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: Z2M6N

Calculation Name: 3HN5-A-Xray312

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3HN5

Chain ID: A

ChEMBL ID:
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UniProt ID: Q5LIG1

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2337650.736431
FMO2-HF: Nuclear repulsion 2255142.146098
FMO2-HF: Total energy -82508.590333
FMO2-MP2: Total energy -82747.249839


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:29:ACE )


Summations of interaction energy for fragment #1(A:29:ACE )
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.
0.1831.042-0.005-0.452-0.401-0.001
Interaction energy analysis for fragmet #1(A:29:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.040
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].
3A31SER 0-0.050-0.0283.8601.0851.939-0.005-0.430-0.419-0.001
4A32MET 0-0.028-0.0186.9540.0720.0720.0000.0000.0000.000
5A33LEU 00.0210.02510.3750.1010.1010.0000.0000.0000.000
6A34THR 0-0.076-0.04613.5290.0320.0320.0000.0000.0000.000
7A35GLY 00.0860.03716.4860.0090.0090.0000.0000.0000.000
8A36ARG 10.8920.93520.1560.1030.1030.0000.0000.0000.000
9A37VAL 00.0120.02223.684-0.003-0.0030.0000.0000.0000.000
10A38MET 0-0.073-0.04426.2600.0110.0110.0000.0000.0000.000
11A39TYR 00.0540.01529.220-0.001-0.0010.0000.0000.0000.000
12A40ASN 0-0.039-0.01232.7980.0040.0040.0000.0000.0000.000
13A41GLY 00.0060.00731.1670.0050.0050.0000.0000.0000.000
14A42GLU -1-0.965-0.97230.926-0.057-0.0570.0000.0000.0000.000
15A43ALA 0-0.024-0.00927.337-0.004-0.0040.0000.0000.0000.000
16A44LEU 00.0210.00529.0440.0080.0080.0000.0000.0000.000
17A45GLN 0-0.023-0.00429.298-0.002-0.0020.0000.0000.0000.000
18A46LEU 00.0180.00627.2490.0030.0030.0000.0000.0000.000
19A47ARG 10.8930.94130.1420.0870.0870.0000.0000.0000.000
20A48GLY 00.0280.02426.488-0.006-0.0060.0000.0000.0000.000
21A49ASN 0-0.066-0.04425.1840.0050.0050.0000.0000.0000.000
22A50GLU -1-0.851-0.94322.734-0.145-0.1450.0000.0000.0000.000
23A51ALA 0-0.070-0.02525.139-0.002-0.0020.0000.0000.0000.000
24A52VAL 00.0200.01426.2880.0030.0030.0000.0000.0000.000
25A53GLN 0-0.021-0.01523.404-0.015-0.0150.0000.0000.0000.000
26A54LEU 0-0.028-0.01621.0690.0160.0160.0000.0000.0000.000
27A55GLN 0-0.007-0.00721.379-0.008-0.0080.0000.0000.0000.000
28A56LEU 00.0240.01515.3850.0130.0130.0000.0000.0000.000
29A57TYR 0-0.026-0.02519.136-0.006-0.0060.0000.0000.0000.000
30A58GLN 00.0830.03413.5170.0190.0190.0000.0000.0000.000
31A59HIS 0-0.055-0.01818.2460.0060.0060.0000.0000.0000.000
32A60GLY 00.0410.02221.7620.0240.0240.0000.0000.0000.000
33A61TYR 00.0640.03424.556-0.002-0.0020.0000.0000.0000.000
