Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 53VVZ

Calculation Name: 1N81-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N81

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IEU2

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2252863.349703
FMO2-HF: Nuclear repulsion 2174580.609459
FMO2-HF: Total energy -78282.740244
FMO2-MP2: Total energy -78513.309846


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:21:TYR)


Summations of interaction energy for fragment #1(A:21:TYR)
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.
-8.612-2.592.788-2.82-5.990.013
Interaction energy analysis for fragmet #1(A:21:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.012
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].
3A23TYR00.0270.0232.464-5.5810.0502.752-2.738-5.6460.012
4A24GLU-1-0.879-0.9304.126-0.772-0.3810.036-0.082-0.3440.001
5A25HIS10.7600.8606.3600.2390.2390.0000.0000.0000.000
6A26GLU-1-0.823-0.9157.597-2.029-2.0290.0000.0000.0000.000
7A27THR0-0.0160.0028.7730.2830.2830.0000.0000.0000.000
8A28HIS0-0.080-0.05210.353-0.013-0.0130.0000.0000.0000.000
9A29ALA00.0440.03613.419-0.041-0.0410.0000.0000.0000.000
10A30PRO0-0.040-0.04714.8270.0140.0140.0000.0000.0000.000
11A31LEU00.0440.04318.7240.0340.0340.0000.0000.0000.000
12A32SER00.0230.02120.155-0.013-0.0130.0000.0000.0000.000
13A33PRO00.012-0.01423.465-0.006-0.0060.0000.0000.0000.000
14A34ARG10.7700.89726.266-0.032-0.0320.0000.0000.0000.000
15A35ILE00.0330.00923.718-0.001-0.0010.0000.0000.0000.000
16A36ARG10.9790.99924.3010.1120.1120.0000.0000.0000.000
17A37LYS10.8610.93526.4550.0420.0420.0000.0000.0000.000
18A38VAL0-0.005-0.01330.0780.0000.0000.0000.0000.0000.000
19A39GLY00.0460.03228.4670.0030.0030.0000.0000.0000.000
20A40ASP-1-0.849-0.92828.799-0.074-0.0740.0000.0000.0000.000
21A41ILE0-0.091-0.05131.0040.0020.0020.0000.0000.0000.000
22A42GLU-1-0.762-0.84832.5560.0070.0070.0000.0000.0000.000
23A43PHE00.0510.01629.1920.0020.0020.0000.0000.0000.000
24A44HIS00.0540.04431.2120.0020.0020.0000.0000.0000.000
25A45ALA0-0.0070.00235.5190.0010.0010.0000.0000.0000.000
26A46CYS0-0.055-0.02135.9170.0030.0030.0000.0000.0000.000
27A47SER0-0.030-0.03035.9160.0010.0010.0000.0000.0000.000
28A48ASP-1-0.804-0.88837.940-0.036-0.0360.0000.0000.0000.000
29A49TYR0-0.060-0.06541.0130.0010.0010.0000.0000.0000.000
30A50ILE00.0330.01238.1220.0020.0020.0000.0000.0000.000
31A51TYR0-0.018-0.01141.9500.0010.0010.0000.0000.0000.000
32A52LEU0-0.054-0.01643.6310.0010.0010.0000.0000.0000.000
33A53LEU00.0090.00043.7410.0010.0010.0000.0000.0000.000
34A54MET0-0.0020.01444.7130.0010.0010.0000.0000.0000.000
35A55THR0-0.072-0.03846.7630.0010.0010.0000.0000.0000.000
36A56LEU0-0.024-0.01449.5600.0010.0010.0000.0000.0000.000
37A57SER0-0.024-0.01548.9260.0020.0020.0000.0000.0000.000
38A58LYS10.7980.88950.8860.0230.0230.0000.0000.0000.000
39A59ASP-1-0.819-0.88054.136-0.012-0.0120.0000.0000.0000.000
