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: LNLM9

Calculation Name: 3AUF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AUF

Chain ID: A

ChEMBL ID:

UniProt ID: E5RXD0

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378336.02636
FMO2-HF: Nuclear repulsion 2297510.90741
FMO2-HF: Total energy -80825.11895
FMO2-MP2: Total energy -81061.476811


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:-11:SER)


Summations of interaction energy for fragment #1(A:-11:SER)
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.
1.9913.69-0.031-0.822-0.8470
Interaction energy analysis for fragmet #1(A:-11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.014
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].
3A-9GLY00.0280.0173.8030.3992.098-0.031-0.822-0.8470.000
4A-8GLU-1-0.826-0.9164.8072.5952.5950.0000.0000.0000.000
5A-7ASN0-0.034-0.0305.263-0.415-0.4150.0000.0000.0000.000
6A-6LEU0-0.017-0.0037.9070.0680.0680.0000.0000.0000.000
7A-5TYR0-0.018-0.01411.514-0.007-0.0070.0000.0000.0000.000
8A-4PHE0-0.047-0.0079.651-0.067-0.0670.0000.0000.0000.000
9A-3GLN00.0560.0219.5590.0670.0670.0000.0000.0000.000
10A-2GLY0-0.014-0.0139.435-0.232-0.2320.0000.0000.0000.000
11A-1HIS0-0.036-0.0077.010-0.727-0.7270.0000.0000.0000.000
12A1MET0-0.0540.00210.719-0.236-0.2360.0000.0000.0000.000
13A2ILE0-0.0140.00013.686-0.084-0.0840.0000.0000.0000.000
14A3ARG10.7950.88016.757-0.490-0.4900.0000.0000.0000.000
15A4ILE00.0370.00719.212-0.017-0.0170.0000.0000.0000.000
16A5GLY00.0420.02622.327-0.025-0.0250.0000.0000.0000.000
17A6VAL0-0.042-0.02125.7700.0020.0020.0000.0000.0000.000
18A7LEU00.0260.02627.908-0.016-0.0160.0000.0000.0000.000
19A8ILE0-0.028-0.01131.1720.0010.0010.0000.0000.0000.000
20A9SER00.029-0.01133.822-0.005-0.0050.0000.0000.0000.000
21A10GLY0-0.005-0.02036.660-0.010-0.0100.0000.0000.0000.000
22A11SER00.0300.01537.2850.0070.0070.0000.0000.0000.000
23A12GLY00.0680.04633.3440.0030.0030.0000.0000.0000.000
24A13THR0-0.017-0.01432.5380.0050.0050.0000.0000.0000.000
25A14ASN00.0840.01328.1790.0170.0170.0000.0000.0000.000
26A15LEU0-0.0030.02027.6190.0170.0170.0000.0000.0000.000
27A16GLN00.0120.01727.7070.0000.0000.0000.0000.0000.000
28A17ALA00.0540.03825.4530.0080.0080.0000.0000.0000.000
29A18ILE0-0.020-0.00222.5530.0250.0250.0000.0000.0000.000
30A19LEU0-0.011-0.01023.1690.0280.0280.0000.0000.0000.000
31A20ASP-1-0.819-0.91224.4780.2490.2490.0000.0000.0000.000
32A21GLY0-0.015-0.00421.3060.0100.0100.0000.0000.0000.000
33A22CYS0-0.047-0.01019.5800.0480.0480.0000.0000.0000.000
34A23ARG10.8380.92020.299-0.235-0.2350.0000.0000.0000.000
35A24GLU-1-0.891-0.93521.6520.2640.2640.0000.0000.0000.000
