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: Z6RYN

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2607956.9002
FMO2-HF: Nuclear repulsion 2517901.628053
FMO2-HF: Total energy -90055.272147
FMO2-MP2: Total energy -90323.765839


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.
-4.996-1.7130.033-1.587-1.7290.001
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 : -0.071 / q_NPA : -0.052
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].
3A35LEU0-0.020-0.0063.333-0.9212.2820.034-1.583-1.6550.001
4A36THR00.0490.0155.765-0.394-0.3940.0000.0000.0000.000
5A37GLU-1-0.853-0.9608.4571.3761.3760.0000.0000.0000.000
6A38GLU-1-0.928-0.95910.5450.6560.6560.0000.0000.0000.000
7A39GLN00.0070.0008.5030.1990.1990.0000.0000.0000.000
8A40LYS10.9230.9774.779-2.716-2.636-0.001-0.004-0.0740.000
9A41GLU-1-0.913-0.9628.4960.8900.8900.0000.0000.0000.000
10A42THR0-0.051-0.02011.350-0.188-0.1880.0000.0000.0000.000
11A43LEU00.0350.0185.811-0.101-0.1010.0000.0000.0000.000
12A44LYS10.9560.9849.998-1.107-1.1070.0000.0000.0000.000
13A45LYS10.9630.99412.001-0.887-0.8870.0000.0000.0000.000
14A46LEU00.0410.02311.811-0.106-0.1060.0000.0000.0000.000
15A47LYS10.9030.9448.700-1.574-1.5740.0000.0000.0000.000
16A48LEU0-0.037-0.01812.826-0.119-0.1190.0000.0000.0000.000
17A49TYR00.0490.00116.215-0.058-0.0580.0000.0000.0000.000
18A50GLN00.0010.02214.763-0.038-0.0380.0000.0000.0000.000
19A51LYS10.8680.93816.884-0.603-0.6030.0000.0000.0000.000
20A52GLU-1-0.827-0.92118.2790.3670.3670.0000.0000.0000.000
21A53TYR0-0.065-0.02119.916-0.039-0.0390.0000.0000.0000.000
22A54TYR0-0.015-0.02316.2310.0070.0070.0000.0000.0000.000
23A55ASP-1-0.911-0.94221.6020.3650.3650.0000.0000.0000.000
24A56TYR0-0.064-0.04524.347-0.046-0.0460.0000.0000.0000.000
25A57GLU-1-0.891-0.94423.2450.3200.3200.0000.0000.0000.000
26A58SER00.0300.00925.529-0.028-0.0280.0000.0000.0000.000
27A59LYS10.8800.94927.444-0.306-0.3060.0000.0000.0000.000
28A60PHE00.0500.03129.476-0.020-0.0200.0000.0000.0000.000
29A61GLU-1-0.911-0.96027.3550.2170.2170.0000.0000.0000.000
30A62TYR0-0.044-0.01331.171-0.017-0.0170.0000.0000.0000.000
31A63GLU-1-0.928-0.97233.3370.1620.1620.0000.0000.0000.000
32A64LEU0-0.037-0.01533.047-0.014-0.0140.0000.0000.0000.000
33A65PHE0-0.036-0.03632.381-0.012-0.0120.0000.0000.0000.000
34A66LEU00.0000.00036.846-0.011-0.0110.0000.0000.0000.000
35A67LEU0-0.045-0.00839.104-0.009-0.0090.0000.0000.0000.000
36A68ARG10.9810.97335.371-0.141-0.1410.0000.0000.0000.000
37A69GLN00.0010.00640.303-0.012-0.0120.0000.0000.0000.000
38A70LYS10.9630.98343.022-0.110-0.1100.0000.0000.0000.000
39A71TYR0-0.011-0.02044.695-0.004-0.0040.0000.0000.0000.000
40A72HIS0-0.0120.01044.762-0.006-0.0060.0000.0000.0000.000
