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: KG3G3

Calculation Name: 5N1I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N1I

Chain ID: A

ChEMBL ID:

UniProt ID: O53623

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 OptHSide
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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1858525.21119
FMO2-HF: Nuclear repulsion 1786783.132255
FMO2-HF: Total energy -71742.078936
FMO2-MP2: Total energy -71951.338979


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:12:SER)


Summations of interaction energy for fragment #1(A:12: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.
-6.988-1.3582.128-3.285-4.47-0.014
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.015
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].
3A14ALA00.0270.0152.753-3.484-0.9310.232-1.212-1.5720.002
4A15THR00.003-0.0112.563-3.023-0.9321.870-1.739-2.221-0.014
5A16ARG10.8800.9494.1981.8912.1190.000-0.063-0.1650.000
6A17GLU-1-0.875-0.9366.155-0.128-0.1280.0000.0000.0000.000
7A18ALA0-0.0020.0087.3480.2660.2660.0000.0000.0000.000
8A19LEU0-0.033-0.0116.9170.2320.2320.0000.0000.0000.000
9A20ILE00.0200.0129.9980.1460.1460.0000.0000.0000.000
10A21THR0-0.010-0.01811.8170.1230.1230.0000.0000.0000.000
11A22GLY00.0230.01212.8420.0620.0620.0000.0000.0000.000
12A23ALA0-0.020-0.02414.0380.0540.0540.0000.0000.0000.000
13A24ARG10.7700.87015.8470.2190.2190.0000.0000.0000.000
14A25LYS10.8820.93117.4900.2220.2220.0000.0000.0000.000
15A26LEU0-0.020-0.01717.5270.0250.0250.0000.0000.0000.000
16A27TRP0-0.032-0.02916.6790.0120.0120.0000.0000.0000.000
17A28GLY00.0480.02921.2760.0150.0150.0000.0000.0000.000
18A29LEU0-0.091-0.03623.0750.0130.0130.0000.0000.0000.000
19A30ARG10.7600.83522.9080.0930.0930.0000.0000.0000.000
20A31GLY00.0690.05024.8690.0080.0080.0000.0000.0000.000
21A32TYR0-0.017-0.03119.808-0.001-0.0010.0000.0000.0000.000
22A33ALA0-0.042-0.02022.8690.0000.0000.0000.0000.0000.000
23A34GLU-1-0.893-0.93425.352-0.047-0.0470.0000.0000.0000.000
24A35VAL0-0.0130.01619.5900.0010.0010.0000.0000.0000.000
25A36GLY0-0.002-0.00219.981-0.002-0.0020.0000.0000.0000.000
26A37THR00.036-0.01214.750-0.009-0.0090.0000.0000.0000.000
27A38PRO0-0.027-0.02414.903-0.014-0.0140.0000.0000.0000.000
28A39GLU-1-0.785-0.85516.034-0.098-0.0980.0000.0000.0000.000
29A40ILE00.0330.02112.811-0.012-0.0120.0000.0000.0000.000
30A41ALA0-0.031-0.00911.502-0.050-0.0500.0000.0000.0000.000
31A42THR0-0.038-0.03012.095-0.027-0.0270.0000.0000.0000.000
32A43GLU-1-0.875-0.91414.679-0.227-0.2270.0000.0000.0000.000
33A44ALA00.0310.0259.888-0.011-0.0110.0000.0000.0000.000
34A45GLY0-0.0340.00410.077-0.088-0.0880.0000.0000.0000.000
35A46VAL0-0.052-0.0276.595-0.037-0.0370.0000.0000.0000.000
36A47THR00.0320.0078.8070.0870.0870.0000.0000.0000.000
37A48ARG11.0260.9879.503-0.057-0.0570.0000.0000.0000.000
38A49GLY00.0090.01310.373-0.033-0.0330.0000.0000.0000.000
39A50ALA00.0030.0075.1220.2620.2620.0000.0000.0000.000
