FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 4LM2N

Calculation Name: 3N3E-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3E

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UUZ6

Base Structure: X-ray

Registration Date: 2025-07-11

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 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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -777422.750084
FMO2-HF: Nuclear repulsion 735596.22054
FMO2-HF: Total energy -41826.529545
FMO2-MP2: Total energy -41948.698727


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:61:GLY)


Summations of interaction energy for fragment #1(A:61: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.
-0.891.135-0.007-0.933-1.086-0.001
Interaction energy analysis for fragmet #1(A:61:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.020
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].
3A62VAL0-0.1320.1124.2770.1720.4290.000-0.115-0.1420.000
4A63SER00.157-0.0163.573-1.0540.589-0.005-0.810-0.828-0.001
5A63SER0-0.0720.0605.697-0.078-0.0780.0000.0000.0000.000
6A64GLU00.054-0.1505.0732.0432.168-0.002-0.008-0.1160.000
7A64GLU-1-0.930-0.7754.983-0.371-0.3710.0000.0000.0000.000
8A65VAL00.048-0.1086.522-0.375-0.3750.0000.0000.0000.000
9A65VAL0-0.0790.10810.0660.0120.0120.0000.0000.0000.000
10A66ARG00.031-0.12010.2000.1180.1180.0000.0000.0000.000
11A66ARG10.8301.0578.3320.2960.2960.0000.0000.0000.000
12A67SER00.103-0.06212.455-0.024-0.0240.0000.0000.0000.000
13A67SER0-0.0450.07216.010-0.007-0.0070.0000.0000.0000.000
14A68ASP00.021-0.07516.1510.0230.0230.0000.0000.0000.000
15A68ASP-1-0.811-0.75518.150-0.011-0.0110.0000.0000.0000.000
16A69ARG00.099-0.08319.1120.0100.0100.0000.0000.0000.000
17A69ARG10.8201.02523.368-0.006-0.0060.0000.0000.0000.000
18A70GLU00.069-0.10521.8050.0080.0080.0000.0000.0000.000
19A70GLU-1-0.932-0.82522.005-0.012-0.0120.0000.0000.0000.000
20A71LYS00.048-0.10219.9230.0010.0010.0000.0000.0000.000
21A71LYS10.7781.00617.6700.0480.0480.0000.0000.0000.000
22A72PHE00.119-0.08816.7100.0130.0130.0000.0000.0000.000
23A72PHE0-0.0870.08215.0010.0100.0100.0000.0000.0000.000
24A73THR00.005-0.08414.110-0.017-0.0170.0000.0000.0000.000
25A73THR0-0.0280.05812.559-0.006-0.0060.0000.0000.0000.000
26A74VAL00.077-0.09411.0520.0910.0910.0000.0000.0000.000
27A74VAL0-0.0820.10110.5580.0140.0140.0000.0000.0000.000
28A75TYR00.063-0.0898.6880.0020.0020.0000.0000.0000.000
29A75TYR0-0.0950.0917.928-0.007-0.0070.0000.0000.0000.000
30A76LEU00.155-0.0997.566-0.077-0.0770.0000.0000.0000.000
31A76LEU0-0.1400.0827.5740.0790.0790.0000.0000.0000.000
32A77ASP00.069-0.0737.1190.3690.3690.0000.0000.0000.000
33A77ASP-1-0.943-0.8646.475-1.929-1.9290.0000.0000.0000.000
34A78VAL0-0.022-0.1418.491-0.008-0.0080.0000.0000.0000.000
35A78VAL0-0.0930.09611.4000.0390.0390.0000.0000.0000.000
36A79LYS00.181-0.07110.9200.1590.1590.0000.0000.0000.000
37A79LYS10.8681.0738.6580.9530.9530.0000.0000.0000.000
38A80HIS00.048-0.09112.7640.0360.0360.0000.0000.0000.000
39A80HIS0-0.1010.06015.637-0.039-0.0390.0000.0000.0000.000
40A81PHE00.075-0.09215.4540.0570.0570.0000.0000.0000.000
41A81PHE0-0.1150.07913.8570.0100.0100.0000.0000.0000.000
