FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: KGYV3

Calculation Name: 2J42-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J42

Chain ID: A

ChEMBL ID:

UniProt ID: O86171

Base Structure: X-ray

Registration Date: 2023-09-24

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 516
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9686653.702538
FMO2-HF: Nuclear repulsion 9484368.087374
FMO2-HF: Total energy -202285.615164
FMO2-MP2: Total energy -202875.988483


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:18:PHE)


Summations of interaction energy for fragment #1(A:18:PHE)
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.
-10.44-1.2212.138-3.382-7.9750.002
Interaction energy analysis for fragmet #1(A:18:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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].
3A20ILE0-0.024-0.0022.865-2.606-0.1080.102-0.843-1.7560.002
4A21ASN0-0.045-0.0292.227-1.9400.3930.908-1.172-2.068-0.008
5A22GLY00.0970.0544.1610.3920.5280.001-0.056-0.0810.000
6A23LEU0-0.0200.0087.9210.0940.0940.0000.0000.0000.000
7A24MET0-0.0120.0239.9190.0180.0180.0000.0000.0000.000
8A25GLY00.0360.00112.7630.0520.0520.0000.0000.0000.000
9A26TYR0-0.0520.00015.8910.0080.0080.0000.0000.0000.000
10A27TYR00.0550.03817.0590.0080.0080.0000.0000.0000.000
11A28PHE0-0.013-0.02122.3310.0100.0100.0000.0000.0000.000
12A29GLU-1-0.797-0.90725.829-0.084-0.0840.0000.0000.0000.000
13A30ASN0-0.025-0.01028.9340.0070.0070.0000.0000.0000.000
14A31ASP-1-0.844-0.92729.701-0.092-0.0920.0000.0000.0000.000
15A32PHE0-0.038-0.03630.363-0.002-0.0020.0000.0000.0000.000
16A33PHE00.0030.00426.0160.0000.0000.0000.0000.0000.000
17A34ASN0-0.047-0.01827.0990.0090.0090.0000.0000.0000.000
18A35LEU00.0150.00521.4500.0060.0060.0000.0000.0000.000
19A36ASN0-0.023-0.01123.6610.0150.0150.0000.0000.0000.000
20A37ILE0-0.035-0.01919.3640.0130.0130.0000.0000.0000.000
21A38ILE0-0.047-0.01115.495-0.007-0.0070.0000.0000.0000.000
22A39SER00.0350.03614.608-0.006-0.0060.0000.0000.0000.000
23A40PRO0-0.001-0.02110.059-0.006-0.0060.0000.0000.0000.000
24A41THR0-0.063-0.04611.3870.1000.1000.0000.0000.0000.000
25A42LEU00.001-0.0017.559-0.139-0.1390.0000.0000.0000.000
26A43ASP-1-0.852-0.9539.038-0.798-0.7980.0000.0000.0000.000
27A44GLY00.0580.03811.4760.0520.0520.0000.0000.0000.000
28A45ASN0-0.053-0.04614.5540.0980.0980.0000.0000.0000.000
29A46LEU0-0.0100.01315.119-0.012-0.0120.0000.0000.0000.000
30A47THR0-0.074-0.04516.9220.0610.0610.0000.0000.0000.000
31A48PHE00.0790.02217.695-0.018-0.0180.0000.0000.0000.000
32A49SER00.0110.01120.0130.0210.0210.0000.0000.0000.000
33A50LYS11.0131.00022.2780.0410.0410.0000.0000.0000.000
34A51GLU-1-1.071-1.04023.2700.0150.0150.0000.0000.0000.000