40A51MET00.0160.0136.321-0.092-0.0920.0000.0000.0000.000
41A52TYR0-0.034-0.0248.529-0.085-0.0850.0000.0000.0000.000
42A53HIS0-0.038-0.0074.135-0.935-0.7050.000-0.037-0.1930.000
43A54GLN0-0.0310.0063.630-1.442-0.9140.026-0.234-0.319-0.002
44A55PHE0-0.0030.0047.075-0.108-0.1080.0000.0000.0000.000
45A56ALA00.0220.01310.8710.0590.0590.0000.0000.0000.000
46A57ASP-1-0.865-0.94313.641-0.028-0.0280.0000.0000.0000.000
47A58LYS10.8600.91115.3690.0470.0470.0000.0000.0000.000
48A59ALA00.0640.03117.205-0.026-0.0260.0000.0000.0000.000
49A60ALA0-0.070-0.03714.239-0.012-0.0120.0000.0000.0000.000
50A61LEU00.0130.01111.397-0.024-0.0240.0000.0000.0000.000
51A62PHE0-0.003-0.00714.261-0.027-0.0270.0000.0000.0000.000
52A63ARG10.9460.98016.6390.1110.1110.0000.0000.0000.000
53A64ASP-1-0.789-0.90211.765-0.440-0.4400.0000.0000.0000.000
54A65VAL0-0.047-0.01915.293-0.005-0.0050.0000.0000.0000.000
55A66VAL0-0.017-0.00816.9800.0150.0150.0000.0000.0000.000
56A67GLU-1-0.821-0.89117.084-0.167-0.1670.0000.0000.0000.000
57A68VAL0-0.024-0.00914.8790.0140.0140.0000.0000.0000.000
58A69VAL0-0.001-0.00418.2650.0180.0180.0000.0000.0000.000
59A70GLU-1-0.881-0.94921.413-0.080-0.0800.0000.0000.0000.000
60A71GLN0-0.040-0.01417.5700.0180.0180.0000.0000.0000.000
61A72ASP-1-0.798-0.88421.075-0.141-0.1410.0000.0000.0000.000
62A73VAL0-0.027-0.01123.5190.0140.0140.0000.0000.0000.000
63A74MET00.005-0.00126.1220.0120.0120.0000.0000.0000.000
64A75ALA0-0.0060.00325.0340.0080.0080.0000.0000.0000.000
65A76ARG10.8560.90627.0170.0760.0760.0000.0000.0000.000
66A77MET00.0070.00728.8170.0060.0060.0000.0000.0000.000
67A78ALA0-0.0010.00130.1400.0050.0050.0000.0000.0000.000
68A79THR0-0.056-0.03229.3750.0040.0040.0000.0000.0000.000
69A80LEU0-0.023-0.01432.0310.0040.0040.0000.0000.0000.000
70A81VAL0-0.0060.00334.8290.0040.0040.0000.0000.0000.000
71A82ALA0-0.0250.00334.6570.0030.0030.0000.0000.0000.000
72A83ALA0-0.017-0.00535.6690.0020.0020.0000.0000.0000.000
73A84SER0-0.074-0.05037.5740.0020.0020.0000.0000.0000.000
74A85GLY0-0.0070.00540.6410.0020.0020.0000.0000.0000.000
75A86ALA0-0.037-0.01141.7620.0020.0020.0000.0000.0000.000
76A87ALA00.0210.00943.2370.0000.0000.0000.0000.0000.000
77A88THR0-0.055-0.04146.0590.0010.0010.0000.0000.0000.000
78A89PRO00.0660.01543.753-0.001-0.0010.0000.0000.0000.000
79A90ALA00.0100.01044.115-0.001-0.0010.0000.0000.0000.000
80A91ASP-1-0.847-0.91345.438-0.026-0.0260.0000.0000.0000.000
81A92ALA00.0210.02040.359-0.002-0.0020.0000.0000.0000.000
82A93ILE0-0.013-0.00340.613-0.002-0.0020.0000.0000.0000.000
83A94ARG10.7550.85341.6300.0230.0230.0000.0000.0000.000
84A95ALA00.0150.01739.853-0.001-0.0010.0000.0000.0000.000
85A96ALA00.0240.00137.221-0.002-0.0020.0000.0000.0000.000
86A97VAL0-0.012-0.00337.284-0.003-0.0030.0000.0000.0000.000
87A98ASP-1-0.837-0.90638.831-0.037-0.0370.0000.0000.0000.000
88A99ALA00.0180.00134.796-0.002-0.0020.0000.0000.0000.000
89A100TRP00.0480.01830.613-0.005-0.0050.0000.0000.0000.000
90A101LEU0-0.0040.01034.471-0.002-0.0020.0000.0000.0000.000