36A25GLY00.0200.02117.674-0.004-0.0040.0000.0000.0000.000
37A26ARG10.8210.88815.912-0.278-0.2780.0000.0000.0000.000
38A27ILE0-0.052-0.01715.6430.0530.0530.0000.0000.0000.000
39A28PRO00.0310.02012.162-0.069-0.0690.0000.0000.0000.000
40A29GLY00.0830.01814.3370.0580.0580.0000.0000.0000.000
41A30ARG10.9310.97317.192-0.454-0.4540.0000.0000.0000.000
42A31VAL00.0170.00920.9470.0060.0060.0000.0000.0000.000
43A32ALA0-0.065-0.02724.053-0.016-0.0160.0000.0000.0000.000
44A33VAL00.0120.00925.582-0.022-0.0220.0000.0000.0000.000
45A34VAL00.0090.01228.3070.0130.0130.0000.0000.0000.000
46A35ILE00.0020.00130.784-0.013-0.0130.0000.0000.0000.000
47A36SER0-0.010-0.02533.5470.0040.0040.0000.0000.0000.000
48A37ASP-1-0.843-0.90836.4110.1320.1320.0000.0000.0000.000
49A38ARG10.9080.94139.042-0.128-0.1280.0000.0000.0000.000
50A39ALA00.0250.02240.4610.0060.0060.0000.0000.0000.000
51A40ASP-1-0.921-0.96142.2310.1080.1080.0000.0000.0000.000
52A41ALA0-0.0200.02038.155-0.001-0.0010.0000.0000.0000.000
53A42TYR00.0340.00137.2180.0030.0030.0000.0000.0000.000
54A43GLY00.008-0.00834.9340.0050.0050.0000.0000.0000.000
55A44LEU00.0330.00234.2440.0110.0110.0000.0000.0000.000
56A45GLU-1-0.833-0.91535.8380.1400.1400.0000.0000.0000.000
57A46ARG10.7770.87932.535-0.166-0.1660.0000.0000.0000.000
58A47ALA00.0100.00131.2730.0080.0080.0000.0000.0000.000
59A48ARG10.9700.99332.033-0.135-0.1350.0000.0000.0000.000
60A49ARG10.8470.92734.200-0.137-0.1370.0000.0000.0000.000
61A50ALA0-0.049-0.01128.6690.0010.0010.0000.0000.0000.000
62A51GLY0-0.016-0.00629.2900.0140.0140.0000.0000.0000.000
63A52VAL0-0.051-0.02127.4590.0090.0090.0000.0000.0000.000
64A53ASP-1-0.830-0.87930.1010.1820.1820.0000.0000.0000.000
65A54ALA0-0.020-0.01531.7480.0090.0090.0000.0000.0000.000
66A55LEU0-0.023-0.02333.862-0.013-0.0130.0000.0000.0000.000
67A56HIS0-0.008-0.00436.227-0.002-0.0020.0000.0000.0000.000
68A57MET0-0.052-0.01736.4130.0000.0000.0000.0000.0000.000
69A58ASP-1-0.803-0.91039.5450.1050.1050.0000.0000.0000.000
70A59PRO0-0.040-0.04040.698-0.002-0.0020.0000.0000.0000.000
71A60ALA0-0.023-0.00242.976-0.003-0.0030.0000.0000.0000.000
72A61ALA0-0.0220.00644.645-0.004-0.0040.0000.0000.0000.000
73A62TYR0-0.023-0.02240.7460.0020.0020.0000.0000.0000.000
74A63PRO00.0200.01544.951-0.002-0.0020.0000.0000.0000.000
75A64SER00.0300.00643.958-0.001-0.0010.0000.0000.0000.000
76A65ARG10.9660.97040.991-0.096-0.0960.0000.0000.0000.000
77A66THR00.0130.00138.8060.0070.0070.0000.0000.0000.000
78A67ALA00.0170.02138.9180.0060.0060.0000.0000.0000.000
79A68PHE00.0130.01837.5900.0040.0040.0000.0000.0000.000
80A69ASP-1-0.788-0.92534.1610.1690.1690.0000.0000.0000.000