35A52ASP-1-0.896-0.93819.902-0.049-0.0490.0000.0000.0000.000
36A53ILE00.0850.04922.174-0.004-0.0040.0000.0000.0000.000
37A54ASN0-0.075-0.03924.900-0.001-0.0010.0000.0000.0000.000
38A55SER0-0.028-0.02624.8220.0090.0090.0000.0000.0000.000
39A56ILE00.0330.03725.4370.0040.0040.0000.0000.0000.000
40A57LEU00.0780.03128.2440.0040.0040.0000.0000.0000.000
41A58GLY00.0530.02231.364-0.002-0.0020.0000.0000.0000.000
42A59ASN0-0.0170.00830.2120.0030.0030.0000.0000.0000.000
43A60LYS10.7210.85727.9180.0360.0360.0000.0000.0000.000
44A61ILE0-0.061-0.02227.865-0.008-0.0080.0000.0000.0000.000
45A62ILE00.0430.03024.2390.0030.0030.0000.0000.0000.000
46A63LYS10.7730.89627.5330.0810.0810.0000.0000.0000.000
47A64SER0-0.029-0.01126.957-0.006-0.0060.0000.0000.0000.000
48A65ALA00.031-0.00121.559-0.002-0.0020.0000.0000.0000.000
49A66ARG10.8630.91821.1570.1980.1980.0000.0000.0000.000
50A67TRP00.0110.02115.8410.0050.0050.0000.0000.0000.000
51A68ILE0-0.027-0.00415.8470.0170.0170.0000.0000.0000.000
52A69GLY00.019-0.00712.919-0.061-0.0610.0000.0000.0000.000
53A70LEU0-0.0210.01011.5000.0850.0850.0000.0000.0000.000
54A71ILE00.0420.00612.258-0.062-0.0620.0000.0000.0000.000
55A72LYS10.8420.9436.8071.4381.4380.0000.0000.0000.000
56A73PRO0-0.0050.02212.403-0.078-0.0780.0000.0000.0000.000
57A74SER00.026-0.01613.894-0.038-0.0380.0000.0000.0000.000
58A75ILE0-0.021-0.03415.4450.0340.0340.0000.0000.0000.000
59A76THR0-0.0160.00319.219-0.015-0.0150.0000.0000.0000.000
60A77GLY00.0120.02221.9440.0180.0180.0000.0000.0000.000
61A78GLU-1-0.954-0.97623.128-0.158-0.1580.0000.0000.0000.000
62A79TYR0-0.013-0.01418.935-0.013-0.0130.0000.0000.0000.000
63A80ILE00.0160.00823.1180.0090.0090.0000.0000.0000.000
64A81LEU0-0.0060.00519.111-0.009-0.0090.0000.0000.0000.000
65A82SER0-0.025-0.00922.4810.0260.0260.0000.0000.0000.000
66A83THR00.022-0.00521.863-0.018-0.0180.0000.0000.0000.000
67A84ASN00.0110.02324.3610.0050.0050.0000.0000.0000.000
68A85SER00.013-0.02326.8550.0140.0140.0000.0000.0000.000
69A86PRO0-0.0280.00227.355-0.006-0.0060.0000.0000.0000.000
70A87ASN00.0150.02628.476-0.008-0.0080.0000.0000.0000.000
71A88CYS00.0410.00624.895-0.007-0.0070.0000.0000.0000.000
72A89ARG10.8100.90825.8610.1650.1650.0000.0000.0000.000
73A90VAL00.007-0.01821.189-0.014-0.0140.0000.0000.0000.000
74A91GLU-1-0.807-0.87922.404-0.155-0.1550.0000.0000.0000.000
75A92LEU00.0130.02319.234-0.015-0.0150.0000.0000.0000.000
76A93ASN0-0.050-0.03520.3370.0020.0020.0000.0000.0000.000
77A94GLY00.0430.02123.5870.0060.0060.0000.0000.0000.000
78A95GLU-1-0.894-0.92526.063-0.140-0.1400.0000.0000.0000.000
79A96ILE0-0.032-0.02026.072-0.011-0.0110.0000.0000.0000.000
80A97PHE00.036-0.00125.2480.0050.0050.0000.0000.0000.000
