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: 4L7GN

Calculation Name: 3A4C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

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 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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -829697.486782
FMO2-HF: Nuclear repulsion 786805.513983
FMO2-HF: Total energy -42891.972798
FMO2-MP2: Total energy -43014.444963


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: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.
-7.466-4.8580.008-1.23-1.3830.005
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 : 0.205 / q_NPA : 0.012
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].
4A453CYS0-0.0840.0694.335-0.1020.1660.001-0.130-0.1390.000
5A454PRO00.087-0.0763.805-2.645-1.284-0.013-0.841-0.5060.006
6A455GLU00.144-0.0336.816-0.338-0.3380.0000.0000.0000.000
7A455GLU-1-1.001-0.8157.974-0.016-0.0160.0000.0000.0000.000
8A456GLN00.096-0.1074.9550.2100.257-0.002-0.003-0.0410.000
9A456GLN0-0.0360.1173.441-0.3040.3690.024-0.206-0.490-0.001
10A457GLU00.110-0.1105.308-0.072-0.063-0.002-0.0070.0000.000
11A457GLU-1-0.969-0.8304.561-5.479-5.403-0.001-0.014-0.0610.000
12A458LEU00.104-0.1085.7710.3870.425-0.0020.000-0.0370.000
13A458LEU0-0.1480.09210.0610.0810.0810.0000.0000.0000.000
14A459ARG00.068-0.1228.9420.1890.1890.0000.0000.0000.000
15A459ARG10.7260.9798.9910.5140.5140.0000.0000.0000.000
16A460LEU00.081-0.1077.8410.4570.4570.0000.0000.0000.000
17A460LEU0-0.0440.1356.483-0.153-0.1530.0000.0000.0000.000
18A461GLN00.140-0.0729.1160.1980.1980.0000.0000.0000.000
19A461GLN0-0.1190.0679.4490.2870.2870.0000.0000.0000.000
20A462ARG00.029-0.09511.2740.1520.1520.0000.0000.0000.000
21A462ARG10.8471.03413.3760.6750.6750.0000.0000.0000.000
22A463LEU00.070-0.11612.6060.1410.1410.0000.0000.0000.000
23A463LEU0-0.0790.10811.2080.0070.0070.0000.0000.0000.000
24A464GLU00.074-0.14013.1100.1530.1530.0000.0000.0000.000
25A464GLU-1-1.003-0.80511.273-1.432-1.4320.0000.0000.0000.000
26A465ARG00.075-0.11614.6200.0690.0690.0000.0000.0000.000
27A465ARG10.8431.04714.7420.7960.7960.0000.0000.0000.000
28A466LEU00.004-0.14117.2640.0660.0660.0000.0000.0000.000
29A466LEU0-0.0960.13016.9870.0090.0090.0000.0000.0000.000
30A467PRO00.029-0.09018.1920.0640.0640.0000.0000.0000.000
31A468GLU00.052-0.05021.1010.0500.0500.0000.0000.0000.000
32A468GLU-1-0.966-0.80821.704-0.428-0.4280.0000.0000.0000.000
33A469LEU00.044-0.13221.8060.0410.0410.0000.0000.0000.000
34A469LEU0-0.0570.12520.0840.0000.0000.0000.0000.0000.000
35A470ALA00.169-0.10223.1730.0300.0300.0000.0000.0000.000
36A470ALA0-0.0690.13423.5680.0020.0020.0000.0000.0000.000
37A471ARG00.087-0.09624.9790.0310.0310.0000.0000.0000.000
38A471ARG10.8771.07326.8020.2480.2480.0000.0000.0000.000
39A472VAL00.020-0.14326.5880.0270.0270.0000.0000.0000.000
40A472VAL0-0.0580.12626.3110.0000.0000.0000.0000.0000.000
41A473LEU00.131-0.10927.1370.0190.0190.0000.0000.0000.000
42A473LEU0-0.1040.11826.6140.0000.0000.0000.0000.0000.000
43A474ARG00.102-0.09628.7380.0180.0180.0000.0000.0000.000
44A474ARG10.7931.03529.9920.1770.1770.0000.0000.0000.000
45A475ASN00.038-0.09831.0230.0170.0170.0000.0000.0000.000
