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

tag_button

FMODB ID: 4J6JN

Calculation Name: 4OPA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OPA

Chain ID: B

ChEMBL ID:

UniProt ID: Q20NS3

Base Structure: X-ray

Registration Date: 2023-09-22

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1981914.695233
FMO2-HF: Nuclear repulsion 1903062.22958
FMO2-HF: Total energy -78852.465654
FMO2-MP2: Total energy -79079.936153


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:2:ASP)


Summations of interaction energy for fragment #1(B:2: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.
14.93718.9883.737-3.608-4.1790.018
Interaction energy analysis for fragmet #1(B:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.837 / q_NPA : -0.933
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].
3B4ASN00.0470.0233.676-15.813-11.7720.055-2.205-1.8910.017
4B5THR0-0.062-0.0211.860-9.743-10.0663.683-1.348-2.0110.001
5B6VAL00.0540.0184.628-6.237-5.904-0.001-0.055-0.2770.000
6B7SER0-0.056-0.0306.663-4.936-4.9360.0000.0000.0000.000
7B8SER0-0.025-0.0427.393-4.178-4.1780.0000.0000.0000.000
8B9PHE0-0.024-0.0128.638-2.447-2.4470.0000.0000.0000.000
9B10GLN00.0500.03010.013-3.379-3.3790.0000.0000.0000.000
10B11VAL00.0550.02812.271-1.803-1.8030.0000.0000.0000.000
11B12ASP-1-0.799-0.85912.97018.66918.6690.0000.0000.0000.000
12B13CYS0-0.074-0.02914.167-1.424-1.4240.0000.0000.0000.000
13B14PHE00.0290.01016.756-1.373-1.3730.0000.0000.0000.000
14B15LEU00.014-0.00816.972-1.118-1.1180.0000.0000.0000.000
15B16TRP0-0.068-0.04419.071-1.010-1.0100.0000.0000.0000.000
16B17HIS00.0380.01320.915-0.872-0.8720.0000.0000.0000.000
17B18VAL0-0.050-0.01422.752-0.732-0.7320.0000.0000.0000.000
18B19ARG10.8310.89720.303-13.921-13.9210.0000.0000.0000.000
19B20LYS10.7730.87125.041-11.118-11.1180.0000.0000.0000.000
20B21ARG10.9840.99025.859-11.972-11.9720.0000.0000.0000.000
21B22PHE0-0.002-0.00228.482-0.367-0.3670.0000.0000.0000.000
22B23ALA0-0.017-0.02929.375-0.341-0.3410.0000.0000.0000.000
23B24ASP-1-0.807-0.87730.6879.9219.9210.0000.0000.0000.000
24B25GLN0-0.096-0.03532.963-0.203-0.2030.0000.0000.0000.000
25B26GLU-1-0.968-0.97834.7127.7747.7740.0000.0000.0000.000
26B27LEU0-0.030-0.01233.542-0.184-0.1840.0000.0000.0000.000
27B28GLY0-0.056-0.01431.757-0.004-0.0040.0000.0000.0000.000
28B29ASP-1-0.832-0.92431.9879.0529.0520.0000.0000.0000.000
29B30ALA00.034-0.00132.2580.2470.2470.0000.0000.0000.000
30B31PRO00.0530.02930.0350.2880.2880.0000.0000.0000.000
31B32PHE0-0.0060.00326.9620.5030.5030.0000.0000.0000.000
32B33LEU00.0450.02527.3230.4860.4860.0000.0000.0000.000
33B34ASP-1-0.943-0.96427.9529.9219.9210.0000.0000.0000.000
34B35ARG10.9400.95423.916-10.318-10.3180.0000.0000.0000.000
35B36LEU0-0.025-0.00423.4060.5620.5620.0000.0000.0000.000
36B37ARG10.9370.95923.719-9.558-9.5580.0000.0000.0000.000
37B38ALA0-0.0050.00122.9520.3240.3240.0000.0000.0000.000
38B39ASP-1-0.748-0.86619.38114.45714.4570.0000.0000.0000.000
39B40GLN00.0130.03118.9310.7810.7810.0000.0000.0000.000
40B41ALA0-0.031-0.02020.1120.5210.5210.0000.0000.0000.000
41B42SER00.0010.00016.5720.7620.7620.0000.0000.0000.000
