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

tag_button

FMODB ID: QNQ5Y

Calculation Name: 3A4C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A4C

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4E9

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 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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -829338.382938
FMO2-HF: Nuclear repulsion 786444.498999
FMO2-HF: Total energy -42893.88394
FMO2-MP2: Total energy -43016.293194


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:452:ARG)


Summations of interaction energy for fragment #1(A:452:ARG)
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.
-4.558-0.7850.009-1.746-2.040.01
Interaction energy analysis for fragmet #1(A:452:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.192 / 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].
4A453CYS0-0.0870.0844.3870.0590.5020.003-0.208-0.2390.000
5A454PRO00.097-0.0903.805-3.053-0.327-0.017-1.681-1.0290.011
6A455GLU00.121-0.0246.816-0.100-0.1000.0000.0000.0000.000
7A455GLU-1-0.992-0.8208.053-0.483-0.4830.0000.0000.0000.000
8A456GLN00.080-0.1044.9740.2540.302-0.002-0.003-0.0430.000
9A456GLN0-0.0550.1053.4470.1730.8080.024-0.187-0.473-0.001
10A457GLU00.140-0.0895.3550.2310.243-0.002-0.007-0.0040.000
11A457GLU-1-0.928-0.7974.467-4.394-4.316-0.001-0.011-0.0650.000
12A458LEU00.092-0.0985.8080.4400.478-0.0020.000-0.0370.000
13A458LEU0-0.1350.08310.0950.0640.0640.0000.0000.0000.000
14A459ARG00.063-0.1169.0120.2060.2060.0000.0000.0000.000
15A459ARG10.7320.9709.0440.3700.3700.0000.0000.0000.000
16A460LEU00.096-0.1027.8680.3970.3970.0000.0000.0000.000
17A460LEU0-0.0600.1256.545-0.125-0.1250.0000.0000.0000.000
18A461GLN00.160-0.0709.1690.2170.2170.0000.0000.0000.000
19A461GLN0-0.1740.0528.9510.2780.2780.0000.0000.0000.000
20A462ARG00.019-0.10611.3060.1420.1420.0000.0000.0000.000
21A462ARG10.8491.03213.3330.6760.6760.0000.0000.0000.000
22A463LEU00.054-0.11912.6650.1040.1040.0000.0000.0000.000
23A463LEU0-0.0790.10511.4630.0070.0070.0000.0000.0000.000
24A464GLU00.084-0.13313.1570.1340.1340.0000.0000.0000.000
25A464GLU-1-0.998-0.81311.049-0.937-0.9370.0000.0000.0000.000
26A465ARG00.086-0.09914.6570.0630.0630.0000.0000.0000.000
27A465ARG10.8401.04714.3460.7130.7130.0000.0000.0000.000
28A466LEU0-0.011-0.14217.3150.0440.0440.0000.0000.0000.000
29A466LEU0-0.0910.11917.0660.0070.0070.0000.0000.0000.000
30A467PRO00.044-0.08818.2450.0430.0430.0000.0000.0000.000
31A468GLU00.040-0.04921.1400.0370.0370.0000.0000.0000.000
32A468GLU-1-0.950-0.81821.472-0.285-0.2850.0000.0000.0000.000
33A469LEU00.040-0.11021.8480.0290.0290.0000.0000.0000.000
34A469LEU0-0.0660.11320.243-0.002-0.0020.0000.0000.0000.000
35A470ALA00.163-0.09423.2220.0140.0140.0000.0000.0000.000
36A470ALA0-0.0660.11623.6010.0030.0030.0000.0000.0000.000
37A471ARG00.103-0.08625.0320.0210.0210.0000.0000.0000.000
38A471ARG10.8621.07026.6260.1400.1400.0000.0000.0000.000
39A472VAL00.051-0.13426.6310.0210.0210.0000.0000.0000.000
40A472VAL0-0.0760.12526.4920.0000.0000.0000.0000.0000.000
41A473LEU00.143-0.10727.1860.0120.0120.0000.0000.0000.000
42A473LEU0-0.1000.10526.561-0.001-0.0010.0000.0000.0000.000
43A474ARG00.105-0.09128.7900.0110.0110.0000.0000.0000.000
