FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: LN389

Calculation Name: 3B5O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5O

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWS1

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:

Apendix: None


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 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2793210.029426
FMO2-HF: Nuclear repulsion 2704072.109942
FMO2-HF: Total energy -89137.919483
FMO2-MP2: Total energy -89398.977361


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
1.536.0651.053-2.28-3.3090.005
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.047
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].
3A2GLU-1-0.861-0.9353.817-4.371-2.3120.001-1.021-1.0390.003
4A3PHE00.0660.0362.8420.2811.1750.174-0.367-0.7020.002
5A4ASN0-0.022-0.0143.5081.3732.2520.023-0.311-0.591-0.001
6A5HIS0-0.004-0.0035.1680.9941.100-0.001-0.009-0.0960.000
7A6LEU0-0.0030.0187.6530.5410.5410.0000.0000.0000.000
8A7THR00.0350.0056.7520.4560.4560.0000.0000.0000.000
9A8LYS10.8850.9579.1351.0341.0340.0000.0000.0000.000
10A9GLN0-0.007-0.01511.1500.2110.2110.0000.0000.0000.000
11A10LEU0-0.0080.00311.5380.1420.1420.0000.0000.0000.000
12A11ASN0-0.010-0.02912.1180.1920.1920.0000.0000.0000.000
13A12GLN0-0.0180.00315.2160.0710.0710.0000.0000.0000.000
14A13LEU0-0.025-0.00616.9170.0550.0550.0000.0000.0000.000
15A14LEU0-0.0090.00218.2200.0490.0490.0000.0000.0000.000
16A15ALA0-0.025-0.02119.5510.0390.0390.0000.0000.0000.000
17A16GLN0-0.101-0.03720.524-0.003-0.0030.0000.0000.0000.000
18A17ASP-1-0.892-0.95122.902-0.316-0.3160.0000.0000.0000.000
19A18TYR0-0.101-0.07422.2490.0040.0040.0000.0000.0000.000
20A19VAL00.0580.02725.5750.0030.0030.0000.0000.0000.000
21A20ALA0-0.031-0.01227.2940.0110.0110.0000.0000.0000.000
22A21PHE00.0260.00923.9370.0070.0070.0000.0000.0000.000
23A22SER0-0.024-0.01525.830-0.002-0.0020.0000.0000.0000.000
24A23ILE00.025-0.00428.0200.0130.0130.0000.0000.0000.000
25A24THR0-0.014-0.01330.2150.0120.0120.0000.0000.0000.000
26A25GLU-1-0.901-0.93130.519-0.168-0.1680.0000.0000.0000.000
27A26ASN00.0180.02229.9490.0110.0110.0000.0000.0000.000
28A27PRO0-0.004-0.01432.0130.0070.0070.0000.0000.0000.000
29A28VAL00.0410.01234.4940.0070.0070.0000.0000.0000.000
30A29VAL0-0.018-0.01433.3200.0070.0070.0000.0000.0000.000
31A30GLN0-0.084-0.05135.7530.0080.0080.0000.0000.0000.000
32A31MET0-0.065-0.00838.0980.0030.0030.0000.0000.0000.000
33A32LEU0-0.009-0.00737.4440.0050.0050.0000.0000.0000.000
34A33SER0-0.061-0.02941.4280.0040.0040.0000.0000.0000.000
35A34GLN0-0.014-0.01243.1600.0040.0040.0000.0000.0000.000
36A35ALA0-0.0240.02142.9330.0030.0030.0000.0000.0000.000