46A475ASN0-0.0350.10631.6580.0030.0030.0000.0000.0000.000
47A476VAL00.105-0.08931.9430.0130.0130.0000.0000.0000.000
48A476VAL0-0.0680.11531.2530.0010.0010.0000.0000.0000.000
49A477PHE00.108-0.09533.1840.0100.0100.0000.0000.0000.000
50A477PHE0-0.1470.07731.5720.0000.0000.0000.0000.0000.000
51A478VAL00.018-0.12635.0380.0120.0120.0000.0000.0000.000
52A478VAL0-0.1070.09235.2880.0000.0000.0000.0000.0000.000
53A479SER00.033-0.08336.7900.0090.0090.0000.0000.0000.000
54A479SER0-0.0450.06437.299-0.002-0.0020.0000.0000.0000.000
55A480GLU00.039-0.09138.1690.0050.0050.0000.0000.0000.000
56A480GLU-1-0.870-0.78437.615-0.112-0.1120.0000.0000.0000.000
57A481ARG00.085-0.07839.4110.0000.0000.0000.0000.0000.000
58A481ARG10.8641.05943.8420.0820.0820.0000.0000.0000.000
59A482LYS0-0.009-0.15141.2400.0050.0050.0000.0000.0000.000
60A482LYS10.8581.06740.3670.0970.0970.0000.0000.0000.000
61A483PRO00.034-0.08738.996-0.005-0.0050.0000.0000.0000.000
62A484ALA00.1050.01036.107-0.005-0.0050.0000.0000.0000.000
63A484ALA0-0.0790.09236.4430.0020.0020.0000.0000.0000.000
64A485LEU0-0.031-0.15435.0570.0080.0080.0000.0000.0000.000
65A485LEU0-0.0540.11634.3000.0000.0000.0000.0000.0000.000
66A486THR00.088-0.04634.049-0.002-0.0020.0000.0000.0000.000
67A486THR00.0100.08034.733-0.003-0.0030.0000.0000.0000.000
68A487MET00.079-0.11129.989-0.005-0.0050.0000.0000.0000.000
69A487MET0-0.0760.14225.437-0.001-0.0010.0000.0000.0000.000
70A488GLU00.181-0.10330.153-0.018-0.0180.0000.0000.0000.000
71A488GLU-1-1.015-0.81932.466-0.128-0.1280.0000.0000.0000.000
72A489VAL00.074-0.09531.912-0.010-0.0100.0000.0000.0000.000
73A489VAL0-0.1210.07634.9890.0020.0020.0000.0000.0000.000
74A490VAL00.032-0.12830.721-0.003-0.0030.0000.0000.0000.000
75A490VAL0-0.0680.10928.9140.0000.0000.0000.0000.0000.000
76A491CYS00.099-0.09927.917-0.011-0.0110.0000.0000.0000.000
77A491CYS0-0.1110.11027.049-0.007-0.0070.0000.0000.0000.000
78A492ALA00.144-0.08128.707-0.022-0.0220.0000.0000.0000.000
79A492ALA0-0.0750.12132.5260.0030.0030.0000.0000.0000.000
80A493ARG00.103-0.07231.355-0.005-0.0050.0000.0000.0000.000
81A493ARG10.7931.00332.5450.1410.1410.0000.0000.0000.000
82A494MET00.111-0.08027.7860.0030.0030.0000.0000.0000.000
83A494MET0-0.1540.07625.0600.0020.0020.0000.0000.0000.000
84A495VAL00.023-0.11827.009-0.015-0.0150.0000.0000.0000.000
85A495VAL0-0.0940.09625.662-0.003-0.0030.0000.0000.0000.000
86A496ASP00.140-0.12627.928-0.015-0.0150.0000.0000.0000.000
87A496ASP-1-1.011-0.83032.133-0.192-0.1920.0000.0000.0000.000
88A497SER0-0.064-0.08830.2370.0080.0080.0000.0000.0000.000
89A497SER0-0.0910.03130.2230.0050.0050.0000.0000.0000.000
90A498CYS00.010-0.08627.4190.0070.0070.0000.0000.0000.000
91A498CYS0-0.1470.06826.243-0.014-0.0140.0000.0000.0000.000
92A499GLN00.111-0.08727.1930.0080.0080.0000.0000.0000.000
93A499GLN0-0.0970.08326.799-0.002-0.0020.0000.0000.0000.000
94A500THR00.090-0.06623.333-0.019-0.0190.0000.0000.0000.000
95A500THR0-0.0310.06222.606-0.018-0.0180.0000.0000.0000.000
96A501ALA00.126-0.06521.0990.0400.0400.0000.0000.0000.000
97A501ALA0-0.0860.09020.179-0.013-0.0130.0000.0000.0000.000
98A502LEU00.011-0.11921.473-0.012-0.0120.0000.0000.0000.000
99A502LEU0-0.1330.07518.377-0.004-0.0040.0000.0000.0000.000
