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: M3GYZ

Calculation Name: 4HVZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q44642

Base Structure: X-ray

Registration Date: 2023-06-20

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1872629.825792
FMO2-HF: Nuclear repulsion 1792166.273674
FMO2-HF: Total energy -80463.552118
FMO2-MP2: Total energy -80694.859566


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:37:PRO)


Summations of interaction energy for fragment #1(A:37:PRO)
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.
-2.392-0.19-0.013-0.961-1.2290.001
Interaction energy analysis for fragmet #1(A:37:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.013
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].
3A39ARG10.9750.9753.543-2.398-0.196-0.013-0.961-1.2290.001
4A40ILE00.0200.0196.0740.2570.2570.0000.0000.0000.000
5A41ALA0-0.006-0.0099.413-0.047-0.0470.0000.0000.0000.000
6A42VAL0-0.0020.00610.9720.0340.0340.0000.0000.0000.000
7A43THR00.0480.04414.606-0.014-0.0140.0000.0000.0000.000
8A44GLY0-0.022-0.01917.4450.0010.0010.0000.0000.0000.000
9A45GLU-1-0.876-0.93420.6200.0120.0120.0000.0000.0000.000
10A46GLY00.000-0.00824.027-0.006-0.0060.0000.0000.0000.000
11A47MET0-0.0310.00426.4130.0030.0030.0000.0000.0000.000
12A48MET0-0.034-0.01330.017-0.002-0.0020.0000.0000.0000.000
13A49THR00.035-0.00333.1970.0020.0020.0000.0000.0000.000
14A50ALA00.0070.00736.777-0.002-0.0020.0000.0000.0000.000
15A51SER00.0260.01139.8320.0020.0020.0000.0000.0000.000
16A52PRO0-0.025-0.00343.153-0.001-0.0010.0000.0000.0000.000
17A53ASP-1-0.890-0.93644.007-0.010-0.0100.0000.0000.0000.000
18A54MET0-0.067-0.03846.5600.0000.0000.0000.0000.0000.000
19A55ALA00.0410.02448.4380.0010.0010.0000.0000.0000.000
20A56ILE0-0.057-0.02546.180-0.001-0.0010.0000.0000.0000.000
21A57LEU00.0370.04050.1030.0010.0010.0000.0000.0000.000
22A58ASN0-0.004-0.01350.981-0.001-0.0010.0000.0000.0000.000
23A59LEU00.0180.01452.9410.0000.0000.0000.0000.0000.000
24A60SER00.0640.02756.3600.0000.0000.0000.0000.0000.000
25A61VAL0-0.020-0.01458.0780.0000.0000.0000.0000.0000.000
26A62LEU00.0400.01161.2090.0000.0000.0000.0000.0000.000
27A63ARG10.8920.94563.8840.0000.0000.0000.0000.0000.000
28A64GLN0-0.009-0.02966.6680.0000.0000.0000.0000.0000.000
29A65ALA0-0.0200.00769.1010.0000.0000.0000.0000.0000.000
30A66LYS10.9300.97271.447-0.003-0.0030.0000.0000.0000.000
31A67THR0-0.018-0.01371.6190.0000.0000.0000.0000.0000.000
32A68ALA00.0800.04867.0230.0000.0000.0000.0000.0000.000
33A69ARG10.9550.97368.4960.0000.0000.0000.0000.0000.000
34A70GLU-1-0.829-0.93769.7360.0010.0010.0000.0000.0000.000
35A71ALA00.0120.02067.6790.0000.0000.0000.0000.0000.000