37A36SER00.0400.01344.9700.0020.0020.0000.0000.0000.000
38A37PHE00.0610.01444.874-0.003-0.0030.0000.0000.0000.000
39A38ALA00.0130.00044.330-0.001-0.0010.0000.0000.0000.000
40A39GLN00.0070.01843.521-0.001-0.0010.0000.0000.0000.000
41A40ILE00.0530.02138.787-0.003-0.0030.0000.0000.0000.000
42A41ALA00.0280.01639.637-0.002-0.0020.0000.0000.0000.000
43A42TYR0-0.050-0.04040.3790.0020.0020.0000.0000.0000.000
44A43VAL00.000-0.00635.601-0.001-0.0010.0000.0000.0000.000
45A44MET00.0100.01533.832-0.005-0.0050.0000.0000.0000.000
46A45GLN0-0.039-0.02836.189-0.001-0.0010.0000.0000.0000.000
47A46GLN00.0470.03336.050-0.001-0.0010.0000.0000.0000.000
48A47TYR0-0.045-0.04727.4500.0040.0040.0000.0000.0000.000
49A48SER0-0.021-0.02231.7780.0000.0000.0000.0000.0000.000
50A49ILE0-0.030-0.02432.6170.0050.0050.0000.0000.0000.000
51A50PHE00.008-0.00224.6630.0040.0040.0000.0000.0000.000
52A51PRO00.0430.02327.1530.0010.0010.0000.0000.0000.000
53A52LYS10.8950.97127.9020.0370.0370.0000.0000.0000.000
54A53GLU-1-0.930-0.98729.131-0.033-0.0330.0000.0000.0000.000
55A54LEU0-0.0030.00523.1620.0010.0010.0000.0000.0000.000
56A55VAL00.0270.04324.1400.0030.0030.0000.0000.0000.000
57A56GLY00.0090.00325.0270.0100.0100.0000.0000.0000.000
58A57PHE00.001-0.01423.4710.0050.0050.0000.0000.0000.000
59A58THR00.0430.00819.493-0.007-0.0070.0000.0000.0000.000
60A59GLU-1-0.745-0.83021.0530.0750.0750.0000.0000.0000.000
61A60LEU0-0.062-0.02723.1920.0150.0150.0000.0000.0000.000
62A61ALA00.0230.01117.9510.0070.0070.0000.0000.0000.000
63A62ARG10.8510.91318.584-0.076-0.0760.0000.0000.0000.000
64A63ARG10.8170.88719.785-0.018-0.0180.0000.0000.0000.000
65A64LYS10.8260.93018.9000.0650.0650.0000.0000.0000.000
66A65ALA00.0230.01115.5660.0090.0090.0000.0000.0000.000
67A66LEU0-0.022-0.01816.8790.0390.0390.0000.0000.0000.000
68A67GLY0-0.056-0.01819.3900.0190.0190.0000.0000.0000.000
69A68ALA0-0.029-0.00415.936-0.004-0.0040.0000.0000.0000.000
70A69GLY0-0.012-0.00416.2490.0270.0270.0000.0000.0000.000
71A70TRP00.000-0.00511.1990.0980.0980.0000.0000.0000.000
72A71ASN0-0.005-0.02614.131-0.055-0.0550.0000.0000.0000.000
73A72GLY00.0190.00612.935-0.038-0.0380.0000.0000.0000.000
74A73VAL00.0220.01910.926-0.024-0.0240.0000.0000.0000.000
75A74ALA0-0.010-0.00813.448-0.065-0.0650.0000.0000.0000.000
76A75GLN0-0.086-0.05816.297-0.042-0.0420.0000.0000.0000.000
77A76GLU-1-0.833-0.92213.0380.1740.1740.0000.0000.0000.000
78A77LEU0-0.026-0.01115.668-0.053-0.0530.0000.0000.0000.000
79A78GLN0-0.068-0.05117.858-0.024-0.0240.0000.0000.0000.000
80A79GLU-1-0.854-0.90318.5150.2430.2430.0000.0000.0000.000
81A80ASN0-0.057-0.03316.328-0.050-0.0500.0000.0000.0000.000
82A81ILE0-0.017-0.00420.304-0.017-0.0170.0000.0000.0000.000