81A70ALA0-0.007-0.00334.6800.0110.0110.0000.0000.0000.000
82A71ALA00.0400.02935.2880.0060.0060.0000.0000.0000.000
83A72LEU0-0.038-0.02233.2280.0070.0070.0000.0000.0000.000
84A73ALA00.043-0.00530.8530.0130.0130.0000.0000.0000.000
85A74GLU-1-0.957-0.96330.7060.1560.1560.0000.0000.0000.000
86A75ARG10.9330.96332.052-0.152-0.1520.0000.0000.0000.000
87A76LEU0-0.002-0.01427.8070.0110.0110.0000.0000.0000.000
88A77GLN00.0180.00227.3730.0090.0090.0000.0000.0000.000
89A78ALA0-0.0130.02427.8950.0110.0110.0000.0000.0000.000
90A79TYR0-0.105-0.08527.152-0.002-0.0020.0000.0000.0000.000
91A80GLY0-0.069-0.04024.4190.0250.0250.0000.0000.0000.000
92A81VAL0-0.069-0.02722.6650.0370.0370.0000.0000.0000.000
93A82ASP-1-0.795-0.87018.3180.5320.5320.0000.0000.0000.000
94A83LEU0-0.026-0.01118.4380.0070.0070.0000.0000.0000.000
95A84VAL00.0350.02521.181-0.016-0.0160.0000.0000.0000.000
96A85CYS0-0.028-0.00422.6490.0130.0130.0000.0000.0000.000
97A86LEU00.0010.00225.359-0.019-0.0190.0000.0000.0000.000
98A87ALA00.0390.00728.5570.0040.0040.0000.0000.0000.000
99A88GLY0-0.002-0.01130.277-0.009-0.0090.0000.0000.0000.000
100A89TYR00.0170.00032.662-0.014-0.0140.0000.0000.0000.000
101A90MET0-0.027-0.01234.401-0.003-0.0030.0000.0000.0000.000
102A91ARG10.8970.95836.134-0.138-0.1380.0000.0000.0000.000
103A92LEU0-0.006-0.00335.3720.0070.0070.0000.0000.0000.000
104A93VAL00.0510.03630.401-0.003-0.0030.0000.0000.0000.000
105A94ARG10.8910.94333.684-0.128-0.1280.0000.0000.0000.000
106A95GLY00.0530.02333.3490.0090.0090.0000.0000.0000.000
107A96PRO00.0100.01032.7980.0070.0070.0000.0000.0000.000
108A97MET00.0400.04529.2550.0100.0100.0000.0000.0000.000
109A98LEU0-0.023-0.01328.7620.0150.0150.0000.0000.0000.000
110A99THR0-0.060-0.04128.0990.0070.0070.0000.0000.0000.000
111A100ALA0-0.028-0.00528.1450.0070.0070.0000.0000.0000.000
112A101PHE0-0.029-0.01723.8890.0170.0170.0000.0000.0000.000
113A102PRO00.0390.03823.3300.0050.0050.0000.0000.0000.000
114A103ASN0-0.039-0.03920.8120.0120.0120.0000.0000.0000.000
115A104ARG10.9240.96016.698-0.472-0.4720.0000.0000.0000.000
116A105ILE00.0090.01621.8430.0010.0010.0000.0000.0000.000
117A106LEU0-0.007-0.00319.768-0.009-0.0090.0000.0000.0000.000
118A107ASN00.001-0.01524.241-0.014-0.0140.0000.0000.0000.000
119A108ILE0-0.0150.02626.2830.0100.0100.0000.0000.0000.000
120A109HIS10.8240.91128.088-0.156-0.1560.0000.0000.0000.000
121A110PRO00.0000.00230.8900.0030.0030.0000.0000.0000.000
122A111SER00.019-0.01332.313-0.008-0.0080.0000.0000.0000.000
123A112LEU00.0050.02830.2450.0110.0110.0000.0000.0000.000
124A113LEU0-0.0050.01329.583-0.008-0.0080.0000.0000.0000.000
125A114PRO00.009-0.02031.0070.0030.0030.0000.0000.0000.000
