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: 3JM5L

Calculation Name: 3K2N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KG60

Base Structure: X-ray

Registration Date: 2023-09-23

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1831281.235883
FMO2-HF: Nuclear repulsion 1762857.319049
FMO2-HF: Total energy -68423.916834
FMO2-MP2: Total energy -68626.496207


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2: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.
-10.314-4.9741.875-3.309-3.9070.028
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.045
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].
3A0ALA00.0150.0172.278-9.055-4.4101.866-3.124-3.3880.027
4A1ALA00.0760.0383.639-1.631-1.0450.009-0.168-0.4270.001
5A2LEU0-0.013-0.0015.1990.2340.2340.0000.0000.0000.000
6A3LYS10.9790.9776.770-0.010-0.0100.0000.0000.0000.000
7A4LEU00.0000.0268.105-0.038-0.0380.0000.0000.0000.000
8A5MET00.006-0.0079.424-0.039-0.0390.0000.0000.0000.000
9A6GLN0-0.023-0.01311.0750.0490.0490.0000.0000.0000.000
10A7TYR0-0.0100.00212.5810.0140.0140.0000.0000.0000.000
11A8ILE0-0.012-0.01213.5510.0050.0050.0000.0000.0000.000
12A9GLY00.0080.00315.3390.0060.0060.0000.0000.0000.000
13A10ASP-1-0.909-0.93617.234-0.047-0.0470.0000.0000.0000.000
14A11ALA00.015-0.00918.4410.0050.0050.0000.0000.0000.000
15A12ILE0-0.042-0.03718.4280.0040.0040.0000.0000.0000.000
16A13GLY0-0.0250.00821.6370.0030.0030.0000.0000.0000.000
17A14THR0-0.070-0.04022.2450.0030.0030.0000.0000.0000.000
18A15ILE0-0.081-0.03321.5630.0030.0030.0000.0000.0000.000
19A16ARG10.9190.96425.6050.0290.0290.0000.0000.0000.000
20A17ASP-1-0.805-0.89429.096-0.018-0.0180.0000.0000.0000.000
21A18PRO00.012-0.00826.839-0.001-0.0010.0000.0000.0000.000
22A19GLN00.0090.00526.1060.0000.0000.0000.0000.0000.000
23A20GLU-1-0.846-0.93926.141-0.025-0.0250.0000.0000.0000.000
24A21LEU0-0.0070.02921.3640.0000.0000.0000.0000.0000.000
25A22PHE00.043-0.00521.527-0.001-0.0010.0000.0000.0000.000
26A23ARG10.9560.99121.4720.0160.0160.0000.0000.0000.000
27A24THR0-0.010-0.01619.1530.0020.0020.0000.0000.0000.000
28A25VAL0-0.027-0.02016.8630.0020.0020.0000.0000.0000.000
29A26THR0-0.024-0.03516.5260.0040.0040.0000.0000.0000.000
30A27ASP-1-0.883-0.94117.485-0.008-0.0080.0000.0000.0000.000
31A28LYS10.8750.93313.5700.0210.0210.0000.0000.0000.000
32A29LEU0-0.0120.00712.5780.0190.0190.0000.0000.0000.000
33A30ARG10.8870.93612.2020.0100.0100.0000.0000.0000.000
34A31LEU0-0.064-0.0209.401-0.004-0.0040.0000.0000.0000.000
35A32LEU0-0.071-0.0335.2410.0410.0410.0000.0000.0000.000
36A33PHE0-0.0100.0009.0000.0120.0120.0000.0000.0000.000
37A34ALA00.0320.01812.143-0.017-0.0170.0000.0000.0000.000
38A35PHE00.0170.00115.0420.0010.0010.0000.0000.0000.000