42B43LEU0-0.008-0.00514.4711.0701.0700.0000.0000.0000.000
43B44ARG10.8970.93515.752-12.160-12.1600.0000.0000.0000.000
44B45GLY00.0130.02516.3490.3150.3150.0000.0000.0000.000
45B46ARG10.8300.8879.948-21.507-21.5070.0000.0000.0000.000
46B47GLY00.0360.02211.3042.0072.0070.0000.0000.0000.000
47B48SER0-0.032-0.01613.488-0.124-0.1240.0000.0000.0000.000
48B49THR0-0.074-0.04210.428-0.109-0.1090.0000.0000.0000.000
49B50LEU0-0.045-0.0056.0731.0951.0950.0000.0000.0000.000
50B51GLY00.0080.0279.2551.7041.7040.0000.0000.0000.000
51B52LEU0-0.057-0.0478.7611.0601.0600.0000.0000.0000.000
52B53ASP-1-0.881-0.93613.01415.42115.4210.0000.0000.0000.000
53B54ILE00.0540.02116.1110.6060.6060.0000.0000.0000.000
54B55GLU-1-0.897-0.93017.62314.49014.4900.0000.0000.0000.000
55B56THR00.001-0.00616.2190.3570.3570.0000.0000.0000.000
56B57ALA00.0280.01213.8670.4760.4760.0000.0000.0000.000
57B58THR0-0.034-0.03515.3610.1910.1910.0000.0000.0000.000
58B59ARG10.8370.89818.276-14.651-14.6510.0000.0000.0000.000
59B60ALA0-0.028-0.01913.725-0.322-0.3220.0000.0000.0000.000
60B61GLY00.0440.00915.4300.2480.2480.0000.0000.0000.000
61B62LYS10.8590.93516.173-14.146-14.1460.0000.0000.0000.000
62B63GLN00.0240.00915.750-1.275-1.2750.0000.0000.0000.000
63B64ILE0-0.037-0.01012.557-0.117-0.1170.0000.0000.0000.000
64B65VAL00.0140.00016.817-0.248-0.2480.0000.0000.0000.000
65B66GLU-1-0.875-0.93119.54813.13413.1340.0000.0000.0000.000
66B67ARG10.9380.96516.869-18.619-18.6190.0000.0000.0000.000
67B68ILE00.0070.00917.224-0.397-0.3970.0000.0000.0000.000
68B69LEU0-0.020-0.01620.916-0.511-0.5110.0000.0000.0000.000
69B70GLU-1-0.800-0.89023.92911.07611.0760.0000.0000.0000.000
70B71GLU-1-1.007-1.01920.24615.78215.7820.0000.0000.0000.000
71B72GLU-1-0.928-0.94424.19512.59012.5900.0000.0000.0000.000
72B73SER0-0.040-0.01625.887-0.538-0.5380.0000.0000.0000.000
73B74ASP-1-0.911-0.97128.3389.9729.9720.0000.0000.0000.000
74B75GLU-1-0.798-0.90430.7289.9829.9820.0000.0000.0000.000
75B76ALA0-0.072-0.02532.5860.0120.0120.0000.0000.0000.000
76B77LEU0-0.054-0.02927.404-0.038-0.0380.0000.0000.0000.000
77B78LYS10.7890.91328.039-10.379-10.3790.0000.0000.0000.000
78B79MET0-0.098-0.05927.544-0.350-0.3500.0000.0000.0000.000
79B80PRO00.0360.02827.6210.3720.3720.0000.0000.0000.000
80B81ALA0-0.018-0.01025.194-0.146-0.1460.0000.0000.0000.000
81B82SER0-0.069-0.03127.1830.0190.0190.0000.0000.0000.000
82B83ARG10.7720.86029.314-11.035-11.0350.0000.0000.0000.000
83B84TYR00.0330.00431.7260.0530.0530.0000.0000.0000.000
84B85LEU0-0.0230.00231.516-0.117-0.1170.0000.0000.0000.000
85B86THR0-0.023-0.02635.700-0.076-0.0760.0000.0000.0000.000
86B87ASP-1-0.701-0.78637.8448.6458.6450.0000.0000.0000.000
87B88MET0-0.103-0.03640.411-0.282-0.2820.0000.0000.0000.000
88B89THR0-0.006-0.03043.6090.0010.0010.0000.0000.0000.000
89B90LEU00.0360.00146.1660.0630.0630.0000.0000.0000.000
90B91GLU-1-0.787-0.84747.7866.2596.2590.0000.0000.0000.000
91B92GLU-1-0.726-0.82046.7197.0387.0380.0000.0000.0000.000
92B93MET0-0.039-0.02142.0080.0670.0670.0000.0000.0000.000
93B94SER0-0.083-0.05446.132-0.025-0.0250.0000.0000.0000.000
94B95ARG10.7700.86749.327-6.418-6.4180.0000.0000.0000.000
