FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: ZN92N

Calculation Name: 3DB5-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKN5

Base Structure: X-ray

Registration Date: 2025-07-08

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1101762.707827
FMO2-HF: Nuclear repulsion 1049841.480158
FMO2-HF: Total energy -51921.227668
FMO2-MP2: Total energy -52070.816572


3D Structure Molmil
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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-1.5360.586-0.003-0.971-1.1480.001
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.025
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].
3A5VAL0-0.0710.1204.1920.0120.4010.001-0.159-0.2310.000
4A6THR00.049-0.0663.563-1.5890.144-0.004-0.812-0.9170.001
5A6THR0-0.0500.0535.8050.1610.1610.0000.0000.0000.000
6A7PHE00.072-0.1035.8780.2850.2850.0000.0000.0000.000
7A7PHE0-0.0870.0915.9630.0100.0100.0000.0000.0000.000
8A8VAL00.064-0.1209.004-0.015-0.0150.0000.0000.0000.000
9A8VAL0-0.0720.11411.433-0.002-0.0020.0000.0000.0000.000
10A9PRO0-0.029-0.10412.5410.0590.0590.0000.0000.0000.000
11A10ASP00.139-0.00415.216-0.017-0.0170.0000.0000.0000.000
12A10ASP-1-0.986-0.83519.204-0.281-0.2810.0000.0000.0000.000
13A11THR0-0.003-0.12518.810-0.021-0.0210.0000.0000.0000.000
14A11THR0-0.0410.08921.0770.0030.0030.0000.0000.0000.000
15A12PRO0-0.070-0.11720.5350.0220.0220.0000.0000.0000.000
16A13ILE00.083-0.00923.0280.0000.0000.0000.0000.0000.000
17A13ILE0-0.0990.10924.9250.0020.0020.0000.0000.0000.000
18A14GLU00.085-0.10326.5200.0020.0020.0000.0000.0000.000
19A14GLU-1-0.982-0.85428.418-0.156-0.1560.0000.0000.0000.000
20A15SER00.054-0.05629.3860.0040.0040.0000.0000.0000.000
21A15SER0-0.0380.01632.5650.0000.0000.0000.0000.0000.000
22A16ARG00.197-0.07032.500-0.004-0.0040.0000.0000.0000.000
23A16ARG10.7091.01235.5910.0750.0750.0000.0000.0000.000
24A17ALA00.042-0.10135.3880.0000.0000.0000.0000.0000.000
25A17ALA0-0.0750.10037.1100.0000.0000.0000.0000.0000.000
26A18ARG00.089-0.12234.0040.0060.0060.0000.0000.0000.000
27A18ARG10.7740.99632.3460.1240.1240.0000.0000.0000.000
28A19LEU00.074-0.08433.985-0.001-0.0010.0000.0000.0000.000
29A19LEU0-0.0950.09130.6090.0000.0000.0000.0000.0000.000
30A20SER0-0.025-0.07134.642-0.001-0.0010.0000.0000.0000.000
31A20SER0-0.0420.04638.7320.0040.0040.0000.0000.0000.000
32A21LEU00.098-0.12637.6560.0070.0070.0000.0000.0000.000
33A21LEU0-0.0990.13337.4170.0000.0000.0000.0000.0000.000
34A22PRO0-0.063-0.12638.776-0.003-0.0030.0000.0000.0000.000
35A23LYS00.1720.04938.854-0.001-0.0010.0000.0000.0000.000
36A23LYS10.7190.97238.9240.0910.0910.0000.0000.0000.000
37A24GLN00.051-0.08339.800-0.004-0.0040.0000.0000.0000.000
38A24GLN0-0.0990.06443.734-0.002-0.0020.0000.0000.0000.000
39A25LEU00.055-0.10041.4750.0030.0030.0000.0000.0000.000
