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: 43MVN

Calculation Name: 2H8R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8R

Chain ID: A

ChEMBL ID:

UniProt ID: P35680

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptH
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1846467.455701
FMO2-HF: Nuclear repulsion 1773410.397983
FMO2-HF: Total energy -73057.057717
FMO2-MP2: Total energy -73271.235458


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:90:SER)


Summations of interaction energy for fragment #1(A:90: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.
-17.766-11.9272.48-3.335-4.9830.019
Interaction energy analysis for fragmet #1(A:90:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.022
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].
3A92LEU00.0730.0752.743-2.1171.0500.797-1.704-2.2600.008
4A93LYS10.9180.9342.451-11.475-9.6821.678-1.165-2.3050.009
5A94GLU-1-0.896-0.9313.619-2.021-1.1420.005-0.466-0.4180.002
6A95LEU0-0.021-0.0305.632-0.318-0.3180.0000.0000.0000.000
7A96GLN0-0.048-0.0206.857-0.173-0.1730.0000.0000.0000.000
8A97ALA0-0.022-0.0097.946-0.295-0.2950.0000.0000.0000.000
9A98LEU0-0.088-0.0419.590-0.268-0.2680.0000.0000.0000.000
10A99ASN0-0.071-0.03811.614-0.159-0.1590.0000.0000.0000.000
11A100THR0-0.0050.02013.4000.0550.0550.0000.0000.0000.000
12A101GLU-1-0.809-0.91615.6400.4100.4100.0000.0000.0000.000
13A102GLU-1-0.852-0.94817.9980.4630.4630.0000.0000.0000.000
14A103ALA00.022-0.01215.208-0.049-0.0490.0000.0000.0000.000
15A104ALA0-0.082-0.07517.050-0.030-0.0300.0000.0000.0000.000
16A105GLU-1-0.790-0.88918.7850.2940.2940.0000.0000.0000.000
17A106GLN0-0.093-0.05817.783-0.039-0.0390.0000.0000.0000.000
18A107ARG10.9060.99616.301-0.471-0.4710.0000.0000.0000.000
19A108ALA00.0750.04120.681-0.030-0.0300.0000.0000.0000.000
20A109GLU-1-0.857-0.89224.1080.1660.1660.0000.0000.0000.000
21A110VAL0-0.008-0.05622.486-0.020-0.0200.0000.0000.0000.000
22A111ASP-1-0.955-1.00223.9730.1500.1500.0000.0000.0000.000
23A112ARG10.9000.97225.680-0.173-0.1730.0000.0000.0000.000
24A113MET0-0.087-0.05227.371-0.007-0.0070.0000.0000.0000.000
25A114LEU0-0.164-0.02825.421-0.012-0.0120.0000.0000.0000.000
26A115SER0-0.044-0.03829.584-0.008-0.0080.0000.0000.0000.000
27A116GLU-1-0.834-0.91732.0210.1030.1030.0000.0000.0000.000
28A117ASP-1-0.894-0.94233.9190.0720.0720.0000.0000.0000.000
29A118PRO00.0490.01833.5260.0060.0060.0000.0000.0000.000
30A119TRP00.0170.01634.2890.0060.0060.0000.0000.0000.000
31A120ARG10.9280.93736.216-0.093-0.0930.0000.0000.0000.000
32A121ALA00.0350.02431.2000.0050.0050.0000.0000.0000.000
33A122ALA00.0090.00932.7440.0050.0050.0000.0000.0000.000
34A123LYS10.8780.96133.739-0.077-0.0770.0000.0000.0000.000
35A124MET00.0610.02031.938-0.001-0.0010.0000.0000.0000.000
36A125ILE00.0770.06228.7340.0040.0040.0000.0000.0000.000
