Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QY71Y

Calculation Name: 3HFD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HFD

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2616207.279981
FMO2-HF: Nuclear repulsion 2526149.21667
FMO2-HF: Total energy -90058.063312
FMO2-MP2: Total energy -90326.495569


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:33:THR)


Summations of interaction energy for fragment #1(A:33:THR)
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.
-2.0470.3460.01-1.041-1.3610.002
Interaction energy analysis for fragmet #1(A:33:THR)
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 : -0.063
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].
3A35LEU0-0.019-0.0073.4620.9753.2420.011-1.027-1.2500.002
4A36THR00.012-0.0285.632-0.026-0.0260.0000.0000.0000.000
5A37GLU-1-0.811-0.8958.2181.6171.6170.0000.0000.0000.000
6A38GLU-1-0.814-0.89010.5520.6580.6580.0000.0000.0000.000
7A39GLN00.0030.0188.0080.1090.1090.0000.0000.0000.000
8A40LYS10.8480.9024.660-1.783-1.657-0.001-0.014-0.1110.000
9A41GLU-1-0.778-0.8748.0021.0271.0270.0000.0000.0000.000
10A42THR0-0.045-0.03011.519-0.182-0.1820.0000.0000.0000.000
11A43LEU00.0150.0195.474-0.151-0.1510.0000.0000.0000.000
12A44LYS10.8100.8799.563-1.300-1.3000.0000.0000.0000.000
13A45LYS10.8950.95311.701-0.972-0.9720.0000.0000.0000.000
14A46LEU00.0460.01811.709-0.106-0.1060.0000.0000.0000.000
15A47LYS10.9160.9609.299-1.757-1.7570.0000.0000.0000.000
16A48LEU00.0030.01112.828-0.113-0.1130.0000.0000.0000.000
17A49TYR00.021-0.00516.241-0.065-0.0650.0000.0000.0000.000
18A50GLN00.0020.01314.834-0.061-0.0610.0000.0000.0000.000
19A51LYS10.7710.87116.552-0.586-0.5860.0000.0000.0000.000
20A52GLU-1-0.820-0.90418.0920.3670.3670.0000.0000.0000.000
21A53TYR0-0.076-0.05619.985-0.043-0.0430.0000.0000.0000.000
22A54TYR00.0180.00716.3150.0020.0020.0000.0000.0000.000
23A55ASP-1-0.792-0.85521.7370.4140.4140.0000.0000.0000.000
24A56TYR0-0.076-0.06024.364-0.054-0.0540.0000.0000.0000.000
25A57GLU-1-0.840-0.89322.8970.3440.3440.0000.0000.0000.000
26A58SER0-0.011-0.02624.695-0.026-0.0260.0000.0000.0000.000
27A59LYS10.8140.90526.978-0.336-0.3360.0000.0000.0000.000
28A60PHE00.0550.02829.604-0.021-0.0210.0000.0000.0000.000
29A61GLU-1-0.936-0.96728.5970.2200.2200.0000.0000.0000.000
30A62TYR00.004-0.00231.254-0.019-0.0190.0000.0000.0000.000
31A63GLU-1-0.926-0.96933.2880.1850.1850.0000.0000.0000.000
32A64LEU0-0.034-0.00733.323-0.017-0.0170.0000.0000.0000.000
33A65PHE0-0.026-0.02633.074-0.014-0.0140.0000.0000.0000.000
34A66LEU0-0.0100.00036.868-0.012-0.0120.0000.0000.0000.000
35A67LEU0-0.032-0.01239.075-0.010-0.0100.0000.0000.0000.000
36A68ARG10.9430.95735.601-0.150-0.1500.0000.0000.0000.000
