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: 5JYMZ

Calculation Name: 2AFR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AFR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EXP7

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2534561.100613
FMO2-HF: Nuclear repulsion 2451414.264141
FMO2-HF: Total energy -83146.836472
FMO2-MP2: Total energy -83390.990657


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:6:GLN)


Summations of interaction energy for fragment #1(A:6:GLN)
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.
-0.8380.549-0.017-0.732-0.6380.001
Interaction energy analysis for fragmet #1(A:6:GLN)
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 : -0.016
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].
3A8THR00.0400.0273.8780.8262.213-0.017-0.732-0.6380.001
4A9ASN00.0530.0186.8680.0470.0470.0000.0000.0000.000
5A10LEU00.0320.0329.2540.0440.0440.0000.0000.0000.000
6A11GLY00.0530.0248.7290.0570.0570.0000.0000.0000.000
7A12ARG10.9370.9525.3910.2520.2520.0000.0000.0000.000
8A13ASN00.0140.0058.9460.1060.1060.0000.0000.0000.000
9A14ILE00.0200.01712.4000.0480.0480.0000.0000.0000.000
10A15GLU-1-0.829-0.8959.2230.9260.9260.0000.0000.0000.000
11A16ASN0-0.029-0.02110.774-0.001-0.0010.0000.0000.0000.000
12A17LYS10.9620.99813.780-0.044-0.0440.0000.0000.0000.000
13A18SER00.008-0.01614.928-0.010-0.0100.0000.0000.0000.000
14A19PHE0-0.031-0.02511.5110.0200.0200.0000.0000.0000.000
15A20SER0-0.020-0.01816.834-0.013-0.0130.0000.0000.0000.000
16A21ILE0-0.0100.00719.534-0.014-0.0140.0000.0000.0000.000
17A22ILE0-0.0040.00217.4620.0020.0020.0000.0000.0000.000
18A23ASP-1-0.814-0.90719.2630.3310.3310.0000.0000.0000.000
19A24GLU-1-1.005-0.98522.2020.0830.0830.0000.0000.0000.000
20A25GLU-1-0.934-0.97824.5570.0960.0960.0000.0000.0000.000
21A26ALA0-0.022-0.00923.964-0.002-0.0020.0000.0000.0000.000
22A27GLY00.0220.02425.957-0.005-0.0050.0000.0000.0000.000
23A28PRO0-0.018-0.01027.5210.0170.0170.0000.0000.0000.000
24A29HIS00.0160.00923.988-0.006-0.0060.0000.0000.0000.000
25A30SER00.0210.01028.394-0.010-0.0100.0000.0000.0000.000
26A31PHE0-0.042-0.00723.3020.0100.0100.0000.0000.0000.000
27A32ALA00.0730.03323.738-0.005-0.0050.0000.0000.0000.000
28A33GLN00.0410.01417.8620.0830.0830.0000.0000.0000.000
29A34GLU-1-0.784-0.87816.8720.7080.7080.0000.0000.0000.000
30A35GLU-1-0.822-0.93217.9210.5160.5160.0000.0000.0000.000
31A36TRP0-0.046-0.03820.0660.0150.0150.0000.0000.0000.000
32A37GLU-1-0.847-0.89814.3110.8420.8420.0000.0000.0000.000
33A38VAL0-0.023-0.00915.4190.0810.0810.0000.0000.0000.000
34A39VAL0-0.013-0.01017.067-0.014-0.0140.0000.0000.0000.000
35A40ARG10.8110.88915.311-0.532-0.5320.0000.0000.0000.000