126A115ALA00.0040.01833.566-0.005-0.0050.0000.0000.0000.000
127A116PHE00.0090.00635.5360.0080.0080.0000.0000.0000.000
128A117PRO00.0600.04635.4550.0070.0070.0000.0000.0000.000
129A118GLY00.0100.00436.171-0.007-0.0070.0000.0000.0000.000
130A119LEU0-0.021-0.03237.6210.0050.0050.0000.0000.0000.000
131A120GLU-1-0.870-0.93539.8050.0840.0840.0000.0000.0000.000
132A121ALA00.0340.02736.783-0.005-0.0050.0000.0000.0000.000
133A122GLN00.0460.01536.738-0.007-0.0070.0000.0000.0000.000
134A123ARG10.8430.91139.691-0.084-0.0840.0000.0000.0000.000
135A124GLN0-0.052-0.02739.817-0.007-0.0070.0000.0000.0000.000
136A125ALA0-0.0040.00839.210-0.004-0.0040.0000.0000.0000.000
137A126LEU0-0.010-0.01841.322-0.004-0.0040.0000.0000.0000.000
138A127GLU-1-0.884-0.94244.2510.0680.0680.0000.0000.0000.000
139A128HIS0-0.042-0.01243.256-0.002-0.0020.0000.0000.0000.000
140A129GLY00.0190.01944.991-0.004-0.0040.0000.0000.0000.000
141A130VAL0-0.083-0.03239.463-0.002-0.0020.0000.0000.0000.000
142A131LYS10.9030.92841.222-0.059-0.0590.0000.0000.0000.000
143A132VAL0-0.022-0.00534.6920.0010.0010.0000.0000.0000.000
144A133ALA00.0110.00835.763-0.001-0.0010.0000.0000.0000.000
145A134GLY00.0320.00131.9090.0010.0010.0000.0000.0000.000
146A135CYS0-0.0640.00228.8310.0000.0000.0000.0000.0000.000
147A136THR00.012-0.01426.5420.0000.0000.0000.0000.0000.000
148A137VAL00.0240.02922.305-0.003-0.0030.0000.0000.0000.000
149A138HIS0-0.027-0.02423.917-0.005-0.0050.0000.0000.0000.000
150A139PHE00.0710.02717.9190.0020.0020.0000.0000.0000.000
151A140VAL0-0.043-0.01424.002-0.026-0.0260.0000.0000.0000.000
152A141THR00.0060.00027.1610.0070.0070.0000.0000.0000.000
153A142ALA00.000-0.02429.360-0.003-0.0030.0000.0000.0000.000
154A143GLY0-0.0120.02032.743-0.006-0.0060.0000.0000.0000.000
155A144VAL0-0.012-0.02532.8670.0100.0100.0000.0000.0000.000
156A145ASP-1-0.851-0.91631.4230.1460.1460.0000.0000.0000.000
157A146GLU-1-0.880-0.94531.4740.1180.1180.0000.0000.0000.000
158A147GLY0-0.040-0.01127.451-0.003-0.0030.0000.0000.0000.000
159A148PRO0-0.017-0.01522.989-0.006-0.0060.0000.0000.0000.000
160A149ILE0-0.0040.00423.8970.0190.0190.0000.0000.0000.000
161A150ILE0-0.024-0.00618.4240.0040.0040.0000.0000.0000.000
162A151LEU00.0170.00318.5330.0020.0020.0000.0000.0000.000
163A152GLN0-0.054-0.03722.317-0.014-0.0140.0000.0000.0000.000
164A153ALA0-0.0110.00725.3360.0030.0030.0000.0000.0000.000
165A154ALA00.0080.00327.662-0.004-0.0040.0000.0000.0000.000
166A155VAL0-0.025-0.01331.1960.0010.0010.0000.0000.0000.000
167A156PRO00.0080.00634.111-0.003-0.0030.0000.0000.0000.000
168A157VAL0-0.0090.00037.6610.0050.0050.0000.0000.0000.000