40A60PRO00.0700.01854.8600.0010.0010.0000.0000.0000.000
41A61GLU-1-0.849-0.91055.952-0.003-0.0030.0000.0000.0000.000
42A62LYS10.7770.86254.6710.0120.0120.0000.0000.0000.000
43A63PHE00.0170.00647.0510.0010.0010.0000.0000.0000.000
44A64ASN0-0.067-0.04450.3400.0010.0010.0000.0000.0000.000
45A65TYR0-0.026-0.00951.0360.0020.0020.0000.0000.0000.000
46A66ALA00.0190.01248.7260.0010.0010.0000.0000.0000.000
47A67LEU00.0400.03445.5190.0000.0000.0000.0000.0000.000
48A68LYS10.8730.91343.680-0.009-0.0090.0000.0000.0000.000
49A69ASP-1-0.739-0.81047.998-0.001-0.0010.0000.0000.0000.000
50A70ARG10.8990.91843.262-0.017-0.0170.0000.0000.0000.000
51A71VAL0-0.050-0.01646.6090.0000.0000.0000.0000.0000.000
52A72SER0-0.028-0.06347.864-0.002-0.0020.0000.0000.0000.000
53A73ILE00.0340.03342.060-0.002-0.0020.0000.0000.0000.000
54A74ARG10.8770.92543.136-0.011-0.0110.0000.0000.0000.000
55A75ARG10.8780.94043.9060.0080.0080.0000.0000.0000.000
56A76TYR00.0270.01642.122-0.002-0.0020.0000.0000.0000.000
57A77VAL00.0190.02138.432-0.004-0.0040.0000.0000.0000.000
58A78ARG10.8880.94239.994-0.002-0.0020.0000.0000.0000.000
59A79LYS10.8660.93041.9180.0330.0330.0000.0000.0000.000
60A80ASN0-0.006-0.02437.075-0.008-0.0080.0000.0000.0000.000
61A81GLN00.0230.00537.478-0.001-0.0010.0000.0000.0000.000
62A82ASN0-0.047-0.02138.487-0.004-0.0040.0000.0000.0000.000
63A83ARG10.9310.98935.5910.0520.0520.0000.0000.0000.000
64A84TYR0-0.031-0.04033.260-0.007-0.0070.0000.0000.0000.000
65A85ASN0-0.054-0.02534.6970.0020.0020.0000.0000.0000.000
66A86TYR00.015-0.00232.3040.0000.0000.0000.0000.0000.000
67A87PHE00.0660.02536.2430.0020.0020.0000.0000.0000.000
68A88LEU0-0.0220.01134.9340.0030.0030.0000.0000.0000.000
69A89ILE0-0.019-0.00835.1260.0030.0030.0000.0000.0000.000
70A90GLU-1-0.818-0.89236.0180.0320.0320.0000.0000.0000.000
71A91GLU-1-0.916-0.95339.3930.0180.0180.0000.0000.0000.000
72A92ARG10.8870.92035.207-0.048-0.0480.0000.0000.0000.000
73A93VAL0-0.0020.00534.5460.0010.0010.0000.0000.0000.000
74A94GLN00.0270.00237.529-0.003-0.0030.0000.0000.0000.000
75A95ASP-1-0.849-0.91739.7080.0170.0170.0000.0000.0000.000
76A96ASN0-0.033-0.04335.874-0.003-0.0030.0000.0000.0000.000
77A97ILE0-0.0180.00935.035-0.001-0.0010.0000.0000.0000.000
78A98VAL0-0.031-0.01937.278-0.003-0.0030.0000.0000.0000.000
79A99ASN0-0.038-0.00839.032-0.004-0.0040.0000.0000.0000.000
80A100ARG10.8160.88033.112-0.023-0.0230.0000.0000.0000.000
81A101ILE0-0.012-0.01137.102-0.003-0.0030.0000.0000.0000.000
82A102SER00.0010.00238.664-0.001-0.0010.0000.0000.0000.000
83A103ASP-1-0.870-0.93938.9920.0160.0160.0000.0000.0000.000
84A104ARG10.7480.84132.0460.0020.0020.0000.0000.0000.000
85A105LEU0-0.049-0.00938.299-0.003-0.0030.0000.0000.0000.000
86A106ILE00.0020.00541.664-0.001-0.0010.0000.0000.0000.000
87A107SER0-0.026-0.02837.628-0.002-0.0020.0000.0000.0000.000
88A108TYR00.008-0.01232.8970.0010.0010.0000.0000.0000.000
89A109CYS0-0.043-0.01139.344-0.005-0.0050.0000.0000.0000.000