36A41ARG10.8540.9289.263-1.143-1.1430.0000.0000.0000.000
37A42ILE0-0.009-0.00415.242-0.044-0.0440.0000.0000.0000.000
38A43ILE0-0.0160.00718.185-0.045-0.0450.0000.0000.0000.000
39A44HIS00.0290.00611.819-0.050-0.0500.0000.0000.0000.000
40A45ALA0-0.071-0.02615.100-0.050-0.0500.0000.0000.0000.000
41A46THR0-0.087-0.06516.374-0.045-0.0450.0000.0000.0000.000
42A47ALA00.0060.02019.808-0.028-0.0280.0000.0000.0000.000
43A48ASP-1-0.806-0.88621.6330.1390.1390.0000.0000.0000.000
44A49PHE00.0710.01523.0170.0320.0320.0000.0000.0000.000
45A50ASP-1-0.811-0.87225.1550.1610.1610.0000.0000.0000.000
46A51TYR00.011-0.00523.0670.0110.0110.0000.0000.0000.000
47A52LYS10.8430.93525.036-0.149-0.1490.0000.0000.0000.000
48A53ASN0-0.032-0.01925.9300.0050.0050.0000.0000.0000.000
49A54ILE0-0.048-0.03726.8810.0000.0000.0000.0000.0000.000
50A55THR0-0.040-0.03922.5150.0050.0050.0000.0000.0000.000
51A56LYS10.8560.93725.954-0.218-0.2180.0000.0000.0000.000
52A57ILE0-0.007-0.00221.0700.0120.0120.0000.0000.0000.000
53A58HIS00.0140.02325.2090.0080.0080.0000.0000.0000.000
54A59PRO00.0340.01325.2110.0320.0320.0000.0000.0000.000
55A60GLN00.0380.03224.936-0.003-0.0030.0000.0000.0000.000
56A61ALA0-0.0080.00222.2810.0260.0260.0000.0000.0000.000
57A62ILE00.0300.01817.3270.0610.0610.0000.0000.0000.000
58A63ASP-1-0.819-0.89919.0580.5130.5130.0000.0000.0000.000
59A64SER0-0.018-0.02420.6750.0130.0130.0000.0000.0000.000
60A65GLY00.0250.01118.6780.0020.0020.0000.0000.0000.000
61A66ILE0-0.043-0.01414.4490.0930.0930.0000.0000.0000.000
62A67GLN0-0.007-0.00816.8600.0410.0410.0000.0000.0000.000
63A68ALA00.0260.00519.527-0.009-0.0090.0000.0000.0000.000
64A69LEU00.004-0.01813.1130.0170.0170.0000.0000.0000.000
65A70LYS10.8410.91412.747-1.068-1.0680.0000.0000.0000.000
66A71LYS10.8980.96016.555-0.429-0.4290.0000.0000.0000.000
67A72GLY00.0630.03317.153-0.054-0.0540.0000.0000.0000.000
68A73CYS0-0.092-0.02418.192-0.027-0.0270.0000.0000.0000.000
69A74PRO00.0150.00719.1350.0400.0400.0000.0000.0000.000
70A75ILE0-0.003-0.01315.7720.0260.0260.0000.0000.0000.000
71A76VAL00.0140.01219.950-0.023-0.0230.0000.0000.0000.000
72A77CYS0-0.018-0.00320.0510.0280.0280.0000.0000.0000.000
73A78ASP-1-0.718-0.85122.7750.2000.2000.0000.0000.0000.000
74A79VAL0-0.008-0.02222.871-0.030-0.0300.0000.0000.0000.000
75A80GLN00.1100.04218.8910.0480.0480.0000.0000.0000.000
76A81MET0-0.0180.01918.9740.0130.0130.0000.0000.0000.000
77A82ILE00.0050.00917.4940.0060.0060.0000.0000.0000.000
78A83LEU00.0370.00916.0350.0630.0630.0000.0000.0000.000
79A84SER0-0.064-0.04414.8940.0140.0140.0000.0000.0000.000
80A85GLY00.0130.02312.572-0.098-0.0980.0000.0000.0000.000
81A86LEU0-0.064-0.02911.3390.1750.1750.0000.0000.0000.000
82A87ASN00.0200.0096.4750.2490.2490.0000.0000.0000.000
