FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 9M6J2

Calculation Name: 1J3E-A-Xray540

Preferred Name:

Target Type:

Ligand Name: n6-methyl-deoxy-adenosine-5'-monophosphate

Ligand 3-letter code: 6MA

Ligand of Interest (LOI):

PDB ID: 1J3E

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFY8

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -956369.937961
FMO2-HF: Nuclear repulsion 909996.725659
FMO2-HF: Total energy -46373.212302
FMO2-MP2: Total energy -46504.981209


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:2:PRO)


Summations of interaction energy for fragment #1(A:2: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.
-0.9681.1217.22-3.415-5.894-0.02
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.005
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].
3A3LEU00.0380.1671.9691.175-1.4956.788-1.219-2.899-0.018
4A4GLY00.019-0.1122.611-1.2191.5620.146-1.352-1.5750.002
5A5SER0-0.0530.0032.7220.2970.9640.047-0.177-0.5370.000
6A5SER00.0460.0833.035-0.6660.4840.240-0.639-0.751-0.004
7A6ALA00.245-0.0474.6660.5060.667-0.001-0.028-0.1320.000
8A6ALA0-0.0490.1346.063-0.070-0.0700.0000.0000.0000.000
9A7MET00.102-0.0936.5810.3940.3940.0000.0000.0000.000
10A7MET0-0.1380.0817.4280.0280.0280.0000.0000.0000.000
11A8ARG00.079-0.0757.4220.1400.1400.0000.0000.0000.000
12A8ARG10.7090.9385.979-0.258-0.2580.0000.0000.0000.000
13A9GLU00.058-0.1398.6390.1440.1440.0000.0000.0000.000
14A9GLU-1-1.018-0.8327.714-0.039-0.0390.0000.0000.0000.000
15A10LEU00.129-0.10010.4810.0850.0850.0000.0000.0000.000
16A10LEU0-0.1340.09511.707-0.009-0.0090.0000.0000.0000.000
17A11LEU00.010-0.11912.3140.0430.0430.0000.0000.0000.000
18A11LEU0-0.0910.06712.2590.0090.0090.0000.0000.0000.000
19A12LEU00.057-0.12313.6120.0140.0140.0000.0000.0000.000
20A12LEU0-0.1020.09612.5160.0140.0140.0000.0000.0000.000
21A13SER00.013-0.04414.8260.0370.0370.0000.0000.0000.000
22A13SER0-0.0380.06514.903-0.010-0.0100.0000.0000.0000.000
23A14ASP00.191-0.10016.3850.0020.0020.0000.0000.0000.000
24A14ASP-1-1.023-0.83120.167-0.040-0.0400.0000.0000.0000.000
25A15GLU00.148-0.12219.4540.0120.0120.0000.0000.0000.000
26A15GLU-1-0.993-0.81818.347-0.219-0.2190.0000.0000.0000.000
27A16TYR00.070-0.11517.5430.0000.0000.0000.0000.0000.000
28A16TYR0-0.1660.03616.798-0.016-0.0160.0000.0000.0000.000
29A17ALA00.029-0.12118.923-0.004-0.0040.0000.0000.0000.000
30A17ALA0-0.0320.13820.3250.0050.0050.0000.0000.0000.000
31A18GLU00.018-0.18721.2090.0160.0160.0000.0000.0000.000
32A18GLU-1-1.021-0.80923.202-0.095-0.0950.0000.0000.0000.000
33A19GLN00.049-0.10822.3910.0110.0110.0000.0000.0000.000
34A19GLN0-0.0490.10621.2340.0050.0050.0000.0000.0000.000
35A20LYS0-0.002-0.13723.9120.0040.0040.0000.0000.0000.000