37A126LYS10.9040.95531.559-0.081-0.0810.0000.0000.0000.000
38A127GLY0-0.026-0.01734.021-0.001-0.0010.0000.0000.0000.000
39A128TYR00.0950.03627.2930.0030.0030.0000.0000.0000.000
40A129MET0-0.130-0.04229.3450.0020.0020.0000.0000.0000.000
41A130GLN0-0.028-0.03931.533-0.006-0.0060.0000.0000.0000.000
42A131GLN0-0.0190.01833.447-0.004-0.0040.0000.0000.0000.000
43A132HIS00.0690.01930.138-0.008-0.0080.0000.0000.0000.000
44A133ASN0-0.087-0.01831.660-0.001-0.0010.0000.0000.0000.000
45A134ILE00.0630.02026.8270.0040.0040.0000.0000.0000.000
46A135PRO0-0.038-0.01827.999-0.010-0.0100.0000.0000.0000.000
47A136GLN00.0140.00628.4670.0040.0040.0000.0000.0000.000
48A137ARG10.9320.94624.637-0.125-0.1250.0000.0000.0000.000
49A138GLU-1-0.872-0.93322.9180.2300.2300.0000.0000.0000.000
50A139VAL00.0500.02223.1290.0070.0070.0000.0000.0000.000
51A140VAL0-0.0200.04423.1550.0030.0030.0000.0000.0000.000
52A141ASP-1-0.866-0.92320.4210.1270.1270.0000.0000.0000.000
53A142VAL00.0750.03017.6770.0030.0030.0000.0000.0000.000
54A143THR0-0.163-0.11918.2810.0040.0040.0000.0000.0000.000
55A144GLY00.0540.04219.787-0.007-0.0070.0000.0000.0000.000
56A145LEU0-0.062-0.03221.169-0.025-0.0250.0000.0000.0000.000
57A146ASN00.0090.00224.751-0.002-0.0020.0000.0000.0000.000
58A147GLN00.0860.01627.683-0.001-0.0010.0000.0000.0000.000
59A148SER00.0890.04929.4070.0030.0030.0000.0000.0000.000
60A149HIS0-0.119-0.06929.804-0.001-0.0010.0000.0000.0000.000
61A150LEU00.0510.05327.4050.0020.0020.0000.0000.0000.000
62A151SER0-0.069-0.03830.7580.0000.0000.0000.0000.0000.000
63A152GLN00.1160.04634.0080.0030.0030.0000.0000.0000.000
64A153HIS0-0.043-0.02831.1670.0080.0080.0000.0000.0000.000
65A154LEU0-0.038-0.02330.9140.0030.0030.0000.0000.0000.000
66A155ASN0-0.089-0.05834.2430.0040.0040.0000.0000.0000.000
67A156LYS10.9330.95037.803-0.045-0.0450.0000.0000.0000.000
68A157GLY00.0530.04136.776-0.002-0.0020.0000.0000.0000.000
69A158THR0-0.018-0.00635.588-0.001-0.0010.0000.0000.0000.000
70A159PRO00.0570.06334.7940.0070.0070.0000.0000.0000.000
71A160MET0-0.009-0.00628.858-0.002-0.0020.0000.0000.0000.000
72A161LYS10.9700.96528.726-0.016-0.0160.0000.0000.0000.000
73A162THR00.1170.02626.3850.0030.0030.0000.0000.0000.000
74A163GLN00.1080.06221.4650.0290.0290.0000.0000.0000.000
75A164LYS10.9620.98723.466-0.021-0.0210.0000.0000.0000.000
76A165ARG10.9821.00124.864-0.079-0.0790.0000.0000.0000.000
77A166ALA00.1200.04323.0410.0150.0150.0000.0000.0000.000
78A167ALA0-0.116-0.03020.9660.0290.0290.0000.0000.0000.000
79A168LEU0-0.067-0.00522.0920.0070.0070.0000.0000.0000.000
80A169TYR00.013-0.01524.0650.0080.0080.0000.0000.0000.000
81A170THR00.1140.02519.1480.0080.0080.0000.0000.0000.000
82A171TRP0-0.0370.02120.3400.0170.0170.0000.0000.0000.000
83A172TYR00.008-0.01421.3690.0120.0120.0000.0000.0000.000
