.0000.0000.000
83A119LEU00.0070.03425.4140.0210.0210.0000.0000.0000.000
84A120LEU0-0.012-0.01228.8080.0200.0200.0000.0000.0000.000
85A121SER0-0.038-0.01331.4060.0220.0220.0000.0000.0000.000
86A122SER00.029-0.01331.0480.0180.0180.0000.0000.0000.000
87A123ILE0-0.018-0.00730.4910.0130.0130.0000.0000.0000.000
88A124ARG10.9130.96233.7930.2370.2370.0000.0000.0000.000
89A125ALA00.0890.04436.8570.0090.0090.0000.0000.0000.000
90A126LEU0-0.009-0.00234.0880.0090.0090.0000.0000.0000.000
91A127MET0-0.071-0.04436.7680.0070.0070.0000.0000.0000.000
92A128ASP-1-0.932-0.96139.412-0.160-0.1600.0000.0000.0000.000
93A129ASP-1-0.909-0.93041.495-0.131-0.1310.0000.0000.0000.000
94A130THR0-0.115-0.05740.8920.0050.0050.0000.0000.0000.000
95A131THR0-0.007-0.02743.2250.0060.0060.0000.0000.0000.000
96A132PRO00.046-0.01245.962-0.003-0.0030.0000.0000.0000.000
97A133SER00.0430.02146.8430.0000.0000.0000.0000.0000.000
98A134ASP-1-0.767-0.81442.017-0.121-0.1210.0000.0000.0000.000
99A135LEU0-0.023-0.00442.653-0.006-0.0060.0000.0000.0000.000
100A136ASP-1-0.885-0.92044.595-0.103-0.1030.0000.0000.0000.000
101A137THR0-0.069-0.02640.7370.0070.0070.0000.0000.0000.000
102A138THR00.0060.00840.623-0.007-0.0070.0000.0000.0000.000
103A139THR00.0140.01437.861-0.004-0.0040.0000.0000.0000.000
104A140THR00.0250.01132.981-0.002-0.0020.0000.0000.0000.000
105A141GLN0-0.0100.01135.4000.0100.0100.0000.0000.0000.000
106A142ILE00.0660.01828.071-0.004-0.0040.0000.0000.0000.000
107A143SER00.0080.01230.796-0.005-0.0050.0000.0000.0000.000
108A144GLY00.0310.02632.1830.0050.0050.0000.0000.0000.000
109A145ALA00.027-0.00229.135-0.001-0.0010.0000.0000.0000.000
110A146LEU00.0210.00025.839-0.010-0.0100.0000.0000.0000.000
111A147THR0-0.015-0.01027.6940.0100.0100.0000.0000.0000.000
112A148LEU0-0.031-0.00829.4090.0060.0060.0000.0000.0000.000
113A149ALA00.0170.00224.209-0.005-0.0050.0000.0000.0000.000
114A150LEU0-0.014-0.01124.039-0.002-0.0020.0000.0000.0000.000
115A151ALA0-0.0080.00925.8320.0180.0180.0000.0000.0000.000
116A152HIS00.0420.01221.4430.0410.0410.0000.0000.0000.000
117A153ILE00.0270.02620.112-0.007-0.0070.0000.0000.0000.000
118A154ASN00.0120.01521.6660.0360.0360.0000.0000.0000.000
119A155LYS10.9290.96523.6870.1820.1820.0000.0000.0000.000
120A156THR0-0.058-0.05018.254-0.006-0.0060.0000.0000.0000.000
121A157ALA00.0160.00919.0140.0030.0030.0000.0000.0000.000
122A158LEU00.0130.00720.1000.0300.0300.0000.0000.0000.000
123A159SER00.0080.00421.1970.0100.0100.0000.0000.0000.000
124A160LEU0-0.0200.00314.301-0.007-0.0070.0000.0000.0000.000
