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: 98YN2

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2377173.027222
FMO2-HF: Nuclear repulsion 2296347.20822
FMO2-HF: Total energy -80825.819002
FMO2-MP2: Total energy -81062.052173


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.
0.6152.473-0.032-0.825-1.0010
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 : -0.006 / q_NPA : -0.013
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-9GLY00.0260.0173.8030.2861.961-0.031-0.812-0.8320.000
4A-8GLU-1-0.812-0.8944.7081.4011.584-0.001-0.013-0.1690.000
5A-7ASN0-0.044-0.0325.235-0.416-0.4160.0000.0000.0000.000
6A-6LEU0-0.0110.0007.8810.0590.0590.0000.0000.0000.000
7A-5TYR00.003-0.00711.489-0.002-0.0020.0000.0000.0000.000
8A-4PHE0-0.049-0.0109.464-0.017-0.0170.0000.0000.0000.000
9A-3GLN00.0510.0189.5330.0420.0420.0000.0000.0000.000
10A-2GLY0-0.010-0.0099.472-0.150-0.1500.0000.0000.0000.000
11A-1HIS0-0.081-0.0537.986-0.372-0.3720.0000.0000.0000.000
12A1MET0-0.0320.01210.635-0.169-0.1690.0000.0000.0000.000
13A2ILE0-0.015-0.00513.686-0.038-0.0380.0000.0000.0000.000
14A3ARG10.8020.87416.668-0.275-0.2750.0000.0000.0000.000
15A4ILE00.0360.00419.035-0.006-0.0060.0000.0000.0000.000
16A5GLY00.0480.02922.217-0.012-0.0120.0000.0000.0000.000
17A6VAL0-0.051-0.02625.664-0.001-0.0010.0000.0000.0000.000
18A7LEU00.0230.02727.805-0.006-0.0060.0000.0000.0000.000
19A8ILE0-0.034-0.01431.071-0.003-0.0030.0000.0000.0000.000
20A9SER00.029-0.02133.7270.0000.0000.0000.0000.0000.000
21A10GLY0-0.001-0.01736.569-0.004-0.0040.0000.0000.0000.000
22A11SER00.0140.00937.1960.0030.0030.0000.0000.0000.000
23A12GLY00.0690.04033.2610.0010.0010.0000.0000.0000.000
24A13THR0-0.010-0.01532.4580.0030.0030.0000.0000.0000.000
25A14ASN00.0640.00128.1520.0020.0020.0000.0000.0000.000
26A15LEU0-0.0050.01327.5430.0050.0050.0000.0000.0000.000
27A16GLN0-0.025-0.00927.6890.0040.0040.0000.0000.0000.000
28A17ALA00.0490.03625.5170.0020.0020.0000.0000.0000.000
29A18ILE0-0.0050.00322.3150.0060.0060.0000.0000.0000.000
30A19LEU00.0070.00423.1800.0130.0130.0000.0000.0000.000
31A20ASP-1-0.806-0.89824.4950.0660.0660.0000.0000.0000.000
32A21GLY0-0.0130.00021.3180.0000.0000.0000.0000.0000.000
33A22CYS0-0.060-0.02319.5990.0170.0170.0000.0000.0000.000
34A23ARG10.8140.89420.322-0.058-0.0580.0000.0000.0000.000
35A24GLU-1-0.858-0.91421.6740.0490.0490.0000.0000.0000.000
36A25GLY00.0150.01917.698-0.012-0.0120.0000.0000.0000.000
37A26ARG10.8110.89015.931-0.045-0.0450.0000.0000.0000.000
38A27ILE0-0.056-0.01315.6520.0080.0080.0000.0000.0000.000
39A28PRO00.0370.02511.915-0.030-0.0300.0000.0000.0000.000