41A73ASP-1-0.897-0.95746.6330.0820.0820.0000.0000.0000.000
42A74LEU0-0.088-0.04648.979-0.004-0.0040.0000.0000.0000.000
43A75TYR0-0.036-0.01046.516-0.002-0.0020.0000.0000.0000.000
44A76GLY00.0620.03851.042-0.003-0.0030.0000.0000.0000.000
45A77PRO00.0580.02452.775-0.003-0.0030.0000.0000.0000.000
46A78ILE0-0.017-0.00754.096-0.003-0.0030.0000.0000.0000.000
47A79TYR00.005-0.00449.537-0.003-0.0030.0000.0000.0000.000
48A80ASP-1-0.883-0.94355.9880.0550.0550.0000.0000.0000.000
49A81LYS10.9130.95158.384-0.058-0.0580.0000.0000.0000.000
50A82ARG10.8580.93054.341-0.058-0.0580.0000.0000.0000.000
51A83ARG10.9390.98257.681-0.052-0.0520.0000.0000.0000.000
52A84GLU-1-0.971-0.99961.0470.0420.0420.0000.0000.0000.000
53A85ALA0-0.021-0.01063.851-0.002-0.0020.0000.0000.0000.000
54A86LEU0-0.0170.00461.051-0.002-0.0020.0000.0000.0000.000
55A87VAL0-0.055-0.03063.035-0.002-0.0020.0000.0000.0000.000
56A88GLY00.0260.02566.081-0.001-0.0010.0000.0000.0000.000
57A89ASN0-0.065-0.05266.401-0.002-0.0020.0000.0000.0000.000
58A90GLY00.0490.04068.4190.0000.0000.0000.0000.0000.000
59A91GLU-1-0.982-0.99570.9330.0260.0260.0000.0000.0000.000
60A92ALA00.007-0.00268.1100.0010.0010.0000.0000.0000.000
61A93LYS10.9170.95669.973-0.026-0.0260.0000.0000.0000.000
62A94ILE00.0090.00768.209-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0770.03665.0000.0010.0010.0000.0000.0000.000
64A96THR0-0.093-0.04462.5450.0000.0000.0000.0000.0000.000
65A97PRO0-0.0100.00765.5850.0000.0000.0000.0000.0000.000
66A98ASN0-0.044-0.01968.154-0.002-0.0020.0000.0000.0000.000
67A99LEU0-0.083-0.04164.6490.0000.0000.0000.0000.0000.000
68A100PRO00.0270.01266.3530.0010.0010.0000.0000.0000.000
69A101GLU-1-0.917-0.96364.9980.0300.0300.0000.0000.0000.000
70A102PHE0-0.0070.00359.0530.0010.0010.0000.0000.0000.000
71A103TRP00.015-0.00955.3790.0020.0020.0000.0000.0000.000
72A104LEU00.0360.03458.8320.0010.0010.0000.0000.0000.000
73A105ARG11.0060.98959.662-0.031-0.0310.0000.0000.0000.000
74A106ALA0-0.0180.00257.4210.0000.0000.0000.0000.0000.000
75A107LEU0-0.057-0.04454.0460.0020.0020.0000.0000.0000.000
76A108ARG10.8490.91655.684-0.031-0.0310.0000.0000.0000.000
77A109ASN0-0.0370.00457.635-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.034-0.01850.0210.0010.0010.0000.0000.0000.000
79A111ASN00.015-0.01251.316-0.002-0.0020.0000.0000.0000.000
80A112THR00.0100.01746.659-0.002-0.0020.0000.0000.0000.000
81A113VAL0-0.024-0.02249.936-0.001-0.0010.0000.0000.0000.000
82A114SER0-0.015-0.01151.819-0.002-0.0020.0000.0000.0000.000
83A115HIS0-0.0020.00850.003-0.002-0.0020.0000.0000.0000.000
84A116VAL00.0320.01650.101-0.002-0.0020.0000.0000.0000.000
85A117ILE0-0.096-0.03153.462-0.001-0.0010.0000.0000.0000.000