39A36ASP-1-0.756-0.86318.4230.0150.0150.0000.0000.0000.000
40A37SER0-0.064-0.02721.918-0.005-0.0050.0000.0000.0000.000
41A38ALA00.0030.00320.2190.0040.0040.0000.0000.0000.000
42A39VAL00.0020.00822.243-0.002-0.0020.0000.0000.0000.000
43A40ILE0-0.010-0.00121.5630.0000.0000.0000.0000.0000.000
44A41ILE0-0.0020.01124.6040.0000.0000.0000.0000.0000.000
45A42THR00.0240.00926.752-0.001-0.0010.0000.0000.0000.000
46A43ILE0-0.054-0.04428.8270.0020.0020.0000.0000.0000.000
47A44ASP-1-0.823-0.90530.881-0.004-0.0040.0000.0000.0000.000
48A45ARG10.8480.90530.363-0.004-0.0040.0000.0000.0000.000
49A46GLU-1-0.912-0.96234.5930.0030.0030.0000.0000.0000.000
50A47ARG10.8310.90038.1660.0020.0020.0000.0000.0000.000
51A48ARG10.7980.88136.418-0.007-0.0070.0000.0000.0000.000
52A49GLU-1-0.856-0.91635.8840.0010.0010.0000.0000.0000.000
53A50ALA0-0.015-0.00931.5250.0000.0000.0000.0000.0000.000
54A51SER00.0440.02231.7930.0010.0010.0000.0000.0000.000
55A52VAL0-0.028-0.00629.170-0.001-0.0010.0000.0000.0000.000
56A53PHE0-0.0060.00425.365-0.001-0.0010.0000.0000.0000.000
57A54PHE0-0.001-0.01822.885-0.002-0.0020.0000.0000.0000.000
58A55GLU-1-0.827-0.90626.2650.0000.0000.0000.0000.0000.000
59A56MET0-0.057-0.01921.722-0.001-0.0010.0000.0000.0000.000
60A57LEU00.0190.01424.3870.0030.0030.0000.0000.0000.000
61A58ARG10.8280.90721.318-0.009-0.0090.0000.0000.0000.000
62A59PHE00.0160.00226.9220.0010.0010.0000.0000.0000.000
63A60GLU-1-0.770-0.86230.653-0.001-0.0010.0000.0000.0000.000
64A61LEU0-0.030-0.01332.5850.0020.0020.0000.0000.0000.000
65A62PRO00.0110.00235.517-0.001-0.0010.0000.0000.0000.000
66A63GLU-1-0.875-0.93638.4270.0000.0000.0000.0000.0000.000
67A64GLN00.0430.01239.989-0.001-0.0010.0000.0000.0000.000
68A65LEU0-0.042-0.00835.8650.0000.0000.0000.0000.0000.000
69A66ARG10.7690.84732.6970.0010.0010.0000.0000.0000.000
70A67HIS00.0040.01136.619-0.001-0.0010.0000.0000.0000.000
71A68GLN0-0.0210.00133.1210.0010.0010.0000.0000.0000.000
72A69THR00.007-0.01234.3620.0000.0000.0000.0000.0000.000
73A70ARG10.8080.89534.251-0.003-0.0030.0000.0000.0000.000
74A71SER00.0410.01736.5150.0000.0000.0000.0000.0000.000
75A72ILE0-0.016-0.01832.4340.0010.0010.0000.0000.0000.000
76A73ALA00.0190.02735.9350.0020.0020.0000.0000.0000.000
77A74GLY0-0.027-0.01537.7530.0000.0000.0000.0000.0000.000
78A75THR0-0.063-0.04134.4550.0020.0020.0000.0000.0000.000
79A76TRP00.0850.00627.0020.0010.0010.0000.0000.0000.000
80A77LEU0-0.0210.00327.4680.0020.0020.0000.0000.0000.000
81A78GLU-1-0.719-0.81929.8650.0090.0090.0000.0000.0000.000
82A79GLY0-0.002-0.00131.3450.0000.0000.0000.0000.0000.000
83A80HIS10.8560.89925.027-0.028-0.0280.0000.0000.0000.000
84A81LEU00.0000.00726.419-0.002-0.0020.0000.0000.0000.000
85A82ASP-1-0.812-0.89826.9190.0050.0050.0000.0000.0000.000