83A88PRO00.0780.0309.1390.3620.3620.0000.0000.0000.000
84A89GLU-1-0.901-0.9476.3260.3450.3450.0000.0000.0000.000
85A90ARG10.8590.9175.227-3.229-3.2290.0000.0000.0000.000
86A91LEU00.0210.0177.572-0.134-0.1340.0000.0000.0000.000
87A92LYS10.9600.97111.123-0.388-0.3880.0000.0000.0000.000
88A93VAL0-0.061-0.0287.768-0.147-0.1470.0000.0000.0000.000
89A94TYR00.016-0.01011.1760.0360.0360.0000.0000.0000.000
90A95GLY0-0.0120.01014.331-0.111-0.1110.0000.0000.0000.000
91A96CYS0-0.0460.00214.749-0.036-0.0360.0000.0000.0000.000
92A97LYS10.9010.96516.691-0.317-0.3170.0000.0000.0000.000
93A98THR00.0340.02415.9230.0030.0030.0000.0000.0000.000
94A99TYR00.008-0.00319.006-0.053-0.0530.0000.0000.0000.000
95A100CYS0-0.048-0.02622.3830.0110.0110.0000.0000.0000.000
96A101PHE00.0360.03124.186-0.014-0.0140.0000.0000.0000.000
97A102ILE0-0.023-0.00925.700-0.017-0.0170.0000.0000.0000.000
98A103SER0-0.054-0.04927.486-0.015-0.0150.0000.0000.0000.000
99A104ASP-1-0.772-0.85528.7200.1040.1040.0000.0000.0000.000
100A105GLU-1-0.856-0.94231.2240.0430.0430.0000.0000.0000.000
101A106ASP-1-0.843-0.90634.1100.0900.0900.0000.0000.0000.000
102A107VAL0-0.015-0.00531.5860.0010.0010.0000.0000.0000.000
103A108ILE0-0.041-0.02232.3660.0010.0010.0000.0000.0000.000
104A109GLU-1-0.783-0.88535.8050.0420.0420.0000.0000.0000.000
105A110ASN0-0.0010.00737.203-0.008-0.0080.0000.0000.0000.000
106A111ALA0-0.0150.00236.5410.0000.0000.0000.0000.0000.000
107A112LYS10.7950.87438.685-0.044-0.0440.0000.0000.0000.000
108A113ARG10.8750.93340.987-0.063-0.0630.0000.0000.0000.000
109A114LYS10.8070.88038.905-0.098-0.0980.0000.0000.0000.000
110A115ASN0-0.058-0.01143.051-0.001-0.0010.0000.0000.0000.000
111A116SER0-0.004-0.01038.8620.0010.0010.0000.0000.0000.000
112A117THR00.028-0.01034.927-0.001-0.0010.0000.0000.0000.000
113A118ARG11.0030.99331.431-0.060-0.0600.0000.0000.0000.000
114A119ALA00.0030.00630.6040.0080.0080.0000.0000.0000.000
115A120ILE00.0030.01231.5740.0120.0120.0000.0000.0000.000
116A121GLU-1-0.765-0.84234.0730.1050.1050.0000.0000.0000.000
117A122SER0-0.031-0.00527.9070.0040.0040.0000.0000.0000.000
118A123ILE00.0150.00927.9240.0100.0100.0000.0000.0000.000
119A124GLN00.027-0.00730.935-0.002-0.0020.0000.0000.0000.000
120A125LYS10.7790.87831.215-0.110-0.1100.0000.0000.0000.000
121A126ALA00.0280.01528.0330.0010.0010.0000.0000.0000.000
122A127ASN00.003-0.00529.9120.0170.0170.0000.0000.0000.000
123A128SER0-0.054-0.02832.421-0.004-0.0040.0000.0000.0000.000
124A129PHE0-0.028-0.02529.230-0.007-0.0070.0000.0000.0000.000
125A130ASN0-0.022-0.01530.4190.0100.0100.0000.0000.0000.000
126A131LEU0-0.037-0.01225.4530.0170.0170.0000.0000.0000.000
127A132LEU00.0210.00525.9300.0280.0280.0000.0000.0000.000