34A62ALA 00.0060.00326.5700.0030.0030.0000.0000.0000.000
35A63LYS 10.9350.96724.7350.1490.1490.0000.0000.0000.000
36A64HIS 10.8040.91026.0880.1340.1340.0000.0000.0000.000
37A65ASP -1-0.864-0.94221.901-0.213-0.2130.0000.0000.0000.000
38A66PRO 0-0.0300.00420.672-0.021-0.0210.0000.0000.0000.000
39A67ILE 00.0450.02414.0210.0060.0060.0000.0000.0000.000
40A68ASN 0-0.041-0.02418.1020.0410.0410.0000.0000.0000.000
41A69VAL 00.0140.01416.686-0.037-0.0370.0000.0000.0000.000
42A70TYR 00.0050.00518.8340.0340.0340.0000.0000.0000.000
43A71VAL 0-0.0160.00020.294-0.014-0.0140.0000.0000.0000.000
44A72ASN 00.0180.00821.6820.0170.0170.0000.0000.0000.000
45A73GLN 00.053-0.00224.019-0.005-0.0050.0000.0000.0000.000
46A74ASP -1-0.924-0.95925.597-0.070-0.0700.0000.0000.0000.000
47A75GLY 00.0420.03726.0660.0020.0020.0000.0000.0000.000
48A76MET 0-0.041-0.02619.9110.0000.0000.0000.0000.0000.000
49A77TYR 0-0.010-0.02516.905-0.008-0.0080.0000.0000.0000.000
50A78SER 0-0.034-0.03813.909-0.020-0.0200.0000.0000.0000.000
51A79ALA 00.0100.01213.4300.0220.0220.0000.0000.0000.000
52A80ASN 0-0.032-0.0077.9530.0440.0440.0000.0000.0000.000
53A81LEU 00.0180.0118.5580.0910.0910.0000.0000.0000.000
54A82PHE 00.0460.0224.519-0.360-0.3550.000-0.0220.0180.000
55A83ASP -1-0.812-0.8737.470-0.540-0.5400.0000.0000.0000.000
56A84GLY 0-0.022-0.0169.3850.0390.0390.0000.0000.0000.000
57A85GLU -1-0.854-0.85113.007-0.240-0.2400.0000.0000.0000.000
58A86TYR 0-0.069-0.05911.0890.0140.0140.0000.0000.0000.000
59A87GLN 0-0.057-0.02317.7700.0320.0320.0000.0000.0000.000
60A88MET 00.0040.01418.338-0.011-0.0110.0000.0000.0000.000
61A89ILE 0-0.0060.00121.5170.0230.0230.0000.0000.0000.000
62A90THR 00.0850.03924.295-0.012-0.0120.0000.0000.0000.000
63A91LYS 10.9731.00126.2110.1410.1410.0000.0000.0000.000
64A92SER 0-0.033-0.03127.7040.0100.0100.0000.0000.0000.000
65A93GLY 00.000-0.00831.3340.0000.0000.0000.0000.0000.000
66A94ASN 0-0.092-0.03627.971-0.007-0.0070.0000.0000.0000.000
67A95GLY 00.041-0.00130.114-0.008-0.0080.0000.0000.0000.000
68A96PRO 0-0.0640.00531.5560.0040.0040.0000.0000.0000.000
69A97TRP 00.001-0.03728.0380.0020.0020.0000.0000.0000.000
70A98THR 00.0200.03134.916-0.002-0.0020.0000.0000.0000.000
71A99SER 0-0.019-0.03234.120-0.004-0.0040.0000.0000.0000.000
72A100GLU -1-0.967-0.98534.912-0.072-0.0720.0000.0000.0000.000
73A101GLY 00.0310.01633.935-0.003-0.0030.0000.0000.0000.000
74A102ARG 10.7780.89728.3930.1210.1210.0000.0000.0000.000
75A103ASP -1-0.853-0.93429.496-0.110-0.1100.0000.0000.0000.000
76A104THR 0-0.142-0.06825.012-0.011-0.0110.0000.0000.0000.000
77A105ILE 00.0330.02422.3270.0100.0100.0000.0000.0000.000
