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: 17RYZ

Calculation Name: 4ONS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ONS

Chain ID: A

ChEMBL ID:

UniProt ID: Q61301

Base Structure: X-ray

Registration Date: 2023-09-20

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2359041.574622
FMO2-HF: Nuclear repulsion 2268687.931629
FMO2-HF: Total energy -90353.642993
FMO2-MP2: Total energy -90615.035457


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:GLU)


Summations of interaction energy for fragment #1(A:18:GLU)
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.
-49.998-46.1822.459-2.46-3.8150.014
Interaction energy analysis for fragmet #1(A:18:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.999 / q_NPA : -1.010
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].
3A20ARG10.8960.9422.083-68.409-64.5932.459-2.460-3.8150.014
4A21THR00.1490.0715.601-1.252-1.2520.0000.0000.0000.000
5A22LEU0-0.0140.0078.683-1.881-1.8810.0000.0000.0000.000
6A23THR0-0.041-0.0329.551-2.164-2.1640.0000.0000.0000.000
7A24VAL00.0740.03111.381-1.124-1.1240.0000.0000.0000.000
8A25GLU-1-0.856-0.95112.97117.71817.7180.0000.0000.0000.000
9A26ARG10.9090.95114.366-18.731-18.7310.0000.0000.0000.000
10A27LEU0-0.019-0.00216.143-0.899-0.8990.0000.0000.0000.000
11A28LEU00.0220.01317.092-0.772-0.7720.0000.0000.0000.000
12A29GLU-1-0.922-0.94319.14712.00512.0050.0000.0000.0000.000
13A30PRO00.024-0.00220.764-0.658-0.6580.0000.0000.0000.000
14A31LEU00.0050.00222.635-0.552-0.5520.0000.0000.0000.000
15A32VAL00.0080.01121.451-0.513-0.5130.0000.0000.0000.000
16A33THR0-0.012-0.00424.510-0.585-0.5850.0000.0000.0000.000
17A34GLN0-0.0030.01326.415-0.182-0.1820.0000.0000.0000.000
18A35VAL0-0.029-0.00927.516-0.405-0.4050.0000.0000.0000.000
19A36THR0-0.035-0.00527.310-0.230-0.2300.0000.0000.0000.000
20A37THR0-0.043-0.02530.080-0.124-0.1240.0000.0000.0000.000
21A38LEU0-0.067-0.03432.573-0.153-0.1530.0000.0000.0000.000
22A39VAL00.0160.01836.061-0.228-0.2280.0000.0000.0000.000
23A52GLY00.0490.02549.169-0.071-0.0710.0000.0000.0000.000
24A53ARG10.9780.99344.603-6.510-6.5100.0000.0000.0000.000
25A54SER0-0.027-0.00945.080-0.142-0.1420.0000.0000.0000.000
26A55LYS11.0000.97845.302-5.739-5.7390.0000.0000.0000.000
27A56LYS10.9820.97145.285-6.079-6.0790.0000.0000.0000.000
28A57ALA00.0290.02341.8040.0980.0980.0000.0000.0000.000
29A58HIS00.0410.01440.6320.2310.2310.0000.0000.0000.000
30A59VAL0-0.0130.01840.6380.1070.1070.0000.0000.0000.000
31A60LEU0-0.012-0.00338.7150.1350.1350.0000.0000.0000.000
32A61ALA00.0420.02136.4880.2080.2080.0000.0000.0000.000
33A62ALA00.0150.01035.7930.1980.1980.0000.0000.0000.000
