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: 2J6KR

Calculation Name: 1FON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FON

Chain ID: A

ChEMBL ID:

UniProt ID: P05805

Base Structure: X-ray

Registration Date: 2023-09-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2766466.565851
FMO2-HF: Nuclear repulsion 2677405.851747
FMO2-HF: Total energy -89060.714104
FMO2-MP2: Total energy -89316.926009


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:9:SER)


Summations of interaction energy for fragment #1(A:9: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.
-38.161-35.9510.64-6.107-6.7430.03
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.002
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].
3A11SER0-0.071-0.0313.8031.3622.885-0.022-0.682-0.8190.002
4A12TRP00.0680.0356.1100.0940.0940.0000.0000.0000.000
5A13GLN0-0.065-0.0287.6090.3820.3820.0000.0000.0000.000
6A14VAL00.016-0.00711.516-0.086-0.0860.0000.0000.0000.000
7A15SER0-0.018-0.01415.1440.1000.1000.0000.0000.0000.000
8A16LEU0-0.0060.00918.182-0.048-0.0480.0000.0000.0000.000
9A17GLN00.031-0.02220.9180.0290.0290.0000.0000.0000.000
10A18TYR0-0.026-0.01724.429-0.011-0.0110.0000.0000.0000.000
11A19GLU-1-0.918-0.95128.152-0.072-0.0720.0000.0000.0000.000
12A20LYS10.8590.90931.045-0.007-0.0070.0000.0000.0000.000
13A21ASP-1-0.923-0.95933.307-0.003-0.0030.0000.0000.0000.000
14A22GLY0-0.0200.00534.944-0.001-0.0010.0000.0000.0000.000
15A23ALA00.0330.00630.293-0.006-0.0060.0000.0000.0000.000
16A24PHE00.0250.01326.3190.0080.0080.0000.0000.0000.000
17A25HIS0-0.055-0.01926.3040.0110.0110.0000.0000.0000.000
18A26HIS00.0040.02518.094-0.049-0.0490.0000.0000.0000.000
19A27THR0-0.071-0.04422.8490.0300.0300.0000.0000.0000.000
20A28CYS0-0.166-0.07420.5450.0470.0470.0000.0000.0000.000
21A29GLY00.0450.04616.365-0.034-0.0340.0000.0000.0000.000
22A30GLY00.0220.00215.359-0.012-0.0120.0000.0000.0000.000
23A31SER0-0.042-0.01613.330-0.015-0.0150.0000.0000.0000.000
24A32LEU00.0520.02812.9610.0240.0240.0000.0000.0000.000
25A33ILE0-0.012-0.00213.298-0.062-0.0620.0000.0000.0000.000
26A34ALA00.0060.00215.599-0.040-0.0400.0000.0000.0000.000
27A35PRO00.0210.00116.9780.0110.0110.0000.0000.0000.000
28A36ASP-1-0.853-0.93218.346-0.334-0.3340.0000.0000.0000.000
29A37TRP00.0560.05519.4760.0590.0590.0000.0000.0000.000
30A38VAL0-0.006-0.00517.097-0.035-0.0350.0000.0000.0000.000
31A39VAL00.0120.01816.9170.0320.0320.0000.0000.0000.000
32A40THR00.018-0.02717.8810.0320.0320.0000.0000.0000.000
33A41ALA0-0.012-0.00220.1610.0050.0050.0000.0000.0000.000
34A42GLY00.0640.03022.922-0.020-0.0200.0000.0000.0000.000
35A43HIS10.7170.81923.457-0.171-0.1710.0000.0000.0000.000