44A474ARG10.8001.03130.0210.1060.1060.0000.0000.0000.000
45A475ASN00.010-0.09531.0710.0120.0120.0000.0000.0000.000
46A475ASN0-0.0430.09431.7150.0050.0050.0000.0000.0000.000
47A476VAL00.134-0.07631.9910.0100.0100.0000.0000.0000.000
48A476VAL0-0.0770.11031.3090.0000.0000.0000.0000.0000.000
49A477PHE00.133-0.09633.2410.0060.0060.0000.0000.0000.000
50A477PHE0-0.1610.07131.6590.0010.0010.0000.0000.0000.000
51A478VAL00.042-0.10335.0900.0080.0080.0000.0000.0000.000
52A478VAL0-0.1130.08535.3250.0000.0000.0000.0000.0000.000
53A479SER00.038-0.08436.8400.0080.0080.0000.0000.0000.000
54A479SER0-0.0370.07537.429-0.002-0.0020.0000.0000.0000.000
55A480GLU00.047-0.08838.2200.0030.0030.0000.0000.0000.000
56A480GLU-1-0.872-0.78537.640-0.093-0.0930.0000.0000.0000.000
57A481ARG00.104-0.06339.4650.0010.0010.0000.0000.0000.000
58A481ARG10.8641.05243.9140.0620.0620.0000.0000.0000.000
59A482LYS0-0.002-0.16641.2270.0050.0050.0000.0000.0000.000
60A482LYS10.8621.07640.3820.0870.0870.0000.0000.0000.000
61A483PRO00.015-0.09039.049-0.004-0.0040.0000.0000.0000.000
62A484ALA00.1140.01836.176-0.002-0.0020.0000.0000.0000.000
63A484ALA0-0.0900.09536.5470.0010.0010.0000.0000.0000.000
64A485LEU0-0.012-0.15035.1240.0060.0060.0000.0000.0000.000
65A485LEU0-0.0710.10434.399-0.001-0.0010.0000.0000.0000.000
66A486THR00.084-0.04034.115-0.001-0.0010.0000.0000.0000.000
67A486THR00.0050.07934.690-0.002-0.0020.0000.0000.0000.000
68A487MET00.072-0.08930.051-0.001-0.0010.0000.0000.0000.000
69A487MET0-0.0620.10125.5150.0000.0000.0000.0000.0000.000
70A488GLU00.162-0.09530.210-0.014-0.0140.0000.0000.0000.000
71A488GLU-1-1.008-0.82032.338-0.143-0.1430.0000.0000.0000.000
72A489VAL00.094-0.08931.962-0.009-0.0090.0000.0000.0000.000
73A489VAL0-0.1200.07535.1240.0020.0020.0000.0000.0000.000
74A490VAL00.046-0.11530.832-0.001-0.0010.0000.0000.0000.000
75A490VAL0-0.0700.10929.1330.0010.0010.0000.0000.0000.000
76A491CYS00.118-0.09927.968-0.003-0.0030.0000.0000.0000.000
77A491CYS0-0.1250.09127.254-0.006-0.0060.0000.0000.0000.000
78A492ALA00.105-0.08128.756-0.018-0.0180.0000.0000.0000.000
79A492ALA0-0.0770.11232.5360.0030.0030.0000.0000.0000.000
80A493ARG00.100-0.07131.397-0.003-0.0030.0000.0000.0000.000
81A493ARG10.7730.98132.6030.1190.1190.0000.0000.0000.000
82A494MET00.139-0.05927.8580.0060.0060.0000.0000.0000.000
83A494MET0-0.1680.09325.3150.0020.0020.0000.0000.0000.000
84A495VAL00.009-0.12527.057-0.005-0.0050.0000.0000.0000.000
85A495VAL0-0.0770.09025.635-0.004-0.0040.0000.0000.0000.000
86A496ASP00.092-0.10327.961-0.011-0.0110.0000.0000.0000.000
87A496ASP-1-1.008-0.84832.317-0.172-0.1720.0000.0000.0000.000
88A497SER0-0.029-0.09730.2560.0080.0080.0000.0000.0000.000
89A497SER0-0.0800.02330.1880.0060.0060.0000.0000.0000.000
90A498CYS00.005-0.08127.4390.0110.0110.0000.0000.0000.000
91A498CYS0-0.1510.06526.414-0.011-0.0110.0000.0000.0000.000
92A499GLN00.104-0.07627.2060.0010.0010.0000.0000.0000.000
93A499GLN0-0.1020.07826.8500.0040.0040.0000.0000.0000.000
94A500THR00.097-0.04223.351-0.014-0.0140.0000.0000.0000.000
95A500THR0-0.0400.03322.551-0.016-0.0160.0000.0000.0000.000
96A501ALA00.127-0.06721.0980.0320.0320.0000.0000.0000.000
97A501ALA0-0.0840.08820.192-0.011-0.0110.0000.0000.0000.000
