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: MNZ9Z

Calculation Name: 4H86-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H86

Chain ID: A

ChEMBL ID:

UniProt ID: P38013

Base Structure: X-ray

Registration Date: 2023-09-23

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1953102.540482
FMO2-HF: Nuclear repulsion 1881801.070755
FMO2-HF: Total energy -71301.469726
FMO2-MP2: Total energy -71508.400946


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:-10:GLY)


Summations of interaction energy for fragment #1(A:-10:GLY)
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.
0.4752.4690.005-1.012-0.9860.002
Interaction energy analysis for fragmet #1(A:-10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.016
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].
3A-8VAL00.0330.0193.444-0.2271.5930.006-0.996-0.8290.002
4A-7PRO00.0090.0204.7270.3830.557-0.001-0.016-0.1570.000
5A-6ARG10.9680.9505.8911.1171.1170.0000.0000.0000.000
6A-5GLY0-0.0020.0049.174-0.022-0.0220.0000.0000.0000.000
7A-4SER0-0.0300.0128.7010.0250.0250.0000.0000.0000.000
8A-3HIS0-0.001-0.01310.2290.0610.0610.0000.0000.0000.000
9A-2MET0-0.004-0.0089.597-0.215-0.2150.0000.0000.0000.000
10A-1ALA00.0170.02712.8540.0880.0880.0000.0000.0000.000
11A0SER0-0.016-0.01216.038-0.047-0.0470.0000.0000.0000.000
12A1MET0-0.0180.00417.6740.0280.0280.0000.0000.0000.000
13A2SER00.0170.00920.4550.0050.0050.0000.0000.0000.000
14A3ASP-1-0.810-0.91623.161-0.102-0.1020.0000.0000.0000.000
15A4LEU0-0.0090.00524.9030.0130.0130.0000.0000.0000.000
16A5VAL00.0030.00525.4630.0090.0090.0000.0000.0000.000
17A6ASN0-0.048-0.02926.5890.0080.0080.0000.0000.0000.000
18A7LYS10.7790.89327.3770.1160.1160.0000.0000.0000.000
19A8LYS10.9620.96932.2800.0570.0570.0000.0000.0000.000
20A9PHE00.0590.02733.753-0.002-0.0020.0000.0000.0000.000
21A10PRO0-0.0180.00432.4780.0070.0070.0000.0000.0000.000
22A11ALA0-0.027-0.01535.7310.0010.0010.0000.0000.0000.000
23A12GLY00.0230.00338.5620.0010.0010.0000.0000.0000.000
24A13ASP-1-0.918-0.96340.863-0.053-0.0530.0000.0000.0000.000
25A14TYR0-0.022-0.00337.3720.0010.0010.0000.0000.0000.000
26A15LYS10.8200.88241.2920.0560.0560.0000.0000.0000.000
27A16PHE0-0.0120.02140.255-0.002-0.0020.0000.0000.0000.000
28A17GLN0-0.007-0.02842.2560.0020.0020.0000.0000.0000.000
29A18TYR0-0.014-0.01543.083-0.007-0.0070.0000.0000.0000.000
30A19ILE0-0.0060.00545.1130.0040.0040.0000.0000.0000.000
31A20ALA00.0190.02247.072-0.004-0.0040.0000.0000.0000.000
32A21ILE0-0.015-0.02845.4500.0010.0010.0000.0000.0000.000
33A22SER00.0550.03049.487-0.001-0.0010.0000.0000.0000.000
34A23GLN0-0.021-0.02151.231-0.001-0.0010.0000.0000.0000.000
35A24SER0-0.029-0.01253.9300.0020.0020.0000.0000.0000.000
36A25ASP-1-0.831-0.93056.600-0.054-0.0540.0000.0000.0000.000
37A26ALA0-0.0170.00654.254-0.001-0.0010.0000.0000.0000.000
38A27ASP-1-0.843-0.91355.233-0.057-0.0570.0000.0000.0000.000
39A28SER00.0120.02556.8300.0010.0010.0000.0000.0000.000
