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: RYJQ8

Calculation Name: 5CN2-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5CN2

Chain ID: A

ChEMBL ID:

UniProt ID: Q06336

Base Structure: X-ray

Registration Date: 2025-07-10

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 OptAll
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 218
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -907269.483315
FMO2-HF: Nuclear repulsion 862708.147997
FMO2-HF: Total energy -44561.335318
FMO2-MP2: Total energy -44691.208742


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:443:GLN)


Summations of interaction energy for fragment #1(A:443:GLN)
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.
0.6612.9040.101-1.048-1.2940.001
Interaction energy analysis for fragmet #1(A:443:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.150 / 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].
4A444ARG10.6730.9414.2071.3001.560-0.001-0.091-0.1690.000
5A445HIS00.058-0.0973.8560.5761.866-0.011-0.655-0.6240.001
6A445HIS0-0.1120.0883.0400.1010.5700.118-0.263-0.3230.000
7A446ILE00.159-0.0876.039-0.188-0.1880.0000.0000.0000.000
8A446ILE0-0.0830.1138.4040.0190.0190.0000.0000.0000.000
9A447LEU00.030-0.1279.5360.0050.0050.0000.0000.0000.000
10A447LEU0-0.1170.08912.091-0.015-0.0150.0000.0000.0000.000
11A448ASN00.057-0.10512.5460.0230.0230.0000.0000.0000.000
12A448ASN0-0.0600.05716.3480.0160.0160.0000.0000.0000.000
13A449GLN00.096-0.06914.284-0.018-0.0180.0000.0000.0000.000
14A449GLN0-0.0990.07214.2090.0320.0320.0000.0000.0000.000
15A450SER00.016-0.04316.1380.0220.0220.0000.0000.0000.000
16A450SER0-0.0330.02820.7630.0000.0000.0000.0000.0000.000
17A451ASP0-0.021-0.12319.3480.0180.0180.0000.0000.0000.000
18A451ASP-1-0.857-0.80423.2720.0600.0600.0000.0000.0000.000
19A452HIS00.034-0.09521.5260.0070.0070.0000.0000.0000.000
20A452HIS0-0.0730.05322.903-0.009-0.0090.0000.0000.0000.000
21A453LEU00.136-0.10218.9760.0010.0010.0000.0000.0000.000
22A453LEU0-0.1330.10617.795-0.009-0.0090.0000.0000.0000.000
23A454ARG00.122-0.08014.4970.0090.0090.0000.0000.0000.000
24A454ARG10.7210.98710.637-0.107-0.1070.0000.0000.0000.000
25A455ILE00.020-0.11613.554-0.032-0.0320.0000.0000.0000.000
26A455ILE0-0.0890.10013.153-0.009-0.0090.0000.0000.0000.000
27A456ASP00.103-0.0529.0280.0760.0760.0000.0000.0000.000
28A456ASP-1-0.834-0.7788.048-0.150-0.1500.0000.0000.0000.000
29A457TYR00.100-0.0927.6570.0360.0360.0000.0000.0000.000
30A457TYR0-0.0840.0877.7470.0510.0510.0000.0000.0000.000
31A458GLU00.101-0.0884.507-0.456-0.476-0.002-0.0290.0510.000
32A458GLU-1-0.863-0.7964.104-2.469-2.311-0.001-0.005-0.1510.000
33A459LEU00.083-0.1174.5640.5980.684-0.002-0.005-0.0780.000
34A459LEU0-0.0780.1045.7430.0370.0370.0000.0000.0000.000
