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: 89M6Y

Calculation Name: 3SH4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SH4

Chain ID: A

ChEMBL ID:

UniProt ID: P98160

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2022706.2193
FMO2-HF: Nuclear repulsion 1951393.128478
FMO2-HF: Total energy -71313.090821
FMO2-MP2: Total energy -71524.981838


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
15.88818.1433.417-2.542-3.132-0.014
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.964
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].
3A3PRO0-0.026-0.0363.980-0.8320.408-0.010-0.601-0.6300.002
4A4GLY0-0.002-0.0057.208-1.421-1.4210.0000.0000.0000.000
5A5GLN0-0.0030.0052.1661.9001.7513.343-1.433-1.761-0.021
6A6TYR00.0300.0013.186-8.589-7.4250.084-0.508-0.7410.005
7A7GLY00.0320.0048.020-2.160-2.1600.0000.0000.0000.000
8A8ALA0-0.0100.00111.0960.5040.5040.0000.0000.0000.000
9A9TYR0-0.027-0.01814.029-0.626-0.6260.0000.0000.0000.000
10A10PHE00.0150.01617.1410.0530.0530.0000.0000.0000.000
11A11HIS00.002-0.04420.4530.3480.3480.0000.0000.0000.000
12A12ASP-1-0.858-0.91523.63311.00811.0080.0000.0000.0000.000
13A13ASP-1-0.897-0.94726.53210.02610.0260.0000.0000.0000.000
14A14GLY0-0.056-0.01322.637-0.030-0.0300.0000.0000.0000.000
15A15PHE0-0.067-0.03921.131-0.054-0.0540.0000.0000.0000.000
16A16LEU00.0280.01714.6940.2770.2770.0000.0000.0000.000
17A17ALA0-0.005-0.00418.952-0.407-0.4070.0000.0000.0000.000
18A18PHE00.0210.01613.6460.4800.4800.0000.0000.0000.000
19A19PRO00.0570.04317.825-0.775-0.7750.0000.0000.0000.000
20A20GLY00.0780.02720.2780.4720.4720.0000.0000.0000.000
21A21HIS0-0.023-0.01518.2650.3310.3310.0000.0000.0000.000
22A22VAL0-0.042-0.02116.1890.5480.5480.0000.0000.0000.000
23A23PHE00.0170.00318.2730.5240.5240.0000.0000.0000.000
24A24SER0-0.048-0.02221.017-0.873-0.8730.0000.0000.0000.000
25A25ARG10.8700.92623.288-11.854-11.8540.0000.0000.0000.000
26A26SER0-0.057-0.05326.320-0.030-0.0300.0000.0000.0000.000
27A27LEU00.0020.01629.109-0.270-0.2700.0000.0000.0000.000
28A28PRO00.026-0.00231.4190.2160.2160.0000.0000.0000.000
29A29GLU-1-0.908-0.97232.8448.6008.6000.0000.0000.0000.000
30A30VAL0-0.059-0.00227.0160.0420.0420.0000.0000.0000.000
31A31PRO00.0100.01727.1970.0650.0650.0000.0000.0000.000
32A32GLU-1-0.815-0.90124.54312.08012.0800.0000.0000.0000.000
33A33THR0-0.011-0.00820.425-0.398-0.3980.0000.0000.0000.000
34A34ILE0-0.026-0.00819.9430.4950.4950.0000.0000.0000.000
35A35GLU-1-0.812-0.87417.23716.07116.0710.0000.0000.0000.000
36A36LEU0-0.029-0.00216.2731.0161.0160.0000.0000.0000.000
37A37GLU-1-0.794-0.86314.01419.81619.8160.0000.0000.0000.000
38A38VAL00.010-0.00316.8660.4770.4770.0000.0000.0000.000
39A39ARG10.9430.97316.983-15.881-15.8810.0000.0000.0000.000
40A40THR0-0.021-0.04620.807-0.044-0.0440.0000.0000.0000.000
41A41SER00.1050.05923.847-0.053-0.0530.0000.0000.0000.000
42A42THR0-0.057-0.02925.930-0.479-0.4790.0000.0000.0000.000
43A43ALA00.0260.01828.3720.1380.1380.0000.0000.0000.000