42A82SER0-0.027-0.10217.160-0.037-0.0370.0000.0000.0000.000
43A82SER0-0.0070.09321.6470.0120.0120.0000.0000.0000.000
44A83PRO00.002-0.11719.9720.0000.0000.0000.0000.0000.000
45A84ASP00.130-0.00521.3150.0070.0070.0000.0000.0000.000
46A84ASP-1-1.006-0.83524.695-0.124-0.1240.0000.0000.0000.000
47A85GLU00.035-0.12020.7520.0250.0250.0000.0000.0000.000
48A85GLU-1-0.923-0.78320.079-0.208-0.2080.0000.0000.0000.000
49A86LEU00.075-0.12118.5760.0070.0070.0000.0000.0000.000
50A86LEU0-0.1060.08315.665-0.008-0.0080.0000.0000.0000.000
51A87SER00.123-0.06119.4400.0020.0020.0000.0000.0000.000
52A87SER0-0.0930.07221.1520.0060.0060.0000.0000.0000.000
53A88VAL00.074-0.12919.4010.0090.0090.0000.0000.0000.000
54A88VAL0-0.0900.12117.816-0.002-0.0020.0000.0000.0000.000
55A89LYS00.036-0.12920.282-0.008-0.0080.0000.0000.0000.000
56A89LYS10.9191.10122.6710.0060.0060.0000.0000.0000.000
57A90VAL00.045-0.10921.1120.0100.0100.0000.0000.0000.000
58A90VAL0-0.0650.11722.289-0.001-0.0010.0000.0000.0000.000
59A91THR00.051-0.05622.624-0.010-0.0100.0000.0000.0000.000
60A91THR0-0.0870.04723.318-0.005-0.0050.0000.0000.0000.000
61A92ASP00.180-0.08523.2690.0140.0140.0000.0000.0000.000
62A92ASP-1-1.031-0.85125.0000.0860.0860.0000.0000.0000.000
63A93ASP00.041-0.08423.7210.0140.0140.0000.0000.0000.000
64A93ASP-1-0.871-0.77023.9030.0960.0960.0000.0000.0000.000
65A94TYR00.059-0.12419.7510.0260.0260.0000.0000.0000.000
66A94TYR0-0.0780.08117.7780.0320.0320.0000.0000.0000.000
67A95VAL00.113-0.09618.170-0.019-0.0190.0000.0000.0000.000
68A95VAL0-0.0770.11317.152-0.003-0.0030.0000.0000.0000.000
69A96GLU00.072-0.14717.0450.0370.0370.0000.0000.0000.000
70A96GLU-1-0.985-0.81819.4690.0710.0710.0000.0000.0000.000
71A97ILE00.087-0.09715.344-0.017-0.0170.0000.0000.0000.000
72A97ILE0-0.0980.08913.370-0.006-0.0060.0000.0000.0000.000
73A98GLN00.031-0.12615.9030.0220.0220.0000.0000.0000.000
74A98GLN0-0.0700.11518.777-0.005-0.0050.0000.0000.0000.000
75A99GLY00.057-0.07416.487-0.027-0.0270.0000.0000.0000.000
76A100LYS00.131-0.02117.4210.0170.0170.0000.0000.0000.000
77A100LYS10.8361.08820.2460.0820.0820.0000.0000.0000.000
78A101HIS00.075-0.10018.4140.0060.0060.0000.0000.0000.000
79A101HIS10.6890.97617.4950.2330.2330.0000.0000.0000.000
80A102GLY0-0.045-0.11419.3450.0070.0070.0000.0000.0000.000
81A103GLU00.030-0.03021.594-0.003-0.0030.0000.0000.0000.000
82A103GLU-1-0.920-0.79618.975-0.271-0.2710.0000.0000.0000.000
83A104ARG00.147-0.09022.5720.0090.0090.0000.0000.0000.000
84A104ARG10.9151.07725.8570.0990.0990.0000.0000.0000.000
85A105GLN00.023-0.08823.189-0.022-0.0220.0000.0000.0000.000
86A105GLN0-0.1180.05920.0730.0000.0000.0000.0000.0000.000
87A106ASP00.086-0.09624.0690.0070.0070.0000.0000.0000.000
88A106ASP-1-0.951-0.85225.316-0.107-0.1070.0000.0000.0000.000
89A107ASP0-0.008-0.14226.3510.0020.0020.0000.0000.0000.000
90A107ASP-1-0.941-0.81428.760-0.065-0.0650.0000.0000.0000.000
91A108HIS0-0.023-0.11329.6390.0030.0030.0000.0000.0000.000
92A108HIS0-0.0980.08331.2000.0000.0000.0000.0000.0000.000
93A109GLY00.082-0.07025.8260.0070.0070.0000.0000.0000.000
94A110TYR00.079-0.03124.275-0.009-0.0090.0000.0000.0000.000