91A102GLU-1-0.914-0.93934.064-0.055-0.0550.0000.0000.0000.000
92A103VAL0-0.001-0.00829.315-0.003-0.0030.0000.0000.0000.000
93A104SER0-0.010-0.01630.550-0.004-0.0040.0000.0000.0000.000
94A105GLY0-0.067-0.05732.2780.0010.0010.0000.0000.0000.000
95A106ASP-1-0.893-0.93727.962-0.087-0.0870.0000.0000.0000.000
96A107PRO0-0.027-0.02529.204-0.002-0.0020.0000.0000.0000.000
97A108GLU-1-0.805-0.88222.010-0.150-0.1500.0000.0000.0000.000
98A109VAL00.0190.00625.609-0.005-0.0050.0000.0000.0000.000
99A110ARG10.8570.92927.1000.0600.0600.0000.0000.0000.000
100A111GLN0-0.056-0.03725.8130.0080.0080.0000.0000.0000.000
101A112LEU00.0250.00221.0550.0010.0010.0000.0000.0000.000
102A113ILE00.0180.00623.5800.0000.0000.0000.0000.0000.000
103A114LEU0-0.030-0.01626.7080.0060.0060.0000.0000.0000.000
104A115LEU0-0.045-0.02029.2190.0060.0060.0000.0000.0000.000
105A116ASP-1-0.786-0.89024.739-0.081-0.0810.0000.0000.0000.000
106A117ALA0-0.0120.00124.7270.0020.0020.0000.0000.0000.000
107A118PRO0-0.011-0.00125.7960.0030.0030.0000.0000.0000.000
108A119VAL0-0.039-0.01528.2120.0050.0050.0000.0000.0000.000
109A120VAL0-0.062-0.02622.0140.0050.0050.0000.0000.0000.000
110A121LEU0-0.037-0.02121.5800.0010.0010.0000.0000.0000.000
111A122GLY00.0120.02424.9020.0060.0060.0000.0000.0000.000
112A123TRP00.040-0.00228.444-0.004-0.0040.0000.0000.0000.000
113A124ALA0-0.016-0.01529.462-0.002-0.0020.0000.0000.0000.000
114A125GLY00.0480.02325.809-0.001-0.0010.0000.0000.0000.000
115A126PHE00.0170.00826.051-0.005-0.0050.0000.0000.0000.000
116A127ARG10.9170.96227.5470.0360.0360.0000.0000.0000.000
117A128ASP-1-0.960-0.97625.283-0.066-0.0660.0000.0000.0000.000
118A129VAL00.0060.01022.921-0.003-0.0030.0000.0000.0000.000
119A130ALA00.0720.03425.599-0.001-0.0010.0000.0000.0000.000
120A131GLN0-0.031-0.01028.6710.0050.0050.0000.0000.0000.000
121A132ARG10.8070.89720.3170.1200.1200.0000.0000.0000.000
122A133TYR0-0.031-0.01420.5360.0000.0000.0000.0000.0000.000
123A134SER00.0310.00427.4160.0050.0050.0000.0000.0000.000
124A135LEU0-0.045-0.01531.1870.0050.0050.0000.0000.0000.000
125A136GLY00.0410.01931.7200.0040.0040.0000.0000.0000.000
126A137MET00.0730.03532.2860.0030.0030.0000.0000.0000.000
127A138THR0-0.023-0.02233.9040.0040.0040.0000.0000.0000.000
128A139GLU-1-0.881-0.97636.222-0.032-0.0320.0000.0000.0000.000
129A140GLN0-0.067-0.02535.2640.0000.0000.0000.0000.0000.000
130A141LEU00.0250.01037.2880.0030.0030.0000.0000.0000.000
131A142ILE00.0070.01140.0670.0020.0020.0000.0000.0000.000
132A143THR0-0.061-0.04440.6590.0030.0030.0000.0000.0000.000
133A144GLU-1-0.913-0.95939.722-0.029-0.0290.0000.0000.0000.000
134A145ALA00.0330.01743.7550.0010.0010.0000.0000.0000.000
135A146ILE0-0.054-0.02245.5370.0020.0020.0000.0000.0000.000
136A147ARG10.8890.95144.5830.0220.0220.0000.0000.0000.000
137A148ALA0-0.015-0.00547.8500.0010.0010.0000.0000.0000.000
138A149GLY00.0100.01649.6740.0010.0010.0000.0000.0000.000
139A150GLN00.006-0.00448.3850.0000.0000.0000.0000.0000.000
140A151LEU00.0280.01446.0490.0000.0000.0000.0000.0000.000