36A45ILE0-0.0030.00425.011-0.013-0.0130.0000.0000.0000.000
37A46SER00.0190.00328.2390.0090.0090.0000.0000.0000.000
38A47THR0-0.005-0.01331.251-0.003-0.0030.0000.0000.0000.000
39A48SER00.004-0.00632.822-0.008-0.0080.0000.0000.0000.000
40A49ARG10.8770.97030.944-0.018-0.0180.0000.0000.0000.000
41A50THR00.0670.03430.713-0.002-0.0020.0000.0000.0000.000
42A51TYR00.0180.00425.8030.0100.0100.0000.0000.0000.000
43A52GLN0-0.015-0.00324.083-0.024-0.0240.0000.0000.0000.000
44A53VAL0-0.008-0.01118.9690.0310.0310.0000.0000.0000.000
45A54VAL0-0.0120.00518.115-0.032-0.0320.0000.0000.0000.000
46A55LEU0-0.024-0.01714.7800.0380.0380.0000.0000.0000.000
47A56GLY00.0630.01613.6080.0300.0300.0000.0000.0000.000
48A57GLU-1-0.882-0.9388.574-2.387-2.3870.0000.0000.0000.000
49A58TYR0-0.034-0.0567.1880.4280.4280.0000.0000.0000.000
50A59ASP-1-0.818-0.9122.957-15.577-13.5650.088-1.151-0.949-0.011
51A60ARG10.8820.9181.826-22.340-23.83210.571-4.223-4.8550.039
52A61SER0-0.107-0.0603.8760.1970.3650.003-0.051-0.1200.000
53A62VAL00.000-0.0166.8370.2070.2070.0000.0000.0000.000
54A63LEU0-0.0120.0228.107-0.605-0.6050.0000.0000.0000.000
55A64GLU-1-0.906-0.9637.791-2.019-2.0190.0000.0000.0000.000
56A65GLY0-0.041-0.01010.9070.0080.0080.0000.0000.0000.000
57A66SER0-0.047-0.03514.3200.1050.1050.0000.0000.0000.000
58A67GLU-1-0.863-0.92916.146-0.369-0.3690.0000.0000.0000.000
59A68GLN0-0.054-0.04216.0990.1070.1070.0000.0000.0000.000
60A69VAL00.0180.01619.5740.0240.0240.0000.0000.0000.000
61A70ILE0-0.061-0.03320.397-0.004-0.0040.0000.0000.0000.000
62A71PRO00.0710.03523.8300.0230.0230.0000.0000.0000.000
63A72ILE0-0.0010.04023.519-0.018-0.0180.0000.0000.0000.000
64A73ASN0-0.0050.00727.6440.0170.0170.0000.0000.0000.000
65A74ALA00.0420.01830.3870.0030.0030.0000.0000.0000.000
66A75GLY0-0.041-0.03631.925-0.003-0.0030.0000.0000.0000.000
67A76ASP-1-0.855-0.90927.654-0.158-0.1580.0000.0000.0000.000
68A77LEU0-0.103-0.05226.478-0.003-0.0030.0000.0000.0000.000
69A78PHE00.0220.00226.6590.0100.0100.0000.0000.0000.000
70A79VAL00.016-0.00227.2080.0070.0070.0000.0000.0000.000
71A80HIS00.0280.03427.915-0.002-0.0020.0000.0000.0000.000
72A81PRO00.022-0.00329.6830.0060.0060.0000.0000.0000.000
73A82LEU0-0.017-0.02632.4600.0030.0030.0000.0000.0000.000
74A83TRP0-0.0390.01429.4010.0180.0180.0000.0000.0000.000
75A84ASN00.0690.02131.670-0.010-0.0100.0000.0000.0000.000
76A85SER0-0.009-0.00132.1050.0080.0080.0000.0000.0000.000
77A86ASN0-0.034-0.01833.0450.0120.0120.0000.0000.0000.000
78A87CYS0-0.100-0.05632.1260.0040.0040.0000.0000.0000.000
79A88VAL00.0900.04628.605-0.001-0.0010.0000.0000.0000.000
80A89ALA00.0010.00630.2220.0070.0070.0000.0000.0000.000
81A91GLY0-0.003-0.00528.795-0.004-0.0040.0000.0000.0000.000