78A106ASN 0-0.009-0.02021.774-0.026-0.0260.0000.0000.0000.000
79A107VAL 00.0030.00016.0920.0100.0100.0000.0000.0000.000
80A108THR 0-0.026-0.07215.045-0.012-0.0120.0000.0000.0000.000
81A109VAL 0-0.086-0.03710.0280.0240.0240.0000.0000.0000.000
82A110ALA 00.0140.00110.629-0.034-0.0340.0000.0000.0000.000
83A111GLY 00.0330.0217.9010.1300.1300.0000.0000.0000.000
84A112ASN 0-0.019-0.0208.980-0.192-0.1920.0000.0000.0000.000
85A113THR 0-0.028-0.00910.8150.0880.0880.0000.0000.0000.000
86A114VAL 0-0.012-0.01414.040-0.018-0.0180.0000.0000.0000.000
87A115GLN 0-0.018-0.01217.4820.0060.0060.0000.0000.0000.000
88A116ASP -1-0.844-0.89620.045-0.150-0.1500.0000.0000.0000.000
89A117VAL 0-0.019-0.01523.039-0.003-0.0030.0000.0000.0000.000
90A118GLU -1-0.819-0.90625.624-0.081-0.0810.0000.0000.0000.000
91A119VAL 0-0.031-0.01629.161-0.003-0.0030.0000.0000.0000.000
92A120THR 00.0600.02031.8140.0070.0070.0000.0000.0000.000
93A121PRO 00.0070.00734.620-0.001-0.0010.0000.0000.0000.000
94A122TYR 00.0120.01236.4440.0050.0050.0000.0000.0000.000
95A123TYR 0-0.042-0.06538.9850.0030.0030.0000.0000.0000.000
96A124LEU 00.0050.00735.757-0.004-0.0040.0000.0000.0000.000
97A125VAL 0-0.028-0.00738.5200.0040.0040.0000.0000.0000.000
98A126ARG 10.8210.89737.0080.0490.0490.0000.0000.0000.000
99A127ASP -1-0.910-0.96541.823-0.032-0.0320.0000.0000.0000.000
100A128ALA 0-0.015-0.00140.4320.0010.0010.0000.0000.0000.000
101A129GLN 0-0.023-0.00742.5450.0020.0020.0000.0000.0000.000
102A130MET 0-0.037-0.01141.913-0.001-0.0010.0000.0000.0000.000
103A131THR 00.0040.01244.6040.0010.0010.0000.0000.0000.000
104A132LEU 00.0060.00345.8260.0000.0000.0000.0000.0000.000
105A133GLU -1-0.886-0.95648.473-0.017-0.0170.0000.0000.0000.000
106A134GLY 0-0.014-0.00552.2410.0000.0000.0000.0000.0000.000
107A135ASN 00.007-0.00251.046-0.001-0.0010.0000.0000.0000.000
108A136LYS 10.8820.91951.1710.0160.0160.0000.0000.0000.000
109A137VAL 00.0090.01545.7000.0000.0000.0000.0000.0000.000
110A138ASN 00.0240.03448.979-0.001-0.0010.0000.0000.0000.000
111A139ALA 00.0010.00445.4220.0000.0000.0000.0000.0000.000
112A140SER 0-0.011-0.00846.4340.0010.0010.0000.0000.0000.000
113A141PHE 00.006-0.00543.758-0.001-0.0010.0000.0000.0000.000
114A142LYS 10.9640.98944.9290.0300.0300.0000.0000.0000.000
115A143VAL 00.0130.02344.176-0.003-0.0030.0000.0000.0000.000
116A144GLU -1-0.839-0.90941.304-0.045-0.0450.0000.0000.0000.000
117A145LYS 10.9230.95342.4680.0380.0380.0000.0000.0000.000
118A146VAL 0-0.017-0.00538.6170.0010.0010.0000.0000.0000.000
119A147ALA 0-0.041-0.01439.8590.0020.0020.0000.0000.0000.000
120A148GLY 0-0.036-0.01441.8490.0030.0030.0000.0000.0000.000
121A149GLY 00.0300.00743.289-0.003-0.0030.0000.0000.0000.000