36A20LYS10.8401.08525.9700.0690.0690.0000.0000.0000.000
37A21ARG00.067-0.12726.0260.0090.0090.0000.0000.0000.000
38A21ARG10.8381.06227.6640.0760.0760.0000.0000.0000.000
39A22ALA00.195-0.05623.922-0.011-0.0110.0000.0000.0000.000
40A22ALA0-0.0780.08524.8000.0020.0020.0000.0000.0000.000
41A23VAL00.021-0.13023.115-0.015-0.0150.0000.0000.0000.000
42A23VAL0-0.1040.08726.0490.0020.0020.0000.0000.0000.000
43A24ASN00.114-0.03323.052-0.019-0.0190.0000.0000.0000.000
44A24ASN0-0.0280.09724.0060.0140.0140.0000.0000.0000.000
45A25ARG00.170-0.06420.048-0.020-0.0200.0000.0000.0000.000
46A25ARG10.8261.03719.6980.1180.1180.0000.0000.0000.000
47A26PHE00.094-0.05518.756-0.033-0.0330.0000.0000.0000.000
48A26PHE0-0.1290.02020.4000.0060.0060.0000.0000.0000.000
49A27MET00.047-0.10119.107-0.029-0.0290.0000.0000.0000.000
50A27MET0-0.1390.06421.7930.0040.0040.0000.0000.0000.000
51A28LEU00.116-0.08618.141-0.028-0.0280.0000.0000.0000.000
52A28LEU0-0.0650.13917.1840.0040.0040.0000.0000.0000.000
53A29LEU00.118-0.07414.562-0.057-0.0570.0000.0000.0000.000
54A29LEU0-0.0770.07914.019-0.001-0.0010.0000.0000.0000.000
55A30LEU00.080-0.08714.146-0.094-0.0940.0000.0000.0000.000
56A30LEU0-0.1130.08016.5380.0090.0090.0000.0000.0000.000
57A31SER00.055-0.10414.923-0.057-0.0570.0000.0000.0000.000
58A31SER0-0.0740.04316.9100.0170.0170.0000.0000.0000.000
59A32THR00.039-0.07112.802-0.011-0.0110.0000.0000.0000.000
60A32THR0-0.0470.06710.8730.0050.0050.0000.0000.0000.000
61A33LEU00.108-0.09410.443-0.173-0.1730.0000.0000.0000.000
62A33LEU0-0.0910.0899.6340.0060.0060.0000.0000.0000.000
63A34TYR00.049-0.09210.882-0.091-0.0910.0000.0000.0000.000
64A34TYR0-0.0870.08714.5680.0210.0210.0000.0000.0000.000
65A35SER0-0.011-0.11211.828-0.014-0.0140.0000.0000.0000.000
66A35SER0-0.0390.07711.5550.0020.0020.0000.0000.0000.000
67A36LEU00.011-0.0987.7540.0350.0350.0000.0000.0000.000
68A36LEU0-0.1010.0785.840-0.129-0.1290.0000.0000.0000.000
69A37ASP00.125-0.0917.376-0.142-0.1420.0000.0000.0000.000
70A37ASP-1-0.906-0.8107.495-0.761-0.7610.0000.0000.0000.000
71A38ALA00.123-0.1029.2710.0620.0620.0000.0000.0000.000
72A38ALA0-0.0890.09213.4610.0130.0130.0000.0000.0000.000
73A39GLN00.020-0.11411.9600.0710.0710.0000.0000.0000.000
74A39GLN0-0.0970.07712.143-0.019-0.0190.0000.0000.0000.000
75A40ALA00.207-0.06210.3710.0830.0830.0000.0000.0000.000
76A40ALA0-0.0570.1179.842-0.022-0.0220.0000.0000.0000.000
77A41PHE00.068-0.10311.8330.0430.0430.0000.0000.0000.000
78A41PHE0-0.1390.07012.6380.0160.0160.0000.0000.0000.000
79A42ALA00.098-0.11113.4440.0390.0390.0000.0000.0000.000
80A42ALA0-0.0920.11216.7080.0030.0030.0000.0000.0000.000
81A43GLU00.117-0.11715.4600.0370.0370.0000.0000.0000.000