44A44SER00.019-0.00231.1540.0050.0050.0000.0000.0000.000
45A45GLY00.0180.01928.130-0.016-0.0160.0000.0000.0000.000
46A46LEU0-0.071-0.03425.2010.1070.1070.0000.0000.0000.000
47A47LEU00.0040.00921.5890.3460.3460.0000.0000.0000.000
48A48LEU00.015-0.00219.9140.6320.6320.0000.0000.0000.000
49A49TRP00.0320.01622.937-0.651-0.6510.0000.0000.0000.000
50A50GLN00.0000.02023.9360.4430.4430.0000.0000.0000.000
51A51GLY00.0390.01126.007-0.305-0.3050.0000.0000.0000.000
52A52VAL0-0.040-0.01929.0510.2980.2980.0000.0000.0000.000
53A53GLU-1-0.850-0.90629.06610.35510.3550.0000.0000.0000.000
54A54VAL00.004-0.00830.835-0.343-0.3430.0000.0000.0000.000
55A55GLY0-0.021-0.01932.8330.0170.0170.0000.0000.0000.000
56A56GLU-1-0.877-0.90933.7728.5438.5430.0000.0000.0000.000
57A57ALA00.000-0.01236.3020.0530.0530.0000.0000.0000.000
58A58GLY0-0.0090.00738.594-0.208-0.2080.0000.0000.0000.000
59A59GLN0-0.066-0.06431.8870.1320.1320.0000.0000.0000.000
60A60GLY00.0260.01835.5410.0980.0980.0000.0000.0000.000
61A61LYS10.9140.93236.030-7.857-7.8570.0000.0000.0000.000
62A62ASP-1-0.764-0.86733.0488.8638.8630.0000.0000.0000.000
63A63PHE0-0.089-0.05430.1790.0540.0540.0000.0000.0000.000
64A64ILE0-0.0070.00326.160-0.223-0.2230.0000.0000.0000.000
65A65SER0-0.047-0.02526.4760.0880.0880.0000.0000.0000.000
66A66LEU00.0430.01622.244-0.177-0.1770.0000.0000.0000.000
67A67GLY00.013-0.00525.6750.1740.1740.0000.0000.0000.000
68A68LEU0-0.0170.01125.4820.0570.0570.0000.0000.0000.000
69A69GLN00.0540.01528.880-0.269-0.2690.0000.0000.0000.000
70A70ASP-1-0.879-0.93132.6818.3898.3890.0000.0000.0000.000
71A71GLY00.016-0.01730.240-0.081-0.0810.0000.0000.0000.000
72A72HIS10.8080.93529.667-8.737-8.7370.0000.0000.0000.000
73A73LEU00.0360.02525.0030.0640.0640.0000.0000.0000.000
74A74VAL0-0.037-0.02028.517-0.404-0.4040.0000.0000.0000.000
75A75PHE00.0070.00326.8420.3950.3950.0000.0000.0000.000
76A76ARG10.8390.89929.295-9.156-9.1560.0000.0000.0000.000
77A77TYR00.0130.00030.4210.3160.3160.0000.0000.0000.000
78A78GLN00.0200.01932.228-0.423-0.4230.0000.0000.0000.000
79A79LEU0-0.015-0.00732.6540.2020.2020.0000.0000.0000.000
80A80GLY00.0990.05135.813-0.075-0.0750.0000.0000.0000.000
81A81SER0-0.082-0.04439.084-0.161-0.1610.0000.0000.0000.000
82A82GLY0-0.023-0.01839.873-0.188-0.1880.0000.0000.0000.000
83A83GLU-1-0.783-0.87636.4188.5738.5730.0000.0000.0000.000
84A84ALA00.0000.01034.432-0.242-0.2420.0000.0000.0000.000
85A85ARG10.8710.91433.950-8.225-8.2250.0000.0000.0000.000
86A86LEU0-0.0560.00431.473-0.268-0.2680.0000.0000.0000.000
87A87VAL0-0.004-0.02231.8880.2560.2560.0000.0000.0000.000
88A88SER00.011-0.00529.709-0.108-0.1080.0000.0000.0000.000
89A89GLU-1-0.882-0.92631.8498.2908.2900.0000.0000.0000.000
90A90ASP-1-0.831-0.91831.9398.8578.8570.0000.0000.0000.000
91A91PRO0-0.148-0.06531.1800.2860.2860.0000.0000.0000.000
92A92ILE00.0570.00524.5040.1630.1630.0000.0000.0000.000
93A93ASN0-0.095-0.03526.1200.3250.3250.0000.0000.0000.000
94A94ASP-1-0.743-0.85726.05511.26411.2640.0000.0000.0000.000
95A95GLY0-0.063-0.01824.485-0.009-0.0090.0000.0000.0000.000
