FMO DATABASE

FMODB ID: 17J8Z

Calculation Name: 1J3E-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: 6MA

PDB ID: 1J3E

Chain ID: A

ChEMBL ID:

UniProt ID: P0AFY8

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-954599.234975
FMO2-HF: Nuclear repulsion	908200.112125
FMO2-HF: Total energy	-46399.12285
FMO2-MP2: Total energy	-46531.289631

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/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.
-1.788	1.93	0.248	-1.543	-2.421	0

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 : 0.030 / q_NPA : -0.006

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 ES EX CT+mix DI(MP2)

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].
3	A	4	GLY	0	0.003	-0.008	2.532	-0.123	2.121	0.159	-1.072	-1.330
4	A	5	SER	0	-0.026	-0.017	3.084	0.474	1.780	0.090	-0.446	-0.949
5	A	6	ALA	0	0.123	0.074	4.844	-0.236	-0.068	-0.001	-0.025	-0.142
6	A	7	MET	0	0.002	0.009	6.767	0.261	0.261	0.000	0.000	0.000
7	A	8	ARG	1	0.773	0.844	6.526	-0.981	-0.981	0.000	0.000	0.000
8	A	9	GLU	-1	-0.925	-0.966	7.145	0.515	0.515	0.000	0.000	0.000
9	A	10	LEU	0	0.008	0.009	10.683	-0.021	-0.021	0.000	0.000	0.000
10	A	11	LEU	0	-0.091	-0.046	12.541	0.018	0.018	0.000	0.000	0.000
11	A	12	LEU	0	-0.030	-0.020	12.993	0.006	0.006	0.000	0.000	0.000
12	A	13	SER	0	-0.036	-0.011	14.727	-0.017	-0.017	0.000	0.000	0.000
13	A	14	ASP	-1	-0.858	-0.931	16.362	0.064	0.064	0.000	0.000	0.000
14	A	15	GLU	-1	-0.853	-0.950	18.345	-0.106	-0.106	0.000	0.000	0.000
15	A	16	TYR	0	-0.057	-0.030	17.064	-0.024	-0.024	0.000	0.000	0.000
16	A	17	ALA	0	-0.004	0.005	19.178	-0.004	-0.004	0.000	0.000	0.000
17	A	18	GLU	-1	-0.911	-0.940	21.507	-0.014	-0.014	0.000	0.000	0.000
18	A	19	GLN	0	-0.047	-0.019	21.353	-0.010	-0.010	0.000	0.000	0.000
19	A	20	LYS	1	0.842	0.891	24.126	0.006	0.006	0.000	0.000	0.000
20	A	21	ARG	1	0.902	0.952	26.159	0.033	0.033	0.000	0.000	0.000
21	A	22	ALA	0	0.050	0.023	24.042	-0.006	-0.006	0.000	0.000	0.000
22	A	23	VAL	0	-0.012	-0.013	23.202	-0.009	-0.009	0.000	0.000	0.000
23	A	24	ASN	0	0.015	0.023	23.113	-0.006	-0.006	0.000	0.000	0.000
24	A	25	ARG	1	0.965	0.984	19.836	0.004	0.004	0.000	0.000	0.000
25	A	26	PHE	0	-0.005	-0.013	18.850	-0.017	-0.017	0.000	0.000	0.000
26	A	27	MET	0	-0.049	-0.032	19.119	-0.019	-0.019	0.000	0.000	0.000
27	A	28	LEU	0	0.065	0.040	17.434	-0.027	-0.027	0.000	0.000	0.000
28	A	29	LEU	0	0.003	0.021	13.969	-0.046	-0.046	0.000	0.000	0.000
29	A	30	LEU	0	0.007	0.007	14.254	-0.070	-0.070	0.000	0.000	0.000
30	A	31	SER	0	-0.007	-0.038	14.918	-0.044	-0.044	0.000	0.000	0.000
31	A	32	THR	0	-0.016	-0.019	10.739	-0.024	-0.024	0.000	0.000	0.000
32	A	33	LEU	0	-0.005	-0.021	9.932	-0.130	-0.130	0.000	0.000	0.000
33	A	34	TYR	0	-0.023	-0.012	10.893	-0.084	-0.084	0.000	0.000	0.000