95B96ASP-1-0.896-0.93050.4966.2096.2090.0000.0000.0000.000
96B97TRP0-0.067-0.05746.938-0.065-0.0650.0000.0000.0000.000
97B98PHE0-0.016-0.02152.5130.0080.0080.0000.0000.0000.000
98B99MET0-0.0520.00449.5460.0770.0770.0000.0000.0000.000
99B100LEU00.001-0.00653.176-0.097-0.0970.0000.0000.0000.000
100B101MET0-0.070-0.04054.000-0.097-0.0970.0000.0000.0000.000
101B102PRO00.000-0.00951.2510.1460.1460.0000.0000.0000.000
102B103LYS10.8840.94245.449-7.121-7.1210.0000.0000.0000.000
103B104GLN00.007-0.00945.2640.1480.1480.0000.0000.0000.000
104B105LYS10.9440.97737.788-8.502-8.5020.0000.0000.0000.000
105B106VAL0-0.0030.01239.5770.0790.0790.0000.0000.0000.000
106B107ALA0-0.057-0.03835.7580.0100.0100.0000.0000.0000.000
107B108GLY00.0330.02034.6730.1760.1760.0000.0000.0000.000
108B109SER00.014-0.01034.6200.0980.0980.0000.0000.0000.000
109B110LEU00.0440.02833.329-0.020-0.0200.0000.0000.0000.000
110B111CYS0-0.050-0.02237.705-0.158-0.1580.0000.0000.0000.000
111B112ILE00.0030.00337.1950.0570.0570.0000.0000.0000.000
112B113ARG10.8600.89841.373-7.274-7.2740.0000.0000.0000.000
113B114MET00.0300.03842.7240.1120.1120.0000.0000.0000.000
114B115ASP-1-0.741-0.86646.6636.0596.0590.0000.0000.0000.000
115B116GLN0-0.018-0.01948.7010.1940.1940.0000.0000.0000.000
116B117ALA0-0.019-0.00751.258-0.035-0.0350.0000.0000.0000.000
117B118ILE0-0.051-0.00850.176-0.095-0.0950.0000.0000.0000.000
118B119MET00.0630.03550.8130.0660.0660.0000.0000.0000.000
119B120ASP-1-0.910-0.92651.1156.0326.0320.0000.0000.0000.000
120B121LYS10.8500.91150.217-6.185-6.1850.0000.0000.0000.000
121B122ASN0-0.031-0.02047.3190.2840.2840.0000.0000.0000.000
122B123ILE0-0.011-0.01943.946-0.065-0.0650.0000.0000.0000.000
123B124ILE0-0.088-0.02240.5330.1780.1780.0000.0000.0000.000
124B125LEU00.0020.00737.985-0.124-0.1240.0000.0000.0000.000
125B126LYS10.8200.89439.240-7.139-7.1390.0000.0000.0000.000
126B127ALA00.003-0.02936.441-0.066-0.0660.0000.0000.0000.000
127B128ASN00.0010.01937.7880.0880.0880.0000.0000.0000.000
128B129PHE00.004-0.01430.8670.0230.0230.0000.0000.0000.000
129B130SER00.030-0.01131.346-0.162-0.1620.0000.0000.0000.000
130B131VAL0-0.032-0.01727.1250.1870.1870.0000.0000.0000.000
131B132ILE00.0320.00324.382-0.201-0.2010.0000.0000.0000.000
132B133PHE00.0530.02720.4690.6190.6190.0000.0000.0000.000
133B134ASP-1-0.827-0.89721.34813.94913.9490.0000.0000.0000.000
134B135ARG10.9040.96318.665-15.758-15.7580.0000.0000.0000.000
135B136LEU0-0.0030.01224.162-0.277-0.2770.0000.0000.0000.000
136B137GLU-1-0.824-0.86926.53911.41111.4110.0000.0000.0000.000
137B138THR0-0.022-0.00728.218-0.111-0.1110.0000.0000.0000.000
138B139LEU0-0.0020.01131.775-0.172-0.1720.0000.0000.0000.000
139B140ILE0-0.067-0.03434.428-0.107-0.1070.0000.0000.0000.000
140B141LEU0-0.030-0.02838.014-0.179-0.1790.0000.0000.0000.000
141B142LEU00.0280.02936.4370.1060.1060.0000.0000.0000.000
142B143ARG10.7930.87139.772-7.093-7.0930.0000.0000.0000.000
143B144ALA0-0.0030.00642.4610.1340.1340.0000.0000.0000.000
144B145PHE0-0.019-0.02744.081-0.182-0.1820.0000.0000.0000.000
145B146THR00.004-0.02846.7790.1180.1180.0000.0000.0000.000
146B147GLU-1-0.883-0.93249.4566.4996.4990.0000.0000.0000.000