82A92ASN00.013-0.01028.251-0.008-0.0080.0000.0000.0000.000
83A93ASP-1-0.711-0.79425.4850.1210.1210.0000.0000.0000.000
84A94ILE0-0.063-0.01621.9280.0210.0210.0000.0000.0000.000
85A95ALA00.0180.00123.343-0.008-0.0080.0000.0000.0000.000
86A96LEU00.0130.02621.8480.0020.0020.0000.0000.0000.000
87A97VAL0-0.036-0.01822.0810.0140.0140.0000.0000.0000.000
88A98LYS10.9700.99722.4330.1720.1720.0000.0000.0000.000
89A99LEU0-0.053-0.03019.1910.0160.0160.0000.0000.0000.000
90A100SER0-0.034-0.05823.799-0.008-0.0080.0000.0000.0000.000
91A101ARG10.9090.95323.3830.3540.3540.0000.0000.0000.000
92A102SER0-0.027-0.01721.0710.0020.0020.0000.0000.0000.000
93A103ALA0-0.0080.00017.3730.0010.0010.0000.0000.0000.000
94A104GLN0-0.050-0.01917.8340.0320.0320.0000.0000.0000.000
95A105LEU00.017-0.00413.261-0.023-0.0230.0000.0000.0000.000
96A106GLY0-0.0090.01312.724-0.210-0.2100.0000.0000.0000.000
97A107ASP-1-0.948-0.99012.069-1.409-1.4090.0000.0000.0000.000
98A108LYS10.9610.9927.2792.5932.5930.0000.0000.0000.000
99A109VAL0-0.044-0.0026.315-0.755-0.7550.0000.0000.0000.000
100A110GLN0-0.032-0.0096.9540.5740.5740.0000.0000.0000.000
101A111LEU0-0.021-0.0128.618-0.016-0.0160.0000.0000.0000.000
102A112ALA0-0.0050.00410.0620.0880.0880.0000.0000.0000.000
103A113ASN0-0.002-0.01611.053-0.005-0.0050.0000.0000.0000.000
104A114LEU00.0520.02914.1730.0900.0900.0000.0000.0000.000
105A115PRO0-0.048-0.00716.923-0.014-0.0140.0000.0000.0000.000
106A116PRO00.0300.00818.305-0.029-0.0290.0000.0000.0000.000
107A117ALA00.0740.02221.7250.0300.0300.0000.0000.0000.000
108A118GLY0-0.072-0.05124.6280.0050.0050.0000.0000.0000.000
109A119ASP-1-0.865-0.91819.8680.2360.2360.0000.0000.0000.000
110A120ILE0-0.051-0.00522.4340.0150.0150.0000.0000.0000.000
111A121LEU00.009-0.00117.0070.0080.0080.0000.0000.0000.000
112A122PRO00.0260.01719.712-0.017-0.0170.0000.0000.0000.000
113A123ASN00.037-0.00321.3430.0490.0490.0000.0000.0000.000
114A124GLU-1-0.995-0.99520.8310.4940.4940.0000.0000.0000.000
115A125ALA0-0.0280.00217.2470.0720.0720.0000.0000.0000.000
116A126PRO0-0.0080.00112.9180.0320.0320.0000.0000.0000.000
117A127CYS00.0180.01011.0810.2210.2210.0000.0000.0000.000
118A128TYR0-0.003-0.0228.7300.2680.2680.0000.0000.0000.000
119A129ILE0-0.0200.00810.774-0.244-0.2440.0000.0000.0000.000
120A130SER00.009-0.0138.1450.4310.4310.0000.0000.0000.000
121A131GLY00.0160.01310.283-0.254-0.2540.0000.0000.0000.000
122A132TRP00.0390.00912.8590.1840.1840.0000.0000.0000.000
123A133GLY0-0.0060.00115.530-0.042-0.0420.0000.0000.0000.000
124A134ARG10.8640.92417.541-0.429-0.4290.0000.0000.0000.000
125A135LEU0-0.053-0.02519.541-0.042-0.0420.0000.0000.0000.000
126A136TYR0-0.037-0.02418.708-0.022-0.0220.0000.0000.0000.000