34	A	35	SER	0	-0.056	-0.033	11.641	-0.033	-0.033	0.000	0.000	0.000
35	A	36	LEU	0	-0.044	-0.017	5.644	-0.121	-0.121	0.000	0.000	0.000
36	A	37	ASP	-1	-0.798	-0.919	7.381	-1.049	-1.049	0.000	0.000	0.000
37	A	38	ALA	0	-0.031	-0.008	9.241	0.101	0.101	0.000	0.000	0.000
38	A	39	GLN	0	-0.048	-0.010	11.944	0.044	0.044	0.000	0.000	0.000
39	A	40	ALA	0	0.078	0.035	10.179	0.065	0.065	0.000	0.000	0.000
40	A	41	PHE	0	-0.043	-0.019	12.175	0.083	0.083	0.000	0.000	0.000
41	A	42	ALA	0	0.006	0.001	13.904	0.061	0.061	0.000	0.000	0.000
42	A	43	GLU	-1	-0.876	-0.933	15.063	-0.316	-0.316	0.000	0.000	0.000
43	A	44	ALA	0	-0.053	-0.027	14.127	0.040	0.040	0.000	0.000	0.000
44	A	45	THR	0	-0.057	-0.037	16.260	0.048	0.048	0.000	0.000	0.000
45	A	46	GLU	-1	-0.998	-0.986	19.090	-0.198	-0.198	0.000	0.000	0.000
46	A	47	SER	0	-0.035	-0.006	19.112	0.022	0.022	0.000	0.000	0.000
47	A	48	LEU	0	-0.058	-0.009	19.573	0.020	0.020	0.000	0.000	0.000
48	A	49	HIS	0	-0.044	-0.046	22.403	0.001	0.001	0.000	0.000	0.000
49	A	50	GLY	0	-0.017	-0.011	26.063	0.005	0.005	0.000	0.000	0.000
50	A	51	ARG	1	0.934	0.965	28.976	0.058	0.058	0.000	0.000	0.000
51	A	52	THR	0	0.001	-0.012	32.037	0.002	0.002	0.000	0.000	0.000
52	A	53	ARG	1	0.841	0.925	30.854	0.068	0.068	0.000	0.000	0.000
53	A	54	VAL	0	0.082	0.052	27.716	-0.003	-0.003	0.000	0.000	0.000
54	A	55	TYR	0	-0.036	-0.031	24.087	0.012	0.012	0.000	0.000	0.000
55	A	56	PHE	0	0.118	0.040	19.934	0.005	0.005	0.000	0.000	0.000
56	A	57	ALA	0	-0.015	-0.014	24.400	0.003	0.003	0.000	0.000	0.000
57	A	58	ALA	0	0.060	0.033	24.973	-0.002	-0.002	0.000	0.000	0.000
58	A	59	ASP	-1	-0.898	-0.931	25.878	-0.115	-0.115	0.000	0.000	0.000
59	A	60	GLU	-1	-0.880	-0.957	29.368	-0.087	-0.087	0.000	0.000	0.000
60	A	61	GLN	0	0.030	-0.002	31.000	0.004	0.004	0.000	0.000	0.000
61	A	62	THR	0	0.016	0.005	30.145	0.008	0.008	0.000	0.000	0.000
62	A	63	LEU	0	-0.025	-0.004	27.214	0.003	0.003	0.000	0.000	0.000
63	A	64	LEU	0	-0.092	-0.051	31.449	0.006	0.006	0.000	0.000	0.000
64	A	65	LYS	1	0.913	0.972	34.674	0.087	0.087	0.000	0.000	0.000
65	A	66	ASN	0	-0.024	-0.009	32.806	0.006	0.006	0.000	0.000	0.000
66	A	67	GLY	0	0.035	0.007	34.550	-0.001	-0.001	0.000	0.000	0.000
67	A	68	ASN	0	0.003	0.013	35.791	0.001	0.001	0.000	0.000	0.000
68	A	69	GLN	0	0.052	0.019	36.531	-0.002	-0.002	0.000	0.000	0.000
69	A	70	THR	0	0.033	0.030	31.716	0.002	0.002	0.000	0.000	0.000
70	A	71	LYS	1	0.852	0.899	31.479	0.058	0.058	0.000	0.000	0.000
71	A	72	PRO	0	0.014	0.027	29.240	-0.004	-0.004	0.000	0.000	0.000
72	A	73	LYS	1	0.930	0.962	26.391	0.090	0.090	0.000	0.000	0.000
73	A	74	HIS	0	0.023	0.010	23.566	0.003	0.003	0.000	0.000	0.000
74	A	75	VAL	0	-0.032	-0.016	18.898	0.008	0.008	0.000	0.000	0.000
