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: K3LL3

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241230.576912
FMO2-HF: Nuclear repulsion 2162950.073627
FMO2-HF: Total energy -78280.503285
FMO2-MP2: Total energy -78511.137074


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.
-6.694-1.2152.307-2.291-5.4930.011
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 : -0.018
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].
3A23TYR00.0380.0352.608-3.8411.2752.255-2.204-5.1660.009
4A24GLU-1-0.890-0.9424.096-0.803-0.4400.052-0.087-0.3270.002
5A25HIS10.7940.9276.3290.4880.4880.0000.0000.0000.000
6A26GLU-1-0.888-1.0027.504-1.978-1.9780.0000.0000.0000.000
7A27THR00.0200.0138.8220.1750.1750.0000.0000.0000.000
8A28HIS0-0.0230.00010.834-0.052-0.0520.0000.0000.0000.000
9A29ALA00.0480.02814.465-0.046-0.0460.0000.0000.0000.000
10A30PRO0-0.021-0.02015.431-0.008-0.0080.0000.0000.0000.000
11A31LEU00.0410.04619.0510.0300.0300.0000.0000.0000.000
12A32SER00.0340.01820.376-0.018-0.0180.0000.0000.0000.000
13A33PRO00.014-0.02223.594-0.006-0.0060.0000.0000.0000.000
14A34ARG10.8300.92426.408-0.058-0.0580.0000.0000.0000.000
15A35ILE00.0320.01924.159-0.001-0.0010.0000.0000.0000.000
16A36ARG11.0101.01123.6130.0750.0750.0000.0000.0000.000
17A37LYS10.9640.98426.9000.0160.0160.0000.0000.0000.000
18A38VAL0-0.026-0.00730.484-0.002-0.0020.0000.0000.0000.000
19A39GLY00.0390.02329.0110.0020.0020.0000.0000.0000.000
20A40ASP-1-0.857-0.93329.604-0.034-0.0340.0000.0000.0000.000
21A41ILE0-0.099-0.04731.5790.0000.0000.0000.0000.0000.000
22A42GLU-1-0.746-0.84833.2230.0370.0370.0000.0000.0000.000
23A43PHE00.034-0.00230.0300.0010.0010.0000.0000.0000.000
24A44HIS00.0480.04031.8520.0010.0010.0000.0000.0000.000
25A45ALA0-0.0110.00335.9390.0000.0000.0000.0000.0000.000
26A46CYS0-0.063-0.03136.3880.0020.0020.0000.0000.0000.000
27A47SER0-0.021-0.02036.1760.0000.0000.0000.0000.0000.000
28A48ASP-1-0.874-0.95138.199-0.017-0.0170.0000.0000.0000.000
29A49TYR0-0.076-0.06741.2600.0000.0000.0000.0000.0000.000
30A50ILE00.0380.01038.5820.0010.0010.0000.0000.0000.000
31A51TYR00.0090.01142.4460.0000.0000.0000.0000.0000.000
32A52LEU0-0.030-0.00843.9480.0000.0000.0000.0000.0000.000
33A53LEU00.0050.00044.2200.0000.0000.0000.0000.0000.000
34A54MET00.0160.01845.2980.0000.0000.0000.0000.0000.000
35A55THR0-0.100-0.05047.3400.0000.0000.0000.0000.0000.000
36A56LEU0-0.053-0.03350.0770.0000.0000.0000.0000.0000.000
37A57SER0-0.0100.00149.6470.0010.0010.0000.0000.0000.000
38A58LYS10.9280.96351.6620.0090.0090.0000.0000.0000.000
39A59ASP-1-0.866-0.94354.7030.0010.0010.0000.0000.0000.000
40A60PRO00.0590.01154.9410.0010.0010.0000.0000.0000.000
41A61GLU-1-0.862-0.91855.8940.0100.0100.0000.0000.0000.000
42A62LYS10.8370.93354.9110.0020.0020.0000.0000.0000.000
43A63PHE0-0.0020.01147.4600.0010.0010.0000.0000.0000.000