86A118GLU-1-0.841-0.91056.6370.0260.0260.0000.0000.0000.000
87A119ASP-1-0.885-0.95859.3560.0260.0260.0000.0000.0000.000
88A120HIS0-0.063-0.04759.271-0.001-0.0010.0000.0000.0000.000
89A121ASP-1-0.719-0.80858.0790.0290.0290.0000.0000.0000.000
90A122GLU-1-0.893-0.94261.2330.0290.0290.0000.0000.0000.000
91A123GLU-1-0.931-0.97563.2650.0230.0230.0000.0000.0000.000
92A124ILE0-0.027-0.03361.1950.0000.0000.0000.0000.0000.000
93A125LEU0-0.025-0.02757.5670.0010.0010.0000.0000.0000.000
94A126VAL00.0130.02561.3670.0020.0020.0000.0000.0000.000
95A127TYR0-0.053-0.02364.0020.0000.0000.0000.0000.0000.000
96A128LEU0-0.0330.00357.0360.0010.0010.0000.0000.0000.000
97A129ASN00.0470.00261.222-0.001-0.0010.0000.0000.0000.000
98A130ASP-1-0.884-0.96557.0770.0510.0510.0000.0000.0000.000
99A131ILE0-0.0210.00452.080-0.001-0.0010.0000.0000.0000.000
100A132ARG10.9260.97951.809-0.056-0.0560.0000.0000.0000.000
101A133CYS0-0.010-0.00245.5980.0010.0010.0000.0000.0000.000
102A134ASP-1-0.887-0.92746.7510.0650.0650.0000.0000.0000.000
103A135TYR00.0370.01840.9460.0030.0030.0000.0000.0000.000
104A136ILE0-0.0060.00040.321-0.004-0.0040.0000.0000.0000.000
105A137LYS10.9170.97241.483-0.071-0.0710.0000.0000.0000.000
106A138LYS10.8200.91136.943-0.092-0.0920.0000.0000.0000.000
107A139ASN0-0.007-0.00539.3780.0050.0050.0000.0000.0000.000
108A140LYS10.8250.88631.099-0.152-0.1520.0000.0000.0000.000
109A141GLU-1-0.830-0.88132.3050.1490.1490.0000.0000.0000.000
110A142LYN0-0.0020.00728.4380.0100.0100.0000.0000.0000.000
111A143LYS10.8970.95029.951-0.095-0.0950.0000.0000.0000.000
112A144GLU-1-0.796-0.91732.5860.1160.1160.0000.0000.0000.000
113A145GLY00.0400.00236.037-0.003-0.0030.0000.0000.0000.000
114A146PHE0-0.045-0.04338.7020.0030.0030.0000.0000.0000.000
115A147ILE0-0.0150.01042.340-0.002-0.0020.0000.0000.0000.000
116A148LEU0-0.0120.01745.8100.0020.0020.0000.0000.0000.000
117A149SER00.020-0.01148.277-0.003-0.0030.0000.0000.0000.000
118A150PHE00.007-0.00650.2250.0000.0000.0000.0000.0000.000
119A151HIS0-0.0010.00254.8630.0000.0000.0000.0000.0000.000
120A152PHE00.0260.00857.0220.0000.0000.0000.0000.0000.000
121A153ALA0-0.0100.00161.2010.0000.0000.0000.0000.0000.000
122A154PRO00.004-0.01364.836-0.001-0.0010.0000.0000.0000.000
123A155ASN00.0220.02563.003-0.002-0.0020.0000.0000.0000.000
124A156PRO0-0.027-0.01967.0870.0000.0000.0000.0000.0000.000
125A157PHE0-0.035-0.01663.558-0.001-0.0010.0000.0000.0000.000
126A158PHE00.0560.00859.808-0.001-0.0010.0000.0000.0000.000
127A159SER0-0.0050.00963.0630.0010.0010.0000.0000.0000.000
128A160ASN0-0.0100.02257.2190.0000.0000.0000.0000.0000.000
129A161SER00.0450.01860.2980.0000.0000.0000.0000.0000.000