86A83ASP-1-0.791-0.85022.1120.0310.0310.0000.0000.0000.000
87A84ARG10.8280.90120.605-0.021-0.0210.0000.0000.0000.000
88A85THR00.0190.01816.888-0.006-0.0060.0000.0000.0000.000
89A86VAL0-0.011-0.00414.6400.0000.0000.0000.0000.0000.000
90A87THR0-0.038-0.00817.5540.0160.0160.0000.0000.0000.000
91A88VAL0-0.018-0.02317.162-0.005-0.0050.0000.0000.0000.000
92A89ALA0-0.010-0.00120.4730.0030.0030.0000.0000.0000.000
93A90SER00.005-0.01323.954-0.005-0.0050.0000.0000.0000.000
94A91ILE0-0.044-0.04026.032-0.002-0.0020.0000.0000.0000.000
95A92ALA00.0090.01228.625-0.002-0.0020.0000.0000.0000.000
96A93ARG10.8540.92328.846-0.039-0.0390.0000.0000.0000.000
97A94ASP-1-0.814-0.89725.5070.0580.0580.0000.0000.0000.000
98A95ILE0-0.038-0.01927.308-0.001-0.0010.0000.0000.0000.000
99A96PRO00.006-0.01030.732-0.002-0.0020.0000.0000.0000.000
100A97SER0-0.016-0.00133.909-0.001-0.0010.0000.0000.0000.000
101A98PHE0-0.042-0.01832.972-0.002-0.0020.0000.0000.0000.000
102A99GLY00.0820.03735.0540.0010.0010.0000.0000.0000.000
103A100ALA0-0.048-0.02938.253-0.001-0.0010.0000.0000.0000.000
104A101ASP-1-0.865-0.91940.3550.0150.0150.0000.0000.0000.000
105A102GLY0-0.005-0.00939.476-0.001-0.0010.0000.0000.0000.000
106A103ALA0-0.047-0.02634.3020.0000.0000.0000.0000.0000.000
107A104PRO00.0510.02835.8330.0010.0010.0000.0000.0000.000
108A105LEU0-0.0130.00731.6190.0000.0000.0000.0000.0000.000
109A106LEU00.0260.01229.3900.0000.0000.0000.0000.0000.000
110A107TRP00.0020.00232.6090.0020.0020.0000.0000.0000.000
111A108THR0-0.007-0.02235.4320.0000.0000.0000.0000.0000.000
112A109LEU0-0.022-0.01428.6270.0000.0000.0000.0000.0000.000
113A110HIS0-0.040-0.01831.3920.0020.0020.0000.0000.0000.000
114A111GLU-1-0.833-0.90432.6250.0150.0150.0000.0000.0000.000
115A112LEU0-0.087-0.04132.128-0.001-0.0010.0000.0000.0000.000
116A113GLY0-0.0220.00431.462-0.001-0.0010.0000.0000.0000.000
117A114MET0-0.060-0.01925.4870.0020.0020.0000.0000.0000.000
118A115ARG10.8220.89026.364-0.024-0.0240.0000.0000.0000.000
119A116GLN0-0.0030.00219.5030.0020.0020.0000.0000.0000.000
120A117ILE0-0.015-0.00823.250-0.005-0.0050.0000.0000.0000.000
121A118VAL0-0.0020.00017.2470.0060.0060.0000.0000.0000.000
122A119LEU0-0.0320.00420.741-0.008-0.0080.0000.0000.0000.000
123A120SER00.021-0.01916.4850.0090.0090.0000.0000.0000.000
124A121PRO0-0.0020.00618.865-0.005-0.0050.0000.0000.0000.000
125A122LEU00.0030.00619.626-0.008-0.0080.0000.0000.0000.000
126A123ARG10.7720.86221.3780.0050.0050.0000.0000.0000.000
127A124SER00.0120.00622.435-0.007-0.0070.0000.0000.0000.000
128A125GLY00.0300.01625.0220.0040.0040.0000.0000.0000.000
129A126GLY0-0.0120.00125.4920.0040.0040.0000.0000.0000.000
130A127ARG10.9630.98426.0370.0160.0160.0000.0000.0000.000
131A128VAL00.0090.00424.781-0.004-0.0040.0000.0000.0000.000