35A460THR0-0.096-0.0915.4670.0020.0020.0000.0000.0000.000
36A460THR0-0.0200.0656.6950.0360.0360.0000.0000.0000.000
37A461ARG00.183-0.0788.1240.0530.0530.0000.0000.0000.000
38A461ARG10.7491.02211.1190.2180.2180.0000.0000.0000.000
39A462GLU00.073-0.10211.512-0.004-0.0040.0000.0000.0000.000
40A462GLU-1-0.905-0.81913.059-0.471-0.4710.0000.0000.0000.000
41A463SER00.020-0.07214.2630.0250.0250.0000.0000.0000.000
42A463SER0-0.0190.06218.2430.0070.0070.0000.0000.0000.000
43A464MET00.098-0.08816.112-0.016-0.0160.0000.0000.0000.000
44A464MET0-0.0370.14118.8090.0000.0000.0000.0000.0000.000
45A465THR00.040-0.09318.3260.0090.0090.0000.0000.0000.000
46A465THR0-0.0660.07420.6090.0090.0090.0000.0000.0000.000
47A466LYS00.096-0.09916.6590.0170.0170.0000.0000.0000.000
48A466LYS10.7721.03015.9390.3600.3600.0000.0000.0000.000
49A467LEU00.013-0.11412.584-0.008-0.0080.0000.0000.0000.000
50A467LEU0-0.0290.10011.5010.0070.0070.0000.0000.0000.000
51A468ARG00.104-0.09411.2280.0810.0810.0000.0000.0000.000
52A468ARG10.8381.08611.0080.7610.7610.0000.0000.0000.000
53A469LEU00.058-0.1249.430-0.175-0.1750.0000.0000.0000.000
54A469LEU0-0.0700.1009.8940.0340.0340.0000.0000.0000.000
55A470VAL00.057-0.0939.0650.2110.2110.0000.0000.0000.000
56A470VAL0-0.1170.0978.5940.0210.0210.0000.0000.0000.000
57A471ILE00.141-0.0939.037-0.311-0.3110.0000.0000.0000.000
58A471ILE0-0.0710.10311.9800.0090.0090.0000.0000.0000.000
59A472PHE00.033-0.10511.0970.0170.0170.0000.0000.0000.000
60A472PHE0-0.0780.0807.9520.0470.0470.0000.0000.0000.000
61A473TYR00.077-0.06712.1470.0380.0380.0000.0000.0000.000
62A473TYR0-0.1000.05716.191-0.007-0.0070.0000.0000.0000.000
63A474SER00.013-0.10115.188-0.027-0.0270.0000.0000.0000.000
64A474SER00.0170.07613.8230.0250.0250.0000.0000.0000.000
65A475ASN00.202-0.02316.2860.0240.0240.0000.0000.0000.000
66A475ASN0-0.1380.06820.8890.0090.0090.0000.0000.0000.000
67A476ILE0-0.053-0.13619.077-0.003-0.0030.0000.0000.0000.000
68A476ILE0-0.0850.10316.9400.0100.0100.0000.0000.0000.000
69A477SER00.069-0.06320.1560.0200.0200.0000.0000.0000.000
70A477SER0-0.0330.05623.971-0.004-0.0040.0000.0000.0000.000
71A478SER00.037-0.10223.922-0.005-0.0050.0000.0000.0000.000
72A478SER0-0.0230.08027.4180.0040.0040.0000.0000.0000.000
73A479ASP00.052-0.08526.351-0.005-0.0050.0000.0000.0000.000
74A479ASP-1-0.922-0.79528.1930.0190.0190.0000.0000.0000.000
75A480PRO0-0.026-0.10625.715-0.003-0.0030.0000.0000.0000.000
76A481ILE00.1490.05123.8990.0050.0050.0000.0000.0000.000
77A481ILE0-0.0940.11021.787-0.002-0.0020.0000.0000.0000.000
78A482THR0-0.009-0.09425.292-0.012-0.0120.0000.0000.0000.000
79A482THR0-0.0750.03728.0000.0030.0030.0000.0000.0000.000
80A483ASN00.081-0.05027.0250.0020.0020.0000.0000.0000.000
81A483ASN0-0.1020.04228.908-0.002-0.0020.0000.0000.0000.000
