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: Q196Y

Calculation Name: 2J92-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J92

Chain ID: B

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-21

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1942462.650437
FMO2-HF: Nuclear repulsion 1870357.130897
FMO2-HF: Total energy -72105.51954
FMO2-MP2: Total energy -72308.807083


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(B:7:ASP)


Summations of interaction energy for fragment #1(B:7:ASP)
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.
-255.418-245.6653.854-6.351-7.2550.069
Interaction energy analysis for fragmet #1(B:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.960
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].
3B9GLN00.0730.0213.323-10.058-7.1820.069-1.359-1.5860.007
4B10LYS10.9871.0152.373-90.180-83.8743.777-4.727-5.3560.061
5B11MET0-0.081-0.0364.119-14.263-13.6920.008-0.265-0.3130.001
6B12VAL00.0420.0156.384-5.532-5.5320.0000.0000.0000.000
7B13MET00.0570.0697.215-5.084-5.0840.0000.0000.0000.000
8B14GLY0-0.029-0.0038.320-3.233-3.2330.0000.0000.0000.000
9B15ASN0-0.073-0.07410.201-2.546-2.5460.0000.0000.0000.000
10B16THR0-0.063-0.02611.501-2.142-2.1420.0000.0000.0000.000
11B17LYS10.8480.94113.728-20.760-20.7600.0000.0000.0000.000
12B18PRO00.0050.02917.073-0.131-0.1310.0000.0000.0000.000
13B19VAL00.028-0.00719.832-0.341-0.3410.0000.0000.0000.000
14B20GLU-1-0.891-0.96123.11213.53813.5380.0000.0000.0000.000
15B21LEU00.0130.01426.549-0.109-0.1090.0000.0000.0000.000
16B22ILE0-0.048-0.03429.702-0.118-0.1180.0000.0000.0000.000
17B23LEU00.0220.01232.763-0.070-0.0700.0000.0000.0000.000
18B24ASP-1-0.910-0.94936.4187.7927.7920.0000.0000.0000.000
19B25GLY0-0.056-0.01935.900-0.022-0.0220.0000.0000.0000.000
20B26LYS10.9290.96933.745-9.345-9.3450.0000.0000.0000.000
21B27THR00.000-0.01028.603-0.058-0.0580.0000.0000.0000.000
22B28VAL0-0.015-0.00531.903-0.097-0.0970.0000.0000.0000.000
23B29ALA00.0150.01428.722-0.016-0.0160.0000.0000.0000.000
24B30ILE0-0.017-0.00423.7820.1520.1520.0000.0000.0000.000
25B31CYS0-0.037-0.01722.221-0.267-0.2670.0000.0000.0000.000
26B32CYS0-0.0440.01717.0490.6560.6560.0000.0000.0000.000
27B33ALA00.0620.03718.127-0.676-0.6760.0000.0000.0000.000
28B34THR0-0.028-0.01213.3051.7811.7810.0000.0000.0000.000
29B35GLY00.0070.01015.330-0.969-0.9690.0000.0000.0000.000
30B36VAL00.002-0.01514.2931.9411.9410.0000.0000.0000.000
31B37PHE00.0570.00614.5560.7270.7270.0000.0000.0000.000
32B38GLY0-0.0030.01916.721-0.719-0.7190.0000.0000.0000.000
33B39THR00.010-0.01119.0700.8570.8570.0000.0000.0000.000
34B40ALA00.0300.02120.003-0.587-0.5870.0000.0000.0000.000
35B41TYR00.003-0.01417.6681.5251.5250.0000.0000.0000.000
36B42LEU0-0.0230.00216.949-0.770-0.7700.0000.0000.0000.000
37B43VAL00.011-0.00219.6000.7500.7500.0000.0000.0000.000
38B44PRO00.001-0.00822.097-0.215-0.2150.0000.0000.0000.000
39B45ARG10.9010.94424.503-10.822-10.8220.0000.0000.0000.000