40A29GLY00.0660.01514.3370.0480.0480.0000.0000.0000.000
41A30ARG10.9240.97217.192-0.231-0.2310.0000.0000.0000.000
42A31VAL00.0070.00220.9470.0070.0070.0000.0000.0000.000
43A32ALA0-0.052-0.01923.987-0.007-0.0070.0000.0000.0000.000
44A33VAL00.0240.01225.582-0.010-0.0100.0000.0000.0000.000
45A34VAL0-0.0080.00228.1970.0050.0050.0000.0000.0000.000
46A35ILE00.0110.00430.628-0.005-0.0050.0000.0000.0000.000
47A36SER00.002-0.01133.4380.0000.0000.0000.0000.0000.000
48A37ASP-1-0.836-0.88936.3070.0530.0530.0000.0000.0000.000
49A38ARG10.8950.93638.938-0.047-0.0470.0000.0000.0000.000
50A39ALA00.0470.02740.3590.0020.0020.0000.0000.0000.000
51A40ASP-1-0.919-0.95642.1280.0370.0370.0000.0000.0000.000
52A41ALA0-0.0290.01138.097-0.001-0.0010.0000.0000.0000.000
53A42TYR00.038-0.00137.1190.0010.0010.0000.0000.0000.000
54A43GLY00.007-0.00634.8380.0010.0010.0000.0000.0000.000
55A44LEU00.0300.00334.1900.0040.0040.0000.0000.0000.000
56A45GLU-1-0.792-0.87135.8380.0450.0450.0000.0000.0000.000
57A46ARG10.8010.89932.525-0.048-0.0480.0000.0000.0000.000
58A47ALA00.008-0.00131.2780.0020.0020.0000.0000.0000.000
59A48ARG10.9540.97632.033-0.048-0.0480.0000.0000.0000.000
60A49ARG10.8210.90234.200-0.040-0.0400.0000.0000.0000.000
61A50ALA0-0.046-0.01128.720-0.001-0.0010.0000.0000.0000.000
62A51GLY0-0.013-0.00429.2960.0060.0060.0000.0000.0000.000
63A52VAL0-0.055-0.02427.4240.0060.0060.0000.0000.0000.000
64A53ASP-1-0.835-0.88430.1010.0810.0810.0000.0000.0000.000
65A54ALA0-0.020-0.01831.7400.0040.0040.0000.0000.0000.000
66A55LEU0-0.016-0.01133.626-0.005-0.0050.0000.0000.0000.000
67A56HIS0-0.031-0.02536.135-0.002-0.0020.0000.0000.0000.000
68A57MET0-0.043-0.01036.3450.0010.0010.0000.0000.0000.000
69A58ASP-1-0.792-0.90639.4320.0440.0440.0000.0000.0000.000
70A59PRO0-0.047-0.04440.7070.0000.0000.0000.0000.0000.000
71A60ALA0-0.037-0.01042.8670.0000.0000.0000.0000.0000.000
72A61ALA0-0.0140.01044.552-0.002-0.0020.0000.0000.0000.000
73A62TYR0-0.019-0.02140.6120.0020.0020.0000.0000.0000.000
74A63PRO00.0230.01644.859-0.001-0.0010.0000.0000.0000.000
75A64SER00.008-0.00743.8480.0000.0000.0000.0000.0000.000
76A65ARG10.9970.98740.933-0.043-0.0430.0000.0000.0000.000
77A66THR00.0100.00038.7130.0030.0030.0000.0000.0000.000
78A67ALA00.0210.02138.8090.0040.0040.0000.0000.0000.000
79A68PHE00.0220.01937.3080.0020.0020.0000.0000.0000.000
80A69ASP-1-0.788-0.91634.3820.0790.0790.0000.0000.0000.000
81A70ALA0-0.025-0.01334.5680.0060.0060.0000.0000.0000.000
82A71ALA00.0330.02435.1710.0040.0040.0000.0000.0000.000
83A72LEU0-0.007-0.00833.1060.0030.0030.0000.0000.0000.000