82A484PHE00.179-0.06222.8740.0070.0070.0000.0000.0000.000
83A484PHE0-0.0940.07418.8720.0020.0020.0000.0000.0000.000
84A485ALA00.064-0.09322.912-0.013-0.0130.0000.0000.0000.000
85A485ALA0-0.0640.11224.5880.0020.0020.0000.0000.0000.000
86A486LEU00.077-0.09319.4180.0240.0240.0000.0000.0000.000
87A486LEU0-0.0900.09516.617-0.005-0.0050.0000.0000.0000.000
88A487LEU00.041-0.11920.927-0.014-0.0140.0000.0000.0000.000
89A487LEU0-0.0860.10023.9910.0030.0030.0000.0000.0000.000
90A488VAL00.051-0.10720.3420.0080.0080.0000.0000.0000.000
91A488VAL0-0.0590.10418.457-0.004-0.0040.0000.0000.0000.000
92A489ALA00.134-0.06921.5070.0040.0040.0000.0000.0000.000
93A489ALA0-0.0980.08823.4140.0040.0040.0000.0000.0000.000
94A490SER00.012-0.11321.200-0.014-0.0140.0000.0000.0000.000
95A490SER0-0.0380.07622.747-0.004-0.0040.0000.0000.0000.000
96A491PRO0-0.012-0.10118.0670.0170.0170.0000.0000.0000.000
97A492LYS00.034-0.00421.248-0.005-0.0050.0000.0000.0000.000
98A492LYS10.8931.06223.6920.0600.0600.0000.0000.0000.000
99A493GLY00.032-0.08822.3290.0110.0110.0000.0000.0000.000
100A494THR0-0.002-0.00820.094-0.002-0.0020.0000.0000.0000.000
101A494THR0-0.0260.05818.178-0.004-0.0040.0000.0000.0000.000
102A495THR00.033-0.04221.3430.0110.0110.0000.0000.0000.000
103A495THR00.0180.11322.1890.0050.0050.0000.0000.0000.000
104A496LEU00.127-0.07319.154-0.022-0.0220.0000.0000.0000.000
105A496LEU0-0.1370.08917.0510.0010.0010.0000.0000.0000.000
106A497SER00.011-0.09119.4210.0200.0200.0000.0000.0000.000
107A497SER0-0.0700.06219.1110.0080.0080.0000.0000.0000.000
108A498LEU00.150-0.11118.601-0.052-0.0520.0000.0000.0000.000
109A498LEU0-0.1180.10217.9840.0010.0010.0000.0000.0000.000
110A499GLN00.048-0.08018.6090.0370.0370.0000.0000.0000.000
111A499GLN0-0.0760.08417.824-0.038-0.0380.0000.0000.0000.000
112A500PRO00.015-0.09519.775-0.006-0.0060.0000.0000.0000.000
113A501GLN00.0840.01618.721-0.039-0.0390.0000.0000.0000.000
114A501GLN0-0.1200.04119.516-0.004-0.0040.0000.0000.0000.000
115A502SER00.025-0.10918.6170.0290.0290.0000.0000.0000.000
116A502SER0-0.0270.09818.252-0.017-0.0170.0000.0000.0000.000
117A503GLY00.001-0.08720.1220.0150.0150.0000.0000.0000.000
118A504ASN00.0790.04322.120-0.016-0.0160.0000.0000.0000.000
119A504ASN0-0.0500.07825.1880.0000.0000.0000.0000.0000.000
120A505MET00.116-0.10523.3030.0110.0110.0000.0000.0000.000
121A505MET0-0.1270.09025.1590.0000.0000.0000.0000.0000.000
122A506LEU00.011-0.12021.099-0.020-0.0200.0000.0000.0000.000
123A506LEU0-0.0880.11218.1590.0020.0020.0000.0000.0000.000
124A507GLN00.140-0.06222.1090.0130.0130.0000.0000.0000.000
125A507GLN0-0.0300.09823.2480.0070.0070.0000.0000.0000.000
126A508SER00.046-0.08822.624-0.002-0.0020.0000.0000.0000.000
127A508SER0-0.0380.05225.851-0.003-0.0030.0000.0000.0000.000