127A137THR00.016-0.00820.585-0.003-0.0030.0000.0000.0000.000
128A138GLY00.0810.05022.873-0.010-0.0100.0000.0000.0000.000
129A139GLY0-0.0400.00223.6870.0140.0140.0000.0000.0000.000
130A140PRO00.0070.01120.960-0.007-0.0070.0000.0000.0000.000
131A141LEU00.0330.02614.3450.0470.0470.0000.0000.0000.000
132A142PRO0-0.024-0.00515.313-0.005-0.0050.0000.0000.0000.000
133A143ASP-1-0.837-0.89814.109-0.332-0.3320.0000.0000.0000.000
134A144LYS10.8580.93511.188-0.542-0.5420.0000.0000.0000.000
135A145LEU0-0.081-0.0057.3300.0470.0470.0000.0000.0000.000
136A146GLN0-0.011-0.01710.1620.4490.4490.0000.0000.0000.000
137A147GLN00.024-0.0055.6251.8091.8090.0000.0000.0000.000
138A148ALA0-0.029-0.0059.5950.0180.0180.0000.0000.0000.000
139A149LEU0-0.0090.00811.636-0.034-0.0340.0000.0000.0000.000
140A150LEU0-0.044-0.03612.841-0.180-0.1800.0000.0000.0000.000
141A151PRO0-0.0070.00015.811-0.023-0.0230.0000.0000.0000.000
142A152THR0-0.024-0.01617.584-0.082-0.0820.0000.0000.0000.000
143A153VAL00.0100.01919.867-0.001-0.0010.0000.0000.0000.000
144A154ASP-1-0.736-0.86923.5940.2990.2990.0000.0000.0000.000
145A155TYR00.0410.00025.374-0.011-0.0110.0000.0000.0000.000
146A156GLU-1-0.909-0.94828.2510.2250.2250.0000.0000.0000.000
147A157HIS10.8290.90427.482-0.319-0.3190.0000.0000.0000.000
148A158CYS0-0.0400.00222.186-0.012-0.0120.0000.0000.0000.000
149A159SER0-0.016-0.02528.456-0.011-0.0110.0000.0000.0000.000
150A160GLN00.0130.01231.011-0.003-0.0030.0000.0000.0000.000
151A161TRP00.011-0.01433.6150.0050.0050.0000.0000.0000.000
152A162ASP-1-0.836-0.89934.5100.2460.2460.0000.0000.0000.000
153A163TRP0-0.019-0.00925.6460.0240.0240.0000.0000.0000.000
154A164TRP0-0.013-0.04326.306-0.024-0.0240.0000.0000.0000.000
155A165GLY0-0.0240.00131.258-0.017-0.0170.0000.0000.0000.000
156A166ILE0-0.008-0.01833.5300.0030.0030.0000.0000.0000.000
157A167THR0-0.035-0.00331.219-0.012-0.0120.0000.0000.0000.000
158A168VAL00.0080.00128.046-0.005-0.0050.0000.0000.0000.000
159A169LYS10.9200.94529.668-0.127-0.1270.0000.0000.0000.000
160A170LYS10.9970.98228.607-0.145-0.1450.0000.0000.0000.000
161A171THR0-0.051-0.00426.9240.0100.0100.0000.0000.0000.000
162A172MET0-0.0080.03524.546-0.004-0.0040.0000.0000.0000.000
163A173VAL00.0400.02819.518-0.002-0.0020.0000.0000.0000.000
164A175ALA00.0600.03617.9190.0200.0200.0000.0000.0000.000
165A176GLY00.004-0.00720.015-0.001-0.0010.0000.0000.0000.000
166A177GLY00.007-0.00520.701-0.039-0.0390.0000.0000.0000.000
167A178ASP-1-0.881-0.94222.7150.4940.4940.0000.0000.0000.000
168A179THR0-0.023-0.01122.1510.0320.0320.0000.0000.0000.000
169A180ARG10.9580.99716.668-0.864-0.8640.0000.0000.0000.000
170A181SER0-0.0070.01019.017-0.059-0.0590.0000.0000.0000.000