95A110TYR0-0.1080.09523.9900.0000.0000.0000.0000.0000.000
96A111ILE00.076-0.12919.7940.0180.0180.0000.0000.0000.000
97A111ILE0-0.1120.12817.599-0.003-0.0030.0000.0000.0000.000
98A112SER00.102-0.07320.294-0.017-0.0170.0000.0000.0000.000
99A112SER0-0.0610.07020.8640.0020.0020.0000.0000.0000.000
100A113ARG00.011-0.11715.7140.0270.0270.0000.0000.0000.000
101A113ARG10.8761.06613.4840.2330.2330.0000.0000.0000.000
102A114GLU00.151-0.12816.501-0.031-0.0310.0000.0000.0000.000
103A114GLU-1-0.963-0.78518.245-0.015-0.0150.0000.0000.0000.000
104A115PHE0-0.003-0.11713.4820.0260.0260.0000.0000.0000.000
105A115PHE0-0.0970.08412.912-0.011-0.0110.0000.0000.0000.000
106A116HIS00.121-0.08914.911-0.033-0.0330.0000.0000.0000.000
107A116HIS0-0.1040.10017.1440.0100.0100.0000.0000.0000.000
108A117ARG00.047-0.14012.7630.0590.0590.0000.0000.0000.000
109A117ARG10.8651.0876.926-0.398-0.3980.0000.0000.0000.000
110A118ARG00.106-0.07613.915-0.051-0.0510.0000.0000.0000.000
111A118ARG10.8971.08616.630-0.173-0.1730.0000.0000.0000.000
112A119TYR0-0.026-0.14514.4240.0850.0850.0000.0000.0000.000
113A119TYR0-0.0540.0798.873-0.067-0.0670.0000.0000.0000.000
114A120ARG00.185-0.05115.134-0.052-0.0520.0000.0000.0000.000
115A120ARG10.8001.04116.180-0.347-0.3470.0000.0000.0000.000
116A121LEU00.022-0.15717.2910.0360.0360.0000.0000.0000.000
117A121LEU0-0.0660.14118.253-0.004-0.0040.0000.0000.0000.000
118A122PRO0-0.035-0.11018.2910.0020.0020.0000.0000.0000.000
119A123SER00.1070.04621.370-0.015-0.0150.0000.0000.0000.000
120A123SER0-0.0560.05926.1320.0030.0030.0000.0000.0000.000
121A124ASN00.073-0.04224.264-0.011-0.0110.0000.0000.0000.000
122A124ASN0-0.1030.04623.3390.0110.0110.0000.0000.0000.000
123A125VAL00.077-0.07521.979-0.011-0.0110.0000.0000.0000.000
124A125VAL0-0.0880.07219.9130.0020.0020.0000.0000.0000.000
125A126ASP00.151-0.08423.3410.0090.0090.0000.0000.0000.000
126A126ASP-1-0.911-0.78025.9820.0060.0060.0000.0000.0000.000
127A127GLN00.125-0.11224.089-0.011-0.0110.0000.0000.0000.000
128A127GLN0-0.0840.10223.871-0.006-0.0060.0000.0000.0000.000
129A128SER0-0.013-0.10125.122-0.010-0.0100.0000.0000.0000.000
130A128SER0-0.0580.06028.880-0.002-0.0020.0000.0000.0000.000
131A129ALA00.071-0.11425.927-0.010-0.0100.0000.0000.0000.000
132A129ALA0-0.0720.11025.6360.0000.0000.0000.0000.0000.000
133A130ILE00.020-0.12621.813-0.014-0.0140.0000.0000.0000.000
134A130ILE0-0.1050.10019.7450.0020.0020.0000.0000.0000.000
135A131THR0-0.035-0.10820.8540.0030.0030.0000.0000.0000.000
136A131THR0-0.0170.08521.060-0.012-0.0120.0000.0000.0000.000
137A132CYS00.157-0.09618.1550.0030.0030.0000.0000.0000.000
138A132CYS0-0.1410.11016.901-0.003-0.0030.0000.0000.0000.000
139A133THR00.006-0.09017.4830.0210.0210.0000.0000.0000.000
140A133THR0-0.0270.06717.3780.0010.0010.0000.0000.0000.000
141A134LEU00.188-0.06016.152-0.042-0.0420.0000.0000.0000.000
142A134LEU0-0.1280.10415.2080.0100.0100.0000.0000.0000.000
143A135SER00.052-0.06215.5670.0690.0690.0000.0000.0000.000
144A135SER0-0.0190.06114.290-0.020-0.0200.0000.0000.0000.000
145A136ALA00.069-0.10816.968-0.017-0.0170.0000.0000.0000.000
146A136ALA0-0.0760.09718.9730.0070.0070.0000.0000.0000.000
147A137ASP00.030-0.13114.5780.0460.0460.0000.0000.0000.000