96A96GLU-1-0.925-0.97022.73012.17312.1730.0000.0000.0000.000
97A97TRP0-0.147-0.10215.1350.5820.5820.0000.0000.0000.000
98A98HIS10.8570.89920.268-12.539-12.5390.0000.0000.0000.000
99A99ARG10.8090.89014.927-17.582-17.5820.0000.0000.0000.000
100A100VAL0-0.025-0.00220.202-0.810-0.8100.0000.0000.0000.000
101A101THR00.038-0.00820.9200.6000.6000.0000.0000.0000.000
102A102ALA0-0.033-0.01622.938-0.701-0.7010.0000.0000.0000.000
103A103LEU0-0.0100.00024.0110.4190.4190.0000.0000.0000.000
104A104ARG10.8090.87426.808-10.958-10.9580.0000.0000.0000.000
105A105GLU-1-0.844-0.90928.92110.14010.1400.0000.0000.0000.000
106A106GLY00.0560.03331.652-0.338-0.3380.0000.0000.0000.000
107A107ARG10.8890.94533.484-7.738-7.7380.0000.0000.0000.000
108A108ARG10.8130.93034.252-9.268-9.2680.0000.0000.0000.000
109A109GLY00.0660.03431.2460.3110.3110.0000.0000.0000.000
110A110SER0-0.043-0.04729.850-0.273-0.2730.0000.0000.0000.000
111A111ILE0-0.0100.00527.6260.3650.3650.0000.0000.0000.000
112A112GLN0-0.014-0.01125.391-0.007-0.0070.0000.0000.0000.000
113A113VAL00.010-0.01524.9690.4910.4910.0000.0000.0000.000
114A114ASP-1-0.734-0.84922.85412.82212.8220.0000.0000.0000.000
115A115GLY0-0.049-0.01524.105-0.087-0.0870.0000.0000.0000.000
116A116GLU-1-0.961-0.97424.98310.44310.4430.0000.0000.0000.000
117A117GLU-1-0.912-0.94828.6799.7619.7610.0000.0000.0000.000
118A118LEU0-0.055-0.03128.5890.0710.0710.0000.0000.0000.000
119A119VAL00.0330.03431.426-0.370-0.3700.0000.0000.0000.000
120A120SER0-0.031-0.03232.4280.2000.2000.0000.0000.0000.000
121A121GLY00.0390.01034.685-0.213-0.2130.0000.0000.0000.000
122A122ARG10.9220.95735.690-7.817-7.8170.0000.0000.0000.000
123A123SER00.0470.05136.504-0.033-0.0330.0000.0000.0000.000
124A124PRO00.0270.01638.266-0.062-0.0620.0000.0000.0000.000
125A125GLY0-0.0350.00140.9730.1520.1520.0000.0000.0000.000
126A126PRO00.003-0.01642.682-0.119-0.1190.0000.0000.0000.000
127A127ASN0-0.011-0.01038.494-0.074-0.0740.0000.0000.0000.000
128A128VAL00.0320.00036.6010.0790.0790.0000.0000.0000.000
129A129ALA0-0.022-0.02133.4010.2900.2900.0000.0000.0000.000
130A130VAL00.0020.01928.846-0.172-0.1720.0000.0000.0000.000
131A131ASN0-0.072-0.05531.3710.1990.1990.0000.0000.0000.000
132A132ALA0-0.054-0.01229.047-0.045-0.0450.0000.0000.0000.000
133A133LYS10.9510.97727.197-9.458-9.4580.0000.0000.0000.000
134A134GLY00.0260.01926.8960.1780.1780.0000.0000.0000.000
135A135SER0-0.037-0.03623.1260.2060.2060.0000.0000.0000.000
136A136VAL0-0.043-0.01119.931-0.411-0.4110.0000.0000.0000.000
137A137TYR0-0.010-0.01020.7030.4670.4670.0000.0000.0000.000
138A138ILE00.010-0.01717.024-0.036-0.0360.0000.0000.0000.000
139A139GLY00.013-0.00220.1070.0560.0560.0000.0000.0000.000
140A140GLY00.0540.02021.503-0.425-0.4250.0000.0000.0000.000
141A141ALA0-0.027-0.01624.1540.2940.2940.0000.0000.0000.000
142A142PRO00.0160.02025.772-0.201-0.2010.0000.0000.0000.000
143A143ASP-1-0.779-0.85528.4348.5028.5020.0000.0000.0000.000
144A144VAL0-0.037-0.01627.9670.0080.0080.0000.0000.0000.000