83A82ASP-1-0.859-0.93123.4040.0940.0940.0000.0000.0000.000
84A83GLU-1-0.835-0.88522.5540.0380.0380.0000.0000.0000.000
85A84GLU-1-0.855-0.92223.206-0.042-0.0420.0000.0000.0000.000
86A85MET0-0.071-0.05125.836-0.006-0.0060.0000.0000.0000.000
87A86GLY00.0330.01927.929-0.001-0.0010.0000.0000.0000.000
88A87SER0-0.091-0.03125.009-0.001-0.0010.0000.0000.0000.000
89A88THR0-0.034-0.04024.5370.0040.0040.0000.0000.0000.000
90A89THR0-0.043-0.03127.871-0.004-0.0040.0000.0000.0000.000
91A90GLY0-0.022-0.01630.899-0.004-0.0040.0000.0000.0000.000
92A91GLY0-0.030-0.01432.0040.0000.0000.0000.0000.0000.000
93A92ILE0-0.053-0.01633.260-0.003-0.0030.0000.0000.0000.000
94A93SER00.0250.02330.501-0.003-0.0030.0000.0000.0000.000
95A94HIS00.1030.02424.6270.0040.0040.0000.0000.0000.000
96A95TYR00.0180.00729.813-0.003-0.0030.0000.0000.0000.000
97A96THR0-0.026-0.01331.868-0.002-0.0020.0000.0000.0000.000
98A97LEU00.0040.01631.080-0.001-0.0010.0000.0000.0000.000
99A98LEU00.0220.01931.492-0.002-0.0020.0000.0000.0000.000
100A99ALA0-0.036-0.02934.282-0.001-0.0010.0000.0000.0000.000
101A100ASP-1-0.851-0.93837.190-0.011-0.0110.0000.0000.0000.000
102A101GLY00.0140.01537.6000.0010.0010.0000.0000.0000.000
103A102LEU0-0.005-0.01736.127-0.002-0.0020.0000.0000.0000.000
104A103GLU-1-0.819-0.90339.778-0.021-0.0210.0000.0000.0000.000
105A104GLU-1-1.000-1.00242.185-0.014-0.0140.0000.0000.0000.000
106A105GLY0-0.005-0.00642.2200.0010.0010.0000.0000.0000.000
107A106LEU0-0.063-0.02940.770-0.001-0.0010.0000.0000.0000.000
108A107GLY0-0.0230.00444.6000.0000.0000.0000.0000.0000.000
109A108VAL0-0.068-0.02741.5120.0000.0000.0000.0000.0000.000
110A109ALA00.0120.00442.4050.0010.0010.0000.0000.0000.000
111A110VAL00.0330.01637.317-0.003-0.0030.0000.0000.0000.000
112A111LYS10.7870.90938.7770.0160.0160.0000.0000.0000.000
113A112ASN0-0.083-0.05140.3250.0000.0000.0000.0000.0000.000
114A113THR00.0270.01438.7870.0000.0000.0000.0000.0000.000
115A114MET0-0.056-0.02739.2640.0010.0010.0000.0000.0000.000
116A115PRO00.011-0.00436.174-0.002-0.0020.0000.0000.0000.000
117A116SER0-0.017-0.02138.1510.0020.0020.0000.0000.0000.000
118A117VAL0-0.011-0.01538.332-0.001-0.0010.0000.0000.0000.000
119A118ALA00.0290.01635.646-0.003-0.0030.0000.0000.0000.000
120A119THR00.0310.00533.215-0.008-0.0080.0000.0000.0000.000
121A120SER0-0.026-0.01033.522-0.002-0.0020.0000.0000.0000.000
122A121LYS10.8190.88533.1630.1100.1100.0000.0000.0000.000
123A122LEU00.0130.03427.454-0.005-0.0050.0000.0000.0000.000
124A123LEU00.0340.01529.534-0.005-0.0050.0000.0000.0000.000
125A124ARG10.9190.95130.0360.0580.0580.0000.0000.0000.000
126A125THR0-0.034-0.02327.428-0.002-0.0020.0000.0000.0000.000
127A126VAL00.0450.02824.310-0.010-0.0100.0000.0000.0000.000