40A25LEU0-0.0760.09241.8820.0010.0010.0000.0000.0000.000
41A26VAL00.064-0.09238.628-0.004-0.0040.0000.0000.0000.000
42A26VAL0-0.0540.10437.992-0.001-0.0010.0000.0000.0000.000
43A27LEU00.077-0.10737.4510.0070.0070.0000.0000.0000.000
44A27LEU0-0.0600.12035.9110.0000.0000.0000.0000.0000.000
45A28ARG00.034-0.10837.093-0.008-0.0080.0000.0000.0000.000
46A28ARG10.8551.04538.6350.0960.0960.0000.0000.0000.000
47A29GLN00.118-0.05138.9280.0040.0040.0000.0000.0000.000
48A29GLN0-0.1240.07139.251-0.005-0.0050.0000.0000.0000.000
49A30SER00.022-0.11040.5420.0000.0000.0000.0000.0000.000
50A30SER0-0.0870.01343.7850.0020.0020.0000.0000.0000.000
51A31ILE00.058-0.07344.150-0.002-0.0020.0000.0000.0000.000
52A31ILE0-0.1340.08248.0090.0010.0010.0000.0000.0000.000
53A32VAL00.020-0.12246.9730.0000.0000.0000.0000.0000.000
54A32VAL0-0.1200.06347.7690.0000.0000.0000.0000.0000.000
55A33GLY00.066-0.09646.1510.0040.0040.0000.0000.0000.000
56A34ALA00.0460.01744.0500.0010.0010.0000.0000.0000.000
57A34ALA0-0.0870.08844.5240.0010.0010.0000.0000.0000.000
58A35GLU00.026-0.15040.6150.0010.0010.0000.0000.0000.000
59A35GLU-1-0.868-0.78340.555-0.077-0.0770.0000.0000.0000.000
60A36VAL00.061-0.08938.7390.0000.0000.0000.0000.0000.000
61A36VAL0-0.0520.11136.584-0.001-0.0010.0000.0000.0000.000
62A37GLY00.075-0.06839.9380.0050.0050.0000.0000.0000.000
63A38VAL00.0880.00041.118-0.006-0.0060.0000.0000.0000.000
64A38VAL0-0.0930.10341.9230.0000.0000.0000.0000.0000.000
65A39TRP00.066-0.09242.2280.0060.0060.0000.0000.0000.000
66A39TRP0-0.1300.07342.0460.0000.0000.0000.0000.0000.000
67A40THR00.105-0.07843.093-0.004-0.0040.0000.0000.0000.000
68A40THR0-0.0990.05846.6210.0000.0000.0000.0000.0000.000
69A41GLY00.020-0.07342.230-0.001-0.0010.0000.0000.0000.000
70A42GLU00.039-0.00443.093-0.002-0.0020.0000.0000.0000.000
71A42GLU-1-0.856-0.78543.915-0.088-0.0880.0000.0000.0000.000
72A43THR00.055-0.07946.3020.0000.0000.0000.0000.0000.000
73A43THR0-0.0510.05051.192-0.001-0.0010.0000.0000.0000.000
74A44ILE00.032-0.10749.708-0.001-0.0010.0000.0000.0000.000
75A44ILE0-0.0930.12146.7280.0000.0000.0000.0000.0000.000
76A45PRO00.055-0.08250.8170.0020.0020.0000.0000.0000.000
77A46VAL00.1390.05354.342-0.001-0.0010.0000.0000.0000.000
78A46VAL0-0.1060.08858.3800.0010.0010.0000.0000.0000.000
79A47ARG00.008-0.08256.7180.0000.0000.0000.0000.0000.000
80A47ARG10.8371.02558.6180.0460.0460.0000.0000.0000.000
81A48THR00.098-0.08952.5440.0010.0010.0000.0000.0000.000
82A48THR0-0.0520.06650.481-0.001-0.0010.0000.0000.0000.000
83A49CYS00.140-0.07852.9080.0000.0000.0000.0000.0000.000
84A49CYS0-0.1360.10253.6650.0000.0000.0000.0000.0000.000
85A50PHE00.023-0.10848.811-0.001-0.0010.0000.0000.0000.000
86A50PHE0-0.0610.09946.954-0.001-0.0010.0000.0000.0000.000
87A51GLY00.011-0.08048.3080.0020.0020.0000.0000.0000.000
88A52PRO0-0.008-0.01748.3750.0000.0000.0000.0000.0000.000