122A150GLY 00.0030.00545.6710.0010.0010.0000.0000.0000.000
123A151ILE 0-0.029-0.01944.613-0.003-0.0030.0000.0000.0000.000
124A152ASP -1-0.959-0.98143.766-0.046-0.0460.0000.0000.0000.000
125A153ARG 10.8900.93142.4050.0470.0470.0000.0000.0000.000
126A154VAL 00.0030.01943.697-0.003-0.0030.0000.0000.0000.000
127A155PHE 0-0.011-0.01738.7100.0010.0010.0000.0000.0000.000
128A156PHE 00.0080.01541.656-0.002-0.0020.0000.0000.0000.000
129A157MET 0-0.073-0.02037.966-0.001-0.0010.0000.0000.0000.000
130A158LEU 00.0220.00540.3800.0010.0010.0000.0000.0000.000
131A159SER 00.002-0.02635.328-0.001-0.0010.0000.0000.0000.000
132A160THR 00.0110.00837.1970.0010.0010.0000.0000.0000.000
133A161THR 0-0.053-0.02732.1940.0010.0010.0000.0000.0000.000
134A162GLN 00.0520.01527.559-0.003-0.0030.0000.0000.0000.000
135A163PHE 0-0.0190.01026.132-0.002-0.0020.0000.0000.0000.000
136A164VAL 00.0120.02230.8820.0020.0020.0000.0000.0000.000
137A165ASN 00.0220.00430.735-0.002-0.0020.0000.0000.0000.000
138A166ASP -1-0.764-0.90234.253-0.066-0.0660.0000.0000.0000.000
139A167ALA 0-0.046-0.01833.6350.0040.0040.0000.0000.0000.000
140A168GLU -1-0.920-0.94729.935-0.068-0.0680.0000.0000.0000.000
141A169HIS 10.9120.94134.6630.0460.0460.0000.0000.0000.000
142A170ASN 0-0.032-0.00136.3040.0030.0030.0000.0000.0000.000
143A171VAL 0-0.0160.00338.8140.0030.0030.0000.0000.0000.000
144A172ASP -1-0.742-0.84441.575-0.029-0.0290.0000.0000.0000.000
145A173ARG 10.7630.84839.6750.0450.0450.0000.0000.0000.000
146A174TYR 0-0.069-0.03843.0190.0020.0020.0000.0000.0000.000
147A175ASP -1-0.734-0.84444.386-0.044-0.0440.0000.0000.0000.000
148A176GLU -1-0.758-0.82746.691-0.027-0.0270.0000.0000.0000.000
149A177THR 00.029-0.02047.939-0.002-0.0020.0000.0000.0000.000
150A178ASP -1-0.890-0.91350.285-0.029-0.0290.0000.0000.0000.000
151A179ASN 0-0.038-0.04353.1350.0000.0000.0000.0000.0000.000
152A180LEU 00.0170.01947.6300.0000.0000.0000.0000.0000.000
153A181ASP -1-0.949-0.97050.789-0.034-0.0340.0000.0000.0000.000
154A182ALA 0-0.0040.00552.5490.0000.0000.0000.0000.0000.000
155A183TYR 0-0.054-0.04449.7790.0010.0010.0000.0000.0000.000
156A184ASP -1-0.815-0.87647.804-0.044-0.0440.0000.0000.0000.000
157A185GLU -1-0.949-0.98049.316-0.035-0.0350.0000.0000.0000.000
158A186THR 00.0490.01246.1020.0000.0000.0000.0000.0000.000
159A187GLY 0-0.036-0.00947.3440.0020.0020.0000.0000.0000.000
160A188LYS 10.8660.94749.1170.0320.0320.0000.0000.0000.000
161A189LEU 0-0.023-0.01448.935-0.001-0.0010.0000.0000.0000.000
162A190TYR 0-0.019-0.04347.8530.0010.0010.0000.0000.0000.000
163A191THR 0-0.044-0.04148.9940.0000.0000.0000.0000.0000.000
164A192PHE 0-0.023-0.00344.9340.0000.0000.0000.0000.0000.000