81A98ASN00.0210.00722.5700.0090.0090.0000.0000.0000.000
82A99LEU0-0.087-0.04126.6390.0120.0120.0000.0000.0000.000
83A100SER0-0.004-0.01428.9610.0040.0040.0000.0000.0000.000
84A101LEU0-0.039-0.01130.1020.0020.0020.0000.0000.0000.000
85A102ASN00.0150.01229.790-0.013-0.0130.0000.0000.0000.000
86A103THR0-0.045-0.00630.864-0.001-0.0010.0000.0000.0000.000
87A104SER0-0.001-0.00127.921-0.004-0.0040.0000.0000.0000.000
88A105ASN0-0.074-0.04729.7310.0130.0130.0000.0000.0000.000
89A106THR0-0.043-0.01427.0470.0000.0000.0000.0000.0000.000
90A107VAL00.1130.03923.0690.0000.0000.0000.0000.0000.000
91A108ASN0-0.045-0.01224.043-0.019-0.0190.0000.0000.0000.000
92A109LEU00.0030.01818.127-0.013-0.0130.0000.0000.0000.000
93A110ILE00.028-0.00220.1570.0090.0090.0000.0000.0000.000
94A111GLN0-0.0210.01214.2250.0000.0000.0000.0000.0000.000
95A112GLY00.0090.00915.2690.0290.0290.0000.0000.0000.000
96A113ASN0-0.111-0.05216.2040.0330.0330.0000.0000.0000.000
97A114VAL00.024-0.00612.413-0.037-0.0370.0000.0000.0000.000
98A115TYR0-0.003-0.01015.2840.0440.0440.0000.0000.0000.000
99A116ASP-1-0.896-0.95416.200-0.332-0.3320.0000.0000.0000.000
100A117ILE0-0.025-0.01014.5070.0290.0290.0000.0000.0000.000
101A118ARG10.7950.85118.0010.2100.2100.0000.0000.0000.000
102A119ILE0-0.013-0.00517.9610.0050.0050.0000.0000.0000.000
103A120GLU-1-0.843-0.88021.430-0.164-0.1640.0000.0000.0000.000
104A121GLN00.0590.01824.1520.0060.0060.0000.0000.0000.000
105A122LEU0-0.039-0.03026.1420.0040.0040.0000.0000.0000.000
106A123MET00.0270.04128.9720.0070.0070.0000.0000.0000.000
107A124SER00.0160.00731.1730.0020.0020.0000.0000.0000.000
108A125GLU-1-0.915-0.95234.459-0.058-0.0580.0000.0000.0000.000
109A126ASN0-0.0030.00730.5050.0020.0020.0000.0000.0000.000
110A127GLN0-0.004-0.01833.4130.0050.0050.0000.0000.0000.000
111A128LEU0-0.048-0.01029.2760.0050.0050.0000.0000.0000.000
112A129LEU00.0770.02731.252-0.003-0.0030.0000.0000.0000.000
113A130LYS10.8060.89428.9380.0320.0320.0000.0000.0000.000
114A131ASN00.0310.02326.7250.0040.0040.0000.0000.0000.000
115A132TYR00.0830.03223.6930.0020.0020.0000.0000.0000.000
116A133GLU-1-0.843-0.91622.707-0.193-0.1930.0000.0000.0000.000
117A134GLY0-0.075-0.06322.2490.0000.0000.0000.0000.0000.000
118A135ILE0-0.0140.01020.0380.0100.0100.0000.0000.0000.000
119A136LYS10.8700.94619.7690.1550.1550.0000.0000.0000.000
120A137LEU00.0260.01116.6320.0240.0240.0000.0000.0000.000
121A138TYR0-0.078-0.07018.228-0.030-0.0300.0000.0000.0000.000
122A139TRP0-0.002-0.02415.421-0.006-0.0060.0000.0000.0000.000
123A140GLU-1-0.909-0.95020.788-0.158-0.1580.0000.0000.0000.000
124A141THR00.0020.00221.9790.0070.0070.0000.0000.0000.000
125A142SER00.0100.00023.9870.0080.0080.0000.0000.0000.000