84A73ALA00.025-0.00930.7440.0060.0060.0000.0000.0000.000
85A74GLU-1-0.876-0.91530.5870.0840.0840.0000.0000.0000.000
86A75ARG10.8690.91431.930-0.072-0.0720.0000.0000.0000.000
87A76LEU00.002-0.01127.4370.0050.0050.0000.0000.0000.000
88A77GLN00.009-0.00127.2450.0050.0050.0000.0000.0000.000
89A78ALA0-0.0160.02227.7700.0070.0070.0000.0000.0000.000
90A79TYR0-0.086-0.07327.1570.0000.0000.0000.0000.0000.000
91A80GLY0-0.068-0.03724.3280.0110.0110.0000.0000.0000.000
92A81VAL0-0.073-0.02922.5410.0200.0200.0000.0000.0000.000
93A82ASP-1-0.806-0.86118.1740.2940.2940.0000.0000.0000.000
94A83LEU0-0.014-0.00818.0960.0040.0040.0000.0000.0000.000
95A84VAL00.0440.02621.072-0.011-0.0110.0000.0000.0000.000
96A85CYS0-0.0230.00222.6790.0040.0040.0000.0000.0000.000
97A86LEU00.0010.00325.264-0.007-0.0070.0000.0000.0000.000
98A87ALA00.0410.01428.443-0.002-0.0020.0000.0000.0000.000
99A88GLY00.000-0.00830.192-0.003-0.0030.0000.0000.0000.000
100A89TYR00.014-0.00132.538-0.005-0.0050.0000.0000.0000.000
101A90MET0-0.028-0.01334.309-0.001-0.0010.0000.0000.0000.000
102A91ARG10.8790.95436.043-0.060-0.0600.0000.0000.0000.000
103A92LEU0-0.006-0.00235.2800.0030.0030.0000.0000.0000.000
104A93VAL00.0410.03230.243-0.001-0.0010.0000.0000.0000.000
105A94ARG10.8940.93933.589-0.062-0.0620.0000.0000.0000.000
106A95GLY00.0600.02433.2480.0050.0050.0000.0000.0000.000
107A96PRO00.0050.00932.6950.0050.0050.0000.0000.0000.000
108A97MET00.0400.04529.0130.0070.0070.0000.0000.0000.000
109A98LEU0-0.023-0.01328.6740.0080.0080.0000.0000.0000.000
110A99THR0-0.054-0.04327.9990.0060.0060.0000.0000.0000.000
111A100ALA0-0.038-0.00628.0380.0070.0070.0000.0000.0000.000
112A101PHE0-0.021-0.01423.8680.0090.0090.0000.0000.0000.000
113A102PRO00.0450.03723.473-0.002-0.0020.0000.0000.0000.000
114A103ASN0-0.053-0.04320.8540.0050.0050.0000.0000.0000.000
115A104ARG10.9160.95216.915-0.264-0.2640.0000.0000.0000.000
116A105ILE00.0060.01521.743-0.002-0.0020.0000.0000.0000.000
117A106LEU0-0.012-0.00319.578-0.005-0.0050.0000.0000.0000.000
118A107ASN0-0.005-0.01824.156-0.004-0.0040.0000.0000.0000.000
119A108ILE00.0020.02625.8920.0000.0000.0000.0000.0000.000
120A109HIS10.7700.87728.021-0.048-0.0480.0000.0000.0000.000
121A110PRO00.0070.00730.839-0.002-0.0020.0000.0000.0000.000
122A111SER00.012-0.01532.269-0.002-0.0020.0000.0000.0000.000
123A112LEU0-0.0090.02630.1600.0030.0030.0000.0000.0000.000
124A113LEU00.0000.01529.470-0.001-0.0010.0000.0000.0000.000
125A114PRO00.013-0.01730.978-0.001-0.0010.0000.0000.0000.000
126A115ALA0-0.0090.01133.5290.0000.0000.0000.0000.0000.000