36A72MET00.013-0.00463.0990.0000.0000.0000.0000.0000.000
37A73THR00.0130.00966.1950.0000.0000.0000.0000.0000.000
38A74ALA00.0290.02368.6900.0000.0000.0000.0000.0000.000
39A75ASN0-0.025-0.01162.2430.0000.0000.0000.0000.0000.000
40A76ASN00.000-0.00464.0710.0000.0000.0000.0000.0000.000
41A77GLU-1-0.947-0.97965.721-0.001-0.0010.0000.0000.0000.000
42A78ALA0-0.004-0.02067.1950.0000.0000.0000.0000.0000.000
43A79MET0-0.0010.00860.7210.0000.0000.0000.0000.0000.000
44A80THR0-0.028-0.03964.3840.0000.0000.0000.0000.0000.000
45A81LYN00.0020.03165.5490.0000.0000.0000.0000.0000.000
46A82VAL00.0150.01562.1170.0000.0000.0000.0000.0000.000
47A83LEU00.0220.01459.2650.0000.0000.0000.0000.0000.000
48A84ASP-1-0.890-0.92462.503-0.004-0.0040.0000.0000.0000.000
49A85ALA0-0.021-0.02365.5780.0000.0000.0000.0000.0000.000
50A86MET00.0000.00460.4010.0000.0000.0000.0000.0000.000
51A87LYS10.8830.93960.7970.0040.0040.0000.0000.0000.000
52A88LYS10.8830.95262.5110.0030.0030.0000.0000.0000.000
53A89ALA0-0.031-0.00662.6020.0000.0000.0000.0000.0000.000
54A90GLY0-0.056-0.01961.6340.0000.0000.0000.0000.0000.000
55A91ILE0-0.019-0.00356.4820.0000.0000.0000.0000.0000.000
56A92GLU-1-0.871-0.95054.492-0.008-0.0080.0000.0000.0000.000
57A93ASP-1-0.873-0.95756.414-0.006-0.0060.0000.0000.0000.000
58A94ARG10.8590.94048.5460.0110.0110.0000.0000.0000.000
59A95ASP-1-0.817-0.89351.470-0.008-0.0080.0000.0000.0000.000
60A96LEU00.0260.01853.0730.0010.0010.0000.0000.0000.000
61A97GLN0-0.005-0.00350.2510.0000.0000.0000.0000.0000.000
62A98THR0-0.0200.00553.5010.0010.0010.0000.0000.0000.000
63A99GLY00.0320.01953.2990.0000.0000.0000.0000.0000.000
64A100GLY0-0.001-0.01053.4270.0000.0000.0000.0000.0000.000
65A101ILE0-0.031-0.02154.0470.0000.0000.0000.0000.0000.000
66A102ASP-1-0.863-0.89556.4060.0030.0030.0000.0000.0000.000
67A103ILE0-0.004-0.01958.3470.0000.0000.0000.0000.0000.000
68A104GLN0-0.0080.00259.6680.0010.0010.0000.0000.0000.000
69A105PRO0-0.026-0.01962.9490.0000.0000.0000.0000.0000.000
70A106ILE00.0520.03765.7820.0000.0000.0000.0000.0000.000
71A107TYR0-0.032-0.02165.1010.0000.0000.0000.0000.0000.000
72A108VAL0-0.017-0.00470.3210.0000.0000.0000.0000.0000.000
73A109TYR00.028-0.00265.9810.0000.0000.0000.0000.0000.000
74A110PRO0-0.024-0.01671.9100.0000.0000.0000.0000.0000.000
75A111ASP-1-0.871-0.93374.4420.0060.0060.0000.0000.0000.000
76A112ASP-1-0.867-0.92177.1130.0060.0060.0000.0000.0000.000
77A113LYS10.8470.92280.638-0.005-0.0050.0000.0000.0000.000
78A114ASN00.0110.00977.3470.0000.0000.0000.0000.0000.000
79A115ASN0-0.037-0.03079.6250.0000.0000.0000.0000.0000.000
80A116LEU0-0.063-0.00575.1040.0000.0000.0000.0000.0000.000
81A117LYS10.8790.93673.136-0.006-0.0060.0000.0000.0000.000