40B46HIS0-0.014-0.02427.673-0.395-0.3950.0000.0000.0000.000
41B47LEU00.0570.03025.388-0.186-0.1860.0000.0000.0000.000
42B48PHE0-0.038-0.02225.239-0.075-0.0750.0000.0000.0000.000
43B49ALA0-0.024-0.00930.195-0.228-0.2280.0000.0000.0000.000
44B50GLU-1-0.974-0.97632.0489.2489.2480.0000.0000.0000.000
45B51GLN0-0.0070.00134.285-0.089-0.0890.0000.0000.0000.000
46B52TYR0-0.068-0.05532.2830.2000.2000.0000.0000.0000.000
47B53ASP-1-0.820-0.91035.1378.3938.3930.0000.0000.0000.000
48B54LYS10.8450.91032.493-9.106-9.1060.0000.0000.0000.000
49B55ILE00.0150.01826.5120.1130.1130.0000.0000.0000.000
50B56MET0-0.040-0.00126.415-0.219-0.2190.0000.0000.0000.000
51B57LEU00.0250.00120.4430.4360.4360.0000.0000.0000.000
52B58ASP-1-0.895-0.97418.71917.74917.7490.0000.0000.0000.000
53B59GLY00.0030.01121.354-0.082-0.0820.0000.0000.0000.000
54B60ARG10.8530.92324.629-12.792-12.7920.0000.0000.0000.000
55B61ALA00.0200.00226.3840.0380.0380.0000.0000.0000.000
56B62MET0-0.081-0.03225.2610.0800.0800.0000.0000.0000.000
57B63THR00.0340.00930.190-0.214-0.2140.0000.0000.0000.000
58B64ASP-1-0.686-0.84031.97610.17310.1730.0000.0000.0000.000
59B65SER0-0.065-0.01733.497-0.015-0.0150.0000.0000.0000.000
60B66ASP-1-0.879-0.93630.07610.14110.1410.0000.0000.0000.000
61B67TYR0-0.054-0.05027.8680.6340.6340.0000.0000.0000.000
62B68ARG10.8370.91728.854-10.229-10.2290.0000.0000.0000.000
63B69VAL00.0240.00927.5370.5260.5260.0000.0000.0000.000
64B70PHE0-0.018-0.01026.680-0.428-0.4280.0000.0000.0000.000
65B71GLU-1-0.840-0.93327.10210.65210.6520.0000.0000.0000.000
66B72PHE0-0.091-0.05422.2580.0720.0720.0000.0000.0000.000
67B73GLU-1-0.914-0.95327.6839.4619.4610.0000.0000.0000.000
68B82LEU0-0.013-0.00830.8700.0590.0590.0000.0000.0000.000
69B83SER0-0.012-0.00224.4800.1570.1570.0000.0000.0000.000
70B84ASP-1-0.805-0.89325.95911.10411.1040.0000.0000.0000.000
71B85ALA0-0.076-0.02521.9680.2520.2520.0000.0000.0000.000
72B86ALA00.0310.01123.962-0.379-0.3790.0000.0000.0000.000
73B87LEU0-0.032-0.03120.4850.8260.8260.0000.0000.0000.000
74B88MET00.0320.03622.900-0.689-0.6890.0000.0000.0000.000
75B89VAL0-0.027-0.02723.4690.7760.7760.0000.0000.0000.000
76B90LEU00.0240.00923.067-0.534-0.5340.0000.0000.0000.000
77B91HIS0-0.0210.01526.2710.3710.3710.0000.0000.0000.000
78B92ARG10.9660.97726.820-10.118-10.1180.0000.0000.0000.000
79B93GLY00.0410.01523.835-0.013-0.0130.0000.0000.0000.000
80B94ASN0-0.0080.00817.650-0.322-0.3220.0000.0000.0000.000
81B95LYS10.9600.98816.673-16.598-16.5980.0000.0000.0000.000
82B96VAL00.0030.02214.9340.8320.8320.0000.0000.0000.000
83B97ARG10.9180.9577.832-31.493-31.4930.0000.0000.0000.000
84B98ASP-1-0.800-0.90412.63519.96819.9680.0000.0000.0000.000
85B99ILE0-0.071-0.0439.0251.7961.7960.0000.0000.0000.000
86B100THR00.0570.02210.9400.7200.7200.0000.0000.0000.000
87B101LYS10.8270.9128.989-23.782-23.7820.0000.0000.0000.000
88B102HIS00.003-0.0035.638-1.099-1.0990.0000.0000.0000.000