89A53LEU00.161-0.02347.137-0.004-0.0040.0000.0000.0000.000
90A53LEU0-0.1360.11146.1480.0000.0000.0000.0000.0000.000
91A54ILE00.007-0.12844.3340.0040.0040.0000.0000.0000.000
92A54ILE0-0.1210.09642.8020.0000.0000.0000.0000.0000.000
93A55GLY00.022-0.12544.033-0.003-0.0030.0000.0000.0000.000
94A56GLN00.1530.02244.8290.0010.0010.0000.0000.0000.000
95A56GLN0-0.0950.10641.2110.0010.0010.0000.0000.0000.000
96A57GLN00.067-0.07245.3980.0010.0010.0000.0000.0000.000
97A57GLN0-0.0730.09748.093-0.001-0.0010.0000.0000.0000.000
98A58SER00.014-0.09748.7170.0000.0000.0000.0000.0000.000
99A58SER0-0.0420.07649.443-0.001-0.0010.0000.0000.0000.000
100A59HIS0-0.040-0.11250.9390.0000.0000.0000.0000.0000.000
101A59HIS00.0730.05052.8440.0000.0000.0000.0000.0000.000
102A71VAL00.1610.03248.2670.0000.0000.0000.0000.0000.000
103A71VAL0-0.1070.08048.8770.0000.0000.0000.0000.0000.000
104A72ASN00.020-0.10148.708-0.002-0.0020.0000.0000.0000.000
105A72ASN0-0.0740.07248.8930.0010.0010.0000.0000.0000.000
106A73HIS00.077-0.07446.8210.0000.0000.0000.0000.0000.000
107A73HIS0-0.1070.08345.401-0.003-0.0030.0000.0000.0000.000
108A74ILE00.143-0.09448.174-0.001-0.0010.0000.0000.0000.000
109A74ILE0-0.0800.08650.0280.0010.0010.0000.0000.0000.000
110A75TRP00.002-0.09450.9500.0010.0010.0000.0000.0000.000
111A75TRP0-0.0370.10148.5410.0010.0010.0000.0000.0000.000
112A76LYS00.131-0.08252.9300.0000.0000.0000.0000.0000.000
113A76LYS10.8541.04556.2320.0350.0350.0000.0000.0000.000
114A77ILE00.066-0.11356.0690.0000.0000.0000.0000.0000.000
115A77ILE0-0.0930.13054.0940.0000.0000.0000.0000.0000.000
116A78TYR00.121-0.07957.0680.0010.0010.0000.0000.0000.000
117A78TYR0-0.0990.07260.2710.0000.0000.0000.0000.0000.000
118A79HIS00.090-0.13360.802-0.001-0.0010.0000.0000.0000.000
119A79HIS0-0.0440.13560.564-0.001-0.0010.0000.0000.0000.000
120A80ASN0-0.025-0.11662.4630.0010.0010.0000.0000.0000.000
121A80ASN0-0.0760.09565.9030.0000.0000.0000.0000.0000.000
122A81GLY00.046-0.10265.4180.0010.0010.0000.0000.0000.000
123A82VAL00.084-0.00264.2300.0010.0010.0000.0000.0000.000
124A82VAL0-0.0380.14062.6790.0000.0000.0000.0000.0000.000
125A83LEU00.114-0.11160.535-0.001-0.0010.0000.0000.0000.000
126A83LEU0-0.1710.07657.4530.0000.0000.0000.0000.0000.000
127A84GLU00.099-0.12858.5750.0010.0010.0000.0000.0000.000
128A84GLU-1-0.985-0.84557.950-0.030-0.0300.0000.0000.0000.000
129A85PHE00.015-0.07454.3410.0010.0010.0000.0000.0000.000
130A85PHE0-0.0830.06752.1810.0000.0000.0000.0000.0000.000
131A86CYS00.101-0.09053.0550.0000.0000.0000.0000.0000.000
132A86CYS0-0.1040.08552.4650.0000.0000.0000.0000.0000.000
133A87ILE00.057-0.08349.3160.0000.0000.0000.0000.0000.000
134A87ILE0-0.0850.10047.7480.0000.0000.0000.0000.0000.000
135A88ILE00.115-0.09147.4680.0000.0000.0000.0000.0000.000
136A88ILE0-0.0990.11845.2570.0000.0000.0000.0000.0000.000