100A503SER00.084-0.06322.2070.0290.0290.0000.0000.0000.000
101A503SER0-0.0280.07922.7270.0120.0120.0000.0000.0000.000
102A504PRO00.038-0.07824.074-0.016-0.0160.0000.0000.0000.000
103A505GLY00.0670.02724.5800.0030.0030.0000.0000.0000.000
104A506GLU00.058-0.04820.5770.0120.0120.0000.0000.0000.000
105A506GLU-1-0.906-0.79819.431-0.457-0.4570.0000.0000.0000.000
106A507MET00.125-0.08820.528-0.045-0.0450.0000.0000.0000.000
107A507MET0-0.0940.12323.833-0.006-0.0060.0000.0000.0000.000
108A508GLU00.161-0.12222.783-0.012-0.0120.0000.0000.0000.000
109A508GLU-1-0.994-0.84424.245-0.184-0.1840.0000.0000.0000.000
110A509LYS00.062-0.08719.5010.0230.0230.0000.0000.0000.000
111A509LYS10.8381.04118.0860.3060.3060.0000.0000.0000.000
112A510HIS00.015-0.10818.788-0.005-0.0050.0000.0000.0000.000
113A510HIS0-0.0670.08317.085-0.077-0.0770.0000.0000.0000.000
114A511LEU00.079-0.10919.772-0.011-0.0110.0000.0000.0000.000
115A511LEU0-0.0790.07823.6270.0060.0060.0000.0000.0000.000
116A512VAL00.052-0.11422.1890.0170.0170.0000.0000.0000.000
117A512VAL0-0.0640.12320.7870.0030.0030.0000.0000.0000.000
118A513LEU00.101-0.07918.0150.0370.0370.0000.0000.0000.000
119A513LEU0-0.0910.08915.165-0.025-0.0250.0000.0000.0000.000
120A514LEU00.127-0.09819.2160.0080.0080.0000.0000.0000.000
121A514LEU0-0.1400.09120.9490.0010.0010.0000.0000.0000.000
122A515ALA00.060-0.08721.6050.0110.0110.0000.0000.0000.000
123A515ALA0-0.0690.08024.2100.0030.0030.0000.0000.0000.000
124A516GLU00.049-0.13120.5130.0270.0270.0000.0000.0000.000
125A516GLU-1-1.014-0.84918.905-0.209-0.2090.0000.0000.0000.000
126A517LEU00.043-0.09719.8960.0320.0320.0000.0000.0000.000
127A517LEU0-0.0980.08716.638-0.009-0.0090.0000.0000.0000.000
128A518LEU0-0.017-0.11920.8040.0170.0170.0000.0000.0000.000
129A518LEU0-0.1090.06622.5570.0000.0000.0000.0000.0000.000
130A519PRO00.100-0.06223.9490.0010.0010.0000.0000.0000.000
131A520ASP00.115-0.01326.7220.0060.0060.0000.0000.0000.000
132A520ASP-1-1.029-0.84929.039-0.085-0.0850.0000.0000.0000.000
133A521TRP00.020-0.09528.2120.0080.0080.0000.0000.0000.000
134A521TRP0-0.1420.04125.516-0.009-0.0090.0000.0000.0000.000
135A522LEU00.148-0.11627.3440.0100.0100.0000.0000.0000.000
136A522LEU0-0.1530.10825.158-0.003-0.0030.0000.0000.0000.000
137A523SER00.061-0.05628.018-0.001-0.0010.0000.0000.0000.000
138A523SER0-0.0530.07231.5640.0050.0050.0000.0000.0000.000
139A524LEU00.098-0.14429.228-0.006-0.0060.0000.0000.0000.000
140A524LEU0-0.0770.13425.9630.0000.0000.0000.0000.0000.000
141A525HIS00.102-0.06530.4940.0080.0080.0000.0000.0000.000
142A525HIS0-0.1090.06834.523-0.001-0.0010.0000.0000.0000.000
143A526ARG00.079-0.09533.589-0.006-0.0060.0000.0000.0000.000
144A526ARG10.8911.08327.9530.0770.0770.0000.0000.0000.000
145A527ILE00.076-0.09934.4050.0080.0080.0000.0000.0000.000
146A527ILE0-0.0860.09637.4660.0000.0000.0000.0000.0000.000
147A528ARG00.091-0.03338.045-0.003-0.0030.0000.0000.0000.000
148A528ARG10.8341.01540.1210.0490.0490.0000.0000.0000.000
149A529THR00.029-0.09736.0130.0010.0010.0000.0000.0000.000
150A529THR0-0.0110.08136.2370.0020.0020.0000.0000.0000.000
151A530ASP00.116-0.09035.121-0.007-0.0070.0000.0000.0000.000