82A43GLU-1-1.000-0.82414.822-0.291-0.2910.0000.0000.0000.000
83A44ALA00.049-0.10714.6510.0430.0430.0000.0000.0000.000
84A44ALA0-0.0590.10313.688-0.008-0.0080.0000.0000.0000.000
85A45THR0-0.071-0.08115.8330.0270.0270.0000.0000.0000.000
86A45THR0-0.1030.03017.6370.0070.0070.0000.0000.0000.000
87A46GLU00.040-0.15418.6080.0210.0210.0000.0000.0000.000
88A46GLU-1-0.993-0.83220.173-0.209-0.2090.0000.0000.0000.000
89A47SER0-0.021-0.10519.9110.0240.0240.0000.0000.0000.000
90A47SER0-0.0540.09518.811-0.002-0.0020.0000.0000.0000.000
91A48LEU00.064-0.12120.8290.0140.0140.0000.0000.0000.000
92A48LEU0-0.1310.09519.5010.0020.0020.0000.0000.0000.000
93A49HIS00.030-0.15021.917-0.004-0.0040.0000.0000.0000.000
94A49HIS0-0.0620.11725.3600.0010.0010.0000.0000.0000.000
95A50GLY0-0.048-0.12025.5570.0030.0030.0000.0000.0000.000
96A51ARG00.1370.01628.454-0.001-0.0010.0000.0000.0000.000
97A51ARG10.8481.06231.9050.0750.0750.0000.0000.0000.000
98A52THR0-0.005-0.10831.5460.0030.0030.0000.0000.0000.000
99A52THR0-0.0260.06934.5770.0000.0000.0000.0000.0000.000
100A53ARG00.082-0.03730.9360.0010.0010.0000.0000.0000.000
101A53ARG10.7410.95330.2820.0940.0940.0000.0000.0000.000
102A54VAL00.110-0.09028.141-0.001-0.0010.0000.0000.0000.000
103A54VAL0-0.0100.16627.1740.0010.0010.0000.0000.0000.000
104A55TYR00.010-0.14924.5980.0080.0080.0000.0000.0000.000
105A55TYR0-0.0790.11323.6200.0060.0060.0000.0000.0000.000
106A56PHE00.178-0.12322.3870.0070.0070.0000.0000.0000.000
107A56PHE0-0.0210.13619.543-0.004-0.0040.0000.0000.0000.000
108A57ALA00.088-0.10123.8720.0010.0010.0000.0000.0000.000
109A57ALA0-0.0930.11427.1120.0040.0040.0000.0000.0000.000
110A58ALA00.140-0.10025.003-0.006-0.0060.0000.0000.0000.000
111A58ALA0-0.0600.14125.1570.0000.0000.0000.0000.0000.000
112A59ASP00.047-0.10025.912-0.002-0.0020.0000.0000.0000.000
113A59ASP-1-1.001-0.85030.389-0.126-0.1260.0000.0000.0000.000
114A60GLU00.135-0.13529.397-0.003-0.0030.0000.0000.0000.000
115A60GLU-1-0.963-0.81130.819-0.107-0.1070.0000.0000.0000.000
116A61GLN00.075-0.13930.9610.0010.0010.0000.0000.0000.000
117A61GLN0-0.0440.12834.6480.0030.0030.0000.0000.0000.000
118A62THR0-0.046-0.11130.8890.0080.0080.0000.0000.0000.000
119A62THR00.0450.11129.8480.0030.0030.0000.0000.0000.000
120A63LEU00.021-0.09230.0990.0030.0030.0000.0000.0000.000
121A63LEU0-0.0610.09926.8290.0020.0020.0000.0000.0000.000
122A64LEU00.010-0.16631.0050.0030.0030.0000.0000.0000.000
123A64LEU0-0.0800.11633.7580.0010.0010.0000.0000.0000.000
124A65LYS00.065-0.06434.2640.0060.0060.0000.0000.0000.000
125A65LYS10.8061.04634.8780.0900.0900.0000.0000.0000.000
126A66ASN00.035-0.11033.1480.0060.0060.0000.0000.0000.000
127A66ASN0-0.1120.07732.2690.0030.0030.0000.0000.0000.000