90A110THR0-0.0040.01242.9550.0000.0000.0000.0000.0000.000
91A111ASP-1-0.932-0.94943.527-0.002-0.0020.0000.0000.0000.000
92A112LYS10.9030.95140.4980.0150.0150.0000.0000.0000.000
93A113GLU-1-0.802-0.89346.094-0.022-0.0220.0000.0000.0000.000
94A114VAL0-0.0010.00443.652-0.002-0.0020.0000.0000.0000.000
95A115THR00.007-0.01844.7630.0000.0000.0000.0000.0000.000
96A116GLU-1-0.844-0.94243.568-0.044-0.0440.0000.0000.0000.000
97A117ASP-1-0.841-0.91441.197-0.045-0.0450.0000.0000.0000.000
98A118TYR0-0.097-0.05639.812-0.002-0.0020.0000.0000.0000.000
99A119ILE00.016-0.00139.2000.0000.0000.0000.0000.0000.000
100A120LYS10.8740.94036.4760.0580.0580.0000.0000.0000.000
101A121LYS10.9500.98434.8970.0360.0360.0000.0000.0000.000
102A122ILE0-0.029-0.01435.0500.0030.0030.0000.0000.0000.000
103A123ASP-1-0.780-0.86533.718-0.050-0.0500.0000.0000.0000.000
104A124ASP-1-0.840-0.91230.570-0.078-0.0780.0000.0000.0000.000
105A125TYR0-0.046-0.02829.662-0.002-0.0020.0000.0000.0000.000
106A126LEU0-0.034-0.02530.2500.0050.0050.0000.0000.0000.000
107A127TRP00.0060.00922.5530.0030.0030.0000.0000.0000.000
108A128VAL00.0160.00825.370-0.003-0.0030.0000.0000.0000.000
109A129GLU-1-0.769-0.85625.4370.0060.0060.0000.0000.0000.000
110A130GLN0-0.053-0.03325.8020.0130.0130.0000.0000.0000.000
111A131ARG10.8580.92517.0990.1450.1450.0000.0000.0000.000
112A132VAL00.000-0.00621.4620.0030.0030.0000.0000.0000.000
113A133ILE0-0.027-0.00921.9810.0190.0190.0000.0000.0000.000
114A134GLU-1-0.860-0.93320.778-0.079-0.0790.0000.0000.0000.000
115A135GLU-1-0.775-0.82815.867-0.107-0.1070.0000.0000.0000.000
116A136VAL0-0.008-0.00417.5230.0330.0330.0000.0000.0000.000
117A137SER0-0.041-0.04119.4450.0260.0260.0000.0000.0000.000
118A138ILE00.0660.03914.3140.0250.0250.0000.0000.0000.000
119A139ASN0-0.042-0.02314.7070.0930.0930.0000.0000.0000.000
120A140VAL0-0.062-0.02816.4520.0490.0490.0000.0000.0000.000
121A141ASP-1-0.855-0.90718.3850.1050.1050.0000.0000.0000.000
122A142HIS0-0.050-0.04711.800-0.050-0.0500.0000.0000.0000.000
123A143ALA0-0.0340.00615.6170.0790.0790.0000.0000.0000.000
124A144ARG10.8770.91216.707-0.526-0.5260.0000.0000.0000.000
125A145GLU-1-0.819-0.89618.6030.3270.3270.0000.0000.0000.000
126A146VAL00.0630.01821.661-0.008-0.0080.0000.0000.0000.000
127A147LYS10.9420.97124.124-0.261-0.2610.0000.0000.0000.000
128A148GLU-1-0.784-0.86917.9370.3130.3130.0000.0000.0000.000
129A149LYS10.8580.94920.129-0.242-0.2420.0000.0000.0000.000
130A150LYS11.0200.99622.158-0.150-0.1500.0000.0000.0000.000
131A151ARG10.7380.83418.404-0.296-0.2960.0000.0000.0000.000
132A152ILE00.0290.00917.418-0.018-0.0180.0000.0000.0000.000
133A153MET0-0.0300.00821.387-0.018-0.0180.0000.0000.0000.000
134A154ASN0-0.068-0.02824.616-0.029-0.0290.0000.0000.0000.000
135A155ASP-1-0.793-0.86720.0060.1930.1930.0000.0000.0000.000
136A156LYS10.9550.95723.107-0.107-0.1070.0000.0000.0000.000
137A157LYS10.8800.93918.496-0.190-0.1900.0000.0000.0000.000
138A158LEU0-0.004-0.00816.581-0.011-0.0110.0000.0000.0000.000