125A161THR0-0.031-0.02718.2920.0320.0320.0000.0000.0000.000
126A162ALA0-0.0040.01319.7650.0260.0260.0000.0000.0000.000
127A163SER0-0.015-0.01317.757-0.012-0.0120.0000.0000.0000.000
128A164ASN0-0.034-0.01314.605-0.037-0.0370.0000.0000.0000.000
129A165THR0-0.042-0.04118.1320.0300.0300.0000.0000.0000.000
130A166ALA0-0.0450.00621.2750.0030.0030.0000.0000.0000.000
131A167ALA00.0010.00118.931-0.013-0.0130.0000.0000.0000.000
132A168ALA0-0.023-0.00620.8640.0080.0080.0000.0000.0000.000
133A198ALA00.0060.00310.4010.0140.0140.0000.0000.0000.000
134A199GLY0-0.007-0.00612.155-0.180-0.1800.0000.0000.0000.000
135A200LEU0-0.031-0.02012.9250.0340.0340.0000.0000.0000.000
136A201HIS0-0.0220.00411.7220.1550.1550.0000.0000.0000.000
137A202ALA0-0.003-0.01313.719-0.154-0.1540.0000.0000.0000.000
138A203ARG10.8750.92113.7130.3160.3160.0000.0000.0000.000
139A204ILE0-0.0140.00017.065-0.060-0.0600.0000.0000.0000.000
140A205LEU0-0.0090.01218.513-0.004-0.0040.0000.0000.0000.000
141A206ILE0-0.014-0.00420.9160.0050.0050.0000.0000.0000.000
142A207ILE00.0000.00323.104-0.012-0.0120.0000.0000.0000.000
143A208SER0-0.023-0.01426.1250.0230.0230.0000.0000.0000.000
144A209VAL0-0.002-0.01729.284-0.008-0.0080.0000.0000.0000.000
145A210SER0-0.001-0.02532.5820.0130.0130.0000.0000.0000.000
146A211ASP-1-0.870-0.92834.476-0.134-0.1340.0000.0000.0000.000
147A212SER0-0.035-0.01934.6240.0000.0000.0000.0000.0000.000
148A213SER00.0380.01336.8610.0060.0060.0000.0000.0000.000
149A214ALA00.0660.01939.4580.0010.0010.0000.0000.0000.000
150A215ALA00.0140.01441.0970.0040.0040.0000.0000.0000.000
151A216GLN0-0.002-0.00936.8860.0010.0010.0000.0000.0000.000
152A217TYR0-0.0090.00935.8390.0000.0000.0000.0000.0000.000
153A218ILE00.0510.01636.1450.0000.0000.0000.0000.0000.000
154A219PRO00.0150.00336.1990.0020.0020.0000.0000.0000.000
155A220THR0-0.023-0.03031.571-0.005-0.0050.0000.0000.0000.000
156A221MET00.0130.00431.562-0.001-0.0010.0000.0000.0000.000
157A222ASN0-0.0120.00931.9000.0170.0170.0000.0000.0000.000
158A223ALA00.0130.00929.5060.0070.0070.0000.0000.0000.000
159A224VAL00.000-0.00327.1130.0010.0010.0000.0000.0000.000
160A225PHE00.007-0.01226.9290.0080.0080.0000.0000.0000.000
161A226ALA0-0.0090.01228.2740.0200.0200.0000.0000.0000.000
162A227ALA00.0170.00623.4450.0170.0170.0000.0000.0000.000
163A228ALA00.0210.01023.1650.0210.0210.0000.0000.0000.000
164A229HIS0-0.0200.00523.6210.0350.0350.0000.0000.0000.000
165A230ALA0-0.044-0.01922.7500.0330.0330.0000.0000.0000.000
166A231ARG10.8610.92918.792-0.250-0.2500.0000.0000.0000.000
167A232ILE0-0.021-0.00218.4280.0090.0090.0000.0000.0000.000