34A63SER0-0.039-0.03136.1330.1180.1180.0000.0000.0000.000
35A64VAL00.0110.01431.2480.1720.1720.0000.0000.0000.000
36A65GLU-1-0.829-0.86431.6359.5239.5230.0000.0000.0000.000
37A66GLN0-0.026-0.01831.9780.3450.3450.0000.0000.0000.000
38A67ALA00.009-0.00331.0460.1620.1620.0000.0000.0000.000
39A68THR0-0.049-0.05926.8850.3910.3910.0000.0000.0000.000
40A69GLN0-0.021-0.03227.5590.5000.5000.0000.0000.0000.000
41A70ASN0-0.038-0.01828.9130.0180.0180.0000.0000.0000.000
42A71PHE0-0.026-0.01321.4250.1910.1910.0000.0000.0000.000
43A72LEU0-0.009-0.01923.0360.4540.4540.0000.0000.0000.000
44A73GLU-1-0.907-0.93424.5619.7989.7980.0000.0000.0000.000
45A74LYS10.9130.94925.291-10.051-10.0510.0000.0000.0000.000
46A75GLY00.0310.02221.3900.3660.3660.0000.0000.0000.000
47A76GLU-1-0.888-0.95320.57411.98511.9850.0000.0000.0000.000
48A77GLN0-0.084-0.03022.1680.1630.1630.0000.0000.0000.000
49A78ILE00.0290.00318.9810.1740.1740.0000.0000.0000.000
50A79ALA00.0060.00617.4670.6210.6210.0000.0000.0000.000
51A80LYS10.8880.95318.192-10.893-10.8930.0000.0000.0000.000
52A81GLU-1-0.984-1.01220.58812.15112.1510.0000.0000.0000.000
53A82SER0-0.035-0.00415.1000.0680.0680.0000.0000.0000.000
54A83GLN0-0.031-0.03616.7370.2140.2140.0000.0000.0000.000
55A84ASP-1-0.863-0.92611.62421.62921.6290.0000.0000.0000.000
56A85LEU00.008-0.0047.695-0.606-0.6060.0000.0000.0000.000
57A86LYS10.9550.99311.096-16.369-16.3690.0000.0000.0000.000
58A87GLU-1-0.917-0.96011.10520.38820.3880.0000.0000.0000.000
59A88GLU-1-0.860-0.9307.70824.91924.9190.0000.0000.0000.000
60A89LEU00.015-0.00410.630-1.039-1.0390.0000.0000.0000.000
61A90VAL00.0020.00013.825-1.011-1.0110.0000.0000.0000.000
62A91ALA00.0060.00912.370-0.927-0.9270.0000.0000.0000.000
63A92ALA0-0.007-0.00613.428-0.644-0.6440.0000.0000.0000.000
64A93VAL0-0.0050.00015.025-0.770-0.7700.0000.0000.0000.000
65A94GLU-1-0.904-0.96417.59612.32712.3270.0000.0000.0000.000
66A95ASP-1-0.934-0.96416.25014.52114.5210.0000.0000.0000.000
67A96VAL00.0130.00818.354-0.673-0.6730.0000.0000.0000.000
68A97ARG10.9020.96320.739-12.412-12.4120.0000.0000.0000.000
69A98LYS10.9150.96118.688-14.103-14.1030.0000.0000.0000.000
70A99GLN0-0.032-0.01919.853-1.023-1.0230.0000.0000.0000.000
71A100GLY00.0280.01823.742-0.420-0.4200.0000.0000.0000.000
72A101GLU-1-0.850-0.93326.4008.9528.9520.0000.0000.0000.000
73A102THR0-0.029-0.00725.886-0.408-0.4080.0000.0000.0000.000
74A103MET0-0.040-0.00627.882-0.341-0.3410.0000.0000.0000.000
75A104ARG10.9010.96529.583-9.188-9.1880.0000.0000.0000.000
76A105ILE0-0.015-0.01630.780-0.330-0.3300.0000.0000.0000.000
77A106ALA0-0.0070.00131.917-0.265-0.2650.0000.0000.0000.000
78A107SER0-0.016-0.04032.958-0.277-0.2770.0000.0000.0000.000