128A509ASN00.025-0.05120.947-0.009-0.0090.0000.0000.0000.000
129A509ASN0-0.1200.05821.074-0.004-0.0040.0000.0000.0000.000
130A510SER00.096-0.08019.5050.0180.0180.0000.0000.0000.000
131A510SER0-0.0510.06919.385-0.014-0.0140.0000.0000.0000.000
132A511ARG00.138-0.07715.215-0.012-0.0120.0000.0000.0000.000
133A511ARG10.8141.03610.103-0.260-0.2600.0000.0000.0000.000
134A512ASP0-0.020-0.11112.6760.0000.0000.0000.0000.0000.000
135A512ASP-1-0.892-0.82110.303-0.278-0.2780.0000.0000.0000.000
136A513GLY00.063-0.07913.846-0.053-0.0530.0000.0000.0000.000
137A514ILE00.049-0.00916.2630.0060.0060.0000.0000.0000.000
138A514ILE0-0.1110.08217.545-0.001-0.0010.0000.0000.0000.000
139A515LYS00.150-0.06414.043-0.018-0.0180.0000.0000.0000.000
140A515LYS10.8141.05410.9550.7900.7900.0000.0000.0000.000
141A516GLN00.108-0.11214.0110.0580.0580.0000.0000.0000.000
142A516GLN0-0.0730.11715.7990.0150.0150.0000.0000.0000.000
143A517ILE00.017-0.11213.764-0.087-0.0870.0000.0000.0000.000
144A517ILE0-0.0700.10013.264-0.006-0.0060.0000.0000.0000.000
145A518ALA00.149-0.06613.9110.0760.0760.0000.0000.0000.000
146A518ALA0-0.0540.10414.4930.0060.0060.0000.0000.0000.000
147A519SER0-0.067-0.06813.987-0.091-0.0910.0000.0000.0000.000
148A519SER00.0070.06015.2840.0120.0120.0000.0000.0000.000
149A520VAL00.128-0.09515.4100.0380.0380.0000.0000.0000.000
150A520VAL0-0.1350.08914.4480.0040.0040.0000.0000.0000.000
151A521GLU00.127-0.12416.485-0.016-0.0160.0000.0000.0000.000
152A521GLU-1-0.913-0.78418.373-0.246-0.2460.0000.0000.0000.000
153A522GLY00.043-0.08319.3260.0180.0180.0000.0000.0000.000
154A523ILE00.1280.02120.629-0.009-0.0090.0000.0000.0000.000
155A523ILE0-0.0510.12224.1610.0010.0010.0000.0000.0000.000
156A524SER00.011-0.09120.3900.0070.0070.0000.0000.0000.000
157A524SER0-0.0280.04819.6480.0040.0040.0000.0000.0000.000
158A525VAL00.107-0.10716.8070.0170.0170.0000.0000.0000.000
159A525VAL0-0.0930.13215.3810.0000.0000.0000.0000.0000.000
160A526ASN00.157-0.04417.273-0.005-0.0050.0000.0000.0000.000
161A526ASN0-0.1350.06721.102-0.008-0.0080.0000.0000.0000.000
162A527LEU0-0.010-0.11319.9770.0070.0070.0000.0000.0000.000
163A527LEU0-0.0930.07621.6540.0030.0030.0000.0000.0000.000
164A528GLY00.030-0.09616.5070.0140.0140.0000.0000.0000.000
165A529LYS00.0640.02316.9280.0180.0180.0000.0000.0000.000
166A529LYS10.8561.04519.6100.0580.0580.0000.0000.0000.000
167A530PRO00.043-0.09215.672-0.019-0.0190.0000.0000.0000.000
168A531ILE00.050-0.00115.3960.0200.0200.0000.0000.0000.000
169A531ILE0-0.0690.12114.866-0.004-0.0040.0000.0000.0000.000
170A532LYS00.120-0.07915.485-0.012-0.0120.0000.0000.0000.000
171A532LYS10.8501.05518.3260.0340.0340.0000.0000.0000.000
172A533LEU00.099-0.10416.0690.0130.0130.0000.0000.0000.000