44A64ASN00.005-0.01050.9160.0020.0020.0000.0000.0000.000
45A65TYR0-0.049-0.02051.7350.0020.0020.0000.0000.0000.000
46A66ALA00.0250.00149.1440.0010.0010.0000.0000.0000.000
47A67LEU00.0130.03246.1370.0010.0010.0000.0000.0000.000
48A68LYS10.9550.96746.418-0.027-0.0270.0000.0000.0000.000
49A69ASP-1-0.777-0.83148.5800.0130.0130.0000.0000.0000.000
50A70ARG10.9040.91143.834-0.033-0.0330.0000.0000.0000.000
51A71VAL0-0.0430.00047.1390.0000.0000.0000.0000.0000.000
52A72SER0-0.048-0.08848.499-0.002-0.0020.0000.0000.0000.000
53A73ILE00.0460.04342.612-0.002-0.0020.0000.0000.0000.000
54A74ARG10.8830.93443.763-0.027-0.0270.0000.0000.0000.000
55A75ARG10.8660.94344.480-0.005-0.0050.0000.0000.0000.000
56A76TYR00.0190.00942.385-0.003-0.0030.0000.0000.0000.000
57A77VAL00.0240.01839.117-0.003-0.0030.0000.0000.0000.000
58A78ARG10.9510.97540.541-0.013-0.0130.0000.0000.0000.000
59A79LYS10.9730.99242.3710.0120.0120.0000.0000.0000.000
60A80ASN0-0.004-0.00337.594-0.007-0.0070.0000.0000.0000.000
61A81GLN00.0550.02837.949-0.003-0.0030.0000.0000.0000.000
62A82ASN0-0.060-0.03738.921-0.005-0.0050.0000.0000.0000.000
63A83ARG10.9781.00435.8680.0330.0330.0000.0000.0000.000
64A84TYR0-0.061-0.03132.643-0.007-0.0070.0000.0000.0000.000
65A85ASN0-0.065-0.02835.3170.0020.0020.0000.0000.0000.000
66A86TYR0-0.001-0.01632.5900.0020.0020.0000.0000.0000.000
67A87PHE00.024-0.00236.6080.0030.0030.0000.0000.0000.000
68A88LEU0-0.0310.00134.9010.0020.0020.0000.0000.0000.000
69A89ILE0-0.030-0.02135.6710.0050.0050.0000.0000.0000.000
70A90GLU-1-0.919-0.95736.7400.0520.0520.0000.0000.0000.000
71A91GLU-1-0.888-0.95039.8870.0350.0350.0000.0000.0000.000
72A92ARG10.9050.95935.194-0.071-0.0710.0000.0000.0000.000
73A93VAL00.0070.00935.2520.0010.0010.0000.0000.0000.000
74A94GLN00.007-0.01537.841-0.001-0.0010.0000.0000.0000.000
75A95ASP-1-0.854-0.92739.9800.0350.0350.0000.0000.0000.000
76A96ASN0-0.073-0.07736.608-0.004-0.0040.0000.0000.0000.000
77A97ILE0-0.0270.01735.5660.0000.0000.0000.0000.0000.000
78A98VAL0-0.018-0.01837.756-0.003-0.0030.0000.0000.0000.000
79A99ASN0-0.0190.00539.958-0.005-0.0050.0000.0000.0000.000
80A100ARG10.8350.90833.764-0.052-0.0520.0000.0000.0000.000
81A101ILE0-0.018-0.01137.797-0.002-0.0020.0000.0000.0000.000
82A102SER0-0.014-0.01039.162-0.001-0.0010.0000.0000.0000.000
83A103ASP-1-0.912-0.96538.8970.0410.0410.0000.0000.0000.000
84A104ARG10.7130.82532.453-0.032-0.0320.0000.0000.0000.000
85A105LEU0-0.043-0.01038.644-0.003-0.0030.0000.0000.0000.000
86A106ILE00.002-0.00342.019-0.002-0.0020.0000.0000.0000.000
87A107SER0-0.0040.00738.123-0.001-0.0010.0000.0000.0000.000
88A108TYR00.017-0.01133.4610.0010.0010.0000.0000.0000.000
89A109CYS0-0.047-0.02240.146-0.005-0.0050.0000.0000.0000.000
90A110THR0-0.0200.00543.654-0.002-0.0020.0000.0000.0000.000
91A111ASP-1-0.871-0.92644.2900.0200.0200.0000.0000.0000.000
92A112LYS10.8780.93140.089-0.008-0.0080.0000.0000.0000.000