79A108SER0-0.037-0.01235.433-0.249-0.2490.0000.0000.0000.000
80A109GLU-1-0.910-0.95136.5987.4177.4170.0000.0000.0000.000
81A110PHE0-0.043-0.01937.634-0.223-0.2230.0000.0000.0000.000
82A111ALA0-0.040-0.02139.357-0.182-0.1820.0000.0000.0000.000
83A112ASP-1-0.899-0.95941.4626.8186.8180.0000.0000.0000.000
84A113ASP-1-0.870-0.94242.9386.7056.7050.0000.0000.0000.000
85A114PRO0-0.022-0.00542.4650.0880.0880.0000.0000.0000.000
86A115CYS0-0.029-0.02643.545-0.018-0.0180.0000.0000.0000.000
87A116SER00.0000.02141.6630.0650.0650.0000.0000.0000.000
88A117SER00.0670.00740.2920.0780.0780.0000.0000.0000.000
89A118VAL00.0250.01337.3240.2070.2070.0000.0000.0000.000
90A119LYS10.9430.98336.414-6.844-6.8440.0000.0000.0000.000
91A120ARG10.9220.98836.291-7.361-7.3610.0000.0000.0000.000
92A121GLY00.004-0.00734.4180.1970.1970.0000.0000.0000.000
93A122THR0-0.057-0.06431.8900.3220.3220.0000.0000.0000.000
94A123MET00.0250.03331.1850.2200.2200.0000.0000.0000.000
95A124VAL0-0.012-0.00330.9170.2550.2550.0000.0000.0000.000
96A125ARG10.9250.95828.078-9.028-9.0280.0000.0000.0000.000
97A126ALA00.0410.03326.6710.3950.3950.0000.0000.0000.000
98A127ALA00.0330.00626.4920.3080.3080.0000.0000.0000.000
99A128ARG10.8680.91924.272-10.104-10.1040.0000.0000.0000.000
100A129ALA00.0070.00622.4060.4760.4760.0000.0000.0000.000
101A130LEU00.0390.02121.7030.5210.5210.0000.0000.0000.000
102A131LEU00.010-0.00822.3310.3990.3990.0000.0000.0000.000
103A132SER0-0.0080.00419.1290.4290.4290.0000.0000.0000.000
104A133ALA00.0530.03817.7480.7800.7800.0000.0000.0000.000
105A134VAL0-0.034-0.01517.9380.5330.5330.0000.0000.0000.000
106A135THR0-0.036-0.03617.2350.2680.2680.0000.0000.0000.000
107A136ARG10.8780.9408.731-21.910-21.9100.0000.0000.0000.000
108A137LEU00.0150.00914.0511.0141.0140.0000.0000.0000.000
109A138LEU0-0.024-0.01415.8350.3780.3780.0000.0000.0000.000
110A139ILE0-0.017-0.00111.6070.4520.4520.0000.0000.0000.000
111A140LEU0-0.018-0.0139.2911.1181.1180.0000.0000.0000.000
112A141ALA0-0.015-0.01612.3950.6040.6040.0000.0000.0000.000
113A142ASP-1-0.902-0.93914.86717.71917.7190.0000.0000.0000.000
114A143MET0-0.040-0.0297.5210.8290.8290.0000.0000.0000.000
115A144ALA0-0.012-0.00411.4541.2091.2090.0000.0000.0000.000
116A145ASP-1-0.887-0.93213.41215.23115.2310.0000.0000.0000.000
117A146VAL0-0.039-0.02512.701-0.539-0.5390.0000.0000.0000.000
118A147MET0-0.014-0.0099.2471.0031.0030.0000.0000.0000.000
119A148ARG10.9871.00713.236-15.391-15.3910.0000.0000.0000.000
120A149LEU0-0.056-0.00416.772-0.929-0.9290.0000.0000.0000.000
121A150LEU0-0.022-0.01812.599-0.755-0.7550.0000.0000.0000.000
122A151SER0-0.033-0.02816.445-0.377-0.3770.0000.0000.0000.000
123A152HIS00.0480.01517.477-0.339-0.3390.0000.0000.0000.000