126A143ASP-1-0.925-0.94524.609-0.135-0.1350.0000.0000.0000.000
127A144ILE0-0.0070.00625.555-0.007-0.0070.0000.0000.0000.000
128A145ILE0-0.063-0.05120.5110.0060.0060.0000.0000.0000.000
129A146LYS10.9250.97422.2090.1600.1600.0000.0000.0000.000
130A147GLU-1-0.942-0.98316.542-0.264-0.2640.0000.0000.0000.000
131A148ILE0-0.094-0.02915.007-0.008-0.0080.0000.0000.0000.000
132A149ILE00.0120.01213.124-0.011-0.0110.0000.0000.0000.000
133A150PRO00.1140.06510.394-0.048-0.0480.0000.0000.0000.000
134A151SER00.045-0.0116.3380.0830.0830.0000.0000.0000.000
135A152GLU-1-0.961-0.9746.476-1.372-1.3720.0000.0000.0000.000
136A153VAL0-0.029-0.0057.7680.0350.0350.0000.0000.0000.000
137A154LEU0-0.0330.0109.5390.1120.1120.0000.0000.0000.000
138A155LEU0-0.065-0.0117.170-0.332-0.3320.0000.0000.0000.000
139A156LYS10.8740.9676.2460.7940.7940.0000.0000.0000.000
140A157PRO00.0260.0069.2800.0670.0670.0000.0000.0000.000
141A158ASN0-0.034-0.0419.074-0.032-0.0320.0000.0000.0000.000
142A159TYR00.035-0.01111.0860.0060.0060.0000.0000.0000.000
143A160SER0-0.053-0.00611.6470.0300.0300.0000.0000.0000.000
144A161ASN00.022-0.01213.3130.0020.0020.0000.0000.0000.000
145A162THR00.0000.02317.042-0.001-0.0010.0000.0000.0000.000
146A163ASN0-0.007-0.00319.5070.0030.0030.0000.0000.0000.000
147A164GLU-1-0.979-0.98521.815-0.054-0.0540.0000.0000.0000.000
148A186ARG10.9310.94627.6220.0770.0770.0000.0000.0000.000
149A187ASP-1-0.786-0.88321.699-0.141-0.1410.0000.0000.0000.000
150A188THR0-0.061-0.04124.822-0.003-0.0030.0000.0000.0000.000
151A189ASH0-0.058-0.04821.445-0.001-0.0010.0000.0000.0000.000
152A190ARG10.8010.90020.8700.1540.1540.0000.0000.0000.000
153A191ASP-1-0.823-0.95017.158-0.144-0.1440.0000.0000.0000.000
154A192GLY0-0.0290.00516.695-0.019-0.0190.0000.0000.0000.000
155A193ILE0-0.017-0.00717.194-0.009-0.0090.0000.0000.0000.000
156A194PRO0-0.0040.00720.4790.0080.0080.0000.0000.0000.000
157A195ASP-1-0.736-0.86824.265-0.074-0.0740.0000.0000.0000.000
158A196GLU-1-0.990-1.00026.445-0.065-0.0650.0000.0000.0000.000
159A197TRP00.013-0.01420.3470.0030.0030.0000.0000.0000.000
160A198GLU-1-0.781-0.86620.982-0.086-0.0860.0000.0000.0000.000
161A199ILE0-0.024-0.00524.2030.0100.0100.0000.0000.0000.000
162A200ASN0-0.107-0.05027.7980.0040.0040.0000.0000.0000.000
163A201GLY00.0330.00024.5940.0080.0080.0000.0000.0000.000
164A202TYR0-0.012-0.02017.631-0.002-0.0020.0000.0000.0000.000
165A203THR0-0.061-0.03020.7410.0090.0090.0000.0000.0000.000
166A204VAL00.031-0.00815.154-0.017-0.0170.0000.0000.0000.000
167A205MET00.0020.03617.2780.0230.0230.0000.0000.0000.000
168A206ASN0-0.004-0.00312.859-0.046-0.0460.0000.0000.0000.000
169A207GLN0-0.005-0.02915.263-0.028-0.0280.0000.0000.0000.000
170A208LYN00.0380.04015.061-0.017-0.0170.0000.0000.0000.000