82A118GLU-1-0.860-0.93570.3960.0080.0080.0000.0000.0000.000
83A119PRO00.0320.01068.4510.0000.0000.0000.0000.0000.000
84A120THR0-0.038-0.03771.6990.0000.0000.0000.0000.0000.000
85A121ILE0-0.0060.00569.3920.0000.0000.0000.0000.0000.000
86A122THR0-0.0030.00771.9750.0000.0000.0000.0000.0000.000
87A123GLY0-0.015-0.01771.7680.0000.0000.0000.0000.0000.000
88A124TYR0-0.033-0.01566.1530.0000.0000.0000.0000.0000.000
89A125SER00.0450.00064.4110.0000.0000.0000.0000.0000.000
90A126VAL0-0.048-0.02362.4250.0000.0000.0000.0000.0000.000
91A127SER00.003-0.00558.6650.0000.0000.0000.0000.0000.000
92A128THR00.0140.02557.9980.0000.0000.0000.0000.0000.000
93A129SER0-0.0340.00053.8940.0000.0000.0000.0000.0000.000
94A130LEU0-0.008-0.04355.299-0.001-0.0010.0000.0000.0000.000
95A131THR0-0.065-0.01450.3920.0000.0000.0000.0000.0000.000
96A132VAL00.0380.01653.484-0.001-0.0010.0000.0000.0000.000
97A133ARG10.8480.91746.3570.0080.0080.0000.0000.0000.000
98A134VAL00.0120.00752.045-0.001-0.0010.0000.0000.0000.000
99A135ARG10.8660.90648.9250.0090.0090.0000.0000.0000.000
100A136GLU-1-0.928-0.96851.787-0.007-0.0070.0000.0000.0000.000
101A137LEU00.0950.04649.7320.0010.0010.0000.0000.0000.000
102A138ALA0-0.017-0.00152.9320.0010.0010.0000.0000.0000.000
103A139ASN0-0.026-0.02456.0660.0010.0010.0000.0000.0000.000
104A140VAL00.0160.01253.5110.0000.0000.0000.0000.0000.000
105A141GLY00.0250.02256.8780.0000.0000.0000.0000.0000.000
106A142LYS10.9080.94659.8810.0040.0040.0000.0000.0000.000
107A143ILE00.0440.02057.6980.0000.0000.0000.0000.0000.000
108A144LEU0-0.046-0.02556.7430.0000.0000.0000.0000.0000.000
109A145ASP-1-0.877-0.91459.4360.0000.0000.0000.0000.0000.000
110A146GLU-1-0.899-0.95062.983-0.002-0.0020.0000.0000.0000.000
111A147SER0-0.108-0.08659.8530.0000.0000.0000.0000.0000.000
112A148VAL00.0350.02661.6730.0000.0000.0000.0000.0000.000
113A149THR0-0.098-0.03163.9760.0000.0000.0000.0000.0000.000
114A150LEU0-0.017-0.01264.3350.0000.0000.0000.0000.0000.000
115A151GLY0-0.080-0.04065.5590.0000.0000.0000.0000.0000.000
116A152VAL0-0.021-0.02559.4670.0000.0000.0000.0000.0000.000
117A153ASN0-0.085-0.03559.9720.0000.0000.0000.0000.0000.000
118A154GLN00.0010.00352.8050.0000.0000.0000.0000.0000.000
119A155GLY00.0710.03856.9000.0000.0000.0000.0000.0000.000
120A156GLY00.026-0.01754.3040.0000.0000.0000.0000.0000.000
121A157ASP-1-0.902-0.95150.5910.0040.0040.0000.0000.0000.000
122A158LEU0-0.097-0.03949.1990.0000.0000.0000.0000.0000.000
123A159ASN00.0190.01646.6260.0000.0000.0000.0000.0000.000
124A160LEU00.006-0.01046.884-0.001-0.0010.0000.0000.0000.000
125A161VAL0-0.0230.00842.8870.0010.0010.0000.0000.0000.000
126A162ASN00.030-0.00340.4250.0000.0000.0000.0000.0000.000