148A137ASP-1-1.029-0.84613.756-0.576-0.5760.0000.0000.0000.000
149A138GLY00.008-0.10613.117-0.107-0.1070.0000.0000.0000.000
150A139LEU00.158-0.00311.057-0.106-0.1060.0000.0000.0000.000
151A139LEU0-0.1470.1038.987-0.013-0.0130.0000.0000.0000.000
152A140LEU00.122-0.09311.5880.1170.1170.0000.0000.0000.000
153A140LEU0-0.1180.09912.5210.0170.0170.0000.0000.0000.000
154A141THR00.011-0.12711.822-0.069-0.0690.0000.0000.0000.000
155A141THR0-0.0320.09213.725-0.018-0.0180.0000.0000.0000.000
156A142LEU00.003-0.11913.8210.0180.0180.0000.0000.0000.000
157A142LEU0-0.0440.12514.2950.0100.0100.0000.0000.0000.000
158A143CYS00.116-0.11415.3620.0170.0170.0000.0000.0000.000
159A143CYS0-0.1350.10618.0400.0030.0030.0000.0000.0000.000
160A144GLY00.052-0.08418.0360.0030.0030.0000.0000.0000.000
161A145PRO00.0220.00720.1760.0150.0150.0000.0000.0000.000
162A146LYS00.1280.02222.9980.0070.0070.0000.0000.0000.000
163A146LYS10.7210.98919.318-0.100-0.1000.0000.0000.0000.000
164A147THR0-0.061-0.10824.279-0.010-0.0100.0000.0000.0000.000
165A147THR00.0180.10527.3210.0020.0020.0000.0000.0000.000
166A148SER00.022-0.08728.0190.0100.0100.0000.0000.0000.000
167A148SER0-0.0400.06930.149-0.001-0.0010.0000.0000.0000.000
168A149GLY0-0.019-0.10730.786-0.006-0.0060.0000.0000.0000.000
169A150ILE00.0470.00133.6480.0060.0060.0000.0000.0000.000
170A150ILE0-0.0750.09337.2010.0000.0000.0000.0000.0000.000
171A151ASP00.112-0.11434.1020.0050.0050.0000.0000.0000.000
172A151ASP-1-0.989-0.84133.7650.0130.0130.0000.0000.0000.000
173A152ALA00.107-0.09130.324-0.003-0.0030.0000.0000.0000.000
174A152ALA0-0.0750.10529.8780.0020.0020.0000.0000.0000.000
175A153GLY0-0.017-0.10128.9350.0010.0010.0000.0000.0000.000
176A154ARG00.087-0.01928.274-0.003-0.0030.0000.0000.0000.000
177A154ARG10.7000.97128.088-0.075-0.0750.0000.0000.0000.000
178A155GLY0-0.016-0.12128.153-0.004-0.0040.0000.0000.0000.000
179A156ASP00.176-0.00726.969-0.003-0.0030.0000.0000.0000.000
180A156ASP-1-0.976-0.80427.5060.0520.0520.0000.0000.0000.000
181A157ARG0-0.031-0.12826.490-0.004-0.0040.0000.0000.0000.000
182A157ARG10.8001.03624.5790.0240.0240.0000.0000.0000.000
183A158THR00.035-0.09325.2510.0060.0060.0000.0000.0000.000
184A158THR0-0.0130.08725.1220.0000.0000.0000.0000.0000.000
185A159ILE00.011-0.12922.6380.0020.0020.0000.0000.0000.000
186A159ILE0-0.0980.10121.0180.0000.0000.0000.0000.0000.000
187A160PRO0-0.015-0.10223.070-0.008-0.0080.0000.0000.0000.000
188A161VAL00.105-0.02320.9830.0010.0010.0000.0000.0000.000
189A161VAL0-0.0600.13919.255-0.004-0.0040.0000.0000.0000.000
190A162THR00.032-0.10021.470-0.001-0.0010.0000.0000.0000.000
191A162THR0-0.0480.08522.4730.0080.0080.0000.0000.0000.000
192A163ARG00.114-0.09920.665-0.026-0.0260.0000.0000.0000.000
193A163ARG10.7691.04119.7500.2840.2840.0000.0000.0000.000
194A164GLU00.076-0.08020.3490.0320.0320.0000.0000.0000.000
195A164GLU-1-0.930-0.80217.381-0.353-0.3530.0000.0000.0000.000
196A165ASP0-0.006-0.15721.819-0.028-0.0280.0000.0000.0000.000
197A165ASP-1-0.966-0.81525.565-0.185-0.1850.0000.0000.0000.000
198A166LYS00.016-0.08718.7890.0010.0010.0000.0000.0000.000
199A166LYS10.9150.93618.6310.3130.3130.0000.0000.0000.000