128A67GLY00.056-0.09434.000-0.001-0.0010.0000.0000.0000.000
129A68ASN00.1060.02135.214-0.001-0.0010.0000.0000.0000.000
130A68ASN0-0.0870.10038.4510.0000.0000.0000.0000.0000.000
131A69GLN00.045-0.09735.991-0.002-0.0020.0000.0000.0000.000
132A69GLN0-0.0500.10136.982-0.003-0.0030.0000.0000.0000.000
133A70THR0-0.013-0.10132.1160.0010.0010.0000.0000.0000.000
134A70THR00.0990.11331.043-0.003-0.0030.0000.0000.0000.000
135A71LYS00.044-0.09531.2030.0030.0030.0000.0000.0000.000
136A71LYS10.7611.03731.0630.0830.0830.0000.0000.0000.000
137A72PRO00.094-0.05628.957-0.007-0.0070.0000.0000.0000.000
138A73LYS00.1020.03527.3550.0100.0100.0000.0000.0000.000
139A73LYS10.8321.03626.3070.1200.1200.0000.0000.0000.000
140A74HIS00.143-0.09725.636-0.008-0.0080.0000.0000.0000.000
141A74HIS0-0.0800.11223.8170.0110.0110.0000.0000.0000.000
142A75VAL00.058-0.15321.0010.0120.0120.0000.0000.0000.000
143A75VAL0-0.0700.13218.901-0.001-0.0010.0000.0000.0000.000
144A76PRO00.004-0.06820.954-0.007-0.0070.0000.0000.0000.000
145A77GLY00.0910.05618.664-0.028-0.0280.0000.0000.0000.000
146A78THR0-0.0320.02118.413-0.023-0.0230.0000.0000.0000.000
147A78THR0-0.0440.04317.2170.0020.0020.0000.0000.0000.000
148A79PRO0-0.017-0.08219.0930.0220.0220.0000.0000.0000.000
149A80TYR00.081-0.02021.4290.0190.0190.0000.0000.0000.000
150A80TYR0-0.0320.12118.2860.0040.0040.0000.0000.0000.000
151A81TRP00.099-0.08922.592-0.006-0.0060.0000.0000.0000.000
152A81TRP0-0.0620.13226.3180.0040.0040.0000.0000.0000.000
153A82VAL00.125-0.11323.586-0.003-0.0030.0000.0000.0000.000
154A82VAL0-0.0530.12921.515-0.001-0.0010.0000.0000.0000.000
155A83ILE00.057-0.10724.7510.0090.0090.0000.0000.0000.000
156A83ILE0-0.1130.11626.4290.0040.0040.0000.0000.0000.000
157A84THR0-0.039-0.10326.152-0.008-0.0080.0000.0000.0000.000
158A84THR0-0.0300.04927.3710.0000.0000.0000.0000.0000.000
159A85ASN00.087-0.11828.3500.0030.0030.0000.0000.0000.000
160A85ASN0-0.0900.11632.2930.0010.0010.0000.0000.0000.000
161A86THR00.022-0.08528.0610.0050.0050.0000.0000.0000.000
162A86THR00.0370.08926.6340.0000.0000.0000.0000.0000.000
163A87ASN00.027-0.05129.037-0.001-0.0010.0000.0000.0000.000
164A87ASN0-0.0090.10128.518-0.005-0.0050.0000.0000.0000.000
165A88THR00.049-0.11025.314-0.010-0.0100.0000.0000.0000.000
166A88THR00.0330.10625.0020.0020.0020.0000.0000.0000.000
167A89GLY00.052-0.05524.057-0.009-0.0090.0000.0000.0000.000
168A90ARG00.1680.03024.217-0.007-0.0070.0000.0000.0000.000
169A90ARG10.8191.05825.4620.1140.1140.0000.0000.0000.000
170A91LYS00.041-0.08322.814-0.010-0.0100.0000.0000.0000.000
171A91LYS10.8111.02322.2010.1320.1320.0000.0000.0000.000
172A92CYS00.133-0.10419.661-0.027-0.0270.0000.0000.0000.000
173A92CYS0-0.0590.11519.4470.0080.0080.0000.0000.0000.000