40A29GLU-1-0.845-0.94256.309-0.054-0.0540.0000.0000.0000.000
41A30SER0-0.046-0.01753.632-0.003-0.0030.0000.0000.0000.000
42A31CYS0-0.035-0.00351.782-0.004-0.0040.0000.0000.0000.000
43A32LYS10.7500.86152.5040.0550.0550.0000.0000.0000.000
44A33MET00.0170.00352.531-0.002-0.0020.0000.0000.0000.000
45A34PRO0-0.050-0.01648.223-0.001-0.0010.0000.0000.0000.000
46A35GLN00.0230.02948.4590.0030.0030.0000.0000.0000.000
47A36THR0-0.013-0.01346.169-0.004-0.0040.0000.0000.0000.000
48A37VAL00.0030.00844.0760.0030.0030.0000.0000.0000.000
49A38GLU-1-0.838-0.90343.999-0.059-0.0590.0000.0000.0000.000
50A39TRP00.0610.00936.676-0.002-0.0020.0000.0000.0000.000
51A40SER00.007-0.00141.034-0.003-0.0030.0000.0000.0000.000
52A41LYS10.8790.94142.6690.0570.0570.0000.0000.0000.000
53A42LEU00.0640.03839.8220.0000.0000.0000.0000.0000.000
54A43ILE0-0.0010.00037.800-0.001-0.0010.0000.0000.0000.000
55A44SER0-0.104-0.05441.3790.0020.0020.0000.0000.0000.000
56A45GLU-1-0.893-0.93544.576-0.061-0.0610.0000.0000.0000.000
57A46ASN0-0.069-0.03942.314-0.001-0.0010.0000.0000.0000.000
58A47LYS10.9360.97041.5580.0770.0770.0000.0000.0000.000
59A48LYS10.8080.91336.2830.1130.1130.0000.0000.0000.000
60A49VAL0-0.006-0.00136.9770.0010.0010.0000.0000.0000.000
61A50ILE00.0120.01632.404-0.006-0.0060.0000.0000.0000.000
62A51ILE0-0.027-0.01532.8110.0090.0090.0000.0000.0000.000
63A52THR0-0.045-0.03929.327-0.015-0.0150.0000.0000.0000.000
64A53GLY00.0570.03129.7940.0140.0140.0000.0000.0000.000
65A54ALA00.013-0.01929.270-0.021-0.0210.0000.0000.0000.000
66A55PRO0-0.052-0.02427.9800.0120.0120.0000.0000.0000.000
67A56ALA00.0500.01730.8360.0110.0110.0000.0000.0000.000
68A57ALA00.0630.04134.199-0.009-0.0090.0000.0000.0000.000
69A58PHE0-0.014-0.01936.8490.0010.0010.0000.0000.0000.000
70A59SER0-0.037-0.01132.464-0.007-0.0070.0000.0000.0000.000
71A60PRO00.0370.00831.045-0.005-0.0050.0000.0000.0000.000
72A61THR00.011-0.01126.0030.0080.0080.0000.0000.0000.000
73A62CYS0-0.0480.00329.450-0.014-0.0140.0000.0000.0000.000
74A63THR00.0060.00431.3760.0050.0050.0000.0000.0000.000
75A64VAL0-0.023-0.01032.0530.0070.0070.0000.0000.0000.000
76A65SER0-0.022-0.01227.6490.0000.0000.0000.0000.0000.000
77A66HIS00.0180.03228.448-0.013-0.0130.0000.0000.0000.000
78A67ILE00.0150.01129.9670.0040.0040.0000.0000.0000.000
79A68PRO00.0180.00333.0890.0060.0060.0000.0000.0000.000
80A69GLY00.0280.02532.0180.0050.0050.0000.0000.0000.000
81A70TYR0-0.027-0.05928.5590.0100.0100.0000.0000.0000.000
82A71ILE0-0.021-0.00134.5580.0090.0090.0000.0000.0000.000
83A72ASN0-0.065-0.02235.2060.0110.0110.0000.0000.0000.000
84A73TYR0-0.027-0.02431.0830.0080.0080.0000.0000.0000.000
85A74LEU0-0.0150.00436.8960.0040.0040.0000.0000.0000.000
86A75ASP-1-0.810-0.89239.232-0.096-0.0960.0000.0000.0000.000
87A76GLU-1-0.837-0.91536.488-0.146-0.1460.0000.0000.0000.000
88A77LEU0-0.028-0.02534.0140.0000.0000.0000.0000.0000.000
89A78VAL0-0.0130.00038.0710.0030.0030.0000.0000.0000.000