128A133ASN00.0140.02127.5280.0090.0090.0000.0000.0000.000
129A134GLU-1-0.878-0.93225.1220.3170.3170.0000.0000.0000.000
130A135SER0-0.072-0.03422.8820.0420.0420.0000.0000.0000.000
131A136ILE0-0.002-0.00217.4110.0110.0110.0000.0000.0000.000
132A137ILE00.0090.00621.417-0.002-0.0020.0000.0000.0000.000
133A138VAL0-0.021-0.01919.0590.0210.0210.0000.0000.0000.000
134A139ILE0-0.017-0.01622.271-0.032-0.0320.0000.0000.0000.000
135A140GLY00.0440.01622.6270.0080.0080.0000.0000.0000.000
136A141ASN0-0.112-0.06123.647-0.028-0.0280.0000.0000.0000.000
137A142ALA00.0880.03326.683-0.011-0.0110.0000.0000.0000.000
138A143PRO00.007-0.01229.9350.0090.0090.0000.0000.0000.000
139A144THR00.015-0.00432.1330.0050.0050.0000.0000.0000.000
140A145ALA00.0210.02629.434-0.002-0.0020.0000.0000.0000.000
141A146LEU00.0010.00128.2140.0080.0080.0000.0000.0000.000
142A147LEU00.0110.00430.9440.0010.0010.0000.0000.0000.000
143A148GLU-1-0.802-0.87733.5420.1290.1290.0000.0000.0000.000
144A149ILE0-0.007-0.00428.9940.0010.0010.0000.0000.0000.000
145A150GLU-1-0.822-0.90232.3780.1430.1430.0000.0000.0000.000
146A151LYS10.7810.87434.742-0.134-0.1340.0000.0000.0000.000
147A152LEU0-0.024-0.01933.065-0.003-0.0030.0000.0000.0000.000
148A153ILE0-0.040-0.01631.0220.0010.0010.0000.0000.0000.000
149A154ARG10.7930.87935.265-0.133-0.1330.0000.0000.0000.000
150A155GLN0-0.041-0.01838.858-0.007-0.0070.0000.0000.0000.000
151A156GLU-1-0.811-0.90537.2310.1250.1250.0000.0000.0000.000
152A157GLY0-0.0050.02237.0130.0020.0020.0000.0000.0000.000
153A158ILE0-0.064-0.02330.5980.0100.0100.0000.0000.0000.000
154A159LYS10.8800.91128.085-0.280-0.2800.0000.0000.0000.000
155A160PRO0-0.0160.01125.6980.0090.0090.0000.0000.0000.000
156A161ALA0-0.011-0.01022.824-0.011-0.0110.0000.0000.0000.000
157A162LEU0-0.057-0.02519.4500.0170.0170.0000.0000.0000.000
158A163ILE00.0100.00923.495-0.003-0.0030.0000.0000.0000.000
159A164VAL00.0050.00519.128-0.001-0.0010.0000.0000.0000.000
160A165GLY00.0530.01822.544-0.019-0.0190.0000.0000.0000.000
161A166VAL0-0.014-0.01321.715-0.014-0.0140.0000.0000.0000.000
162A167PRO00.0020.01425.116-0.008-0.0080.0000.0000.0000.000
163A168VAL0-0.016-0.00126.098-0.003-0.0030.0000.0000.0000.000
164A169GLY00.002-0.00428.699-0.010-0.0100.0000.0000.0000.000
165A170PHE0-0.029-0.05232.1780.0040.0040.0000.0000.0000.000
166A171VAL00.0050.02235.778-0.003-0.0030.0000.0000.0000.000
167A172SER00.0360.01135.810-0.003-0.0030.0000.0000.0000.000
168A173ALA00.0040.01631.1640.0070.0070.0000.0000.0000.000
169A174LYS10.8230.91132.527-0.105-0.1050.0000.0000.0000.000
170A175GLU-1-0.784-0.89634.2730.1280.1280.0000.0000.0000.000
171A176SER0-0.009-0.01932.1830.0080.0080.0000.0000.0000.000