137A89THR00.035-0.10344.295-0.002-0.0020.0000.0000.0000.000
138A89THR0-0.1080.06544.7800.0010.0010.0000.0000.0000.000
139A90THR00.157-0.05742.357-0.002-0.0020.0000.0000.0000.000
140A90THR0-0.0280.06341.3310.0010.0010.0000.0000.0000.000
141A91ASP00.099-0.10638.668-0.004-0.0040.0000.0000.0000.000
142A91ASP-1-0.914-0.77637.118-0.078-0.0780.0000.0000.0000.000
143A92GLU00.113-0.11635.9520.0040.0040.0000.0000.0000.000
144A92GLU-1-0.813-0.70234.336-0.114-0.1140.0000.0000.0000.000
145A93ASN00.059-0.09635.505-0.004-0.0040.0000.0000.0000.000
146A93ASN0-0.1150.05133.211-0.006-0.0060.0000.0000.0000.000
147A94GLU00.021-0.12036.2240.0000.0000.0000.0000.0000.000
148A94GLU-1-0.913-0.81239.162-0.062-0.0620.0000.0000.0000.000
149A95CYS00.023-0.14039.4830.0050.0050.0000.0000.0000.000
150A95CYS0-0.0900.09340.8730.0020.0020.0000.0000.0000.000
151A96ASN00.156-0.01239.532-0.005-0.0050.0000.0000.0000.000
152A96ASN0-0.1030.03741.9580.0010.0010.0000.0000.0000.000
153A97TRP00.104-0.11040.2290.0020.0020.0000.0000.0000.000
154A97TRP0-0.0430.11939.9580.0010.0010.0000.0000.0000.000
155A98MET0-0.003-0.12341.058-0.002-0.0020.0000.0000.0000.000
156A98MET0-0.1170.10545.1130.0010.0010.0000.0000.0000.000
157A99MET00.104-0.10942.6940.0040.0040.0000.0000.0000.000
158A99MET0-0.0910.11339.535-0.001-0.0010.0000.0000.0000.000
159A100PHE0-0.053-0.12541.4280.0030.0030.0000.0000.0000.000
160A100PHE0-0.0550.09436.777-0.001-0.0010.0000.0000.0000.000
161A101VAL00.081-0.10242.644-0.002-0.0020.0000.0000.0000.000
162A101VAL0-0.0860.10245.3660.0000.0000.0000.0000.0000.000
163A102ARG00.084-0.09946.0150.0030.0030.0000.0000.0000.000
164A102ARG10.8341.07241.6180.0760.0760.0000.0000.0000.000
165A103LYS00.120-0.10147.8520.0000.0000.0000.0000.0000.000
166A103LYS10.7801.04151.4580.0470.0470.0000.0000.0000.000
167A104ALA00.132-0.08751.569-0.001-0.0010.0000.0000.0000.000
168A104ALA0-0.0900.10854.2560.0000.0000.0000.0000.0000.000
169A105ARG0-0.021-0.13453.7650.0020.0020.0000.0000.0000.000
170A105ARG10.7691.01151.2140.0570.0570.0000.0000.0000.000
171A106ASN00.016-0.11255.3980.0020.0020.0000.0000.0000.000
172A106ASN0-0.0790.07456.2650.0000.0000.0000.0000.0000.000
173A107ARG00.121-0.07157.756-0.002-0.0020.0000.0000.0000.000
174A107ARG10.8731.04361.8800.0390.0390.0000.0000.0000.000
175A108GLU0-0.006-0.08759.4840.0000.0000.0000.0000.0000.000
176A108GLU-1-0.954-0.85859.060-0.043-0.0430.0000.0000.0000.000
177A109GLU00.160-0.13254.9930.0000.0000.0000.0000.0000.000
178A109GLU-1-0.833-0.76753.760-0.055-0.0550.0000.0000.0000.000
179A110GLN00.144-0.04154.248-0.003-0.0030.0000.0000.0000.000
180A110GLN0-0.1830.06056.6610.0010.0010.0000.0000.0000.000
181A111ASN0-0.012-0.07754.0940.0020.0020.0000.0000.0000.000
182A111ASN0-0.0690.06051.162-0.001-0.0010.0000.0000.0000.000
183A112LEU00.052-0.12752.8020.0000.0000.0000.0000.0000.000