90A79LYS10.7870.87441.6400.0970.0970.0000.0000.0000.000
91A80GLU-1-0.918-0.95939.395-0.102-0.1020.0000.0000.0000.000
92A81LYS10.7650.88234.7340.1340.1340.0000.0000.0000.000
93A82GLU-1-0.873-0.92338.024-0.101-0.1010.0000.0000.0000.000
94A83VAL0-0.032-0.01836.3910.0010.0010.0000.0000.0000.000
95A84ASP-1-0.796-0.88939.479-0.088-0.0880.0000.0000.0000.000
96A85GLN0-0.061-0.02640.2780.0040.0040.0000.0000.0000.000
97A86VAL00.0230.01635.547-0.006-0.0060.0000.0000.0000.000
98A87ILE0-0.039-0.02636.6090.0050.0050.0000.0000.0000.000
99A88VAL00.0400.02834.611-0.010-0.0100.0000.0000.0000.000
100A89VAL0-0.023-0.01233.5370.0100.0100.0000.0000.0000.000
101A90THR0-0.003-0.02733.708-0.008-0.0080.0000.0000.0000.000
102A91VAL00.0380.01434.2690.0060.0060.0000.0000.0000.000
103A92ASP-1-0.835-0.86436.977-0.111-0.1110.0000.0000.0000.000
104A93ASN00.0230.02639.6170.0030.0030.0000.0000.0000.000
105A94PRO00.0800.03043.124-0.003-0.0030.0000.0000.0000.000
106A95PHE00.0250.00644.625-0.002-0.0020.0000.0000.0000.000
107A96ALA0-0.020-0.00742.346-0.001-0.0010.0000.0000.0000.000
108A97ASN00.0490.00538.812-0.008-0.0080.0000.0000.0000.000
109A98GLN0-0.052-0.01341.923-0.004-0.0040.0000.0000.0000.000
110A99ALA00.0130.00044.964-0.001-0.0010.0000.0000.0000.000
111A100TRP0-0.010-0.00134.159-0.001-0.0010.0000.0000.0000.000
112A101ALA00.0530.03241.157-0.004-0.0040.0000.0000.0000.000
113A102LYS10.8630.92142.1050.0760.0760.0000.0000.0000.000
114A103SER0-0.122-0.06641.880-0.001-0.0010.0000.0000.0000.000
115A104LEU0-0.008-0.00536.851-0.002-0.0020.0000.0000.0000.000
116A105GLY00.0010.00840.673-0.004-0.0040.0000.0000.0000.000
117A106VAL0-0.021-0.01141.6850.0040.0040.0000.0000.0000.000
118A107LYS10.8890.94244.2160.0960.0960.0000.0000.0000.000
119A108ASP-1-0.812-0.89346.646-0.075-0.0750.0000.0000.0000.000
120A109THR00.0290.02444.891-0.004-0.0040.0000.0000.0000.000
121A110THR0-0.063-0.03645.8680.0000.0000.0000.0000.0000.000
122A111HIS00.009-0.01642.7140.0030.0030.0000.0000.0000.000
123A112ILE0-0.0010.01538.309-0.006-0.0060.0000.0000.0000.000
124A113LYS10.8070.89240.4130.0940.0940.0000.0000.0000.000
125A114PHE00.0190.00037.982-0.007-0.0070.0000.0000.0000.000
126A115ALA00.0040.00838.2050.0060.0060.0000.0000.0000.000
127A116SER0-0.005-0.03338.314-0.006-0.0060.0000.0000.0000.000
128A117ASP-1-0.738-0.85335.462-0.098-0.0980.0000.0000.0000.000
129A118PRO00.018-0.00437.984-0.002-0.0020.0000.0000.0000.000
130A119GLY00.000-0.00138.2810.0020.0020.0000.0000.0000.000
131A120CYS0-0.099-0.03931.897-0.003-0.0030.0000.0000.0000.000
132A121ALA00.0050.01734.354-0.003-0.0030.0000.0000.0000.000
133A122PHE00.0190.00034.2020.0000.0000.0000.0000.0000.000
134A123THR0-0.007-0.02930.323-0.005-0.0050.0000.0000.0000.000
135A124LYS10.8540.92930.4430.0800.0800.0000.0000.0000.000
136A125SER0-0.109-0.04930.8550.0010.0010.0000.0000.0000.000
137A126ILE0-0.024-0.00529.7520.0030.0030.0000.0000.0000.000
138A127GLY00.0290.02826.717-0.010-0.0100.0000.0000.0000.000