128A127LEU00.0100.01225.347-0.003-0.0030.0000.0000.0000.000
129A128SER0-0.109-0.06826.414-0.001-0.0010.0000.0000.0000.000
130A129LEU0-0.022-0.00922.043-0.005-0.0050.0000.0000.0000.000
131A130PHE00.006-0.02020.231-0.010-0.0100.0000.0000.0000.000
132A131ASP-1-0.869-0.93822.923-0.036-0.0360.0000.0000.0000.000
133A132ARG10.7430.88120.4530.2100.2100.0000.0000.0000.000
134A133GLN0-0.065-0.04515.9360.0410.0410.0000.0000.0000.000
135A134VAL00.0520.01814.380-0.028-0.0280.0000.0000.0000.000
136A135ASP-1-0.767-0.89512.284-0.231-0.2310.0000.0000.0000.000
137A136TYR0-0.0220.00413.947-0.052-0.0520.0000.0000.0000.000
138A137VAL0-0.018-0.00616.616-0.018-0.0180.0000.0000.0000.000
139A138LEU00.0260.00812.5600.0020.0020.0000.0000.0000.000
140A139GLY00.0130.02413.571-0.048-0.0480.0000.0000.0000.000
141A140ALA0-0.002-0.00814.506-0.012-0.0120.0000.0000.0000.000
142A141THR0-0.014-0.03715.6700.0270.0270.0000.0000.0000.000
143A142TYR0-0.047-0.02411.020-0.120-0.1200.0000.0000.0000.000
144A143ALA00.0120.00814.295-0.013-0.0130.0000.0000.0000.000
145A144ILE00.0160.03417.1630.0120.0120.0000.0000.0000.000
146A145GLU-1-0.855-0.92212.902-0.296-0.2960.0000.0000.0000.000
147A146ALA0-0.035-0.02915.0080.0020.0020.0000.0000.0000.000
148A147THR0-0.058-0.05716.6790.0190.0190.0000.0000.0000.000
149A148SER00.0120.00819.6760.0310.0310.0000.0000.0000.000
150A149ILE00.0410.02418.9090.0150.0150.0000.0000.0000.000
151A150PRO0-0.0170.00420.9500.0170.0170.0000.0000.0000.000
152A151GLU-1-0.826-0.89723.784-0.118-0.1180.0000.0000.0000.000
153A152LEU00.0240.00825.0750.0140.0140.0000.0000.0000.000
154A153THR0-0.016-0.02525.5940.0110.0110.0000.0000.0000.000
155A154LEU0-0.046-0.02627.6300.0100.0100.0000.0000.0000.000
156A155ILE0-0.015-0.00229.5640.0090.0090.0000.0000.0000.000
157A156VAL00.0180.02130.4920.0080.0080.0000.0000.0000.000
158A157LYS10.9440.98732.4900.1030.1030.0000.0000.0000.000
159A158LEU0-0.025-0.01733.9700.0060.0060.0000.0000.0000.000
160A159VAL00.008-0.00735.1950.0060.0060.0000.0000.0000.000
161A160GLU-1-0.939-0.97235.982-0.063-0.0630.0000.0000.0000.000
162A161TRP0-0.087-0.03938.4750.0030.0030.0000.0000.0000.000
163A162LEU0-0.048-0.02439.2040.0030.0030.0000.0000.0000.000
164A163HIS0-0.046-0.02939.5840.0070.0070.0000.0000.0000.000
165A164GLU-1-0.907-0.93943.157-0.039-0.0390.0000.0000.0000.000
166A165GLY0-0.053-0.03545.5590.0000.0000.0000.0000.0000.000
167A166ALA0-0.062-0.03342.099-0.002-0.0020.0000.0000.0000.000
168A167ILE00.0430.03035.7340.0010.0010.0000.0000.0000.000
169A168PRO00.0180.01939.5100.0020.0020.0000.0000.0000.000
170A169LYS10.8360.89537.915-0.001-0.0010.0000.0000.0000.000
171A170ASP-1-0.826-0.90536.294-0.002-0.0020.0000.0000.0000.000