127A163ASP-1-0.875-0.93342.097-0.010-0.0100.0000.0000.0000.000
128A164ASN0-0.071-0.03938.2260.0000.0000.0000.0000.0000.000
129A165PRO00.0640.04335.978-0.001-0.0010.0000.0000.0000.000
130A166SER00.0170.02033.894-0.001-0.0010.0000.0000.0000.000
131A167ALA00.0160.00132.970-0.003-0.0030.0000.0000.0000.000
132A168VAL00.0670.03133.455-0.002-0.0020.0000.0000.0000.000
133A169ILE0-0.004-0.00830.009-0.001-0.0010.0000.0000.0000.000
134A170ASN0-0.030-0.01928.306-0.002-0.0020.0000.0000.0000.000
135A171GLU-1-0.832-0.89828.614-0.037-0.0370.0000.0000.0000.000
136A172ALA00.0230.01428.781-0.003-0.0030.0000.0000.0000.000
137A173ARG10.8560.91423.9430.0290.0290.0000.0000.0000.000
138A174LYS10.8790.93224.2490.0370.0370.0000.0000.0000.000
139A175ARG10.8550.91924.4090.0190.0190.0000.0000.0000.000
140A176ALA00.0690.04422.656-0.003-0.0030.0000.0000.0000.000
141A177VAL0-0.021-0.00718.457-0.002-0.0020.0000.0000.0000.000
142A178ALA00.0340.01519.853-0.006-0.0060.0000.0000.0000.000
143A179ASN0-0.052-0.03521.436-0.003-0.0030.0000.0000.0000.000
144A180ALA00.0420.01017.450-0.001-0.0010.0000.0000.0000.000
145A181ILE0-0.026-0.01216.542-0.009-0.0090.0000.0000.0000.000
146A182ALA0-0.072-0.04517.582-0.007-0.0070.0000.0000.0000.000
147A183LYS10.9080.94818.2450.0000.0000.0000.0000.0000.000
148A184ALA00.0410.02413.6360.0090.0090.0000.0000.0000.000
149A185LYS10.9310.97415.6530.0670.0670.0000.0000.0000.000
150A186THR00.0020.00917.6090.0030.0030.0000.0000.0000.000
151A187LEU0-0.042-0.02415.1620.0070.0070.0000.0000.0000.000
152A188ALA0-0.007-0.01813.8600.0050.0050.0000.0000.0000.000
153A189ASP-1-0.839-0.91215.021-0.056-0.0560.0000.0000.0000.000
154A190ALA0-0.025-0.01218.1240.0060.0060.0000.0000.0000.000
155A191ALA0-0.043-0.01814.7670.0150.0150.0000.0000.0000.000
156A192GLY0-0.069-0.00515.4040.0040.0040.0000.0000.0000.000
157A193VAL0-0.090-0.05910.144-0.015-0.0150.0000.0000.0000.000
158A194GLY00.0450.02412.4670.0080.0080.0000.0000.0000.000
159A195LEU0-0.046-0.01811.078-0.053-0.0530.0000.0000.0000.000
160A196GLY00.0070.0009.5260.0280.0280.0000.0000.0000.000
161A197ARG10.9280.9648.7750.3790.3790.0000.0000.0000.000
162A198VAL00.0190.0069.302-0.050-0.0500.0000.0000.0000.000
163A199VAL0-0.043-0.0245.407-0.011-0.0110.0000.0000.0000.000
164A200GLU-1-0.944-0.9638.5850.0170.0170.0000.0000.0000.000
165A201ILE00.008-0.00110.9000.0200.0200.0000.0000.0000.000
166A202SER0-0.030-0.02513.8170.0060.0060.0000.0000.0000.000
167A203GLU-1-0.808-0.90016.387-0.013-0.0130.0000.0000.0000.000
168A204LEU00.011-0.00917.136-0.003-0.0030.0000.0000.0000.000
169A205SER0-0.0250.00120.8690.0080.0080.0000.0000.0000.000
170A206ARG10.9620.98223.254-0.033-0.0330.0000.0000.0000.000