147B148GLU-1-0.895-0.91950.6746.0906.0900.0000.0000.0000.000
148B149GLY0-0.0040.00250.183-0.079-0.0790.0000.0000.0000.000
149B150ALA00.0010.00551.0280.0210.0210.0000.0000.0000.000
150B151ILE0-0.022-0.00547.0150.1100.1100.0000.0000.0000.000
151B152VAL00.0210.00747.148-0.121-0.1210.0000.0000.0000.000
152B153GLY00.013-0.00744.8900.0220.0220.0000.0000.0000.000
153B154GLU-1-0.805-0.88142.9727.1127.1120.0000.0000.0000.000
154B155ILE00.0200.02436.6630.0350.0350.0000.0000.0000.000
155B156SER00.008-0.00139.850-0.034-0.0340.0000.0000.0000.000
156B157PRO00.0310.02036.764-0.024-0.0240.0000.0000.0000.000
157B158LEU0-0.074-0.02638.330-0.267-0.2670.0000.0000.0000.000
158B159PRO00.0280.00138.9230.1780.1780.0000.0000.0000.000
159B160SER0-0.045-0.01240.3330.1090.1090.0000.0000.0000.000
160B161LEU0-0.040-0.01537.324-0.001-0.0010.0000.0000.0000.000
161B162PRO00.0260.01132.7810.0520.0520.0000.0000.0000.000
162B163GLY00.0370.03531.528-0.138-0.1380.0000.0000.0000.000
163B164HIS00.0130.01631.0130.1700.1700.0000.0000.0000.000
164B165THR0-0.008-0.04025.8980.3110.3110.0000.0000.0000.000
165B166ASP-1-0.841-0.95224.24112.93312.9330.0000.0000.0000.000
166B167GLU-1-0.848-0.91323.61212.99112.9910.0000.0000.0000.000
167B168ASP-1-0.841-0.88526.83510.63210.6320.0000.0000.0000.000
168B169VAL0-0.017-0.01029.855-0.423-0.4230.0000.0000.0000.000
169B170LYS10.8650.94224.802-13.047-13.0470.0000.0000.0000.000
170B171ASN0-0.047-0.03627.874-0.450-0.4500.0000.0000.0000.000
171B172ALA0-0.023-0.01631.560-0.331-0.3310.0000.0000.0000.000
172B173ILE00.0230.00432.729-0.367-0.3670.0000.0000.0000.000
173B174GLY00.0380.03133.800-0.256-0.2560.0000.0000.0000.000
174B175VAL0-0.080-0.04735.029-0.286-0.2860.0000.0000.0000.000
175B176LEU0-0.022-0.00637.625-0.289-0.2890.0000.0000.0000.000
176B177ILE00.0330.01135.979-0.225-0.2250.0000.0000.0000.000
177B178GLY00.0680.04638.949-0.161-0.1610.0000.0000.0000.000
178B179GLY0-0.079-0.06740.376-0.224-0.2240.0000.0000.0000.000
179B180LEU0-0.003-0.01242.461-0.204-0.2040.0000.0000.0000.000
180B181GLU-1-0.855-0.93140.4687.9287.9280.0000.0000.0000.000
181B182TRP0-0.097-0.04142.075-0.174-0.1740.0000.0000.0000.000
182B183ASN0-0.111-0.03846.124-0.120-0.1200.0000.0000.0000.000
183B184ASP-1-0.882-0.94847.8006.4226.4220.0000.0000.0000.000
184B185ASN0-0.103-0.06346.451-0.198-0.1980.0000.0000.0000.000
185B186THR00.0310.01744.1650.1780.1780.0000.0000.0000.000
186B187VAL0-0.015-0.01240.337-0.076-0.0760.0000.0000.0000.000
187B188ARG10.9090.96139.881-7.078-7.0780.0000.0000.0000.000
188B189VAL00.0630.02134.523-0.104-0.1040.0000.0000.0000.000
189B190SER0-0.008-0.01836.8070.0840.0840.0000.0000.0000.000
190B191GLU-1-0.888-0.96333.61110.05110.0510.0000.0000.0000.000
191B192THR00.027-0.00832.9270.3980.3980.0000.0000.0000.000
192B193LEU0-0.009-0.00931.7010.4380.4380.0000.0000.0000.000
193B194GLN0-0.098-0.04931.3180.4670.4670.0000.0000.0000.000
194B195ARG10.8650.94226.409-11.261-11.2610.0000.0000.0000.000
195B196PHE0-0.076-0.04726.2140.4750.4750.0000.0000.0000.000
196B197ALA00.0390.01727.2910.3450.3450.0000.0000.0000.000
197B198TRP0-0.095-0.03825.493-0.191-0.1910.0000.0000.0000.000