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: YQ2J2

Calculation Name: 1S7H-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1S7H

Chain ID: A

ChEMBL ID:

UniProt ID: O34911

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1972864.740721
FMO2-HF: Nuclear repulsion 1899995.460419
FMO2-HF: Total energy -72869.280302
FMO2-MP2: Total energy -73078.458441


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:7:ACE )


Summations of interaction energy for fragment #1(A:7:ACE )
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.
-0.9230.2236.697-4.64-3.202-0.017
Interaction energy analysis for fragmet #1(A:7:ACE )
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 : -0.018
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].
3A9ARG 10.8050.9033.8291.4002.229-0.005-0.357-0.466-0.001
4A10ILE 0-0.046-0.0142.4320.1310.1141.443-0.808-0.618-0.003
5A11ALA 00.0290.0266.053-0.096-0.0960.0000.0000.0000.000
6A12GLY 00.020-0.0149.4520.1530.1530.0000.0000.0000.000
7A13PHE 00.002-0.01511.927-0.052-0.0520.0000.0000.0000.000
8A14ARG 10.9200.97315.524-0.110-0.1100.0000.0000.0000.000
9A15PHE 00.002-0.00317.925-0.021-0.0210.0000.0000.0000.000
10A16SER 00.022-0.00321.2220.0130.0130.0000.0000.0000.000
11A17LEU 0-0.011-0.00624.530-0.005-0.0050.0000.0000.0000.000
12A18TYR 00.007-0.02127.0230.0010.0010.0000.0000.0000.000
13A19PRO 0-0.026-0.00130.373-0.004-0.0040.0000.0000.0000.000
14A20MET 0-0.056-0.03033.217-0.001-0.0010.0000.0000.0000.000
15A21THR 00.010-0.00736.037-0.002-0.0020.0000.0000.0000.000
16A22ASP -1-0.888-0.94937.3850.0400.0400.0000.0000.0000.000
17A23ASP -1-0.937-0.96337.2950.0580.0580.0000.0000.0000.000
18A24PHE 00.033-0.00332.3630.0050.0050.0000.0000.0000.000
19A25ILE 00.001-0.00531.4710.0060.0060.0000.0000.0000.000
20A26SER 0-0.030-0.02131.1670.0080.0080.0000.0000.0000.000
21A27VAL 00.0150.02131.0950.0060.0060.0000.0000.0000.000
22A28ILE 00.0070.00226.5260.0050.0050.0000.0000.0000.000
23A29LYS 10.9310.97326.860-0.095-0.0950.0000.0000.0000.000
24A30SER 0-0.025-0.02727.1930.0100.0100.0000.0000.0000.000
25A31ALA 00.0690.04726.3170.0040.0040.0000.0000.0000.000
26A32LEU 00.0160.00121.0600.0080.0080.0000.0000.0000.000
27A33LYS 10.8630.94122.886-0.126-0.1260.0000.0000.0000.000
28A34LYS 10.9180.95324.834-0.070-0.0700.0000.0000.0000.000
29A35THR 0-0.0250.00819.930-0.007-0.0070.0000.0000.0000.000
30A36ASP -1-0.841-0.89918.8660.2110.2110.0000.0000.0000.000
31A37THR 0-0.003-0.02616.6570.0060.0060.0000.0000.0000.000
32A38SER 0-0.056-0.04015.3660.0470.0470.0000.0000.0000.000
33A39LYS 10.8560.93812.410-0.230-0.2300.0000.0000.0000.000
34A40VAL 00.004-0.00710.6100.0300.0300.0000.0000.0000.000
35A41TRP 00.0090.0379.678-0.029-0.0290.0000.0000.0000.000
36A42THR 0-0.006-0.02011.446-0.072-0.0720.0000.0000.0000.000
37A43LYS 10.9480.98214.759-0.233-0.2330.0000.0000.0000.000
38A44THR 00.0190.00316.827-0.009-0.0090.0000.0000.0000.000
39A45ASP -1-0.918-0.93220.3610.1300.1300.0000.0000.0000.000
40A46HIS 00.005-0.01122.7760.0020.0020.0000.0000.0000.000