141A152ALA00.0260.02250.0590.0000.0000.0000.0000.0000.000
142A153ARG10.9930.98849.8370.0150.0150.0000.0000.0000.000
143A154GLN0-0.018-0.00947.1580.0010.0010.0000.0000.0000.000
144A155PRO0-0.018-0.01345.5660.0000.0000.0000.0000.0000.000
145A156VAL00.0720.02340.3910.0000.0000.0000.0000.0000.000
146A157ARG10.9801.00835.1840.0310.0310.0000.0000.0000.000
147A158PRO0-0.021-0.02840.483-0.001-0.0010.0000.0000.0000.000
148A159LEU00.0260.03442.9090.0000.0000.0000.0000.0000.000
149A160ALA00.0410.01238.005-0.001-0.0010.0000.0000.0000.000
150A161GLN0-0.020-0.01235.882-0.003-0.0030.0000.0000.0000.000
151A162VAL0-0.012-0.00139.091-0.001-0.0010.0000.0000.0000.000
152A163LEU0-0.013-0.00840.5840.0000.0000.0000.0000.0000.000
153A164ILE00.0170.00934.4970.0000.0000.0000.0000.0000.000
154A165GLY00.0260.01737.314-0.002-0.0020.0000.0000.0000.000
155A166ALA0-0.011-0.00238.9770.0000.0000.0000.0000.0000.000
156A167LEU0-0.018-0.02037.5200.0000.0000.0000.0000.0000.000
157A168ASP-1-0.889-0.94134.143-0.054-0.0540.0000.0000.0000.000
158A169GLU-1-0.940-0.96636.314-0.037-0.0370.0000.0000.0000.000
159A170ALA0-0.045-0.02439.1330.0000.0000.0000.0000.0000.000
160A171ALA0-0.009-0.00734.6240.0000.0000.0000.0000.0000.000
161A172MET00.0280.01734.166-0.003-0.0030.0000.0000.0000.000
162A173PHE00.0010.01436.5980.0010.0010.0000.0000.0000.000
163A174ILE0-0.060-0.03937.9210.0010.0010.0000.0000.0000.000
164A175ALA0-0.039-0.01534.1740.0000.0000.0000.0000.0000.000
165A176THR0-0.023-0.01936.141-0.001-0.0010.0000.0000.0000.000
166A177ALA00.0060.01938.2820.0020.0020.0000.0000.0000.000
167A178ASP-1-0.895-0.94440.940-0.030-0.0300.0000.0000.0000.000
168A179ASP-1-0.885-0.95443.010-0.032-0.0320.0000.0000.0000.000
169A180PRO00.0350.00938.9440.0000.0000.0000.0000.0000.000
170A181LYS10.9260.95937.9460.0440.0440.0000.0000.0000.000
171A182ARG10.8290.87942.6790.0260.0260.0000.0000.0000.000
172A183ALA00.0560.04542.4080.0010.0010.0000.0000.0000.000
173A184ARG10.9180.98836.1200.0480.0480.0000.0000.0000.000
174A185ARG10.9020.96242.1270.0300.0300.0000.0000.0000.000
175A186GLU-1-0.832-0.90045.369-0.025-0.0250.0000.0000.0000.000
176A187THR00.0390.00542.3000.0010.0010.0000.0000.0000.000
177A188ARG10.8830.94039.6600.0380.0380.0000.0000.0000.000
178A189GLN0-0.0020.01444.6010.0020.0020.0000.0000.0000.000
179A190VAL0-0.001-0.00147.1510.0010.0010.0000.0000.0000.000
180A191LEU00.0350.01741.7000.0010.0010.0000.0000.0000.000
181A192ARG10.8830.94644.7580.0300.0300.0000.0000.0000.000
182A193ARG10.8750.91347.6100.0220.0220.0000.0000.0000.000
183A194LEU00.0030.01345.9580.0010.0010.0000.0000.0000.000
184A195ILE00.0150.00743.9530.0010.0010.0000.0000.0000.000
185A196ASP-1-0.813-0.91947.913-0.024-0.0240.0000.0000.0000.000
186A197GLY0-0.053-0.00651.0760.0010.0010.0000.0000.0000.000
187A198MET0-0.072-0.03448.5320.0000.0000.0000.0000.0000.000
188A199LEU0-0.041-0.00946.4570.0000.0000.0000.0000.0000.000
189A200ASN0-0.051-0.01650.8910.0010.0010.0000.0000.0000.000
190A201GLY00.0020.00550.812-0.001-0.0010.0000.0000.0000.000