145A145ALA00.0480.04330.565-0.062-0.0620.0000.0000.0000.000
146A146THR0-0.032-0.05134.035-0.211-0.2110.0000.0000.0000.000
147A147LEU0-0.053-0.00727.030-0.038-0.0380.0000.0000.0000.000
148A148THR0-0.045-0.03429.893-0.085-0.0850.0000.0000.0000.000
149A149GLY0-0.031-0.00432.525-0.162-0.1620.0000.0000.0000.000
150A150GLY0-0.019-0.01735.570-0.230-0.2300.0000.0000.0000.000
151A151ARG10.6960.83533.651-8.772-8.7720.0000.0000.0000.000
152A152PHE00.0040.00029.9510.0560.0560.0000.0000.0000.000
153A153SER00.028-0.00432.653-0.126-0.1260.0000.0000.0000.000
154A154SER00.0410.03329.855-0.188-0.1880.0000.0000.0000.000
155A155GLY00.0590.02825.7190.0860.0860.0000.0000.0000.000
156A156ILE0-0.060-0.02221.041-0.350-0.3500.0000.0000.0000.000
157A157THR00.0230.02123.5640.1730.1730.0000.0000.0000.000
158A158GLY00.0090.00921.195-0.269-0.2690.0000.0000.0000.000
159A159CYS0-0.171-0.04411.819-1.118-1.1180.0000.0000.0000.000
160A160VAL00.0560.03515.695-0.577-0.5770.0000.0000.0000.000
161A161LYS10.8350.90911.424-20.454-20.4540.0000.0000.0000.000
162A162ASN0-0.067-0.0489.7921.0001.0000.0000.0000.0000.000
163A163LEU00.0450.04111.965-1.126-1.1260.0000.0000.0000.000
164A164VAL00.0100.00013.5071.2421.2420.0000.0000.0000.000
165A165LEU0-0.0010.00015.614-1.385-1.3850.0000.0000.0000.000
166A166HIS00.026-0.00118.1060.8510.8510.0000.0000.0000.000
167A167SER00.0220.02920.172-0.743-0.7430.0000.0000.0000.000
168A168ALA0-0.026-0.02423.0270.3990.3990.0000.0000.0000.000
169A169ARG10.9660.98924.148-12.892-12.8920.0000.0000.0000.000
170A170PRO00.034-0.00525.1030.3710.3710.0000.0000.0000.000
171A171GLY0-0.0070.00025.435-0.077-0.0770.0000.0000.0000.000
172A172ALA0-0.073-0.01621.4770.3530.3530.0000.0000.0000.000
173A173PRO00.0220.00416.718-0.168-0.1680.0000.0000.0000.000
174A174PRO00.001-0.01115.585-0.341-0.3410.0000.0000.0000.000
175A175PRO00.0040.02115.5320.8590.8590.0000.0000.0000.000
176A176GLN0-0.009-0.0169.6561.5291.5290.0000.0000.0000.000
177A177PRO0-0.010-0.0029.045-1.494-1.4940.0000.0000.0000.000
178A178LEU0-0.032-0.0059.6662.1122.1120.0000.0000.0000.000
179A179ASP-1-0.795-0.8906.59033.86833.8680.0000.0000.0000.000
180A180LEU0-0.035-0.0438.837-1.981-1.9810.0000.0000.0000.000
181A181GLN00.0140.0138.564-2.399-2.3990.0000.0000.0000.000
182A182HIS0-0.072-0.0396.204-2.057-2.0570.0000.0000.0000.000
183A183ARG10.8850.94110.849-23.341-23.3410.0000.0000.0000.000
184A184ALA00.0180.03713.284-0.943-0.9430.0000.0000.0000.000
185A185GLN0-0.037-0.03316.027-0.264-0.2640.0000.0000.0000.000
186A186ALA00.005-0.00219.421-0.674-0.6740.0000.0000.0000.000
187A187GLY00.0410.01619.5660.7090.7090.0000.0000.0000.000
188A188ALA0-0.053-0.01920.723-0.349-0.3490.0000.0000.0000.000
189A189ASN0-0.0140.00221.7120.3650.3650.0000.0000.0000.000
190A190THR00.0400.00817.0080.3490.3490.0000.0000.0000.000
191A191ARG10.9320.98115.614-14.539-14.5390.0000.0000.0000.000
192A192PRO00.0510.02910.284-0.051-0.0510.0000.0000.0000.000
193A194PRO0-0.0080.00610.8071.6101.6100.0000.0000.0000.000
194A195SER00.010-0.00411.126-1.880-1.8800.0000.0000.0000.000