139A128PHE0-0.009-0.01624.443-0.024-0.0240.0000.0000.0000.000
140A129GLU-1-0.862-0.94326.051-0.160-0.1600.0000.0000.0000.000
141A130LEU00.0160.00524.701-0.021-0.0210.0000.0000.0000.000
142A131ALA0-0.013-0.00227.0710.0120.0120.0000.0000.0000.000
143A132VAL0-0.032-0.02127.724-0.011-0.0110.0000.0000.0000.000
144A133GLY00.0310.01930.1630.0000.0000.0000.0000.0000.000
145A134ASP-1-0.919-0.95732.190-0.067-0.0670.0000.0000.0000.000
146A135GLY0-0.019-0.00333.6590.0040.0040.0000.0000.0000.000
147A136VAL0-0.028-0.01234.6410.0000.0000.0000.0000.0000.000
148A137TYR00.022-0.01029.525-0.002-0.0020.0000.0000.0000.000
149A138TRP00.0170.01130.7350.0020.0020.0000.0000.0000.000
150A139SER00.0470.00529.7230.0030.0030.0000.0000.0000.000
151A140GLY00.0230.02026.150-0.006-0.0060.0000.0000.0000.000
152A141ARG10.8070.87924.7730.2620.2620.0000.0000.0000.000
153A142TRP00.0010.00124.570-0.025-0.0250.0000.0000.0000.000
154A143ALA00.0040.02126.1830.0110.0110.0000.0000.0000.000
155A144MET0-0.023-0.01027.050-0.004-0.0040.0000.0000.0000.000
156A145VAL00.0220.02429.5560.0030.0030.0000.0000.0000.000
157A146VAL0-0.010-0.00531.8880.0020.0020.0000.0000.0000.000
158A147GLU-1-0.773-0.87733.754-0.126-0.1260.0000.0000.0000.000
159A148ASN0-0.057-0.03736.7500.0070.0070.0000.0000.0000.000
160A149GLY00.0390.02738.6320.0050.0050.0000.0000.0000.000
161A150ILE0-0.067-0.03532.8890.0020.0020.0000.0000.0000.000
162A151VAL00.0160.01629.310-0.004-0.0040.0000.0000.0000.000
163A152THR0-0.018-0.03230.138-0.003-0.0030.0000.0000.0000.000
164A153TYR0-0.024-0.03623.224-0.020-0.0200.0000.0000.0000.000
165A154ALA00.009-0.00425.5670.0150.0150.0000.0000.0000.000
166A155ALA00.0150.01821.540-0.012-0.0120.0000.0000.0000.000
167A156LYS10.8230.90721.7750.2210.2210.0000.0000.0000.000
168A157GLU-1-0.745-0.82520.118-0.432-0.4320.0000.0000.0000.000
169A158THR0-0.004-0.00114.9840.0100.0100.0000.0000.0000.000
170A159ASN0-0.052-0.03415.7570.0540.0540.0000.0000.0000.000
171A160PRO00.0090.01219.8270.0060.0060.0000.0000.0000.000
172A161GLY00.0030.01423.3520.0200.0200.0000.0000.0000.000
173A162THR0-0.039-0.03620.3990.0260.0260.0000.0000.0000.000
174A163ASP-1-0.812-0.88518.348-0.514-0.5140.0000.0000.0000.000
175A164VAL0-0.018-0.03121.6240.0390.0390.0000.0000.0000.000
176A165THR00.001-0.00618.033-0.013-0.0130.0000.0000.0000.000
177A166VAL00.0030.02319.1400.0270.0270.0000.0000.0000.000
178A167SER0-0.028-0.04621.8640.0380.0380.0000.0000.0000.000
179A168SER00.0200.02523.9310.0310.0310.0000.0000.0000.000
180A169VAL00.0290.02126.4190.0030.0030.0000.0000.0000.000
181A170GLU-1-0.812-0.90626.209-0.235-0.2350.0000.0000.0000.000
182A171SER0-0.035-0.03222.736-0.005-0.0050.0000.0000.0000.000
183A172VAL0-0.0100.00525.1650.0060.0060.0000.0000.0000.000
184A173LEU00.0340.01228.3470.0100.0100.0000.0000.0000.000
185A174ALA0-0.061-0.02525.2680.0110.0110.0000.0000.0000.000
186A175HIS10.7670.87023.0510.2640.2640.0000.0000.0000.000
187A176LEU00.0290.04028.1780.0140.0140.0000.0000.0000.000