173A533LEU0-0.0640.12614.005-0.006-0.0060.0000.0000.0000.000
174A534LYS00.071-0.07917.4110.0100.0100.0000.0000.0000.000
175A534LYS10.8601.04621.9840.0630.0630.0000.0000.0000.000
176A535TRP00.015-0.11219.087-0.013-0.0130.0000.0000.0000.000
177A535TRP0-0.0680.09616.899-0.011-0.0110.0000.0000.0000.000
178A536LYS00.115-0.08720.5340.0190.0190.0000.0000.0000.000
179A536LYS10.7160.97824.0780.0490.0490.0000.0000.0000.000
180A537ALA00.081-0.10421.164-0.021-0.0210.0000.0000.0000.000
181A537ALA0-0.0510.11120.259-0.001-0.0010.0000.0000.0000.000
182A538ASN00.052-0.07922.4130.0150.0150.0000.0000.0000.000
183A538ASN0-0.1220.06226.406-0.004-0.0040.0000.0000.0000.000
184A539TYR00.085-0.07524.725-0.014-0.0140.0000.0000.0000.000
185A539TYR0-0.0890.03722.3010.0020.0020.0000.0000.0000.000
186A540CYS00.108-0.10026.1950.0090.0090.0000.0000.0000.000
187A540CYS0-0.1240.11930.037-0.003-0.0030.0000.0000.0000.000
188A541THR00.104-0.01027.986-0.008-0.0080.0000.0000.0000.000
189A541THR0-0.0170.06526.9910.0000.0000.0000.0000.0000.000
190A542LYS00.014-0.13528.872-0.003-0.0030.0000.0000.0000.000
191A542LYS10.8181.06829.3100.0270.0270.0000.0000.0000.000
192A543GLY00.027-0.12731.9310.0050.0050.0000.0000.0000.000
193A544ASP00.0630.00331.3560.0010.0010.0000.0000.0000.000
194A544ASP-1-0.890-0.79630.0530.0040.0040.0000.0000.0000.000
195A545SER00.041-0.09330.346-0.004-0.0040.0000.0000.0000.000
196A545SER0-0.0670.07531.619-0.002-0.0020.0000.0000.0000.000
197A546LYS00.077-0.08126.9600.0010.0010.0000.0000.0000.000
198A546LYS10.8041.02025.579-0.012-0.0120.0000.0000.0000.000
199A547GLU00.054-0.09625.658-0.010-0.0100.0000.0000.0000.000
200A547GLU-1-0.889-0.80626.469-0.036-0.0360.0000.0000.0000.000
201A548GLU00.063-0.13421.7580.0140.0140.0000.0000.0000.000
202A548GLU-1-0.813-0.71719.672-0.015-0.0150.0000.0000.0000.000
203A549SER0-0.034-0.09221.764-0.017-0.0170.0000.0000.0000.000
204A549SER0-0.0240.07523.5840.0010.0010.0000.0000.0000.000
205A550GLY00.098-0.06219.4880.0180.0180.0000.0000.0000.000
206A551THR00.0210.04319.424-0.018-0.0180.0000.0000.0000.000
207A551THR0-0.0780.00420.3310.0030.0030.0000.0000.0000.000
208A552THR0-0.021-0.08814.9530.0290.0290.0000.0000.0000.000
209A552THR00.0040.10513.062-0.003-0.0030.0000.0000.0000.000
210A553SER00.052-0.07215.048-0.044-0.0440.0000.0000.0000.000
211A553SER0-0.0360.05414.6820.0030.0030.0000.0000.0000.000
212A554LEU00.052-0.08011.1960.0240.0240.0000.0000.0000.000
213A554LEU0-0.0570.10510.662-0.007-0.0070.0000.0000.0000.000
214A555PRO0-0.019-0.0977.4030.0440.0440.0000.0000.0000.000
215A556THR00.0290.02310.359-0.068-0.0680.0000.0000.0000.000
216A556THR00.0050.07611.2880.0060.0060.0000.0000.0000.000
217A557ILE0-0.077-0.1329.789-0.020-0.0200.0000.0000.0000.000
218A557ILE00.0460.04712.933-0.002-0.0020.0000.0000.0000.000