174A93SER00.126-0.03619.321-0.021-0.0210.0000.0000.0000.000
175A93SER0-0.0500.04622.2130.0050.0050.0000.0000.0000.000
176A94MET00.073-0.05019.966-0.005-0.0050.0000.0000.0000.000
177A94MET0-0.1410.03020.2460.0030.0030.0000.0000.0000.000
178A95ILE00.097-0.08816.424-0.017-0.0170.0000.0000.0000.000
179A95ILE0-0.0770.08514.8900.0020.0020.0000.0000.0000.000
180A96GLU00.101-0.10515.159-0.058-0.0580.0000.0000.0000.000
181A96GLU-1-1.019-0.85517.198-0.136-0.1360.0000.0000.0000.000
182A97HIS00.105-0.10415.543-0.017-0.0170.0000.0000.0000.000
183A97HIS0-0.1120.10018.1270.0110.0110.0000.0000.0000.000
184A98ILE00.125-0.08614.6220.0050.0050.0000.0000.0000.000
185A98ILE0-0.1050.08212.6360.0000.0000.0000.0000.0000.000
186A99MET00.082-0.07210.884-0.050-0.0500.0000.0000.0000.000
187A99MET0-0.1390.0609.7740.0310.0310.0000.0000.0000.000
188A100GLN00.075-0.10210.673-0.056-0.0560.0000.0000.0000.000
189A100GLN0-0.0650.08214.7040.0150.0150.0000.0000.0000.000
190A101SER00.029-0.02912.3700.0120.0120.0000.0000.0000.000
191A101SER00.0410.07513.557-0.005-0.0050.0000.0000.0000.000
192A102MET00.011-0.0879.1440.0460.0460.0000.0000.0000.000
193A102MET0-0.1650.0688.136-0.022-0.0220.0000.0000.0000.000
194A103GLN00.044-0.1257.605-0.136-0.1360.0000.0000.0000.000
195A103GLN0-0.1240.0828.5960.0020.0020.0000.0000.0000.000
196A104PHE00.070-0.0947.324-0.085-0.0850.0000.0000.0000.000
197A104PHE0-0.0940.0846.190-0.077-0.0770.0000.0000.0000.000
198A105PRO0-0.036-0.0926.6110.1010.1010.0000.0000.0000.000
199A106ALA00.2340.0079.552-0.039-0.0390.0000.0000.0000.000
200A106ALA0-0.0440.13914.3960.0070.0070.0000.0000.0000.000
201A107GLU00.120-0.07012.732-0.029-0.0290.0000.0000.0000.000
202A107GLU-1-0.853-0.76510.1630.1450.1450.0000.0000.0000.000
203A108LEU00.086-0.1309.4990.0360.0360.0000.0000.0000.000
204A108LEU0-0.1400.0987.2160.0020.0020.0000.0000.0000.000
205A109ILE00.123-0.08911.005-0.037-0.0370.0000.0000.0000.000
206A109ILE0-0.0620.11511.472-0.005-0.0050.0000.0000.0000.000
207A110GLU00.039-0.13813.009-0.020-0.0200.0000.0000.0000.000
208A110GLU-1-0.987-0.84416.129-0.033-0.0330.0000.0000.0000.000
209A111LYS00.068-0.08613.8060.0060.0060.0000.0000.0000.000
210A111LYS10.7771.01511.739-0.049-0.0490.0000.0000.0000.000
211A112VAL00.067-0.11513.9900.0280.0280.0000.0000.0000.000
212A112VAL0-0.0370.12812.043-0.007-0.0070.0000.0000.0000.000
213A113CYS00.071-0.11014.8530.0080.0080.0000.0000.0000.000
214A113CYS0-0.0980.16216.898-0.001-0.0010.0000.0000.0000.000
215A114GLY00.003-0.07318.2040.0090.0090.0000.0000.0000.000
216A115THR0-0.011-0.00718.1240.0210.0210.0000.0000.0000.000
217A115THR0-0.0290.07516.446-0.012-0.0120.0000.0000.0000.000
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