37A69GLN00.0220.00940.049-0.012-0.0120.0000.0000.0000.000
38A70LYS10.9310.97843.056-0.115-0.1150.0000.0000.0000.000
39A71TYR0-0.004-0.01444.378-0.004-0.0040.0000.0000.0000.000
40A72HIS0-0.040-0.01945.029-0.006-0.0060.0000.0000.0000.000
41A73ASP-1-0.850-0.91846.8510.0910.0910.0000.0000.0000.000
42A74LEU0-0.076-0.03648.758-0.004-0.0040.0000.0000.0000.000
43A75TYR0-0.013-0.01246.419-0.003-0.0030.0000.0000.0000.000
44A76GLY00.0460.03851.183-0.004-0.0040.0000.0000.0000.000
45A77PRO00.0390.00852.856-0.004-0.0040.0000.0000.0000.000
46A78ILE0-0.063-0.03153.775-0.003-0.0030.0000.0000.0000.000
47A79TYR00.0300.01549.820-0.003-0.0030.0000.0000.0000.000
48A80ASP-1-0.758-0.85455.9890.0600.0600.0000.0000.0000.000
49A81LYS10.9270.96758.523-0.063-0.0630.0000.0000.0000.000
50A82ARG10.8240.93054.740-0.061-0.0610.0000.0000.0000.000
51A83ARG10.7900.88158.231-0.056-0.0560.0000.0000.0000.000
52A84GLU-1-0.835-0.92861.6990.0470.0470.0000.0000.0000.000
53A85ALA0-0.034-0.01764.143-0.002-0.0020.0000.0000.0000.000
54A86LEU0-0.024-0.00261.465-0.002-0.0020.0000.0000.0000.000
55A87VAL0-0.050-0.03663.884-0.002-0.0020.0000.0000.0000.000
56A88GLY00.0090.01766.892-0.001-0.0010.0000.0000.0000.000
57A89ASN0-0.053-0.03166.162-0.002-0.0020.0000.0000.0000.000
58A90GLY00.0180.02568.6930.0010.0010.0000.0000.0000.000
59A91GLU-1-0.951-0.98971.6510.0300.0300.0000.0000.0000.000
60A92ALA00.0330.01468.1600.0010.0010.0000.0000.0000.000
61A93LYS10.8490.92569.271-0.029-0.0290.0000.0000.0000.000
62A94ILE0-0.040-0.01368.552-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0470.02365.4530.0010.0010.0000.0000.0000.000
64A96THR0-0.071-0.05363.201-0.001-0.0010.0000.0000.0000.000
65A97PRO00.0010.01066.208-0.001-0.0010.0000.0000.0000.000
66A98ASN0-0.055-0.02568.607-0.002-0.0020.0000.0000.0000.000
67A99LEU0-0.071-0.03265.3080.0000.0000.0000.0000.0000.000
68A100PRO00.0560.02967.0010.0010.0010.0000.0000.0000.000
69A101GLU-1-0.843-0.90565.6480.0300.0300.0000.0000.0000.000
70A102PHE0-0.0050.00959.6350.0010.0010.0000.0000.0000.000
71A103TRP00.000-0.02755.8370.0010.0010.0000.0000.0000.000
72A104LEU00.0170.02459.3400.0010.0010.0000.0000.0000.000
73A105ARG10.9170.92860.557-0.031-0.0310.0000.0000.0000.000
74A106ALA0-0.021-0.00557.9570.0000.0000.0000.0000.0000.000
75A107LEU0-0.034-0.02754.5900.0010.0010.0000.0000.0000.000
76A108ARG10.8110.87456.505-0.031-0.0310.0000.0000.0000.000
77A109ASN0-0.052-0.01058.656-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.024-0.01651.0170.0010.0010.0000.0000.0000.000
79A111ASN0-0.016-0.01451.8880.0010.0010.0000.0000.0000.000
80A112THR00.001-0.01047.455-0.002-0.0020.0000.0000.0000.000
81A113VAL0-0.007-0.02050.611-0.001-0.0010.0000.0000.0000.000
82A114SER0-0.021-0.00352.547-0.002-0.0020.0000.0000.0000.000