172A177LYS10.8320.93028.549-0.187-0.1870.0000.0000.0000.000
173A178GLU-1-0.827-0.91031.7830.1340.1340.0000.0000.0000.000
174A179SER0-0.069-0.03534.147-0.001-0.0010.0000.0000.0000.000
175A180ILE00.0460.01929.673-0.002-0.0020.0000.0000.0000.000
176A181LEU00.0060.00331.037-0.001-0.0010.0000.0000.0000.000
177A182LYS10.8750.93334.218-0.137-0.1370.0000.0000.0000.000
178A183LEU00.0020.01334.301-0.006-0.0060.0000.0000.0000.000
179A184GLU-1-0.797-0.87532.3400.2250.2250.0000.0000.0000.000
180A185TYR0-0.037-0.01435.700-0.007-0.0070.0000.0000.0000.000
181A186TYR0-0.057-0.04138.687-0.006-0.0060.0000.0000.0000.000
182A187ASN0-0.062-0.03238.131-0.001-0.0010.0000.0000.0000.000
183A188VAL0-0.0110.00838.407-0.001-0.0010.0000.0000.0000.000
184A189THR0-0.011-0.01133.8540.0060.0060.0000.0000.0000.000
185A190SER00.0140.00931.743-0.007-0.0070.0000.0000.0000.000
186A191ILE0-0.025-0.00728.2150.0160.0160.0000.0000.0000.000
187A192PRO00.0260.02824.767-0.002-0.0020.0000.0000.0000.000
188A193TYR0-0.038-0.05725.0950.0150.0150.0000.0000.0000.000
189A194ILE00.012-0.00219.4330.0170.0170.0000.0000.0000.000
190A195LEU0-0.0210.00723.615-0.006-0.0060.0000.0000.0000.000
191A196THR00.0190.00023.6250.0130.0130.0000.0000.0000.000
192A197MET0-0.0170.00326.778-0.014-0.0140.0000.0000.0000.000
193A198GLY00.0500.02430.318-0.005-0.0050.0000.0000.0000.000
194A199ARG10.9430.95331.665-0.088-0.0880.0000.0000.0000.000
195A200LYS10.8250.88827.005-0.149-0.1490.0000.0000.0000.000
196A201GLY00.0610.02824.6580.0100.0100.0000.0000.0000.000
197A202GLY00.0060.00122.808-0.022-0.0220.0000.0000.0000.000
198A203SER00.013-0.01819.7980.0370.0370.0000.0000.0000.000
199A204THR00.0450.00916.3410.0530.0530.0000.0000.0000.000
200A205ILE00.0260.03416.6470.0670.0670.0000.0000.0000.000
201A206ALA00.0330.00917.9470.0670.0670.0000.0000.0000.000
202A207VAL0-0.0110.00012.9270.0870.0870.0000.0000.0000.000
203A208ALA0-0.0070.00313.3180.1900.1900.0000.0000.0000.000
204A209ILE00.003-0.00113.9030.1550.1550.0000.0000.0000.000
205A210LEU00.0090.00313.7900.1010.1010.0000.0000.0000.000
206A211HIS0-0.007-0.0199.3010.6180.6180.0000.0000.0000.000
207A212ALA0-0.0130.0139.7770.4300.4300.0000.0000.0000.000
208A213LEU00.0250.01111.9720.1060.1060.0000.0000.0000.000
209A214LEU00.002-0.0078.5980.0270.0270.0000.0000.0000.000
210A215LEU0-0.027-0.0066.7240.4680.4680.0000.0000.0000.000
211A216LEU00.004-0.0028.693-0.154-0.1540.0000.0000.0000.000
212A217SER00.0230.02310.988-0.153-0.1530.0000.0000.0000.000
213A218SER0-0.051-0.0216.578-0.268-0.2680.0000.0000.0000.000
214A219LYS10.8610.9239.682-1.052-1.0520.0000.0000.0000.000
215A220ARG10.7330.81711.367-0.807-0.8070.0000.0000.0000.000
216A221GLY0-0.068-0.01612.375-0.173-0.1730.0000.0000.0000.000