89B103PHE00.0340.04110.0500.8350.8350.0000.0000.0000.000
90B104ARG10.9130.95110.308-22.492-22.4920.0000.0000.0000.000
91B105ASP-1-0.764-0.87415.83814.11514.1150.0000.0000.0000.000
92B106THR0-0.0010.04318.623-0.788-0.7880.0000.0000.0000.000
93B107ALA0-0.0130.00116.5460.7420.7420.0000.0000.0000.000
94B108ARG10.9090.94418.176-13.297-13.2970.0000.0000.0000.000
95B109MET0-0.0090.02616.6490.7740.7740.0000.0000.0000.000
96B110LYS10.8630.92717.632-16.643-16.6430.0000.0000.0000.000
97B111LYS10.9030.96120.052-12.123-12.1230.0000.0000.0000.000
98B112GLY0-0.0050.00421.098-0.146-0.1460.0000.0000.0000.000
99B113THR0-0.072-0.04015.8690.7610.7610.0000.0000.0000.000
100B114PRO00.0410.01512.871-0.213-0.2130.0000.0000.0000.000
101B115VAL0-0.057-0.02213.5490.8050.8050.0000.0000.0000.000
102B116VAL0-0.029-0.0248.6100.3150.3150.0000.0000.0000.000
103B117GLY00.0340.02611.837-0.027-0.0270.0000.0000.0000.000
104B118VAL0-0.062-0.0368.7621.1831.1830.0000.0000.0000.000
105B119VAL00.009-0.01211.668-1.519-1.5190.0000.0000.0000.000
106B120ASN0-0.032-0.05513.9410.7010.7010.0000.0000.0000.000
107B121ASN00.0290.01116.107-0.713-0.7130.0000.0000.0000.000
108B122ALA00.0620.02419.9100.3090.3090.0000.0000.0000.000
109B123ASP-1-0.878-0.91022.66013.18813.1880.0000.0000.0000.000
110B124VAL0-0.041-0.02218.424-0.102-0.1020.0000.0000.0000.000
111B125GLY00.0280.03618.4880.6200.6200.0000.0000.0000.000
112B126ARG10.8520.89210.030-26.627-26.6270.0000.0000.0000.000
113B127LEU00.0120.01014.0690.1110.1110.0000.0000.0000.000
114B128ILE00.004-0.0018.8941.0811.0810.0000.0000.0000.000
115B129PHE0-0.0020.01612.144-1.118-1.1180.0000.0000.0000.000
116B130SER0-0.001-0.00713.4991.0611.0610.0000.0000.0000.000
117B131GLY00.0390.00515.010-1.273-1.2730.0000.0000.0000.000
118B132GLU-1-0.890-0.93716.73614.79714.7970.0000.0000.0000.000
119B133ALA0-0.0040.01418.560-0.732-0.7320.0000.0000.0000.000
120B134LEU00.008-0.00720.164-0.401-0.4010.0000.0000.0000.000
121B135THR0-0.006-0.02023.104-0.666-0.6660.0000.0000.0000.000
122B136TYR0-0.052-0.03222.8510.7420.7420.0000.0000.0000.000
123B137LYS10.8160.89120.909-13.192-13.1920.0000.0000.0000.000
124B138ASP-1-0.789-0.87621.74912.89412.8940.0000.0000.0000.000
125B139ILE0-0.0340.00119.009-0.350-0.3500.0000.0000.0000.000
126B140VAL0-0.017-0.06022.079-0.066-0.0660.0000.0000.0000.000
127B148MET00.0200.01026.5740.3290.3290.0000.0000.0000.000
128B149PRO00.0240.01222.162-0.165-0.1650.0000.0000.0000.000
129B150GLY00.0390.02924.523-0.013-0.0130.0000.0000.0000.000
130B151LEU00.0550.02723.7210.4630.4630.0000.0000.0000.000
131B152PHE00.011-0.01016.735-0.213-0.2130.0000.0000.0000.000
132B153ALA00.0420.02721.4660.3150.3150.0000.0000.0000.000
133B154TYR00.000-0.04619.3130.4330.4330.0000.0000.0000.000
134B155LYS10.8780.95721.302-12.865-12.8650.0000.0000.0000.000
135B156ALA00.0480.00319.1770.7780.7780.0000.0000.0000.000
136B157ALA0-0.032-0.00120.784-0.672-0.6720.0000.0000.0000.000
137B158THR0-0.032-0.01819.3290.5970.5970.0000.0000.0000.000