93A113GLU-1-0.904-0.93046.066-0.005-0.0050.0000.0000.0000.000
94A114VAL00.0160.00844.188-0.002-0.0020.0000.0000.0000.000
95A115THR00.011-0.00545.174-0.002-0.0020.0000.0000.0000.000
96A116GLU-1-0.923-0.97443.953-0.025-0.0250.0000.0000.0000.000
97A117ASP-1-0.860-0.93941.638-0.028-0.0280.0000.0000.0000.000
98A118TYR0-0.149-0.08840.2040.0000.0000.0000.0000.0000.000
99A119ILE00.028-0.00539.3880.0010.0010.0000.0000.0000.000
100A120LYS10.9730.99237.0020.0370.0370.0000.0000.0000.000
101A121LYS10.9801.01035.6130.0030.0030.0000.0000.0000.000
102A122ILE0-0.059-0.02734.8000.0020.0020.0000.0000.0000.000
103A123ASP-1-0.819-0.90133.937-0.019-0.0190.0000.0000.0000.000
104A124ASP-1-0.881-0.94830.700-0.036-0.0360.0000.0000.0000.000
105A125TYR0-0.060-0.03229.9360.0020.0020.0000.0000.0000.000
106A126LEU0-0.050-0.02530.6320.0080.0080.0000.0000.0000.000
107A127TRP00.0190.01322.5720.0030.0030.0000.0000.0000.000
108A128VAL0-0.0060.00125.8530.0020.0020.0000.0000.0000.000
109A129GLU-1-0.765-0.85725.7190.0490.0490.0000.0000.0000.000
110A130GLN0-0.024-0.02026.4770.0090.0090.0000.0000.0000.000
111A131ARG10.9280.96318.1180.0640.0640.0000.0000.0000.000
112A132VAL00.001-0.00421.8390.0110.0110.0000.0000.0000.000
113A133ILE0-0.031-0.00922.1680.0210.0210.0000.0000.0000.000
114A134GLU-1-0.918-0.97221.317-0.003-0.0030.0000.0000.0000.000
115A135GLU-1-0.849-0.90715.4680.0650.0650.0000.0000.0000.000
116A136VAL0-0.019-0.02118.0140.0400.0400.0000.0000.0000.000
117A137SER0-0.071-0.05919.8230.0250.0250.0000.0000.0000.000
118A138ILE00.0470.03414.7710.0110.0110.0000.0000.0000.000
119A139ASN0-0.041-0.02514.5230.0940.0940.0000.0000.0000.000
120A140VAL0-0.049-0.02816.4190.0420.0420.0000.0000.0000.000
121A141ASP-1-0.876-0.94018.4110.1630.1630.0000.0000.0000.000
122A142HIS0-0.052-0.03112.472-0.062-0.0620.0000.0000.0000.000
123A143ALA0-0.0220.01615.2860.0780.0780.0000.0000.0000.000
124A144ARG10.9440.96116.194-0.595-0.5950.0000.0000.0000.000
125A145GLU-1-0.900-0.95718.4850.3390.3390.0000.0000.0000.000
126A146VAL00.0730.02521.752-0.003-0.0030.0000.0000.0000.000
127A147LYS10.9440.97024.419-0.283-0.2830.0000.0000.0000.000
128A148GLU-1-0.782-0.87717.9480.3920.3920.0000.0000.0000.000
129A149LYS10.8860.96619.961-0.288-0.2880.0000.0000.0000.000
130A150LYS11.0000.99722.110-0.175-0.1750.0000.0000.0000.000
131A151ARG10.7490.84318.181-0.365-0.3650.0000.0000.0000.000
132A152ILE00.006-0.00217.539-0.015-0.0150.0000.0000.0000.000
133A153MET0-0.0090.02221.344-0.018-0.0180.0000.0000.0000.000
134A154ASN0-0.057-0.01124.363-0.030-0.0300.0000.0000.0000.000
135A155ASP-1-0.818-0.89720.1980.2600.2600.0000.0000.0000.000
136A156LYS10.9930.97423.099-0.135-0.1350.0000.0000.0000.000
137A157LYS10.9280.99119.388-0.263-0.2630.0000.0000.0000.000
138A158LEU00.0100.00816.932-0.006-0.0060.0000.0000.0000.000
139A159ILE00.0230.00820.192-0.016-0.0160.0000.0000.0000.000