127A116PHE00.0130.00535.4960.0020.0020.0000.0000.0000.000
128A117PRO00.0640.05135.3420.0020.0020.0000.0000.0000.000
129A118GLY00.0020.00036.119-0.002-0.0020.0000.0000.0000.000
130A119LEU0-0.024-0.03237.5580.0000.0000.0000.0000.0000.000
131A120GLU-1-0.834-0.89339.7390.0250.0250.0000.0000.0000.000
132A121ALA00.0390.03136.678-0.002-0.0020.0000.0000.0000.000
133A122GLN00.0480.01636.498-0.002-0.0020.0000.0000.0000.000
134A123ARG10.7890.85039.644-0.025-0.0250.0000.0000.0000.000
135A124GLN0-0.034-0.02039.884-0.002-0.0020.0000.0000.0000.000
136A125ALA0-0.0040.00739.165-0.002-0.0020.0000.0000.0000.000
137A126LEU0-0.011-0.01941.287-0.002-0.0020.0000.0000.0000.000
138A127GLU-1-0.882-0.92844.2170.0180.0180.0000.0000.0000.000
139A128HIS0-0.040-0.01443.2150.0000.0000.0000.0000.0000.000
140A129GLY00.0160.01644.951-0.001-0.0010.0000.0000.0000.000
141A130VAL0-0.078-0.03039.289-0.002-0.0020.0000.0000.0000.000
142A131LYS10.8870.90641.209-0.005-0.0050.0000.0000.0000.000
143A132VAL0-0.036-0.01334.794-0.002-0.0020.0000.0000.0000.000
144A133ALA00.0210.01135.7320.0020.0020.0000.0000.0000.000
145A134GLY00.0320.00331.882-0.003-0.0030.0000.0000.0000.000
146A135CYS0-0.0580.00128.8790.0020.0020.0000.0000.0000.000
147A136THR00.007-0.01426.586-0.004-0.0040.0000.0000.0000.000
148A137VAL00.0270.02922.3700.0040.0040.0000.0000.0000.000
149A138HIS0-0.031-0.02023.859-0.006-0.0060.0000.0000.0000.000
150A139PHE00.0750.02617.7750.0030.0030.0000.0000.0000.000
151A140VAL0-0.050-0.01823.928-0.012-0.0120.0000.0000.0000.000
152A141THR00.0120.00027.0780.0060.0060.0000.0000.0000.000
153A142ALA0-0.003-0.01929.281-0.003-0.0030.0000.0000.0000.000
154A143GLY00.0080.02932.686-0.004-0.0040.0000.0000.0000.000
155A144VAL0-0.012-0.02732.7960.0030.0030.0000.0000.0000.000
156A145ASP-1-0.797-0.88531.3480.0510.0510.0000.0000.0000.000
157A146GLU-1-0.874-0.93631.4150.0540.0540.0000.0000.0000.000
158A147GLY0-0.030-0.00327.3860.0000.0000.0000.0000.0000.000
159A148PRO0-0.021-0.01722.825-0.006-0.0060.0000.0000.0000.000
160A149ILE0-0.0010.00423.8410.0070.0070.0000.0000.0000.000
161A150ILE0-0.028-0.00818.4000.0000.0000.0000.0000.0000.000
162A151LEU00.0320.01118.669-0.010-0.0100.0000.0000.0000.000
163A152GLN0-0.060-0.04422.2830.0030.0030.0000.0000.0000.000
164A153ALA0-0.0090.00825.317-0.007-0.0070.0000.0000.0000.000
165A154ALA00.0060.00327.6410.0040.0040.0000.0000.0000.000
166A155VAL0-0.020-0.01431.180-0.003-0.0030.0000.0000.0000.000
167A156PRO00.0170.01234.0960.0010.0010.0000.0000.0000.000
168A157VAL0-0.0150.00137.6490.0020.0020.0000.0000.0000.000
169A158LEU0-0.034-0.01940.608-0.002-0.0020.0000.0000.0000.000