98A502LEU00.001-0.11521.481-0.023-0.0230.0000.0000.0000.000
99A502LEU0-0.1180.07518.405-0.003-0.0030.0000.0000.0000.000
100A503SER00.109-0.06222.2320.0330.0330.0000.0000.0000.000
101A503SER0-0.0680.03322.7130.0090.0090.0000.0000.0000.000
102A504PRO00.034-0.08724.110-0.011-0.0110.0000.0000.0000.000
103A505GLY00.0530.01924.6210.0050.0050.0000.0000.0000.000
104A506GLU00.101-0.03920.6220.0060.0060.0000.0000.0000.000
105A506GLU-1-0.865-0.73519.226-0.475-0.4750.0000.0000.0000.000
106A507MET00.099-0.08320.576-0.035-0.0350.0000.0000.0000.000
107A507MET0-0.1040.11723.877-0.001-0.0010.0000.0000.0000.000
108A508GLU00.142-0.10222.8380.0020.0020.0000.0000.0000.000
109A508GLU-1-0.969-0.83324.263-0.240-0.2400.0000.0000.0000.000
110A509LYS00.184-0.05019.6570.0280.0280.0000.0000.0000.000
111A509LYS10.7511.01618.7210.3030.3030.0000.0000.0000.000
112A510HIS0-0.070-0.14418.855-0.003-0.0030.0000.0000.0000.000
113A510HIS0-0.0670.07317.096-0.059-0.0590.0000.0000.0000.000
114A511LEU00.118-0.08719.8320.0050.0050.0000.0000.0000.000
115A511LEU0-0.1080.07223.5390.0050.0050.0000.0000.0000.000
116A512VAL00.055-0.11222.3060.0260.0260.0000.0000.0000.000
117A512VAL0-0.0760.10521.0000.0020.0020.0000.0000.0000.000
118A513LEU00.116-0.06218.0420.0350.0350.0000.0000.0000.000
119A513LEU0-0.0980.07815.463-0.022-0.0220.0000.0000.0000.000
120A514LEU00.162-0.06619.2900.0220.0220.0000.0000.0000.000
121A514LEU0-0.1470.08021.4150.0010.0010.0000.0000.0000.000
122A515ALA00.055-0.10921.6770.0210.0210.0000.0000.0000.000
123A515ALA0-0.0870.07524.2550.0000.0000.0000.0000.0000.000
124A516GLU00.021-0.14120.4440.0270.0270.0000.0000.0000.000
125A516GLU-1-0.982-0.85618.388-0.214-0.2140.0000.0000.0000.000
126A517LEU00.035-0.07219.8990.0300.0300.0000.0000.0000.000
127A517LEU0-0.0920.08616.575-0.005-0.0050.0000.0000.0000.000
128A518LEU0-0.010-0.11620.8850.0260.0260.0000.0000.0000.000
129A518LEU0-0.1070.06122.6230.0000.0000.0000.0000.0000.000
130A519PRO00.113-0.06123.918-0.003-0.0030.0000.0000.0000.000
131A520ASP00.052-0.03026.714-0.001-0.0010.0000.0000.0000.000
132A520ASP-1-0.991-0.86028.747-0.032-0.0320.0000.0000.0000.000
133A521TRP00.009-0.07728.2840.0060.0060.0000.0000.0000.000
134A521TRP0-0.1340.04625.716-0.006-0.0060.0000.0000.0000.000
135A522LEU00.164-0.09427.3960.0060.0060.0000.0000.0000.000
136A522LEU0-0.1730.10225.070-0.002-0.0020.0000.0000.0000.000
137A523SER00.111-0.06428.098-0.002-0.0020.0000.0000.0000.000
138A523SER0-0.0720.06931.7760.0020.0020.0000.0000.0000.000
139A524LEU00.064-0.12329.180-0.004-0.0040.0000.0000.0000.000
140A524LEU0-0.0760.11226.081-0.002-0.0020.0000.0000.0000.000
141A525HIS00.102-0.08030.5020.0050.0050.0000.0000.0000.000
142A525HIS0-0.0940.08234.527-0.001-0.0010.0000.0000.0000.000
143A526ARG00.083-0.08533.590-0.005-0.0050.0000.0000.0000.000
144A526ARG10.8951.07427.6130.1090.1090.0000.0000.0000.000
145A527ILE00.053-0.09834.4100.0070.0070.0000.0000.0000.000
146A527ILE0-0.0830.09437.5420.0010.0010.0000.0000.0000.000
147A528ARG00.113-0.02038.050-0.003-0.0030.0000.0000.0000.000
148A528ARG10.8381.00840.2260.0640.0640.0000.0000.0000.000
149A529THR00.033-0.10236.0330.0000.0000.0000.0000.0000.000
150A529THR0-0.0050.08136.4960.0020.0020.0000.0000.0000.000
151A530ASP00.119-0.11035.129-0.010-0.0100.0000.0000.0000.000