139A159ILE00.0310.01020.040-0.021-0.0210.0000.0000.0000.000
140A160ARG10.7240.84922.870-0.033-0.0330.0000.0000.0000.000
141A161MET00.0830.05917.337-0.002-0.0020.0000.0000.0000.000
142A162LEU00.0100.01516.464-0.023-0.0230.0000.0000.0000.000
143A163PHE00.026-0.00520.181-0.022-0.0220.0000.0000.0000.000
144A164ASP-1-0.847-0.90221.9240.0080.0080.0000.0000.0000.000
145A165THR0-0.061-0.02617.527-0.017-0.0170.0000.0000.0000.000
146A166TYR0-0.032-0.06417.390-0.031-0.0310.0000.0000.0000.000
147A167GLU-1-0.780-0.88622.884-0.015-0.0150.0000.0000.0000.000
148A168TYR00.0020.01121.499-0.003-0.0030.0000.0000.0000.000
149A169VAL0-0.043-0.02620.209-0.008-0.0080.0000.0000.0000.000
150A170LYS10.8090.90523.6340.0860.0860.0000.0000.0000.000
151A171ASP-1-0.926-0.94227.073-0.067-0.0670.0000.0000.0000.000
152A172VAL0-0.059-0.02128.8160.0080.0080.0000.0000.0000.000
153A173LYS10.8720.92629.6900.0010.0010.0000.0000.0000.000
154A174PHE0-0.0440.00029.7790.0010.0010.0000.0000.0000.000
155A175THR00.016-0.00632.9100.0030.0030.0000.0000.0000.000
156A176ASP-1-0.813-0.92432.8240.0140.0140.0000.0000.0000.000
157A177ASP-1-0.820-0.89234.1700.0290.0290.0000.0000.0000.000
158A178GLN00.0360.01834.7300.0010.0010.0000.0000.0000.000
159A179TYR00.0050.00826.8630.0020.0020.0000.0000.0000.000
160A180LYS10.7800.87431.061-0.024-0.0240.0000.0000.0000.000
161A181ASP-1-0.845-0.91132.9980.0250.0250.0000.0000.0000.000
162A182ALA0-0.003-0.00530.1920.0020.0020.0000.0000.0000.000
163A183ALA00.0140.00428.3260.0030.0030.0000.0000.0000.000
164A184ALA0-0.042-0.01429.2470.0080.0080.0000.0000.0000.000
165A185ARG10.8370.91031.803-0.005-0.0050.0000.0000.0000.000
166A186ILE00.0210.01625.1930.0000.0000.0000.0000.0000.000
167A187SER0-0.018-0.03327.1670.0040.0040.0000.0000.0000.000
168A188GLN0-0.032-0.00328.5610.0010.0010.0000.0000.0000.000
169A189PHE00.0200.00427.5200.0020.0020.0000.0000.0000.000
170A190LEU00.005-0.00523.7750.0020.0020.0000.0000.0000.000
171A191ILE0-0.025-0.02227.3290.0060.0060.0000.0000.0000.000
172A192ASP-1-0.776-0.84429.8050.0440.0440.0000.0000.0000.000
173A193VAL0-0.051-0.01528.653-0.004-0.0040.0000.0000.0000.000
174A194VAL0-0.0030.00523.878-0.005-0.0050.0000.0000.0000.000
175A195ASP-1-0.860-0.96226.8710.0470.0470.0000.0000.0000.000
176A196SER0-0.042-0.05422.5800.0110.0110.0000.0000.0000.000
177A197TYR0-0.022-0.00724.3190.0190.0190.0000.0000.0000.000
178A198ILE0-0.063-0.02225.9360.0070.0070.0000.0000.0000.000
179A199ILE00.0070.00027.154-0.012-0.0120.0000.0000.0000.000
180A200LYS10.9370.97330.968-0.058-0.0580.0000.0000.0000.000
181A201PRO0-0.0020.00534.7230.0030.0030.0000.0000.0000.000
182A202ILE00.0270.00735.522-0.005-0.0050.0000.0000.0000.000
183A203PRO0-0.023-0.01138.2440.0000.0000.0000.0000.0000.000
184A204ALA00.0240.02041.6630.0010.0010.0000.0000.0000.000
185A205LEU00.0400.02044.722-0.003-0.0030.0000.0000.0000.000
186A206PRO0-0.055-0.02247.223-0.003-0.0030.0000.0000.0000.000