130A162VAL0-0.009-0.01854.2960.0010.0010.0000.0000.0000.000
131A163LEU0-0.0120.02454.019-0.001-0.0010.0000.0000.0000.000
132A164THR0-0.001-0.00949.3620.0010.0010.0000.0000.0000.000
133A165LYS10.8880.95544.487-0.050-0.0500.0000.0000.0000.000
134A166THR0-0.041-0.02742.2930.0030.0030.0000.0000.0000.000
135A167TYR00.001-0.02939.793-0.001-0.0010.0000.0000.0000.000
136A168HIS0-0.037-0.02736.9940.0120.0120.0000.0000.0000.000
137A169MET00.034-0.00134.337-0.003-0.0030.0000.0000.0000.000
138A170LYS10.8950.95526.433-0.163-0.1630.0000.0000.0000.000
139A178PRO00.011-0.02231.0010.0020.0020.0000.0000.0000.000
140A179VAL00.0080.02828.098-0.007-0.0070.0000.0000.0000.000
141A180LEU00.0300.00731.5600.0020.0020.0000.0000.0000.000
142A181LEU0-0.097-0.04031.283-0.002-0.0020.0000.0000.0000.000
143A182HIS0-0.018-0.01734.511-0.008-0.0080.0000.0000.0000.000
144A183THR00.0370.02338.1760.0030.0030.0000.0000.0000.000
145A184GLU-1-0.862-0.91941.7370.0540.0540.0000.0000.0000.000
146A185ALA00.0230.02944.9700.0030.0030.0000.0000.0000.000
147A186THR0-0.062-0.01748.461-0.002-0.0020.0000.0000.0000.000
148A187VAL00.016-0.00151.906-0.001-0.0010.0000.0000.0000.000
149A188ILE0-0.0150.00454.1180.0000.0000.0000.0000.0000.000
150A189ASP-1-0.917-0.95857.1090.0260.0260.0000.0000.0000.000
151A190TRP0-0.041-0.04057.6200.0000.0000.0000.0000.0000.000
152A191TYR0-0.020-0.00262.336-0.001-0.0010.0000.0000.0000.000
153A192ASP-1-0.913-0.96765.9560.0150.0150.0000.0000.0000.000
154A193ASN0-0.078-0.04467.7240.0000.0000.0000.0000.0000.000
155A194LYS10.8850.94565.662-0.021-0.0210.0000.0000.0000.000
156A195ASN00.0100.01259.3900.0020.0020.0000.0000.0000.000
157A196ILE00.0280.03159.844-0.001-0.0010.0000.0000.0000.000
158A197LEU00.0290.02755.580-0.001-0.0010.0000.0000.0000.000
159A198LYS10.8830.94558.756-0.018-0.0180.0000.0000.0000.000
160A199LYS10.8250.93761.221-0.011-0.0110.0000.0000.0000.000
161A200ASN00.006-0.01264.0540.0000.0000.0000.0000.0000.000
162A201VAL00.0890.14267.366-0.001-0.0010.0000.0000.0000.000
163A202VAL0-0.030-0.05870.1650.0000.0000.0000.0000.0000.000
164A203LYS10.9020.90872.987-0.007-0.0070.0000.0000.0000.000
165A216VAL00.0300.00672.9340.0000.0000.0000.0000.0000.000
166A217GLN00.0570.05569.5480.0000.0000.0000.0000.0000.000
167A218GLN00.004-0.00968.355-0.001-0.0010.0000.0000.0000.000
168A219THR0-0.0080.00063.4040.0010.0010.0000.0000.0000.000
169A220VAL00.058-0.00560.708-0.001-0.0010.0000.0000.0000.000
170A221ASN0-0.040-0.02656.3170.0010.0010.0000.0000.0000.000
171A222ARG10.9260.97158.082-0.021-0.0210.0000.0000.0000.000
172A223ASP-1-0.878-0.92853.2810.0240.0240.0000.0000.0000.000
173A224SER0-0.067-0.09454.9150.0000.0000.0000.0000.0000.000
174A225PHE00.0970.04852.0520.0010.0010.0000.0000.0000.000