165A193ALA 00.0070.01450.3950.0010.0010.0000.0000.0000.000
166A194THR 0-0.049-0.04451.3670.0000.0000.0000.0000.0000.000
167A195ARG 10.8200.91047.9270.0280.0280.0000.0000.0000.000
168A196ASP -1-0.814-0.85451.172-0.017-0.0170.0000.0000.0000.000
169A197TYR 0-0.037-0.06446.794-0.001-0.0010.0000.0000.0000.000
170A198THR 0-0.031-0.06950.3230.0010.0010.0000.0000.0000.000
171A199ASP -1-0.894-0.93952.476-0.015-0.0150.0000.0000.0000.000
172A200ASN 0-0.0350.00045.2930.0000.0000.0000.0000.0000.000
173A201SER 00.0520.00946.8350.0010.0010.0000.0000.0000.000
174A202MET 0-0.020-0.00440.3070.0010.0010.0000.0000.0000.000
175A203PHE 00.0860.03443.2470.0000.0000.0000.0000.0000.000
176A204GLN 0-0.029-0.01245.1730.0020.0020.0000.0000.0000.000
177A205THR 0-0.104-0.05742.2270.0020.0020.0000.0000.0000.000
178A206ALA 00.0170.01241.2390.0010.0010.0000.0000.0000.000
179A207LEU 00.0430.01942.5700.0010.0010.0000.0000.0000.000
180A208LYS 10.8920.95945.3540.0110.0110.0000.0000.0000.000
181A209ARG 10.9250.94338.2140.0180.0180.0000.0000.0000.000
182A210GLY 0-0.0110.01041.4100.0010.0010.0000.0000.0000.000
183A211THR 0-0.090-0.05337.5470.0000.0000.0000.0000.0000.000
184A212LEU 0-0.0090.01239.621-0.001-0.0010.0000.0000.0000.000
185A213PHE 00.0110.00534.3670.0010.0010.0000.0000.0000.000
186A214GLY 00.0350.00238.2590.0000.0000.0000.0000.0000.000
187A215ARG 10.7630.87531.1220.0660.0660.0000.0000.0000.000
188A216ILE 00.0650.02538.3160.0020.0020.0000.0000.0000.000
189A217CYS 0-0.045-0.00137.964-0.004-0.0040.0000.0000.0000.000
190A218ILE 00.0410.03139.4440.0040.0040.0000.0000.0000.000
191A219TRP 0-0.009-0.01736.389-0.003-0.0030.0000.0000.0000.000
192A220PRO 0-0.0160.00338.6950.0030.0030.0000.0000.0000.000
193A221LYS 10.9530.96941.3510.0400.0400.0000.0000.0000.000
194A222GLY 0-0.011-0.00641.751-0.001-0.0010.0000.0000.0000.000
195A223SER 0-0.034-0.01536.670-0.006-0.0060.0000.0000.0000.000
196A224ASP -1-0.788-0.88432.780-0.093-0.0930.0000.0000.0000.000
197A225GLN 0-0.034-0.02731.587-0.001-0.0010.0000.0000.0000.000
198A226GLY 00.0510.04935.0160.0030.0030.0000.0000.0000.000
199A227ILE 0-0.026-0.01033.703-0.006-0.0060.0000.0000.0000.000
200A228TYR 00.023-0.01333.6760.0060.0060.0000.0000.0000.000
201A229SER 00.0010.00235.9570.0000.0000.0000.0000.0000.000
202A230LYS 11.0040.99233.1130.0460.0460.0000.0000.0000.000
203A231VAL 00.0050.02132.2340.0030.0030.0000.0000.0000.000
204A232ILE 0-0.0090.00034.9580.0020.0020.0000.0000.0000.000
205A233ARG 10.8190.87835.9760.0200.0200.0000.0000.0000.000
206A234LEU 0-0.043-0.02438.7700.0010.0010.0000.0000.0000.000
207A235LYS 00.0930.08540.703-0.004-0.0040.0000.0000.0000.000