138B159ARG10.8950.93521.786-14.267-14.2670.0000.0000.0000.000
139B160ALA00.0740.03022.9110.5230.5230.0000.0000.0000.000
140B161GLY00.0720.04023.1810.1700.1700.0000.0000.0000.000
141B162TYR0-0.031-0.02218.8140.5720.5720.0000.0000.0000.000
142B163ALA00.0070.01318.9960.8550.8550.0000.0000.0000.000
143B164GLY00.0460.02019.545-0.070-0.0700.0000.0000.0000.000
144B165GLY00.0160.02415.6310.8700.8700.0000.0000.0000.000
145B166ALA0-0.016-0.00411.812-0.736-0.7360.0000.0000.0000.000
146B167VAL00.0200.00813.2100.7540.7540.0000.0000.0000.000
147B168LEU0-0.049-0.0327.1900.8170.8170.0000.0000.0000.000
148B169ALA00.0400.02111.213-1.135-1.1350.0000.0000.0000.000
149B170LYS10.8370.8908.704-26.222-26.2220.0000.0000.0000.000
150B171ASP-1-0.814-0.91212.64215.31815.3180.0000.0000.0000.000
151B172GLY0-0.004-0.00514.213-0.008-0.0080.0000.0000.0000.000
152B173ALA00.0360.01112.2170.2720.2720.0000.0000.0000.000
153B174ASP-1-0.832-0.8899.38226.32126.3210.0000.0000.0000.000
154B175THR0-0.075-0.0396.581-2.549-2.5490.0000.0000.0000.000
155B176PHE0-0.030-0.0188.1701.5491.5490.0000.0000.0000.000
156B177ILE00.013-0.0049.7920.6340.6340.0000.0000.0000.000
157B178VAL0-0.005-0.00512.018-1.478-1.4780.0000.0000.0000.000
158B179GLY00.0510.01215.351-1.261-1.2610.0000.0000.0000.000
159B180THR0-0.0030.01515.8851.2611.2610.0000.0000.0000.000
160B181HIS00.0190.02617.680-0.363-0.3630.0000.0000.0000.000
161B182SER00.003-0.00419.4740.0560.0560.0000.0000.0000.000
162B183ALA00.0550.03323.179-0.528-0.5280.0000.0000.0000.000
163B184GLY0-0.010-0.01123.9840.5600.5600.0000.0000.0000.000
164B185GLY00.0270.02825.406-0.301-0.3010.0000.0000.0000.000
165B186ASN00.0180.00828.1600.1090.1090.0000.0000.0000.000
166B187GLY0-0.0140.00326.0070.0190.0190.0000.0000.0000.000
167B188VAL00.002-0.00224.5580.4670.4670.0000.0000.0000.000
168B189GLY00.0170.01621.952-0.280-0.2800.0000.0000.0000.000
169B190TYR00.022-0.00322.795-0.053-0.0530.0000.0000.0000.000
170B191CYS0-0.0280.00818.9400.3810.3810.0000.0000.0000.000
171B192SER00.0520.01421.016-0.675-0.6750.0000.0000.0000.000
172B193CYS0-0.074-0.03419.5610.6520.6520.0000.0000.0000.000
173B194VAL00.0180.00018.304-0.722-0.7220.0000.0000.0000.000
174B195SER00.0460.01017.8620.8180.8180.0000.0000.0000.000
175B196ARG10.9610.98713.806-17.780-17.7800.0000.0000.0000.000
176B197SER0-0.014-0.03017.650-0.497-0.4970.0000.0000.0000.000
177B198MET0-0.054-0.00121.248-0.388-0.3880.0000.0000.0000.000
178B199LEU00.0480.02516.319-0.302-0.3020.0000.0000.0000.000
179B200GLN0-0.023-0.01518.1930.1890.1890.0000.0000.0000.000
180B201LYS10.9200.95820.820-12.255-12.2550.0000.0000.0000.000
181B202MET00.0310.03222.789-0.440-0.4400.0000.0000.0000.000
182B203LYS10.8730.93620.003-13.416-13.4160.0000.0000.0000.000
183B204ALA0-0.043-0.02422.544-0.186-0.1860.0000.0000.0000.000
184B205HIS00.0240.02425.419-0.287-0.2870.0000.0000.0000.000
185B206VAL0-0.076-0.02224.387-0.200-0.2000.0000.0000.0000.000