83A115HIS0-0.016-0.00151.579-0.002-0.0020.0000.0000.0000.000
84A116VAL0-0.023-0.00850.538-0.001-0.0010.0000.0000.0000.000
85A117ILE0-0.070-0.02253.9460.0000.0000.0000.0000.0000.000
86A118GLU-1-0.843-0.92457.3980.0230.0230.0000.0000.0000.000
87A119ASP-1-0.833-0.91460.1040.0260.0260.0000.0000.0000.000
88A120HIS0-0.073-0.05360.095-0.001-0.0010.0000.0000.0000.000
89A121ASP-1-0.741-0.84658.6470.0310.0310.0000.0000.0000.000
90A122GLU-1-0.853-0.92061.7540.0310.0310.0000.0000.0000.000
91A123GLU-1-0.864-0.93263.8730.0240.0240.0000.0000.0000.000
92A124ILE0-0.024-0.01661.5130.0000.0000.0000.0000.0000.000
93A125LEU00.011-0.00658.1660.0010.0010.0000.0000.0000.000
94A126VAL00.0010.01162.2040.0010.0010.0000.0000.0000.000
95A127TYR0-0.024-0.02064.6230.0000.0000.0000.0000.0000.000
96A128LEU0-0.047-0.00357.5390.0010.0010.0000.0000.0000.000
97A129ASN00.027-0.01061.259-0.001-0.0010.0000.0000.0000.000
98A130ASP-1-0.854-0.93657.4220.0560.0560.0000.0000.0000.000
99A131ILE0-0.0020.01152.736-0.001-0.0010.0000.0000.0000.000
100A132ARG10.8210.90852.179-0.062-0.0620.0000.0000.0000.000
101A133CYS00.0380.00445.9230.0010.0010.0000.0000.0000.000
102A134ASP-1-0.906-0.92047.2900.0730.0730.0000.0000.0000.000
103A135TYR00.0120.00541.1540.0020.0020.0000.0000.0000.000
104A136ILE0-0.0020.01240.456-0.003-0.0030.0000.0000.0000.000
105A137LYS10.8970.94741.793-0.082-0.0820.0000.0000.0000.000
106A138LYS10.8140.90636.900-0.115-0.1150.0000.0000.0000.000
107A139ASN0-0.015-0.00939.3560.0060.0060.0000.0000.0000.000
108A140LYS10.8060.87331.601-0.181-0.1810.0000.0000.0000.000
109A141GLU-1-0.838-0.88332.7610.1740.1740.0000.0000.0000.000
110A142LYN0-0.020-0.00528.8200.0140.0140.0000.0000.0000.000
111A143LYS10.8960.95130.422-0.121-0.1210.0000.0000.0000.000
112A144GLU-1-0.689-0.84432.9350.1330.1330.0000.0000.0000.000
113A145GLY00.0500.00536.217-0.004-0.0040.0000.0000.0000.000
114A146PHE0-0.039-0.02939.0130.0030.0030.0000.0000.0000.000
115A147ILE00.0270.01542.641-0.002-0.0020.0000.0000.0000.000
116A148LEU0-0.0180.00646.0590.0020.0020.0000.0000.0000.000
117A149SER0-0.012-0.02948.652-0.003-0.0030.0000.0000.0000.000
118A150PHE00.0320.01550.7070.0000.0000.0000.0000.0000.000
119A151HIS00.001-0.00455.4310.0000.0000.0000.0000.0000.000
120A152PHE00.0430.00557.463-0.001-0.0010.0000.0000.0000.000
121A153ALA00.0110.01761.9320.0000.0000.0000.0000.0000.000
122A154PRO0-0.007-0.02165.482-0.001-0.0010.0000.0000.0000.000
123A155ASN00.0420.04863.588-0.002-0.0020.0000.0000.0000.000
124A156PRO0-0.020-0.01667.7690.0000.0000.0000.0000.0000.000
125A157PHE0-0.007-0.00464.098-0.001-0.0010.0000.0000.0000.000
126A158PHE00.0290.00660.408-0.001-0.0010.0000.0000.0000.000
127A159SER0-0.041-0.00562.9630.0010.0010.0000.0000.0000.000