124A153LEU0-0.063-0.03017.407-0.647-0.6470.0000.0000.0000.000
125A154LYS10.9850.99014.514-20.042-20.0420.0000.0000.0000.000
126A155ILE00.0660.05019.034-0.482-0.4820.0000.0000.0000.000
127A156VAL0-0.037-0.02522.024-0.716-0.7160.0000.0000.0000.000
128A157GLU-1-0.943-0.98219.62315.55915.5590.0000.0000.0000.000
129A158GLU-1-0.893-0.95419.35215.06315.0630.0000.0000.0000.000
130A159ALA0-0.040-0.01623.421-0.590-0.5900.0000.0000.0000.000
131A160LEU0-0.070-0.05226.169-0.635-0.6350.0000.0000.0000.000
132A161GLU-1-0.911-0.95022.30813.49913.4990.0000.0000.0000.000
133A162ALA0-0.017-0.00626.909-0.387-0.3870.0000.0000.0000.000
134A163VAL0-0.047-0.03129.547-0.434-0.4340.0000.0000.0000.000
135A164LYS10.9030.97127.653-11.569-11.5690.0000.0000.0000.000
136A165ASN0-0.058-0.03527.791-0.441-0.4410.0000.0000.0000.000
137A166ALA00.0300.04231.810-0.083-0.0830.0000.0000.0000.000
138A167THR00.0060.00534.824-0.212-0.2120.0000.0000.0000.000
139A168ASN00.028-0.00937.878-0.106-0.1060.0000.0000.0000.000
140A169GLU-1-0.774-0.92839.9237.6897.6890.0000.0000.0000.000
141A170GLN0-0.0290.00241.337-0.031-0.0310.0000.0000.0000.000
142A171ASP-1-0.889-0.94336.3358.6218.6210.0000.0000.0000.000
143A172LEU00.0170.01536.3500.2220.2220.0000.0000.0000.000
144A173ALA00.0110.01436.7990.1600.1600.0000.0000.0000.000
145A174ASN0-0.029-0.02735.7180.0730.0730.0000.0000.0000.000
146A175ARG10.9460.97031.884-9.497-9.4970.0000.0000.0000.000
147A176PHE00.0100.00132.5530.2780.2780.0000.0000.0000.000
148A177LYS10.8590.92734.695-7.952-7.9520.0000.0000.0000.000
149A178GLU-1-0.924-0.96230.77310.03010.0300.0000.0000.0000.000
150A179PHE00.0940.05028.5790.1630.1630.0000.0000.0000.000
151A180GLY00.0160.01530.1710.2020.2020.0000.0000.0000.000
152A181LYS10.8940.94332.023-8.974-8.9740.0000.0000.0000.000
153A182GLU-1-0.839-0.93126.44011.79611.7960.0000.0000.0000.000
154A183MET0-0.051-0.00427.4610.3880.3880.0000.0000.0000.000
155A184VAL0-0.038-0.02029.0290.0670.0670.0000.0000.0000.000
156A185LYS10.9220.95427.176-10.875-10.8750.0000.0000.0000.000
157A186LEU00.0570.04122.8610.2700.2700.0000.0000.0000.000
158A187ASN0-0.051-0.04625.9990.3000.3000.0000.0000.0000.000
159A188TYR0-0.0180.01126.298-0.023-0.0230.0000.0000.0000.000
160A189VAL00.0550.02321.494-0.149-0.1490.0000.0000.0000.000
161A190ALA00.0320.01024.4280.1210.1210.0000.0000.0000.000
162A191ALA0-0.047-0.01725.351-0.129-0.1290.0000.0000.0000.000
163A192ARG10.9310.94525.711-11.412-11.4120.0000.0000.0000.000
164A193ARG10.9701.00720.430-14.313-14.3130.0000.0000.0000.000
165A194GLN00.0770.04624.4530.1980.1980.0000.0000.0000.000
166A195GLN0-0.074-0.03927.122-0.110-0.1100.0000.0000.0000.000