152A530ASP-1-0.996-0.84236.307-0.089-0.0890.0000.0000.0000.000
153A531THR00.015-0.11431.5740.0090.0090.0000.0000.0000.000
154A531THR0-0.0100.10929.8210.0000.0000.0000.0000.0000.000
155A532TYR00.066-0.10532.886-0.011-0.0110.0000.0000.0000.000
156A532TYR0-0.1290.07835.5490.0010.0010.0000.0000.0000.000
157A533VAL00.117-0.10431.1530.0060.0060.0000.0000.0000.000
158A533VAL0-0.0480.12829.493-0.002-0.0020.0000.0000.0000.000
159A534LYS00.109-0.07032.0260.0010.0010.0000.0000.0000.000
160A534LYS10.8591.04834.0770.0850.0850.0000.0000.0000.000
161A535LEU00.052-0.11631.913-0.003-0.0030.0000.0000.0000.000
162A535LEU0-0.0720.10529.507-0.001-0.0010.0000.0000.0000.000
163A536ASP00.099-0.12832.4240.0070.0070.0000.0000.0000.000
164A536ASP-1-0.910-0.77132.971-0.094-0.0940.0000.0000.0000.000
165A537LYS00.023-0.10433.767-0.007-0.0070.0000.0000.0000.000
166A537LYS10.8221.01935.6960.1200.1200.0000.0000.0000.000
167A538ALA00.105-0.10835.999-0.003-0.0030.0000.0000.0000.000
168A538ALA0-0.0640.12836.8700.0020.0020.0000.0000.0000.000
169A539VAL0-0.008-0.13532.4030.0070.0070.0000.0000.0000.000
170A539VAL0-0.0770.09530.909-0.002-0.0020.0000.0000.0000.000
171A540ASP00.143-0.10432.905-0.005-0.0050.0000.0000.0000.000
172A540ASP-1-0.928-0.82432.757-0.146-0.1460.0000.0000.0000.000
173A541LEU00.094-0.09529.343-0.004-0.0040.0000.0000.0000.000
174A541LEU0-0.1120.08527.3250.0020.0020.0000.0000.0000.000
175A542ALA00.037-0.11428.137-0.024-0.0240.0000.0000.0000.000
176A542ALA0-0.0400.14530.7830.0020.0020.0000.0000.0000.000
177A543GLY0-0.001-0.10728.111-0.007-0.0070.0000.0000.0000.000
178A544LEU00.022-0.07826.7710.0010.0010.0000.0000.0000.000
179A544LEU0-0.0290.15826.3600.0000.0000.0000.0000.0000.000
180A545THR00.053-0.04524.104-0.012-0.0120.0000.0000.0000.000
181A545THR0-0.0770.03123.577-0.007-0.0070.0000.0000.0000.000
182A546ALA00.134-0.07823.021-0.034-0.0340.0000.0000.0000.000
183A546ALA0-0.0900.10825.6850.0050.0050.0000.0000.0000.000
184A547ARG00.076-0.09022.917-0.011-0.0110.0000.0000.0000.000
185A547ARG10.8631.05724.3350.1460.1460.0000.0000.0000.000
186A548LEU00.116-0.09920.8060.0080.0080.0000.0000.0000.000
187A548LEU0-0.1270.10618.9970.0010.0010.0000.0000.0000.000
188A549ALA00.097-0.09318.657-0.037-0.0370.0000.0000.0000.000
189A549ALA0-0.0580.10919.8480.0030.0030.0000.0000.0000.000
190A550HIS00.100-0.08118.011-0.042-0.0420.0000.0000.0000.000
191A550HIS0-0.1520.05821.3740.0180.0180.0000.0000.0000.000
192A551HIS00.064-0.09218.2450.0080.0080.0000.0000.0000.000
193A551HIS0-0.0810.08118.4260.0040.0040.0000.0000.0000.000
194A552VAL00.129-0.07414.7460.0310.0310.0000.0000.0000.000
195A552VAL0-0.1090.09313.249-0.011-0.0110.0000.0000.0000.000
196A553HIS00.092-0.07713.486-0.076-0.0760.0000.0000.0000.000
197A553HIS0-0.1050.06515.668-0.041-0.0410.0000.0000.0000.000
198A554ALA00.080-0.11014.115-0.015-0.0150.0000.0000.0000.000
199A554ALA0-0.0850.10917.2390.0110.0110.0000.0000.0000.000
200A555GLU0-0.033-0.15312.4060.1120.1120.0000.0000.0000.000
201A555GLU-1-0.841-0.73511.532-0.445-0.4450.0000.0000.0000.000
202A556GLY0-0.026-0.09510.8930.0890.0890.0000.0000.0000.000
203A557LEU0-0.096-0.0646.8130.2240.2240.0000.0000.0000.000
204A557LEU00.0110.0374.194-0.751-0.6150.003-0.029-0.1090.000