41A47ILE 0-0.018-0.00224.233-0.009-0.0090.0000.0000.0000.000
42A48SER 0-0.024-0.00921.250-0.005-0.0050.0000.0000.0000.000
43A49THR 00.0140.00518.1920.0070.0070.0000.0000.0000.000
44A50VAL 0-0.076-0.02813.483-0.015-0.0150.0000.0000.0000.000
45A51LEU 0-0.013-0.00713.6230.0400.0400.0000.0000.0000.000
46A52ARG 10.8040.8926.039-0.702-0.7020.0000.0000.0000.000
47A53GLY 00.0680.0347.1670.1150.1150.0000.0000.0000.000
48A54SER 0-0.0100.0007.904-0.131-0.1310.0000.0000.0000.000
49A55ILE 00.0660.0198.7760.0220.0220.0000.0000.0000.000
50A56ASP -1-0.871-0.92711.9890.0110.0110.0000.0000.0000.000
51A57HIS 00.0120.00111.0090.0450.0450.0000.0000.0000.000
52A58VAL 0-0.0170.01110.9850.0070.0070.0000.0000.0000.000
53A59PHE 00.0420.01113.653-0.009-0.0090.0000.0000.0000.000
54A60ASP -1-0.890-0.93316.2150.1240.1240.0000.0000.0000.000
55A61ALA 00.0300.01016.250-0.008-0.0080.0000.0000.0000.000
56A62ALA 0-0.018-0.00317.689-0.011-0.0110.0000.0000.0000.000
57A63LYS 10.9620.98919.544-0.058-0.0580.0000.0000.0000.000
58A64ALA 0-0.0100.00221.384-0.007-0.0070.0000.0000.0000.000
59A65ILE 0-0.013-0.00719.540-0.005-0.0050.0000.0000.0000.000
60A66TYR 0-0.021-0.03723.474-0.005-0.0050.0000.0000.0000.000
61A67LEU 00.0300.00825.708-0.005-0.0050.0000.0000.0000.000
62A68HIS 0-0.011-0.01024.805-0.010-0.0100.0000.0000.0000.000
63A69ALA 0-0.032-0.01327.655-0.003-0.0030.0000.0000.0000.000
64A70ALA 00.0170.01129.340-0.005-0.0050.0000.0000.0000.000
65A71ASN 0-0.049-0.02931.207-0.005-0.0050.0000.0000.0000.000
66A72SER 0-0.081-0.02232.900-0.002-0.0020.0000.0000.0000.000
67A73GLU -1-0.940-0.99034.5820.0350.0350.0000.0000.0000.000
68A74GLN 0-0.0320.00135.062-0.002-0.0020.0000.0000.0000.000
69A75HIS 00.0050.03435.1240.0010.0010.0000.0000.0000.000
70A76ILE 0-0.0300.00029.5630.0030.0030.0000.0000.0000.000
71A77VAL 00.0290.02229.171-0.002-0.0020.0000.0000.0000.000
72A78MET 0-0.0500.00422.4200.0060.0060.0000.0000.0000.000
73A79ASN 0-0.0090.00025.596-0.008-0.0080.0000.0000.0000.000
74A80GLY 00.0430.00821.5200.0130.0130.0000.0000.0000.000
75A81THR 0-0.049-0.01718.430-0.017-0.0170.0000.0000.0000.000
76A82PHE 00.0000.01915.6290.0240.0240.0000.0000.0000.000
77A83SER 0-0.024-0.02013.850-0.037-0.0370.0000.0000.0000.000
78A84ILE 00.0470.0189.6210.0380.0380.0000.0000.0000.000
79A85GLY 00.0470.0219.981-0.010-0.0100.0000.0000.0000.000
80A86CYS 0-0.0270.00111.0430.0210.0210.0000.0000.0000.000
81A87PRO 00.0360.00710.889-0.058-0.0580.0000.0000.0000.000
82A88GLY 0-0.014-0.00810.9720.0510.0510.0000.0000.0000.000
83A89ASP -1-0.910-0.9387.4650.0960.0960.0000.0000.0000.000
84A90THR 00.0190.0177.202-0.082-0.0820.0000.0000.0000.000
85A91GLN 0-0.024-0.0192.262-2.295-2.4551.334-0.977-0.196-0.002
86A92GLY 0-0.001-0.0043.0290.7442.1800.185-0.724-0.897-0.007
87A93ASP -1-0.916-0.9585.7430.6750.6750.0000.0000.0000.000
88A94THR 00.022-0.0093.457-0.384-0.2920.014-0.054-0.0520.000
89A95TYR 0-0.0130.0156.9170.0450.0450.0000.0000.0000.000
90A96LEU 0-0.037-0.0262.1770.306-0.7283.726-1.720-0.973-0.004