171A182GLY00.0510.01417.3160.0980.0980.0000.0000.0000.000
172A183CYS0-0.098-0.08218.229-0.039-0.0390.0000.0000.0000.000
173A184ASN00.0210.00513.5820.1190.1190.0000.0000.0000.000
174A185GLY00.0500.04614.4820.0340.0340.0000.0000.0000.000
175A186ASP-1-0.787-0.90615.4700.3080.3080.0000.0000.0000.000
176A187SER00.0390.02517.7490.0180.0180.0000.0000.0000.000
177A188GLY00.0560.01719.720-0.026-0.0260.0000.0000.0000.000
178A189GLY0-0.0100.00815.766-0.034-0.0340.0000.0000.0000.000
179A190PRO00.0220.02411.6090.0210.0210.0000.0000.0000.000
180A191LEU0-0.057-0.01613.0680.1520.1520.0000.0000.0000.000
181A192ASN00.006-0.0028.844-0.342-0.3420.0000.0000.0000.000
182A194PRO00.0110.0229.656-0.120-0.1200.0000.0000.0000.000
183A195ALA00.0260.01411.253-0.019-0.0190.0000.0000.0000.000
184A196ALA0-0.012-0.01813.5980.0510.0510.0000.0000.0000.000
185A197ASP-1-0.924-0.96614.079-0.025-0.0250.0000.0000.0000.000
186A198GLY00.0180.01211.309-0.056-0.0560.0000.0000.0000.000
187A199SER0-0.050-0.0099.4910.0480.0480.0000.0000.0000.000
188A200TRP00.0150.0016.8140.3940.3940.0000.0000.0000.000
189A201GLN00.0520.02410.020-0.125-0.1250.0000.0000.0000.000
190A202VAL0-0.007-0.00112.7080.1420.1420.0000.0000.0000.000
191A203HIS00.015-0.01314.019-0.005-0.0050.0000.0000.0000.000
192A204GLY0-0.038-0.02815.965-0.035-0.0350.0000.0000.0000.000
193A205VAL00.0250.03016.3770.0190.0190.0000.0000.0000.000
194A206THR0-0.085-0.05717.3360.0160.0160.0000.0000.0000.000
195A207SER0-0.055-0.05419.837-0.042-0.0420.0000.0000.0000.000
196A208PHE0-0.009-0.02323.605-0.014-0.0140.0000.0000.0000.000
197A209VAL00.0180.00823.2730.0380.0380.0000.0000.0000.000
198A210SER00.0430.01725.877-0.037-0.0370.0000.0000.0000.000
199A211ALA00.0280.01629.0270.0030.0030.0000.0000.0000.000
200A212PHE0-0.057-0.03530.652-0.006-0.0060.0000.0000.0000.000
201A213GLY00.0300.02927.2450.0070.0070.0000.0000.0000.000
202A215ASN00.009-0.02222.6500.0230.0230.0000.0000.0000.000
203A216THR00.0110.03023.952-0.033-0.0330.0000.0000.0000.000
204A217ILE00.0390.00526.2180.0120.0120.0000.0000.0000.000
205A218LYS10.7850.89227.511-0.310-0.3100.0000.0000.0000.000
206A219LYS10.8530.93827.406-0.289-0.2890.0000.0000.0000.000
207A220PRO0-0.0280.00423.0830.0140.0140.0000.0000.0000.000
208A221THR00.0050.01219.909-0.039-0.0390.0000.0000.0000.000
209A222VAL00.0180.01322.0800.0170.0170.0000.0000.0000.000
210A223PHE0-0.004-0.00916.654-0.003-0.0030.0000.0000.0000.000
211A224THR0-0.033-0.03421.323-0.005-0.0050.0000.0000.0000.000
212A225ARG10.8860.93020.936-0.159-0.1590.0000.0000.0000.000
213A226VAL00.0450.02118.065-0.030-0.0300.0000.0000.0000.000
214A227SER00.005-0.00521.052-0.029-0.0290.0000.0000.0000.000
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