140A160ARG10.8230.91623.137-0.094-0.0940.0000.0000.0000.000
141A161MET00.002-0.00618.102-0.002-0.0020.0000.0000.0000.000
142A162LEU00.0190.00517.146-0.019-0.0190.0000.0000.0000.000
143A163PHE00.003-0.02320.443-0.024-0.0240.0000.0000.0000.000
144A164ASP-1-0.847-0.90222.2610.0720.0720.0000.0000.0000.000
145A165THR0-0.044-0.01517.954-0.015-0.0150.0000.0000.0000.000
146A166TYR0-0.013-0.02717.953-0.036-0.0360.0000.0000.0000.000
147A167GLU-1-0.805-0.89423.1760.0270.0270.0000.0000.0000.000
148A168TYR0-0.017-0.00322.126-0.007-0.0070.0000.0000.0000.000
149A169VAL0-0.049-0.02420.692-0.011-0.0110.0000.0000.0000.000
150A170LYS10.8380.92423.9850.0490.0490.0000.0000.0000.000
151A171ASP-1-0.944-0.94427.189-0.029-0.0290.0000.0000.0000.000
152A172VAL0-0.0230.00129.0890.0030.0030.0000.0000.0000.000
153A173LYS10.9000.93429.980-0.032-0.0320.0000.0000.0000.000
154A174PHE0-0.066-0.01530.136-0.001-0.0010.0000.0000.0000.000
155A175THR00.000-0.00733.1720.0030.0030.0000.0000.0000.000
156A176ASP-1-0.867-0.95534.0190.0560.0560.0000.0000.0000.000
157A177ASP-1-0.925-0.95734.8460.0530.0530.0000.0000.0000.000
158A178GLN00.0090.00135.0660.0020.0020.0000.0000.0000.000
159A179TYR00.0010.01127.0690.0050.0050.0000.0000.0000.000
160A180LYS10.9580.97131.464-0.067-0.0670.0000.0000.0000.000
161A181ASP-1-0.924-0.96533.1230.0590.0590.0000.0000.0000.000
162A182ALA0-0.018-0.01630.6180.0020.0020.0000.0000.0000.000
163A183ALA00.0060.00028.5480.0040.0040.0000.0000.0000.000
164A184ALA0-0.031-0.01229.4480.0090.0090.0000.0000.0000.000
165A185ARG10.8980.95332.027-0.041-0.0410.0000.0000.0000.000
166A186ILE00.0350.03025.7650.0010.0010.0000.0000.0000.000
167A187SER0-0.010-0.02427.0430.0030.0030.0000.0000.0000.000
168A188GLN0-0.033-0.01128.618-0.001-0.0010.0000.0000.0000.000
169A189PHE0-0.009-0.01227.877-0.001-0.0010.0000.0000.0000.000
170A190LEU00.008-0.00224.1880.0000.0000.0000.0000.0000.000
171A191ILE0-0.038-0.02827.8110.0030.0030.0000.0000.0000.000
172A192ASP-1-0.809-0.88129.8770.0720.0720.0000.0000.0000.000
173A193VAL0-0.055-0.02429.164-0.006-0.0060.0000.0000.0000.000
174A194VAL00.0090.02424.601-0.006-0.0060.0000.0000.0000.000
175A195ASP-1-0.912-0.97227.4750.0720.0720.0000.0000.0000.000
176A196SER0-0.032-0.02922.8190.0060.0060.0000.0000.0000.000
177A197TYR0-0.022-0.00924.1520.0110.0110.0000.0000.0000.000
178A198ILE0-0.044-0.01425.5950.0050.0050.0000.0000.0000.000
179A199ILE00.0200.01827.003-0.007-0.0070.0000.0000.0000.000
180A200LYS10.9160.95530.819-0.073-0.0730.0000.0000.0000.000
181A201PRO0-0.005-0.00934.5720.0010.0010.0000.0000.0000.000
182A202ILE00.0290.02535.313-0.005-0.0050.0000.0000.0000.000
183A203PRO0-0.018-0.00838.0350.0000.0000.0000.0000.0000.000
184A204ALA00.0160.00741.3720.0000.0000.0000.0000.0000.000
185A205LEU00.0260.01044.501-0.003-0.0030.0000.0000.0000.000
186A206PRO0-0.023-0.00346.579-0.002-0.0020.0000.0000.0000.000