84A173VAL00.010-0.01521.1070.0110.0110.0000.0000.0000.000
85A174ARG10.9140.93914.763-0.508-0.5080.0000.0000.0000.000
86A175LYS10.8910.95120.192-0.249-0.2490.0000.0000.0000.000
87A176GLN00.0250.03622.366-0.013-0.0130.0000.0000.0000.000
88A177ARG10.8990.88020.371-0.359-0.3590.0000.0000.0000.000
89A178GLU-1-0.954-0.97619.1400.3600.3600.0000.0000.0000.000
90A179ILE0-0.020-0.03121.290-0.017-0.0170.0000.0000.0000.000
91A180LEU0-0.0690.04924.240-0.016-0.0160.0000.0000.0000.000
92A181ARG10.9670.98817.360-0.509-0.5090.0000.0000.0000.000
93A182GLN0-0.139-0.05723.559-0.003-0.0030.0000.0000.0000.000
94A183PHE00.030-0.02025.067-0.018-0.0180.0000.0000.0000.000
95A184ASN0-0.0690.00727.713-0.006-0.0060.0000.0000.0000.000
96A185GLN00.047-0.00225.554-0.016-0.0160.0000.0000.0000.000
97A186THR0-0.0530.00825.508-0.012-0.0120.0000.0000.0000.000
98A187VAL00.0210.02727.882-0.010-0.0100.0000.0000.0000.000
99A231MET00.0750.03118.1080.0040.0040.0000.0000.0000.000
100A232ARG10.9170.94919.570-0.094-0.0940.0000.0000.0000.000
101A233ARG10.9751.02522.950-0.103-0.1030.0000.0000.0000.000
102A234ASN0-0.004-0.03625.466-0.018-0.0180.0000.0000.0000.000
103A235ARG10.9720.96627.607-0.078-0.0780.0000.0000.0000.000
104A236PHE0-0.0380.01031.1840.0020.0020.0000.0000.0000.000
105A237LYS10.9140.95534.111-0.094-0.0940.0000.0000.0000.000
106A238TRP00.0820.05636.1590.0060.0060.0000.0000.0000.000
107A239GLY00.0480.03639.1370.0000.0000.0000.0000.0000.000
108A240PRO0-0.010-0.02839.649-0.004-0.0040.0000.0000.0000.000
109A241ALA00.0980.03041.575-0.004-0.0040.0000.0000.0000.000
110A242SER0-0.057-0.05040.463-0.003-0.0030.0000.0000.0000.000
111A243GLN00.038-0.01642.773-0.007-0.0070.0000.0000.0000.000
112A244GLN0-0.0640.01145.128-0.005-0.0050.0000.0000.0000.000
113A245ILE00.0030.01446.082-0.004-0.0040.0000.0000.0000.000
114A246LEU00.036-0.00244.971-0.002-0.0020.0000.0000.0000.000
115A247TYR0-0.012-0.01347.372-0.003-0.0030.0000.0000.0000.000
116A248GLN00.0200.00451.120-0.001-0.0010.0000.0000.0000.000
117A249ALA0-0.002-0.02351.549-0.002-0.0020.0000.0000.0000.000
118A250TYR0-0.080-0.01852.209-0.002-0.0020.0000.0000.0000.000
119A251ASP-1-0.980-0.97254.0260.0420.0420.0000.0000.0000.000
120A252ARG10.9731.00153.894-0.051-0.0510.0000.0000.0000.000
121A253GLN00.012-0.01356.146-0.001-0.0010.0000.0000.0000.000
122A254LYS11.0201.02055.297-0.031-0.0310.0000.0000.0000.000
123A255ASN0-0.053-0.03454.4410.0010.0010.0000.0000.0000.000
124A256PRO00.0770.06751.479-0.001-0.0010.0000.0000.0000.000
125A257SER0-0.0520.00252.4840.0010.0010.0000.0000.0000.000
126A258LYS10.9890.97447.052-0.054-0.0540.0000.0000.0000.000
127A259GLU-1-0.894-0.92649.6550.0510.0510.0000.0000.0000.000
128A260GLU-1-0.874-0.96150.5130.0520.0520.0000.0000.0000.000
129A261ARG10.9170.91847.768-0.048-0.0480.0000.0000.0000.000
130A262GLU-1-0.917-0.97045.8280.0650.0650.0000.0000.0000.000