132A129ILE0-0.026-0.01824.7530.0010.0010.0000.0000.0000.000
133A130GLY00.0540.01625.8890.0000.0000.0000.0000.0000.000
134A131PHE0-0.037-0.01022.7490.0000.0000.0000.0000.0000.000
135A132LEU00.0170.03316.803-0.002-0.0020.0000.0000.0000.000
136A133SER0-0.050-0.04720.8440.0050.0050.0000.0000.0000.000
137A134PHE00.004-0.00814.841-0.003-0.0030.0000.0000.0000.000
138A135VAL00.0380.01220.7310.0030.0030.0000.0000.0000.000
139A136SER0-0.001-0.01719.893-0.005-0.0050.0000.0000.0000.000
140A137ALA00.0550.03223.0030.0010.0010.0000.0000.0000.000
141A138GLU-1-0.866-0.90722.0550.0310.0310.0000.0000.0000.000
142A139GLU-1-0.813-0.90422.2190.0570.0570.0000.0000.0000.000
143A140LYS10.7480.86716.978-0.030-0.0300.0000.0000.0000.000
144A141LEU00.0080.00715.7180.0040.0040.0000.0000.0000.000
145A142TRP00.005-0.00212.4450.0100.0100.0000.0000.0000.000
146A143SER0-0.035-0.03910.6910.0190.0190.0000.0000.0000.000
147A144ASP-1-0.809-0.91712.8090.1700.1700.0000.0000.0000.000
148A145GLY00.0120.0278.809-0.038-0.0380.0000.0000.0000.000
149A146ASP-1-0.797-0.8668.6000.3300.3300.0000.0000.0000.000
150A147LYS10.9080.9389.734-0.227-0.2270.0000.0000.0000.000
151A148SER0-0.027-0.0079.310-0.056-0.0560.0000.0000.0000.000
152A149LEU0-0.020-0.0213.980-0.241-0.1320.000-0.017-0.0920.000
153A150LEU0-0.0050.0138.337-0.044-0.0440.0000.0000.0000.000
154A151SER00.019-0.00111.771-0.008-0.0080.0000.0000.0000.000
155A152GLY0-0.0040.00710.468-0.002-0.0020.0000.0000.0000.000
156A153VAL00.0280.00810.7790.0110.0110.0000.0000.0000.000
157A154SER00.0130.00612.4000.0290.0290.0000.0000.0000.000
158A155SER0-0.029-0.00414.8660.0170.0170.0000.0000.0000.000
159A156SER0-0.031-0.03314.514-0.001-0.0010.0000.0000.0000.000
160A157ILE00.0180.00916.2900.0110.0110.0000.0000.0000.000
161A158ALA00.0320.02018.8520.0080.0080.0000.0000.0000.000
162A159ILE0-0.0160.01319.8240.0060.0060.0000.0000.0000.000
163A160ALA00.0140.01621.0050.0050.0050.0000.0000.0000.000
164A161VAL0-0.012-0.00822.7770.0040.0040.0000.0000.0000.000
165A162SER0-0.039-0.03824.2920.0030.0030.0000.0000.0000.000
166A163ASN0-0.0010.00525.6970.0030.0030.0000.0000.0000.000
167A164ALA00.0140.00827.1950.0020.0020.0000.0000.0000.000
168A165LEU00.021-0.01028.7510.0020.0020.0000.0000.0000.000
169A166ALA0-0.0110.00930.3270.0020.0020.0000.0000.0000.000
170A167TYR0-0.020-0.01529.5140.0010.0010.0000.0000.0000.000
171A168GLU-1-0.782-0.85433.373-0.012-0.0120.0000.0000.0000.000
172A169GLU-1-0.852-0.90434.768-0.009-0.0090.0000.0000.0000.000
173A170LEU0-0.020-0.01735.3420.0010.0010.0000.0000.0000.000
174A171ARG10.8170.89237.3150.0130.0130.0000.0000.0000.000
175A172GLN0-0.068-0.04537.9260.0010.0010.0000.0000.0000.000
176A173ARG10.7220.85539.9300.0100.0100.0000.0000.0000.000
177A174GLU-1-0.979-0.98042.309-0.010-0.0100.0000.0000.0000.000