175A226PHE0-0.011-0.02852.9650.0020.0020.0000.0000.0000.000
176A227HIS0-0.009-0.00451.2170.0000.0000.0000.0000.0000.000
177A228PHE0-0.0090.00246.7490.0010.0010.0000.0000.0000.000
178A229PHE0-0.054-0.02948.6560.0030.0030.0000.0000.0000.000
179A230THR0-0.024-0.00747.688-0.003-0.0030.0000.0000.0000.000
180A231SER0-0.016-0.01544.6300.0030.0030.0000.0000.0000.000
181A232HIS00.0240.01441.032-0.001-0.0010.0000.0000.0000.000
182A233LYS10.9050.92937.940-0.030-0.0300.0000.0000.0000.000
183A234VAL00.1200.04533.182-0.001-0.0010.0000.0000.0000.000
184A235PRO0-0.0400.01731.2990.0030.0030.0000.0000.0000.000
185A247GLU-1-0.947-0.97937.842-0.007-0.0070.0000.0000.0000.000
186A248VAL00.025-0.02133.5990.0030.0030.0000.0000.0000.000
187A249ALA00.0680.05536.9630.0050.0050.0000.0000.0000.000
188A250GLN00.0170.00838.5900.0030.0030.0000.0000.0000.000
189A251LEU0-0.054-0.02737.5910.0020.0020.0000.0000.0000.000
190A252GLU-1-0.932-0.95934.5030.0520.0520.0000.0000.0000.000
191A253MET0-0.001-0.00537.9570.0030.0030.0000.0000.0000.000
192A254ILE0-0.016-0.01441.0360.0010.0010.0000.0000.0000.000
193A255ILE0-0.053-0.03236.9900.0020.0020.0000.0000.0000.000
194A256GLU-1-0.926-0.97136.2010.0600.0600.0000.0000.0000.000
195A257GLY00.0210.02239.9320.0020.0020.0000.0000.0000.000
196A258ASP-1-0.851-0.89842.9750.0520.0520.0000.0000.0000.000
197A259TYR00.016-0.01737.6130.0040.0040.0000.0000.0000.000
198A260GLU-1-0.905-0.94641.8330.0590.0590.0000.0000.0000.000
199A261VAL00.0140.02343.2530.0010.0010.0000.0000.0000.000
200A262ALA0-0.007-0.01243.5690.0010.0010.0000.0000.0000.000
201A263LEU0-0.0190.01040.0060.0010.0010.0000.0000.0000.000
202A264THR0-0.010-0.01443.7190.0020.0020.0000.0000.0000.000
203A265ILE00.005-0.00246.8150.0000.0000.0000.0000.0000.000
204A266LYS10.9080.95241.117-0.088-0.0880.0000.0000.0000.000
205A267GLU-1-0.936-0.98741.4630.0920.0920.0000.0000.0000.000
206A268ARG10.9250.95944.643-0.068-0.0680.0000.0000.0000.000
207A269ILE0-0.0040.01049.079-0.001-0.0010.0000.0000.0000.000
208A270ILE00.0010.00748.861-0.001-0.0010.0000.0000.0000.000
209A271PRO0-0.0100.00448.189-0.002-0.0020.0000.0000.0000.000
210A272TYR00.0070.00047.4960.0000.0000.0000.0000.0000.000
211A273ALA0-0.0020.02353.837-0.002-0.0020.0000.0000.0000.000
212A274VAL00.0640.00456.151-0.002-0.0020.0000.0000.0000.000
213A275ASP-1-0.892-0.92156.0380.0530.0530.0000.0000.0000.000
214A276TYR0-0.005-0.01051.0070.0010.0010.0000.0000.0000.000
215A277PHE0-0.027-0.01157.307-0.002-0.0020.0000.0000.0000.000
216A278LEU0-0.074-0.05460.749-0.002-0.0020.0000.0000.0000.000
217A279GLY0-0.0090.01359.861-0.001-0.0010.0000.0000.0000.000
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