172A171LEU00.0300.03233.9860.0000.0000.0000.0000.0000.000
173A172GLN00.001-0.00133.175-0.005-0.0050.0000.0000.0000.000
174A173TYR0-0.027-0.01029.351-0.003-0.0030.0000.0000.0000.000
175A174PHE00.0120.00028.047-0.001-0.0010.0000.0000.0000.000
176A175PHE00.0510.01328.655-0.005-0.0050.0000.0000.0000.000
177A176SER00.018-0.02028.118-0.006-0.0060.0000.0000.0000.000
178A177LYS10.7010.84425.072-0.008-0.0080.0000.0000.0000.000
179A178HIS0-0.065-0.03422.9700.0060.0060.0000.0000.0000.000
180A179LEU0-0.049-0.02023.269-0.017-0.0170.0000.0000.0000.000
181A180ASP-1-0.958-0.93824.422-0.068-0.0680.0000.0000.0000.000
182A188ALA00.024-0.00710.0990.0060.0060.0000.0000.0000.000
183A189GLY00.0750.0659.2940.0630.0630.0000.0000.0000.000
184A190LEU00.0950.06210.5390.1240.1240.0000.0000.0000.000
185A191ARG10.8960.9495.4651.2391.2390.0000.0000.0000.000
186A192THR0-0.072-0.0675.453-0.045-0.0450.0000.0000.0000.000
187A193SER00.0220.0106.4420.7070.7070.0000.0000.0000.000
188A194VAL00.017-0.0087.5780.1880.1880.0000.0000.0000.000
189A195ALA0-0.059-0.0222.546-0.877-0.4580.857-0.545-0.7310.001
190A196ALA0-0.044-0.0144.2220.8561.034-0.001-0.027-0.1500.000
191A197TYR0-0.024-0.0056.606-0.217-0.2170.0000.0000.0000.000
192A198ILE0-0.0390.0155.657-0.198-0.1980.0000.0000.0000.000
193A199GLN0-0.020-0.0196.497-0.071-0.0710.0000.0000.0000.000
194A200PRO00.014-0.0147.219-0.154-0.1540.0000.0000.0000.000
195A201GLU-1-0.934-0.9719.002-0.300-0.3000.0000.0000.0000.000
196A202GLU-1-0.847-0.91411.202-0.227-0.2270.0000.0000.0000.000
197A203PHE0-0.041-0.0294.953-0.153-0.1530.0000.0000.0000.000
198A204GLY0-0.005-0.00310.7610.0140.0140.0000.0000.0000.000
199A205GLU-1-0.753-0.86714.320-0.232-0.2320.0000.0000.0000.000
200A206PHE0-0.0100.00810.498-0.018-0.0180.0000.0000.0000.000
201A207ALA0-0.007-0.02013.2320.0290.0290.0000.0000.0000.000
202A208ALA0-0.0110.00014.6020.0540.0540.0000.0000.0000.000
203A209GLY00.0270.01516.8340.0420.0420.0000.0000.0000.000
204A210PHE0-0.013-0.00314.4250.0230.0230.0000.0000.0000.000
205A211ARG10.9010.93617.1120.3960.3960.0000.0000.0000.000
206A212ALA00.0010.00619.8400.0330.0330.0000.0000.0000.000
207A213MET0-0.0090.00519.9670.0340.0340.0000.0000.0000.000
208A214ILE00.0240.01019.3190.0210.0210.0000.0000.0000.000
209A215ASP-1-0.829-0.88722.333-0.244-0.2440.0000.0000.0000.000
210A216ALA0-0.036-0.01325.0170.0210.0210.0000.0000.0000.000
211A217MET0-0.0030.00223.2140.0110.0110.0000.0000.0000.000
212A218GLN00.0350.01426.3930.0130.0130.0000.0000.0000.000
213A219VAL0-0.018-0.01128.0690.0130.0130.0000.0000.0000.000
214A220TRP0-0.0090.00529.0240.0090.0090.0000.0000.0000.000
215A221TRP00.0510.02127.8060.0140.0140.0000.0000.0000.000
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