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: 89Y3Y

Calculation Name: 1S7H-A-Xray372

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: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964575.909312
FMO2-HF: Nuclear repulsion 1891876.407223
FMO2-HF: Total energy -72699.502089
FMO2-MP2: Total energy -72908.063276


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:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
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.
-6.042-3.0557.077-4.87-5.193-0.023
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.019
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].
3A10ILE0-0.038-0.0082.883-0.5661.8590.251-1.113-1.5630.005
4A11ALA00.0290.0225.345-0.771-0.743-0.001-0.003-0.0230.000
5A12GLY00.024-0.0109.139-0.063-0.0630.0000.0000.0000.000
6A13PHE00.001-0.01611.5560.0120.0120.0000.0000.0000.000
7A14ARG10.8490.91615.2960.0630.0630.0000.0000.0000.000
8A15PHE00.007-0.00117.6330.0050.0050.0000.0000.0000.000
9A16SER00.0270.00121.093-0.018-0.0180.0000.0000.0000.000
10A17LEU0-0.008-0.00624.5550.0130.0130.0000.0000.0000.000
11A18TYR0-0.003-0.02427.283-0.012-0.0120.0000.0000.0000.000
12A19PRO0-0.0210.01130.7630.0040.0040.0000.0000.0000.000
13A20MET0-0.038-0.02133.571-0.010-0.0100.0000.0000.0000.000
14A21THR00.022-0.00736.5490.0000.0000.0000.0000.0000.000
15A22ASP-1-0.893-0.94637.8340.0260.0260.0000.0000.0000.000
16A23ASP-1-0.901-0.92038.1940.0420.0420.0000.0000.0000.000
17A24PHE00.0420.00332.9880.0050.0050.0000.0000.0000.000
18A25ILE0-0.011-0.01432.3410.0050.0050.0000.0000.0000.000
19A26SER0-0.059-0.05632.1060.0020.0020.0000.0000.0000.000
20A27VAL00.0170.01531.8850.0080.0080.0000.0000.0000.000
21A28ILE00.0010.00127.1270.0120.0120.0000.0000.0000.000
22A29LYS10.9410.97427.840-0.033-0.0330.0000.0000.0000.000
23A30SER0-0.023-0.02528.4800.0080.0080.0000.0000.0000.000
24A31ALA00.0400.03327.3080.0100.0100.0000.0000.0000.000
25A32LEU00.0250.01322.2900.0180.0180.0000.0000.0000.000
26A33LYS10.8690.94324.319-0.082-0.0820.0000.0000.0000.000
27A34LYS10.9220.95426.513-0.111-0.1110.0000.0000.0000.000
28A35THR0-0.0260.00221.3790.0160.0160.0000.0000.0000.000
29A36ASP-1-0.834-0.88220.7330.2760.2760.0000.0000.0000.000
30A37THR0-0.014-0.03418.2550.0360.0360.0000.0000.0000.000
31A38SER0-0.052-0.05017.1830.0170.0170.0000.0000.0000.000
32A39LYS10.8000.89114.430-0.457-0.4570.0000.0000.0000.000
33A40VAL00.000-0.00912.2340.1510.1510.0000.0000.0000.000
34A41TRP0-0.0260.03311.041-0.098-0.0980.0000.0000.0000.000
35A42THR0-0.007-0.02412.9110.0150.0150.0000.0000.0000.000
36A43LYS10.9530.98315.8490.1210.1210.0000.0000.0000.000
37A44THR00.004-0.01017.7220.0150.0150.0000.0000.0000.000
38A45ASP-1-0.877-0.92320.863-0.088-0.0880.0000.0000.0000.000
39A46HIS00.005-0.01123.4310.0160.0160.0000.0000.0000.000
40A47ILE0-0.0080.01024.2900.0090.0090.0000.0000.0000.000
41A48SER0-0.0060.01321.1970.0090.0090.0000.0000.0000.000