91A97SER 00.014-0.0176.418-0.056-0.0560.0000.0000.0000.000
92A98LYS 10.9510.9759.0750.0010.0010.0000.0000.0000.000
93A99GLY 0-0.001-0.00410.621-0.032-0.0320.0000.0000.0000.000
94A100ASP -1-0.818-0.87912.9580.2640.2640.0000.0000.0000.000
95A101LYS 10.9260.96714.699-0.092-0.0920.0000.0000.0000.000
96A102ARG 10.7890.86216.449-0.016-0.0160.0000.0000.0000.000
97A103VAL 0-0.007-0.00616.868-0.011-0.0110.0000.0000.0000.000
98A104ASN 0-0.006-0.00718.946-0.016-0.0160.0000.0000.0000.000
99A105GLU -1-0.950-0.96121.2310.0390.0390.0000.0000.0000.000
100A106ASP -1-0.915-0.97923.0750.0550.0550.0000.0000.0000.000
101A107ALA 0-0.053-0.01825.012-0.005-0.0050.0000.0000.0000.000
102A108VAL 00.014-0.00524.193-0.005-0.0050.0000.0000.0000.000
103A109ARG 10.9580.99827.075-0.049-0.0490.0000.0000.0000.000
104A110GLY 0-0.054-0.03028.368-0.005-0.0050.0000.0000.0000.000
105A111LEU 0-0.0430.00028.368-0.001-0.0010.0000.0000.0000.000
106A112LYS 10.9080.95530.783-0.026-0.0260.0000.0000.0000.000
107A113ALA 00.005-0.01730.5470.0030.0030.0000.0000.0000.000
108A114GLU -1-0.874-0.92031.5030.0180.0180.0000.0000.0000.000
109A115ALA 0-0.038-0.02428.8240.0050.0050.0000.0000.0000.000
110A116PRO 00.0580.07130.473-0.003-0.0030.0000.0000.0000.000
111A117CYS 0-0.079-0.05426.4890.0040.0040.0000.0000.0000.000
112A118GLN 0-0.0070.01529.470-0.003-0.0030.0000.0000.0000.000
113A119PHE 00.006-0.02224.9130.0040.0040.0000.0000.0000.000
114A120ALA 00.0320.02425.331-0.005-0.0050.0000.0000.0000.000
115A121LEU 00.0020.00320.7840.0030.0030.0000.0000.0000.000
116A122TYR 0-0.031-0.02921.4550.0020.0020.0000.0000.0000.000
117A123PRO 00.0360.01120.282-0.008-0.0080.0000.0000.0000.000
118A124MET 0-0.022-0.01818.7550.0110.0110.0000.0000.0000.000
119A125ASN 0-0.094-0.05220.281-0.007-0.0070.0000.0000.0000.000
120A126GLU -1-0.758-0.87122.050-0.142-0.1420.0000.0000.0000.000
121A127PRO 0-0.051-0.03723.8100.0130.0130.0000.0000.0000.000
122A128ASP -1-0.896-0.96026.517-0.071-0.0710.0000.0000.0000.000
123A129TYR 00.0140.01125.2650.0040.0040.0000.0000.0000.000
124A130MET 0-0.038-0.02226.3900.0060.0060.0000.0000.0000.000
125A131GLY 00.0400.02929.2640.0050.0050.0000.0000.0000.000
126A132LEU 00.0210.00922.2500.0030.0030.0000.0000.0000.000
127A133ILE 0-0.040-0.01226.2280.0050.0050.0000.0000.0000.000
128A134MET 0-0.047-0.02027.6010.0070.0070.0000.0000.0000.000
129A135GLU -1-0.783-0.91226.258-0.080-0.0800.0000.0000.0000.000
130A136ALA 0-0.040-0.02425.5090.0040.0040.0000.0000.0000.000
131A137VAL 0-0.039-0.01926.8960.0070.0070.0000.0000.0000.000
132A138ASP -1-0.902-0.95530.376-0.033-0.0330.0000.0000.0000.000
133A139ILE 0-0.034-0.00924.3900.0020.0020.0000.0000.0000.000
134A140ALA 00.0220.00028.5150.0040.0040.0000.0000.0000.000
135A141LYS 10.8750.95029.8170.0280.0280.0000.0000.0000.000
136A142ALA 0-0.0290.00130.6830.0030.0030.0000.0000.0000.000
137A143GLN 0-0.037-0.02626.031-0.004-0.0040.0000.0000.0000.000
138A144GLY 0-0.048-0.01330.9790.0040.0040.0000.0000.0000.000
139A145THR 00.003-0.01429.1590.0010.0010.0000.0000.0000.000