152A530ASP-1-0.917-0.79636.388-0.096-0.0960.0000.0000.0000.000
153A531THR00.001-0.07931.6180.0080.0080.0000.0000.0000.000
154A531THR0-0.0140.09129.798-0.002-0.0020.0000.0000.0000.000
155A532TYR00.042-0.10932.954-0.010-0.0100.0000.0000.0000.000
156A532TYR0-0.1830.04335.6440.0020.0020.0000.0000.0000.000
157A533VAL00.119-0.10231.2970.0040.0040.0000.0000.0000.000
158A533VAL0-0.0570.11429.682-0.002-0.0020.0000.0000.0000.000
159A534LYS00.124-0.05332.0960.0010.0010.0000.0000.0000.000
160A534LYS10.8541.04834.1980.0670.0670.0000.0000.0000.000
161A535LEU00.042-0.12231.962-0.003-0.0030.0000.0000.0000.000
162A535LEU0-0.0630.09929.9440.0000.0000.0000.0000.0000.000
163A536ASP00.084-0.11532.4980.0030.0030.0000.0000.0000.000
164A536ASP-1-0.910-0.78133.242-0.051-0.0510.0000.0000.0000.000
165A537LYS00.020-0.08733.837-0.002-0.0020.0000.0000.0000.000
166A537LYS10.7860.98335.7120.0810.0810.0000.0000.0000.000
167A538ALA00.106-0.09836.067-0.001-0.0010.0000.0000.0000.000
168A538ALA0-0.0590.11836.9660.0010.0010.0000.0000.0000.000
169A539VAL0-0.003-0.11932.5350.0070.0070.0000.0000.0000.000
170A539VAL0-0.0890.09631.2200.0000.0000.0000.0000.0000.000
171A540ASP00.154-0.10332.965-0.007-0.0070.0000.0000.0000.000
172A540ASP-1-0.919-0.81632.961-0.064-0.0640.0000.0000.0000.000
173A541LEU00.101-0.09029.4180.0010.0010.0000.0000.0000.000
174A541LEU0-0.1070.08827.1100.0000.0000.0000.0000.0000.000
175A542ALA00.020-0.12028.191-0.013-0.0130.0000.0000.0000.000
176A542ALA0-0.0330.13230.8450.0010.0010.0000.0000.0000.000
177A543GLY00.010-0.10428.1650.0020.0020.0000.0000.0000.000
178A544LEU00.008-0.04826.8140.0100.0100.0000.0000.0000.000
179A544LEU0-0.0410.12826.4920.0000.0000.0000.0000.0000.000
180A545THR00.068-0.05324.155-0.005-0.0050.0000.0000.0000.000
181A545THR0-0.0700.02923.582-0.007-0.0070.0000.0000.0000.000
182A546ALA00.123-0.06223.076-0.015-0.0150.0000.0000.0000.000
183A546ALA0-0.0910.09625.8160.0030.0030.0000.0000.0000.000
184A547ARG00.093-0.08122.9760.0080.0080.0000.0000.0000.000
185A547ARG10.8611.05224.4620.0430.0430.0000.0000.0000.000
186A548LEU00.093-0.09920.8770.0160.0160.0000.0000.0000.000
187A548LEU0-0.1110.09819.278-0.002-0.0020.0000.0000.0000.000
188A549ALA00.095-0.08418.708-0.020-0.0200.0000.0000.0000.000
189A549ALA0-0.0680.10319.9360.0020.0020.0000.0000.0000.000
190A550HIS00.103-0.07718.069-0.001-0.0010.0000.0000.0000.000
191A550HIS0-0.1710.04121.3170.0210.0210.0000.0000.0000.000
192A551HIS00.071-0.07918.3110.0350.0350.0000.0000.0000.000
193A551HIS0-0.0880.08918.5860.0120.0120.0000.0000.0000.000
194A552VAL00.146-0.07914.8160.0380.0380.0000.0000.0000.000
195A552VAL0-0.1120.08713.350-0.011-0.0110.0000.0000.0000.000
196A553HIS00.095-0.07513.553-0.012-0.0120.0000.0000.0000.000
197A553HIS0-0.1160.06415.970-0.023-0.0230.0000.0000.0000.000
198A554ALA00.084-0.10714.1750.0650.0650.0000.0000.0000.000
199A554ALA0-0.0880.10017.212-0.002-0.0020.0000.0000.0000.000
200A555GLU0-0.045-0.14812.3250.1010.1010.0000.0000.0000.000
201A555GLU-1-0.813-0.74411.377-0.266-0.2660.0000.0000.0000.000
202A556GLY0-0.028-0.08410.8740.1130.1130.0000.0000.0000.000
203A557LEU0-0.102-0.0646.7550.2760.2760.0000.0000.0000.000
204A557LEU00.0380.0373.4300.011-0.1960.0060.351-0.1500.000