167A196GLU-1-0.916-0.95223.48612.46712.4670.0000.0000.0000.000
168A197LEU0-0.0510.01023.0910.1540.1540.0000.0000.0000.000
169A198LYS10.9650.98226.135-11.178-11.1780.0000.0000.0000.000
170A199ASP-1-0.832-0.92226.68510.85310.8530.0000.0000.0000.000
171A200PRO0-0.004-0.01528.4180.1220.1220.0000.0000.0000.000
172A201HIS00.0420.02927.604-0.407-0.4070.0000.0000.0000.000
173A202CYS00.005-0.00924.8670.2870.2870.0000.0000.0000.000
174A203ARG10.8250.90426.629-9.889-9.8890.0000.0000.0000.000
175A204ASP-1-0.901-0.94428.9369.6799.6790.0000.0000.0000.000
176A205GLU-1-0.914-0.95924.56512.79812.7980.0000.0000.0000.000
177A206MET0-0.0190.00322.8310.1620.1620.0000.0000.0000.000
178A207ALA0-0.036-0.03026.559-0.032-0.0320.0000.0000.0000.000
179A208ALA0-0.0010.01929.130-0.268-0.2680.0000.0000.0000.000
180A209ALA00.0300.02125.117-0.178-0.1780.0000.0000.0000.000
181A210ARG10.9040.92327.183-10.836-10.8360.0000.0000.0000.000
182A211GLY0-0.031-0.01228.222-0.285-0.2850.0000.0000.0000.000
183A212ALA0-0.040-0.02228.572-0.326-0.3260.0000.0000.0000.000
184A213LEU00.0570.03225.629-0.261-0.2610.0000.0000.0000.000
185A214LYS10.9420.98328.774-9.218-9.2180.0000.0000.0000.000
186A215LYS10.9840.99332.039-9.193-9.1930.0000.0000.0000.000
187A216ASN00.021-0.00530.260-0.346-0.3460.0000.0000.0000.000
188A217ALA00.0850.06430.410-0.046-0.0460.0000.0000.0000.000
189A218THR0-0.077-0.06431.886-0.245-0.2450.0000.0000.0000.000
190A219MET0-0.022-0.01534.369-0.182-0.1820.0000.0000.0000.000
191A220LEU00.0430.02729.668-0.175-0.1750.0000.0000.0000.000
192A221TYR0-0.0060.01333.688-0.105-0.1050.0000.0000.0000.000
193A222THR0-0.005-0.01536.287-0.251-0.2510.0000.0000.0000.000
194A223ALA0-0.018-0.00735.273-0.189-0.1890.0000.0000.0000.000
195A224SER0-0.009-0.02934.3530.0220.0220.0000.0000.0000.000
196A225GLN0-0.046-0.02036.607-0.138-0.1380.0000.0000.0000.000
197A226ALA0-0.059-0.03640.146-0.194-0.1940.0000.0000.0000.000
198A227PHE00.011-0.00537.416-0.056-0.0560.0000.0000.0000.000
199A228LEU0-0.047-0.01038.639-0.084-0.0840.0000.0000.0000.000
200A229ARG10.8840.94741.497-7.299-7.2990.0000.0000.0000.000
201A230HIS0-0.039-0.01243.226-0.213-0.2130.0000.0000.0000.000
202A231PRO00.0260.02241.0970.1410.1410.0000.0000.0000.000
203A232ASP-1-0.878-0.93141.2527.3417.3410.0000.0000.0000.000
204A233VAL0-0.046-0.00442.548-0.038-0.0380.0000.0000.0000.000
205A234ALA00.0580.03639.3850.1970.1970.0000.0000.0000.000
206A235ALA00.026-0.00138.2930.2500.2500.0000.0000.0000.000
207A236THR0-0.019-0.03138.4060.2050.2050.0000.0000.0000.000
208A237ARG10.9650.98832.305-9.301-9.3010.0000.0000.0000.000
209A238ALA0-0.0020.00734.1620.3050.3050.0000.0000.0000.000
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