171A209ALA00.000-0.00917.102-0.013-0.0130.0000.0000.0000.000
172A210VAL00.0800.04320.6670.0120.0120.0000.0000.0000.000
173A211ALA0-0.044-0.02223.8880.0060.0060.0000.0000.0000.000
174A212TRP0-0.027-0.01425.720-0.002-0.0020.0000.0000.0000.000
175A213ASP-1-0.955-0.99128.5420.0050.0050.0000.0000.0000.000
176A214ASP-1-0.825-0.91730.0980.0020.0020.0000.0000.0000.000
177A215LYS10.8270.90027.481-0.005-0.0050.0000.0000.0000.000
178A216PHE00.0240.01323.2940.0070.0070.0000.0000.0000.000
179A217ALA00.0300.02426.4930.0080.0080.0000.0000.0000.000
180A218ALA0-0.035-0.00927.6360.0080.0080.0000.0000.0000.000
181A219ASN0-0.067-0.04025.047-0.003-0.0030.0000.0000.0000.000
182A220GLY00.0420.04225.4250.0120.0120.0000.0000.0000.000
183A221TYR0-0.045-0.02921.0520.0090.0090.0000.0000.0000.000
184A222LYS10.9250.97117.685-0.073-0.0730.0000.0000.0000.000
185A223LYS10.9070.97521.0400.0070.0070.0000.0000.0000.000
186A224TYR0-0.0150.00216.1520.0240.0240.0000.0000.0000.000
187A225VAL00.000-0.00921.630-0.007-0.0070.0000.0000.0000.000
188A226SER00.002-0.01820.8000.0070.0070.0000.0000.0000.000
189A227ASN00.0200.01022.5400.0020.0020.0000.0000.0000.000
190A228PRO00.0690.04923.203-0.006-0.0060.0000.0000.0000.000
191A229PHE0-0.008-0.02325.182-0.005-0.0050.0000.0000.0000.000
192A230LYS10.7550.86922.5330.0300.0300.0000.0000.0000.000
193A231PRO00.0700.05518.7850.0030.0030.0000.0000.0000.000
194A232CYS00.0470.02616.779-0.010-0.0100.0000.0000.0000.000
195A233THR0-0.048-0.02218.6310.0130.0130.0000.0000.0000.000
196A234ALA0-0.017-0.01718.0800.0060.0060.0000.0000.0000.000
197A235ASN0-0.047-0.01119.9440.0020.0020.0000.0000.0000.000
198A236ASP-1-0.803-0.92014.288-0.008-0.0080.0000.0000.0000.000
199A237PRO00.0040.01112.757-0.011-0.0110.0000.0000.0000.000
200A238TYR0-0.046-0.0338.408-0.006-0.0060.0000.0000.0000.000
201A239THR00.0330.00712.2610.0070.0070.0000.0000.0000.000
202A240ASP-1-0.752-0.89113.474-0.071-0.0710.0000.0000.0000.000
203A241PHE00.0060.01912.545-0.008-0.0080.0000.0000.0000.000
204A242GLU-1-0.826-0.9229.547-0.320-0.3200.0000.0000.0000.000
205A243LYS10.7870.8879.561-0.016-0.0160.0000.0000.0000.000
206A244VAL0-0.035-0.00611.0930.0130.0130.0000.0000.0000.000
207A245SER0-0.064-0.03210.2320.0130.0130.0000.0000.0000.000
208A246GLY0-0.025-0.0098.1330.0140.0140.0000.0000.0000.000
209A247GLN0-0.078-0.0485.336-0.105-0.1050.0000.0000.0000.000
210A248ILE00.0160.0234.9430.1550.1550.0000.0000.0000.000
211A249ASP-1-0.771-0.8714.131-0.1890.043-0.001-0.041-0.1910.000
212A250PRO0-0.010-0.0123.360-0.817-0.0710.048-0.218-0.5760.001
213A251SER00.008-0.0276.057-0.009-0.0090.0000.0000.0000.000
214A252VAL0-0.0450.0028.769-0.072-0.0720.0000.0000.0000.000
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