170A159GLU-1-0.816-0.89443.4420.0050.0050.0000.0000.0000.000
171A160GLY0-0.008-0.00747.126-0.001-0.0010.0000.0000.0000.000
172A161ASP-1-0.737-0.81641.8550.0090.0090.0000.0000.0000.000
173A162THR0-0.0100.00045.3190.0010.0010.0000.0000.0000.000
174A163VAL00.030-0.01342.4060.0010.0010.0000.0000.0000.000
175A164GLU-1-0.829-0.90341.6580.0240.0240.0000.0000.0000.000
176A165ASP-1-0.829-0.90440.9550.0120.0120.0000.0000.0000.000
177A166LEU0-0.0070.00237.9560.0000.0000.0000.0000.0000.000
178A167ARG10.8500.91137.487-0.025-0.0250.0000.0000.0000.000
179A168ARG10.8630.91936.171-0.017-0.0170.0000.0000.0000.000
180A169ARG10.7760.84735.282-0.007-0.0070.0000.0000.0000.000
181A170ILE00.0020.00432.381-0.001-0.0010.0000.0000.0000.000
182A171LEU0-0.0130.00131.5150.0020.0020.0000.0000.0000.000
183A172ALA0-0.025-0.01030.7280.0040.0040.0000.0000.0000.000
184A173GLU-1-0.784-0.88727.5340.0040.0040.0000.0000.0000.000
185A174GLU-1-0.892-0.94726.7720.0470.0470.0000.0000.0000.000
186A175HIS0-0.027-0.04126.1470.0100.0100.0000.0000.0000.000
187A176ARG10.8580.93522.4570.0020.0020.0000.0000.0000.000
188A177ILE00.033-0.00521.9960.0060.0060.0000.0000.0000.000
189A178TYR0-0.022-0.02521.5200.0140.0140.0000.0000.0000.000
190A179PRO0-0.006-0.02220.6020.0180.0180.0000.0000.0000.000
191A180GLU-1-0.915-0.95317.2740.0290.0290.0000.0000.0000.000
192A181ALA00.0170.00616.5230.0180.0180.0000.0000.0000.000
193A182ILE00.000-0.00716.9690.0260.0260.0000.0000.0000.000
194A183ARG10.8540.92811.873-0.056-0.0560.0000.0000.0000.000
195A184LEU0-0.008-0.00212.2860.0690.0690.0000.0000.0000.000
196A185PHE0-0.025-0.02012.2730.0510.0510.0000.0000.0000.000
197A186ALA00.003-0.00112.8050.0440.0440.0000.0000.0000.000
198A187GLU-1-0.793-0.8798.2810.2900.2900.0000.0000.0000.000
199A188GLY0-0.0180.0017.8120.1260.1260.0000.0000.0000.000
200A189ARG10.7850.8698.1340.0340.0340.0000.0000.0000.000
201A190LEU0-0.0320.00710.763-0.074-0.0740.0000.0000.0000.000
202A191VAL00.0120.00013.2120.0350.0350.0000.0000.0000.000
203A192ILE0-0.0150.00215.906-0.030-0.0300.0000.0000.0000.000
204A193GLU-1-0.817-0.89619.2630.1160.1160.0000.0000.0000.000
205A194GLY00.0000.00421.859-0.014-0.0140.0000.0000.0000.000
206A195ARG10.8620.91024.972-0.056-0.0560.0000.0000.0000.000
207A196ARG10.8870.93222.073-0.068-0.0680.0000.0000.0000.000
208A197VAL00.0310.01017.6940.0150.0150.0000.0000.0000.000
209A198ARG10.8680.93613.719-0.172-0.1720.0000.0000.0000.000
210A199ILE00.012-0.00113.7450.0370.0370.0000.0000.0000.000
211A200LEU0-0.028-0.0099.064-0.025-0.0250.0000.0000.0000.000
212A201ASP-1-0.900-0.9337.780-0.223-0.2230.0000.0000.0000.000