128A160ASN0-0.025-0.02158.2650.0000.0000.0000.0000.0000.000
129A161SER00.0400.01960.7830.0000.0000.0000.0000.0000.000
130A162VAL0-0.039-0.02855.1320.0010.0010.0000.0000.0000.000
131A163LEU0-0.0030.02654.739-0.001-0.0010.0000.0000.0000.000
132A164THR0-0.012-0.03050.1900.0010.0010.0000.0000.0000.000
133A165LYS10.8060.89645.125-0.057-0.0570.0000.0000.0000.000
134A166THR0-0.044-0.01442.4130.0030.0030.0000.0000.0000.000
135A167TYR00.005-0.02740.251-0.002-0.0020.0000.0000.0000.000
136A168HIS0-0.020-0.01137.2000.0140.0140.0000.0000.0000.000
137A169MET00.004-0.00834.708-0.003-0.0030.0000.0000.0000.000
138A170LYS10.8940.94126.693-0.194-0.1940.0000.0000.0000.000
139A178PRO00.006-0.01531.8360.0020.0020.0000.0000.0000.000
140A179VAL0-0.0020.01028.567-0.009-0.0090.0000.0000.0000.000
141A180LEU00.0240.02132.0030.0040.0040.0000.0000.0000.000
142A181LEU0-0.079-0.03631.2540.0010.0010.0000.0000.0000.000
143A182HIS0-0.061-0.04734.880-0.008-0.0080.0000.0000.0000.000
144A183THR00.0180.02138.4750.0050.0050.0000.0000.0000.000
145A184GLU-1-0.846-0.91642.1040.0700.0700.0000.0000.0000.000
146A185ALA00.0410.02645.4010.0020.0020.0000.0000.0000.000
147A186THR0-0.052-0.00549.052-0.001-0.0010.0000.0000.0000.000
148A187VAL00.0220.00352.519-0.001-0.0010.0000.0000.0000.000
149A188ILE00.0060.01554.3890.0000.0000.0000.0000.0000.000
150A189ASP-1-0.877-0.91857.5350.0330.0330.0000.0000.0000.000
151A190TRP0-0.029-0.03858.095-0.001-0.0010.0000.0000.0000.000
152A191TYR0-0.032-0.00662.731-0.001-0.0010.0000.0000.0000.000
153A192ASP-1-0.829-0.92666.2230.0180.0180.0000.0000.0000.000
154A193ASN0-0.140-0.08568.3720.0000.0000.0000.0000.0000.000
155A194LYS10.8100.91566.961-0.024-0.0240.0000.0000.0000.000
156A195ASN00.0260.01559.9350.0010.0010.0000.0000.0000.000
157A196ILE00.0310.02660.634-0.001-0.0010.0000.0000.0000.000
158A197LEU00.0170.03656.044-0.001-0.0010.0000.0000.0000.000
159A198LYS10.9120.95359.445-0.021-0.0210.0000.0000.0000.000
160A199LYS10.8150.91062.149-0.013-0.0130.0000.0000.0000.000
161A200ASN00.0350.02264.8240.0000.0000.0000.0000.0000.000
162A201VAL00.0430.01767.858-0.001-0.0010.0000.0000.0000.000
163A202VAL0-0.035-0.01371.151-0.001-0.0010.0000.0000.0000.000
164A203LYS10.8900.92373.677-0.008-0.0080.0000.0000.0000.000
165A216VAL00.0220.00073.8020.0000.0000.0000.0000.0000.000
166A217GLN00.0590.04769.7740.0000.0000.0000.0000.0000.000
167A218GLN00.0330.02268.957-0.001-0.0010.0000.0000.0000.000
168A219THR0-0.019-0.00564.2840.0010.0010.0000.0000.0000.000
169A220VAL00.0390.02060.839-0.001-0.0010.0000.0000.0000.000
170A221ASN00.003-0.00456.4600.0010.0010.0000.0000.0000.000
171A222ARG10.8510.92158.484-0.023-0.0230.0000.0000.0000.000
172A223ASP-1-0.854-0.90454.3260.0240.0240.0000.0000.0000.000
173A224SER0-0.019-0.04755.6710.0000.0000.0000.0000.0000.000