169A158LEU0-0.043-0.02940.626-0.004-0.0040.0000.0000.0000.000
170A159GLU-1-0.832-0.91643.4610.0570.0570.0000.0000.0000.000
171A160GLY0-0.008-0.00847.142-0.001-0.0010.0000.0000.0000.000
172A161ASP-1-0.742-0.83341.9220.0850.0850.0000.0000.0000.000
173A162THR0-0.0200.01544.927-0.001-0.0010.0000.0000.0000.000
174A163VAL00.055-0.01242.4710.0040.0040.0000.0000.0000.000
175A164GLU-1-0.883-0.93941.2120.1120.1120.0000.0000.0000.000
176A165ASP-1-0.845-0.91440.9970.0860.0860.0000.0000.0000.000
177A166LEU0-0.011-0.00137.9430.0050.0050.0000.0000.0000.000
178A167ARG10.8430.89937.526-0.101-0.1010.0000.0000.0000.000
179A168ARG10.9300.95936.219-0.102-0.1020.0000.0000.0000.000
180A169ARG10.8000.88335.283-0.085-0.0850.0000.0000.0000.000
181A170ILE00.0000.00332.4940.0060.0060.0000.0000.0000.000
182A171LEU0-0.0100.00331.5560.0120.0120.0000.0000.0000.000
183A172ALA0-0.038-0.01730.7340.0140.0140.0000.0000.0000.000
184A173GLU-1-0.799-0.89528.1520.1780.1780.0000.0000.0000.000
185A174GLU-1-0.891-0.96126.7890.1970.1970.0000.0000.0000.000
186A175HIS0-0.017-0.03326.2010.0210.0210.0000.0000.0000.000
187A176ARG10.8760.94422.905-0.194-0.1940.0000.0000.0000.000
188A177ILE00.027-0.00922.0400.0320.0320.0000.0000.0000.000
189A178TYR0-0.022-0.01421.5710.0340.0340.0000.0000.0000.000
190A179PRO00.000-0.02020.6710.0380.0380.0000.0000.0000.000
191A180GLU-1-0.926-0.95617.0910.4300.4300.0000.0000.0000.000
192A181ALA00.0220.00616.5760.0690.0690.0000.0000.0000.000
193A182ILE0-0.007-0.00817.0390.0480.0480.0000.0000.0000.000
194A183ARG10.9060.96611.884-0.703-0.7030.0000.0000.0000.000
195A184LEU0-0.0060.00012.4430.1660.1660.0000.0000.0000.000
196A185PHE0-0.030-0.02312.3450.1070.1070.0000.0000.0000.000
197A186ALA0-0.003-0.00612.9050.0610.0610.0000.0000.0000.000
198A187GLU-1-0.870-0.9458.1981.4801.4800.0000.0000.0000.000
199A188GLY0-0.0140.0057.8970.3710.3710.0000.0000.0000.000
200A189ARG10.8280.9028.498-0.976-0.9760.0000.0000.0000.000
201A190LEU0-0.0330.00510.812-0.185-0.1850.0000.0000.0000.000
202A191VAL00.0150.00613.3740.0120.0120.0000.0000.0000.000
203A192ILE0-0.0100.00315.952-0.048-0.0480.0000.0000.0000.000
204A193GLU-1-0.859-0.93119.2630.1370.1370.0000.0000.0000.000
205A194GLY00.0020.00621.894-0.015-0.0150.0000.0000.0000.000
206A195ARG10.8870.93125.019-0.135-0.1350.0000.0000.0000.000
207A196ARG10.9270.95023.084-0.110-0.1100.0000.0000.0000.000
208A197VAL00.0460.02017.9290.0100.0100.0000.0000.0000.000
209A198ARG10.8620.94213.720-0.232-0.2320.0000.0000.0000.000
210A199ILE00.003-0.00313.7830.0620.0620.0000.0000.0000.000
211A200LEU0-0.037-0.0148.937-0.085-0.0850.0000.0000.0000.000
212A201ASP-1-0.905-0.9387.8520.3360.3360.0000.0000.0000.000