75	A	76	PRO	0	0.051	0.023	20.954	-0.009	-0.009	0.000	0.000	0.000
76	A	77	GLY	0	0.041	0.029	18.715	-0.021	-0.021	0.000	0.000	0.000
77	A	78	THR	0	-0.009	0.015	17.194	-0.025	-0.025	0.000	0.000	0.000
78	A	79	PRO	0	0.003	0.019	19.247	0.026	0.026	0.000	0.000	0.000
79	A	80	TYR	0	0.034	0.006	17.949	0.009	0.009	0.000	0.000	0.000
80	A	81	TRP	0	0.022	0.018	22.568	0.009	0.009	0.000	0.000	0.000
81	A	82	VAL	0	0.058	0.021	22.140	-0.006	-0.006	0.000	0.000	0.000
82	A	83	ILE	0	-0.058	-0.008	25.137	0.015	0.015	0.000	0.000	0.000
83	A	84	THR	0	0.029	-0.006	26.564	-0.003	-0.003	0.000	0.000	0.000
84	A	85	ASN	0	-0.063	-0.004	28.600	0.006	0.006	0.000	0.000	0.000
85	A	86	THR	0	0.053	0.026	26.967	0.001	0.001	0.000	0.000	0.000
86	A	87	ASN	0	0.038	0.022	28.655	-0.003	-0.003	0.000	0.000	0.000
87	A	88	THR	0	0.086	0.018	25.118	-0.008	-0.008	0.000	0.000	0.000
88	A	89	GLY	0	0.046	0.041	24.067	-0.005	-0.005	0.000	0.000	0.000
89	A	90	ARG	1	0.932	0.960	24.172	0.075	0.075	0.000	0.000	0.000
90	A	91	LYS	1	0.832	0.920	22.277	0.068	0.068	0.000	0.000	0.000
91	A	92	CYS	0	0.077	0.027	19.646	-0.014	-0.014	0.000	0.000	0.000
92	A	93	SER	0	0.003	0.017	19.248	-0.015	-0.015	0.000	0.000	0.000
93	A	94	MET	0	-0.073	-0.031	20.257	-0.010	-0.010	0.000	0.000	0.000
94	A	95	ILE	0	0.023	0.008	14.865	-0.020	-0.020	0.000	0.000	0.000
95	A	96	GLU	-1	-0.921	-0.975	15.423	-0.116	-0.116	0.000	0.000	0.000
96	A	97	HIS	0	-0.049	-0.011	15.882	-0.003	-0.003	0.000	0.000	0.000
97	A	98	ILE	0	0.013	-0.001	13.326	-0.017	-0.017	0.000	0.000	0.000
98	A	99	MET	0	-0.025	-0.014	9.675	-0.024	-0.024	0.000	0.000	0.000
99	A	100	GLN	0	-0.013	-0.015	11.124	-0.031	-0.031	0.000	0.000	0.000
100	A	101	SER	0	0.055	0.043	12.688	-0.021	-0.021	0.000	0.000	0.000
101	A	102	MET	0	-0.097	-0.027	8.651	0.009	0.009	0.000	0.000	0.000
102	A	103	GLN	0	-0.035	-0.038	7.987	-0.163	-0.163	0.000	0.000	0.000
103	A	104	PHE	0	0.008	0.015	6.490	-0.141	-0.141	0.000	0.000	0.000
104	A	105	PRO	0	-0.032	-0.015	6.906	0.088	0.088	0.000	0.000	0.000
105	A	106	ALA	0	0.093	0.029	9.892	0.004	0.004	0.000	0.000	0.000
106	A	107	GLU	-1	-0.695	-0.803	10.361	0.522	0.522	0.000	0.000	0.000
107	A	108	LEU	0	-0.056	-0.012	7.233	0.012	0.012	0.000	0.000	0.000
108	A	109	ILE	0	0.035	0.007	11.114	-0.037	-0.037	0.000	0.000	0.000
109	A	110	GLU	-1	-0.944	-0.978	13.014	0.059	0.059	0.000	0.000	0.000
110	A	111	LYS	1	0.811	0.888	12.376	-0.319	-0.319	0.000	0.000	0.000
111	A	112	VAL	0	0.044	0.031	12.048	-0.003	-0.003	0.000	0.000	0.000
112	A	113	CYS	0	0.011	0.027	14.984	-0.011	-0.011	0.000	0.000	0.000
113	A	114	GLY	0	0.012	0.026	18.285	-0.003	-0.003	0.000	0.000	0.000
114	A	115	THR	0	-0.030	-0.016	17.045	-0.002	-0.002	0.000	0.000	0.000
115	A	116	ILE	0	-0.081	-0.022	18.093	-0.007	-0.007	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)