131A263ALA00.0560.07146.3260.0040.0040.0000.0000.0000.000
132A264LEU0-0.023-0.02946.7100.0040.0040.0000.0000.0000.000
133A265VAL0-0.117-0.02941.2490.0040.0040.0000.0000.0000.000
134A266GLU-1-0.883-0.96842.1730.0920.0920.0000.0000.0000.000
135A267GLU-1-0.985-0.97843.8210.0690.0690.0000.0000.0000.000
136A268CYS00.0040.01641.7050.0020.0020.0000.0000.0000.000
137A269ASN00.0990.04138.4710.0080.0080.0000.0000.0000.000
138A270ARG10.9571.00639.176-0.076-0.0760.0000.0000.0000.000
139A271ALA0-0.0020.00140.7490.0050.0050.0000.0000.0000.000
140A272GLU-1-0.808-0.89436.9800.1100.1100.0000.0000.0000.000
141A273CYS0-0.023-0.02836.7360.0110.0110.0000.0000.0000.000
142A274LEU00.0570.04437.7250.0040.0040.0000.0000.0000.000
143A275GLN0-0.133-0.07036.611-0.001-0.0010.0000.0000.0000.000
144A276ARG10.7790.89931.953-0.139-0.1390.0000.0000.0000.000
145A277GLY0-0.036-0.01934.2840.0100.0100.0000.0000.0000.000
146A278VAL0-0.048-0.01233.0030.0090.0090.0000.0000.0000.000
147A279SER00.1120.10735.848-0.008-0.0080.0000.0000.0000.000
148A280PRO0-0.014-0.01837.1110.0020.0020.0000.0000.0000.000
149A281SER0-0.112-0.10636.729-0.005-0.0050.0000.0000.0000.000
150A282LYN00.1140.02228.0490.0050.0050.0000.0000.0000.000
151A283ALA00.0810.04933.6850.0080.0080.0000.0000.0000.000
152A284HIS0-0.032-0.03229.797-0.007-0.0070.0000.0000.0000.000
153A285GLY00.0300.01829.4240.0080.0080.0000.0000.0000.000
154A286LEU0-0.035-0.00629.3520.0100.0100.0000.0000.0000.000
155A287GLY0-0.0020.01628.9490.0020.0020.0000.0000.0000.000
156A288SER00.014-0.05528.712-0.014-0.0140.0000.0000.0000.000
157A289ASN0-0.116-0.02430.455-0.022-0.0220.0000.0000.0000.000
158A290LEU00.0200.02632.735-0.007-0.0070.0000.0000.0000.000
159A291VAL0-0.0160.00234.662-0.005-0.0050.0000.0000.0000.000
160A292THR00.050-0.01137.2400.0010.0010.0000.0000.0000.000
161A293GLU-1-0.724-0.83640.1180.0760.0760.0000.0000.0000.000
162A294VAL00.0750.00740.378-0.003-0.0030.0000.0000.0000.000
163A295ARG10.8240.92033.485-0.103-0.1030.0000.0000.0000.000
164A296VAL00.0960.03041.247-0.002-0.0020.0000.0000.0000.000
165A297TYR0-0.098-0.02644.339-0.005-0.0050.0000.0000.0000.000
166A298ASN0-0.094-0.06141.599-0.006-0.0060.0000.0000.0000.000
167A299TRP0-0.045-0.03743.707-0.002-0.0020.0000.0000.0000.000
168A300PHE0-0.0160.04745.716-0.002-0.0020.0000.0000.0000.000
169A301ALA00.103-0.00647.927-0.002-0.0020.0000.0000.0000.000
170A302ASN0-0.057-0.01944.355-0.005-0.0050.0000.0000.0000.000
171A303ARG10.9360.94347.077-0.045-0.0450.0000.0000.0000.000
172A304ARG10.7650.90950.465-0.042-0.0420.0000.0000.0000.000
173A305LYS10.8990.90247.008-0.039-0.0390.0000.0000.0000.000
174A306GLU-1-0.910-0.92348.2500.0420.0420.0000.0000.0000.000
175A307GLU-1-0.925-0.95352.2220.0310.0310.0000.0000.0000.000
176A308ALA0-0.048-0.01055.262-0.002-0.0020.0000.0000.0000.000