171A207PRO00.0370.00926.939-0.001-0.0010.0000.0000.0000.000
172A208PRO0-0.0220.01027.3650.0020.0020.0000.0000.0000.000
173A209MET0-0.007-0.01629.830-0.001-0.0010.0000.0000.0000.000
174A210PRO00.0210.01733.3720.0010.0010.0000.0000.0000.000
175A211MET0-0.0070.00333.4360.0020.0020.0000.0000.0000.000
176A212PRO00.0480.04936.699-0.001-0.0010.0000.0000.0000.000
177A213ILE0-0.0160.00738.1780.0020.0020.0000.0000.0000.000
178A214ALA00.0400.00240.756-0.001-0.0010.0000.0000.0000.000
179A215ARG10.9720.97542.559-0.010-0.0100.0000.0000.0000.000
180A216GLY00.0150.00042.2710.0000.0000.0000.0000.0000.000
181A217GLN00.0020.00336.4240.0020.0020.0000.0000.0000.000
182A218PHE00.0150.01238.4430.0000.0000.0000.0000.0000.000
183A219ARG10.9980.99935.156-0.022-0.0220.0000.0000.0000.000
184A220THR0-0.029-0.03234.225-0.001-0.0010.0000.0000.0000.000
185A221MET00.0560.04433.6330.0000.0000.0000.0000.0000.000
186A222LEU00.0040.00134.452-0.001-0.0010.0000.0000.0000.000
187A223ALA0-0.042-0.02533.912-0.001-0.0010.0000.0000.0000.000
188A224ALA0-0.030-0.00830.2630.0000.0000.0000.0000.0000.000
189A225ALA0-0.046-0.01030.725-0.002-0.0020.0000.0000.0000.000
190A226PRO0-0.047-0.04531.438-0.001-0.0010.0000.0000.0000.000
191A227ASP-1-0.868-0.91331.938-0.005-0.0050.0000.0000.0000.000
192A228ASN0-0.090-0.05634.549-0.001-0.0010.0000.0000.0000.000
193A229SER00.0040.02135.636-0.002-0.0020.0000.0000.0000.000
194A230VAL0-0.030-0.02137.5800.0010.0010.0000.0000.0000.000
195A231PRO00.0040.00039.5660.0000.0000.0000.0000.0000.000
196A232ILE0-0.0090.00138.250-0.001-0.0010.0000.0000.0000.000
197A233ALA0-0.015-0.00641.0450.0010.0010.0000.0000.0000.000
198A234ALA0-0.031-0.02643.0880.0000.0000.0000.0000.0000.000
199A235GLY0-0.0090.00343.892-0.001-0.0010.0000.0000.0000.000
200A236GLU-1-0.821-0.89840.864-0.005-0.0050.0000.0000.0000.000
201A237ASN0-0.017-0.01738.6760.0030.0030.0000.0000.0000.000
202A238SER0-0.047-0.04834.765-0.001-0.0010.0000.0000.0000.000
203A239TYR0-0.038-0.03832.1650.0010.0010.0000.0000.0000.000
204A240ASN00.0100.00228.224-0.003-0.0030.0000.0000.0000.000
205A241VAL0-0.038-0.01623.8250.0010.0010.0000.0000.0000.000
206A242SER0-0.012-0.01122.2620.0000.0000.0000.0000.0000.000
207A243VAL0-0.015-0.00618.129-0.001-0.0010.0000.0000.0000.000
208A244ASN00.010-0.00214.1910.0040.0040.0000.0000.0000.000
209A245VAL0-0.025-0.01112.920-0.016-0.0160.0000.0000.0000.000
210A246VAL00.0250.0187.0930.0230.0230.0000.0000.0000.000
211A247PHE00.0330.0079.035-0.048-0.0480.0000.0000.0000.000
212A248GLU-1-0.904-0.9574.903-0.879-0.8790.0000.0000.0000.000
213A249ILE0-0.0350.0025.8030.2260.2260.0000.0000.0000.000
214A250LYS10.9550.9726.2090.1510.1510.0000.0000.0000.000