42A49THR00.0000.01518.883-0.019-0.0190.0000.0000.0000.000
43A50VAL0-0.057-0.01813.6470.0090.0090.0000.0000.0000.000
44A51LEU00.0020.00314.253-0.009-0.0090.0000.0000.0000.000
45A52ARG10.7870.8626.0500.9000.9000.0000.0000.0000.000
46A53GLY00.0710.0388.436-0.078-0.0780.0000.0000.0000.000
47A54SER0-0.025-0.0188.1830.2290.2290.0000.0000.0000.000
48A55ILE00.0720.0199.143-0.295-0.2950.0000.0000.0000.000
49A56ASP-1-0.862-0.92811.4260.9940.9940.0000.0000.0000.000
50A57HIS00.0240.01912.026-0.010-0.0100.0000.0000.0000.000
51A58VAL0-0.0140.00911.370-0.134-0.1340.0000.0000.0000.000
52A59PHE00.0510.01514.328-0.106-0.1060.0000.0000.0000.000
53A60ASP-1-0.887-0.93116.8380.3710.3710.0000.0000.0000.000
54A61ALA00.0200.00417.193-0.061-0.0610.0000.0000.0000.000
55A62ALA0-0.0020.00418.391-0.052-0.0520.0000.0000.0000.000
56A63LYS10.9200.95920.120-0.372-0.3720.0000.0000.0000.000
57A64ALA0-0.0130.00122.309-0.031-0.0310.0000.0000.0000.000
58A65ILE0-0.015-0.00620.483-0.032-0.0320.0000.0000.0000.000
59A66TYR0-0.015-0.03124.356-0.022-0.0220.0000.0000.0000.000
60A67LEU00.0320.01226.339-0.018-0.0180.0000.0000.0000.000
61A68HIS0-0.005-0.00426.055-0.029-0.0290.0000.0000.0000.000
62A69ALA0-0.029-0.01228.337-0.015-0.0150.0000.0000.0000.000
63A70ALA00.0200.02530.141-0.013-0.0130.0000.0000.0000.000
64A71ASN0-0.062-0.04032.076-0.012-0.0120.0000.0000.0000.000
65A72SER0-0.091-0.04233.750-0.008-0.0080.0000.0000.0000.000
66A73GLU-1-0.951-0.98935.5220.0760.0760.0000.0000.0000.000
67A74GLN0-0.0150.00735.707-0.010-0.0100.0000.0000.0000.000
68A75HIS00.0250.03635.1460.0020.0020.0000.0000.0000.000
69A76ILE0-0.042-0.02029.462-0.007-0.0070.0000.0000.0000.000
70A77VAL00.0130.01229.1760.0060.0060.0000.0000.0000.000
71A78MET0-0.0400.01323.3080.0010.0010.0000.0000.0000.000
72A79ASN0-0.021-0.01225.2510.0030.0030.0000.0000.0000.000
73A80GLY00.0500.01221.142-0.009-0.0090.0000.0000.0000.000
74A81THR0-0.048-0.01617.3040.0000.0000.0000.0000.0000.000
75A82PHE00.0110.02115.302-0.008-0.0080.0000.0000.0000.000
76A83SER0-0.032-0.02312.822-0.047-0.0470.0000.0000.0000.000
77A84ILE00.0490.0207.7580.0790.0790.0000.0000.0000.000
78A85GLY00.0480.0207.8790.0250.0250.0000.0000.0000.000
79A86CYS0-0.043-0.0048.860-0.007-0.0070.0000.0000.0000.000
80A87PRO00.0530.0149.191-0.352-0.3520.0000.0000.0000.000
81A88GLY0-0.025-0.0109.2970.0890.0890.0000.0000.0000.000
82A89ASP-1-0.868-0.9046.623-1.272-1.2720.0000.0000.0000.000
83A90THR00.0040.0036.584-0.852-0.8520.0000.0000.0000.000
84A91GLN0-0.027-0.0202.285-5.060-4.8656.819-3.653-3.360-0.029
85A92GLY0-0.0010.0044.4000.6020.675-0.001-0.003-0.0690.000
86A93ASP-1-0.897-0.9577.041-0.374-0.3740.0000.0000.0000.000
87A94THR00.010-0.0225.0160.1170.1170.0000.0000.0000.000
88A95TYR00.0030.0208.414-0.192-0.1920.0000.0000.0000.000
89A96LEU0-0.025-0.0223.9490.1510.4170.009-0.098-0.1780.001
90A97SER0-0.001-0.0248.489-0.247-0.2470.0000.0000.0000.000