174A225PHE00.0720.03252.8600.0010.0010.0000.0000.0000.000
175A226PHE0-0.021-0.03053.7730.0020.0020.0000.0000.0000.000
176A227HIS0-0.033-0.02152.0490.0020.0020.0000.0000.0000.000
177A228PHE00.0070.02447.0700.0020.0020.0000.0000.0000.000
178A229PHE0-0.035-0.00649.2980.0030.0030.0000.0000.0000.000
179A230THR0-0.036-0.03047.575-0.003-0.0030.0000.0000.0000.000
180A231SER0-0.019-0.01045.0570.0030.0030.0000.0000.0000.000
181A232HIS00.0180.01441.715-0.001-0.0010.0000.0000.0000.000
182A233LYS10.9260.94838.251-0.042-0.0420.0000.0000.0000.000
183A234VAL00.0500.02534.061-0.005-0.0050.0000.0000.0000.000
184A235PRO0-0.0030.01632.1190.0040.0040.0000.0000.0000.000
185A247GLU-1-0.945-0.98738.841-0.004-0.0040.0000.0000.0000.000
186A248VAL0-0.008-0.02134.0510.0040.0040.0000.0000.0000.000
187A249ALA00.0650.03837.4510.0050.0050.0000.0000.0000.000
188A250GLN00.0320.01738.9710.0040.0040.0000.0000.0000.000
189A251LEU0-0.037-0.02038.7650.0030.0030.0000.0000.0000.000
190A252GLU-1-0.941-0.96834.3180.0500.0500.0000.0000.0000.000
191A253MET00.0330.02238.5370.0030.0030.0000.0000.0000.000
192A254ILE0-0.007-0.00841.5670.0020.0020.0000.0000.0000.000
193A255ILE0-0.041-0.02137.5730.0030.0030.0000.0000.0000.000
194A256GLU-1-0.937-0.96737.9430.0560.0560.0000.0000.0000.000
195A257GLY00.0120.01140.8050.0020.0020.0000.0000.0000.000
196A258ASP-1-0.803-0.87343.5890.0560.0560.0000.0000.0000.000
197A259TYR00.041-0.00438.8320.0040.0040.0000.0000.0000.000
198A260GLU-1-0.868-0.90842.4990.0570.0570.0000.0000.0000.000
199A261VAL00.0400.02443.9910.0010.0010.0000.0000.0000.000
200A262ALA0-0.016-0.00143.9090.0010.0010.0000.0000.0000.000
201A263LEU0-0.023-0.01140.5330.0020.0020.0000.0000.0000.000
202A264THR0-0.028-0.02344.1090.0020.0020.0000.0000.0000.000
203A265ILE00.022-0.00147.317-0.001-0.0010.0000.0000.0000.000
204A266LYS10.8070.89341.410-0.096-0.0960.0000.0000.0000.000
205A267GLU-1-0.892-0.93841.8830.1000.1000.0000.0000.0000.000
206A268ARG10.9310.96444.820-0.066-0.0660.0000.0000.0000.000
207A269ILE00.0090.01349.679-0.001-0.0010.0000.0000.0000.000
208A270ILE00.0000.01149.474-0.001-0.0010.0000.0000.0000.000
209A271PRO0-0.0080.00148.651-0.001-0.0010.0000.0000.0000.000
210A272TYR00.0070.00247.9660.0000.0000.0000.0000.0000.000
211A273ALA00.0160.02554.347-0.003-0.0030.0000.0000.0000.000
212A274VAL00.0220.00056.879-0.002-0.0020.0000.0000.0000.000
213A275ASP-1-0.860-0.93556.4710.0530.0530.0000.0000.0000.000
214A276TYR0-0.002-0.00551.9470.0000.0000.0000.0000.0000.000
215A277PHE0-0.019-0.00158.016-0.002-0.0020.0000.0000.0000.000
216A278LEU0-0.060-0.03861.539-0.002-0.0020.0000.0000.0000.000
217A279GLY00.0010.01460.490-0.001-0.0010.0000.0000.0000.000
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