168A233ALA00.0090.00617.102-0.013-0.0130.0000.0000.0000.000
169A234ILE00.003-0.01219.156-0.042-0.0420.0000.0000.0000.000
170A235ASP-1-0.790-0.87816.986-0.370-0.3700.0000.0000.0000.000
171A236THR0-0.023-0.01920.5850.0030.0030.0000.0000.0000.000
172A237LEU0-0.0060.00622.513-0.008-0.0080.0000.0000.0000.000
173A238ALA0-0.016-0.01124.5140.0060.0060.0000.0000.0000.000
174A239LEU0-0.006-0.00426.599-0.005-0.0050.0000.0000.0000.000
175A240ARG10.9260.96029.8180.1770.1770.0000.0000.0000.000
176A241GLY00.0090.02232.813-0.002-0.0020.0000.0000.0000.000
177A242SER0-0.032-0.02634.033-0.005-0.0050.0000.0000.0000.000
178A243ALA00.0330.01331.1560.0110.0110.0000.0000.0000.000
179A244THR00.0420.00931.331-0.005-0.0050.0000.0000.0000.000
180A245PHE00.013-0.00131.6780.0040.0040.0000.0000.0000.000
181A246LEU00.0300.00327.7160.0070.0070.0000.0000.0000.000
182A247GLU-1-0.791-0.84926.978-0.145-0.1450.0000.0000.0000.000
183A248GLN0-0.033-0.03027.3580.0060.0060.0000.0000.0000.000
184A249ALA00.0270.01226.6780.0150.0150.0000.0000.0000.000
185A250SER0-0.029-0.00122.7480.0060.0060.0000.0000.0000.000
186A251PHE0-0.0110.00822.9770.0150.0150.0000.0000.0000.000
187A252ILE0-0.015-0.00424.7100.0220.0220.0000.0000.0000.000
188A253THR0-0.072-0.05421.9430.0180.0180.0000.0000.0000.000
189A254ARG10.9080.95719.498-0.124-0.1240.0000.0000.0000.000
190A255GLY0-0.0190.00018.593-0.003-0.0030.0000.0000.0000.000
191A256THR0-0.023-0.01417.2490.0410.0410.0000.0000.0000.000
192A257PHE00.0260.00520.127-0.019-0.0190.0000.0000.0000.000
193A258ILE0-0.021-0.00219.9070.0000.0000.0000.0000.0000.000
194A259ARG10.8250.87924.3590.1560.1560.0000.0000.0000.000
195A260ALA0-0.015-0.00326.556-0.004-0.0040.0000.0000.0000.000
196A261ALA00.0280.02027.7840.0180.0180.0000.0000.0000.000
197A262GLU-1-0.932-0.96728.892-0.273-0.2730.0000.0000.0000.000
198A263PRO00.0380.01328.490-0.031-0.0310.0000.0000.0000.000
199A264ARG10.8790.93128.6180.2330.2330.0000.0000.0000.000
200A265GLY0-0.0010.01326.018-0.021-0.0210.0000.0000.0000.000
201A266LEU0-0.023-0.00624.058-0.038-0.0380.0000.0000.0000.000
202A267LEU0-0.001-0.01219.722-0.024-0.0240.0000.0000.0000.000
203A268GLN00.0150.00219.864-0.048-0.0480.0000.0000.0000.000
204A269TYR00.0370.01819.346-0.040-0.0400.0000.0000.0000.000
205A270LEU0-0.041-0.02418.871-0.025-0.0250.0000.0000.0000.000
206A271MET0-0.054-0.01513.533-0.060-0.0600.0000.0000.0000.000
207A272PHE0-0.031-0.02414.414-0.127-0.1270.0000.0000.0000.000
208A273GLY00.0090.02515.8990.0250.0250.0000.0000.0000.000
209A274PHE0-0.031-0.01612.5400.0680.0680.0000.0000.0000.000