184A112LEU0-0.0110.12949.5550.0000.0000.0000.0000.0000.000
185A113VAL00.123-0.06554.2460.0000.0000.0000.0000.0000.000
186A113VAL0-0.1310.08957.5570.0010.0010.0000.0000.0000.000
187A114ALA00.131-0.09754.343-0.001-0.0010.0000.0000.0000.000
188A114ALA0-0.0890.09953.5920.0000.0000.0000.0000.0000.000
189A115TYR0-0.018-0.15355.2540.0020.0020.0000.0000.0000.000
190A115TYR0-0.0720.09256.0750.0010.0010.0000.0000.0000.000
191A116PRO00.009-0.09756.099-0.001-0.0010.0000.0000.0000.000
192A117HIS00.069-0.00256.6540.0010.0010.0000.0000.0000.000
193A117HIS0-0.1070.08557.1770.0000.0000.0000.0000.0000.000
194A118ASP00.096-0.11456.736-0.001-0.0010.0000.0000.0000.000
195A118ASP-1-0.954-0.80757.399-0.037-0.0370.0000.0000.0000.000
196A119GLY00.009-0.11456.626-0.001-0.0010.0000.0000.0000.000
197A120LYS0-0.009-0.05953.2370.0000.0000.0000.0000.0000.000
198A120LYS10.8681.08650.0020.0470.0470.0000.0000.0000.000
199A121ILE00.072-0.08152.0970.0020.0020.0000.0000.0000.000
200A121ILE0-0.0570.09551.4400.0000.0000.0000.0000.0000.000
201A122PHE00.123-0.07951.445-0.003-0.0030.0000.0000.0000.000
202A122PHE0-0.0550.10351.9690.0000.0000.0000.0000.0000.000
203A123PHE00.050-0.08651.3060.0020.0020.0000.0000.0000.000
204A123PHE0-0.0580.08647.6380.0000.0000.0000.0000.0000.000
205A124CYS00.184-0.07052.461-0.002-0.0020.0000.0000.0000.000
206A124CYS0-0.1430.09355.7840.0010.0010.0000.0000.0000.000
207A125THR00.009-0.09354.2130.0010.0010.0000.0000.0000.000
208A125THR0-0.0510.06252.3340.0000.0000.0000.0000.0000.000
209A126SER0-0.011-0.09854.8650.0010.0010.0000.0000.0000.000
210A126SER0-0.0420.07557.7320.0000.0000.0000.0000.0000.000
211A127GLN00.031-0.09456.7060.0020.0020.0000.0000.0000.000
212A127GLN0-0.0340.09156.2840.0010.0010.0000.0000.0000.000
213A128ASP00.144-0.08355.159-0.001-0.0010.0000.0000.0000.000
214A128ASP-1-0.909-0.82555.477-0.053-0.0530.0000.0000.0000.000
215A129ILE00.011-0.12851.8020.0020.0020.0000.0000.0000.000
216A129ILE0-0.1260.11750.2680.0000.0000.0000.0000.0000.000
217A130PRO00.006-0.10551.060-0.002-0.0020.0000.0000.0000.000
218A131PRO00.0520.02946.2270.0000.0000.0000.0000.0000.000
219A132GLU00.0440.03145.0040.0030.0030.0000.0000.0000.000
220A132GLU-1-1.016-0.88543.313-0.093-0.0930.0000.0000.0000.000
221A133ASN00.122-0.11545.9650.0010.0010.0000.0000.0000.000
222A133ASN0-0.1470.05149.3440.0030.0030.0000.0000.0000.000
223A134GLU00.106-0.11746.325-0.003-0.0030.0000.0000.0000.000
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226A135LEU0-0.0860.07746.1380.0000.0000.0000.0000.0000.000
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230A137PHE0-0.0850.09049.6800.0010.0010.0000.0000.0000.000
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232A138TYR0-0.0620.09356.8340.0010.0010.0000.0000.0000.000
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238A141ARG10.9360.98761.4830.0390.0390.0000.0000.0000.000