91A98LYS10.9160.9578.657-1.418-1.4180.0000.0000.0000.000
92A99GLY00.0060.00410.587-0.084-0.0840.0000.0000.0000.000
93A100ASP-1-0.784-0.84213.7830.4720.4720.0000.0000.0000.000
94A101LYS10.8120.89415.208-0.287-0.2870.0000.0000.0000.000
95A102ARG10.7610.83115.741-0.671-0.6710.0000.0000.0000.000
96A103VAL00.008-0.00318.350-0.036-0.0360.0000.0000.0000.000
97A104ASN0-0.034-0.01720.246-0.080-0.0800.0000.0000.0000.000
98A105GLU-1-0.853-0.91321.4710.3910.3910.0000.0000.0000.000
99A106ASP-1-0.846-0.92723.8550.2660.2660.0000.0000.0000.000
100A107ALA0-0.049-0.00926.450-0.020-0.0200.0000.0000.0000.000
101A108VAL00.023-0.00525.388-0.017-0.0170.0000.0000.0000.000
102A109ARG10.9050.96127.902-0.232-0.2320.0000.0000.0000.000
103A110GLY0-0.051-0.02928.956-0.006-0.0060.0000.0000.0000.000
104A111LEU0-0.0410.00329.623-0.013-0.0130.0000.0000.0000.000
105A112LYS10.8660.91731.356-0.174-0.1740.0000.0000.0000.000
106A113ALA00.019-0.00131.073-0.009-0.0090.0000.0000.0000.000
107A114GLU-1-0.885-0.92831.8050.1560.1560.0000.0000.0000.000
108A115ALA0-0.035-0.02928.813-0.002-0.0020.0000.0000.0000.000
109A116PRO00.0590.06330.2910.0090.0090.0000.0000.0000.000
110A117CYS0-0.087-0.04826.006-0.002-0.0020.0000.0000.0000.000
111A118GLN0-0.039-0.01228.864-0.006-0.0060.0000.0000.0000.000
112A119PHE00.009-0.01823.7760.0030.0030.0000.0000.0000.000
113A120ALA00.0250.01524.187-0.009-0.0090.0000.0000.0000.000
114A121LEU0-0.012-0.00118.5420.0090.0090.0000.0000.0000.000
115A122TYR0-0.012-0.02219.800-0.027-0.0270.0000.0000.0000.000
116A123PRO00.0350.01917.536-0.009-0.0090.0000.0000.0000.000
117A124MET0-0.022-0.01916.345-0.026-0.0260.0000.0000.0000.000
118A125ASN0-0.088-0.05316.8410.0090.0090.0000.0000.0000.000
119A126GLU-1-0.776-0.87017.9570.1720.1720.0000.0000.0000.000
120A127PRO0-0.043-0.03420.0290.0000.0000.0000.0000.0000.000
121A128ASP-1-0.897-0.95022.2560.1450.1450.0000.0000.0000.000
122A129TYR00.0100.00421.9450.0170.0170.0000.0000.0000.000
123A130MET0-0.030-0.01922.8430.0100.0100.0000.0000.0000.000
124A131GLY00.0440.03025.4850.0040.0040.0000.0000.0000.000
125A132LEU00.0370.01918.3440.0110.0110.0000.0000.0000.000
126A133ILE0-0.049-0.01722.7310.0190.0190.0000.0000.0000.000
127A134MET0-0.019-0.01224.8070.0000.0000.0000.0000.0000.000
128A135GLU-1-0.805-0.90422.2210.2990.2990.0000.0000.0000.000
129A136ALA0-0.031-0.02422.9980.0130.0130.0000.0000.0000.000
130A137VAL0-0.037-0.02224.4640.0000.0000.0000.0000.0000.000
131A138ASP-1-0.821-0.90427.6570.1680.1680.0000.0000.0000.000
132A139ILE0-0.029-0.00521.8300.0040.0040.0000.0000.0000.000
133A140ALA00.022-0.00526.108-0.001-0.0010.0000.0000.0000.000
134A141LYS10.8080.90827.906-0.165-0.1650.0000.0000.0000.000
135A142ALA0-0.038-0.00628.224-0.007-0.0070.0000.0000.0000.000
136A143GLN0-0.036-0.03124.3120.0220.0220.0000.0000.0000.000
137A144GLY0-0.051-0.01429.105-0.004-0.0040.0000.0000.0000.000
138A145THR0-0.001-0.01927.792-0.011-0.0110.0000.0000.0000.000