140A146PHE 0-0.032-0.01632.2560.0010.0010.0000.0000.0000.000
141A147VAL 0-0.0100.02033.3920.0000.0000.0000.0000.0000.000
142A148GLN 0-0.062-0.05035.090-0.002-0.0020.0000.0000.0000.000
143A149GLY 0-0.0040.01134.481-0.001-0.0010.0000.0000.0000.000
144A150VAL 0-0.015-0.00334.1510.0010.0010.0000.0000.0000.000
145A151HIS 00.001-0.01434.823-0.003-0.0030.0000.0000.0000.000
146A152TYR 0-0.061-0.04231.5420.0030.0030.0000.0000.0000.000
147A153ALA 00.0020.01230.0970.0000.0000.0000.0000.0000.000
148A154SER 0-0.0080.00729.264-0.002-0.0020.0000.0000.0000.000
149A155GLU -1-0.897-0.95830.3590.0070.0070.0000.0000.0000.000
150A156LEU 0-0.037-0.03727.108-0.003-0.0030.0000.0000.0000.000
151A157ASP -1-0.865-0.95031.6440.0140.0140.0000.0000.0000.000
152A158GLY 00.0690.05332.679-0.002-0.0020.0000.0000.0000.000
153A159ASP -1-0.749-0.89730.7540.0330.0330.0000.0000.0000.000
154A160ALA 00.029-0.00227.125-0.001-0.0010.0000.0000.0000.000
155A161HIS 0-0.086-0.03926.2360.0010.0010.0000.0000.0000.000
156A162ASP -1-0.894-0.94426.1400.0080.0080.0000.0000.0000.000
157A163VAL 00.0080.01526.487-0.005-0.0050.0000.0000.0000.000
158A164PHE 0-0.014-0.04621.451-0.001-0.0010.0000.0000.0000.000
159A165SER 0-0.0400.00322.139-0.005-0.0050.0000.0000.0000.000
160A166THR 00.0470.03823.159-0.009-0.0090.0000.0000.0000.000
161A167LEU 0-0.009-0.01021.807-0.008-0.0080.0000.0000.0000.000
162A168GLU -1-0.750-0.86017.067-0.002-0.0020.0000.0000.0000.000
163A169ALA 0-0.0090.00819.123-0.018-0.0180.0000.0000.0000.000
164A170VAL 00.0060.00221.362-0.014-0.0140.0000.0000.0000.000
165A171PHE 0-0.025-0.02813.486-0.013-0.0130.0000.0000.0000.000
166A172ARG 10.8090.88213.9000.0440.0440.0000.0000.0000.000
167A173MET 0-0.0350.03017.667-0.020-0.0200.0000.0000.0000.000
168A174ALA 00.0450.00019.672-0.013-0.0130.0000.0000.0000.000
169A175GLU -1-0.969-0.99213.210-0.282-0.2820.0000.0000.0000.000
170A176GLN 0-0.048-0.01915.391-0.040-0.0400.0000.0000.0000.000
171A177GLN 0-0.034-0.00717.427-0.014-0.0140.0000.0000.0000.000
172A178THR 0-0.005-0.00718.388-0.001-0.0010.0000.0000.0000.000
173A179ASN 0-0.021-0.01914.012-0.068-0.0680.0000.0000.0000.000
174A180HIS 0-0.0100.01013.868-0.041-0.0410.0000.0000.0000.000
175A181ILE 00.0430.03915.3060.0250.0250.0000.0000.0000.000
176A182THR 0-0.044-0.03115.9960.0130.0130.0000.0000.0000.000
177A183MET 00.0070.00518.324-0.006-0.0060.0000.0000.0000.000
178A184THR 0-0.0200.00220.4060.0130.0130.0000.0000.0000.000
179A185VAL 00.0180.00322.176-0.005-0.0050.0000.0000.0000.000
180A186ASN 00.012-0.00824.6000.0110.0110.0000.0000.0000.000
181A187LEU 00.0410.02224.887-0.004-0.0040.0000.0000.0000.000
182A188SER 00.005-0.00228.8400.0060.0060.0000.0000.0000.000
183A189ALA 00.0680.03231.081-0.002-0.0020.0000.0000.0000.000
184A190ASN 0-0.035-0.03633.066-0.002-0.0020.0000.0000.0000.000
185A191SER 0-0.021-0.01536.6160.0000.0000.0000.0000.0000.000
186A192PRO 0-0.007-0.00937.999-0.001-0.0010.0000.0000.0000.000
187A193SER 0-0.050-0.03240.494-0.001-0.0010.0000.0000.0000.000
188A194NME 00.0310.03441.2270.0000.0000.0000.0000.0000.000