139A146PHE0-0.030-0.01730.397-0.010-0.0100.0000.0000.0000.000
140A147VAL0-0.0010.01031.838-0.007-0.0070.0000.0000.0000.000
141A148GLN0-0.078-0.05433.730-0.013-0.0130.0000.0000.0000.000
142A149GLY0-0.0010.01133.0400.0100.0100.0000.0000.0000.000
143A150VAL0-0.014-0.00833.143-0.008-0.0080.0000.0000.0000.000
144A151HIS00.000-0.01633.2790.0040.0040.0000.0000.0000.000
145A152TYR0-0.054-0.03930.053-0.003-0.0030.0000.0000.0000.000
146A153ALA0-0.0050.01428.6670.0020.0020.0000.0000.0000.000
147A154SER00.0080.01427.838-0.003-0.0030.0000.0000.0000.000
148A155GLU-1-0.873-0.92329.3370.1040.1040.0000.0000.0000.000
149A156LEU0-0.046-0.02826.0300.0090.0090.0000.0000.0000.000
150A157ASP-1-0.842-0.94030.7000.1190.1190.0000.0000.0000.000
151A158GLY00.0390.03831.8650.0120.0120.0000.0000.0000.000
152A159ASP-1-0.702-0.85830.6370.1930.1930.0000.0000.0000.000
153A160ALA00.025-0.00227.5040.0140.0140.0000.0000.0000.000
154A161HIS0-0.047-0.01226.1050.0510.0510.0000.0000.0000.000
155A162ASP-1-0.872-0.93225.5950.2570.2570.0000.0000.0000.000
156A163VAL00.0100.02626.2170.0220.0220.0000.0000.0000.000
157A164PHE0-0.013-0.04121.3160.0180.0180.0000.0000.0000.000
158A165SER0-0.0390.01021.4260.0360.0360.0000.0000.0000.000
159A166THR00.0280.02121.7650.0280.0280.0000.0000.0000.000
160A167LEU0-0.007-0.01021.0870.0190.0190.0000.0000.0000.000
161A168GLU-1-0.724-0.81315.8740.7530.7530.0000.0000.0000.000
162A169ALA0-0.0050.00917.3220.0740.0740.0000.0000.0000.000
163A170VAL00.0030.00318.9920.0240.0240.0000.0000.0000.000
164A171PHE0-0.001-0.01912.2650.0230.0230.0000.0000.0000.000
165A172ARG10.8010.87511.825-0.965-0.9650.0000.0000.0000.000
166A173MET0-0.0300.01314.9770.0510.0510.0000.0000.0000.000
167A174ALA00.0480.01216.6350.0070.0070.0000.0000.0000.000
168A175GLU-1-0.883-0.9199.5401.5851.5850.0000.0000.0000.000
169A176GLN0-0.090-0.04710.7050.0330.0330.0000.0000.0000.000
170A177GLN0-0.063-0.02813.2180.0220.0220.0000.0000.0000.000
171A178THR0-0.013-0.01814.209-0.063-0.0630.0000.0000.0000.000
172A179ASN0-0.027-0.0209.6100.1380.1380.0000.0000.0000.000
173A180HIS00.0210.02210.5560.0300.0300.0000.0000.0000.000
174A181ILE00.0320.03312.840-0.024-0.0240.0000.0000.0000.000
175A182THR0-0.043-0.03414.1920.0000.0000.0000.0000.0000.000
176A183MET0-0.0010.00416.8070.0270.0270.0000.0000.0000.000
177A184THR0-0.0030.01019.3960.0120.0120.0000.0000.0000.000
178A185VAL00.012-0.00321.5610.0180.0180.0000.0000.0000.000
179A186ASN00.005-0.00123.936-0.018-0.0180.0000.0000.0000.000
180A187LEU00.0430.01624.4020.0020.0020.0000.0000.0000.000
181A188SER0-0.010-0.00728.643-0.010-0.0100.0000.0000.0000.000
182A189ALA00.0530.03131.4070.0050.0050.0000.0000.0000.000
183A190ASN0-0.048-0.06133.285-0.005-0.0050.0000.0000.0000.000
184A191SER0-0.0080.01036.584-0.005-0.0050.0000.0000.0000.000
185A192PRO00.003-0.00638.0590.0010.0010.0000.0000.0000.000
186A193SER0-0.0190.00140.3650.0000.0000.0000.0000.0000.000