FMO DATABASE

FMODB ID: G6QZ1

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	OptAll
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	-954415.076276
FMO2-HF: Nuclear repulsion	908015.307294
FMO2-HF: Total energy	-46399.768982
FMO2-MP2: Total energy	-46531.820132

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.
-3.655	-0.636	0.104	-1.135	-1.987	0.002

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 : 0.033 / q_NPA : -0.007

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

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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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	4	GLY	0	0.006	-0.003	2.683	-0.694	1.265	0.082	-0.828	-1.213	0.002
4	A	5	SER	0	-0.047	-0.017	3.547	-0.107	0.831	0.023	-0.286	-0.674	0.000
5	A	6	ALA	0	0.124	0.068	4.778	-0.236	-0.114	-0.001	-0.021	-0.100	0.000
6	A	7	MET	0	-0.006	0.006	6.879	0.112	0.112	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.775	0.846	7.364	-1.579	-1.579	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.905	-0.967	6.823	0.044	0.044	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.008	0.007	10.695	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.064	-0.027	12.730	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.046	-0.020	12.892	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.027	-0.005	14.744	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.862	-0.939	16.473	0.045	0.045	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.867	-0.943	18.155	-0.082	-0.082	0.000	0.000	0.000	0.000
15	A	16	TYR	0	-0.034	-0.030	17.174	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.015	0.010	19.285	0.006	0.006	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.965	-0.970	21.839	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.002	-0.007	21.176	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.845	0.920	23.967	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.919	0.962	26.810	0.006	0.006	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.074	0.030	24.233	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.045	-0.029	23.496	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.007	-0.001	23.637	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.900	0.946	20.064	-0.061	-0.061	0.000	0.000	0.000	0.000
25	A	26	PHE	0	0.008	0.000	18.964	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.041	-0.021	19.117	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.063	0.034	17.139	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.009	0.018	14.078	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.021	-0.001	14.236	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.005	-0.028	15.076	-0.033	-0.033	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.011	-0.006	10.490	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	33	LEU	0	0.008	-0.005	9.661	-0.113	-0.113	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.002	-0.004	10.681	-0.094	-0.094	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.073	-0.055	11.184	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.048	-0.020	5.547	-0.109	-0.109	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.827	-0.923	7.017	-0.921	-0.921	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.015	0.004	9.311	0.103	0.103	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.075	-0.025	12.209	0.044	0.044	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.078	0.031	10.492	0.063	0.063	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.014	-0.010	12.500	0.080	0.080	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.011	0.011	14.096	0.056	0.056	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.862	-0.922	15.301	-0.235	-0.235	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.027	-0.007	14.671	0.040	0.040	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.070	-0.055	16.816	0.041	0.041	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.994	-1.003	19.660	-0.148	-0.148	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.045	-0.017	19.371	0.018	0.018	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.043	-0.001	19.393	0.020	0.020	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.049	-0.049	22.522	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.008	0.000	26.161	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.918	0.950	28.931	0.007	0.007	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.007	0.002	32.308	0.001	0.001	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.851	0.922	30.714	0.020	0.020	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.083	0.055	27.899	0.001	0.001	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.042	-0.024	24.005	0.010	0.010	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.097	0.030	20.099	0.003	0.003	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.020	-0.007	24.738	0.003	0.003	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.082	0.045	25.088	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.911	-0.946	26.004	-0.086	-0.086	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.857	-0.947	29.502	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	61	GLN	0	0.067	0.011	31.028	0.006	0.006	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.022	-0.006	30.300	0.007	0.007	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.006	0.020	27.210	0.003	0.003	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.038	-0.017	31.487	0.006	0.006	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.848	0.922	35.111	0.057	0.057	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.002	0.004	32.956	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.038	-0.006	34.356	0.002	0.002	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.016	0.023	35.475	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.050	0.026	36.748	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.015	0.029	31.896	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.807	0.882	31.480	0.026	0.026	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.038	0.047	29.454	0.000	0.000	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.915	0.944	26.130	0.050	0.050	0.000	0.000	0.000	0.000
73	A	74	HIS	0	0.036	0.032	23.324	0.005	0.005	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.001	-0.006	18.687	0.011	0.011	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.028	0.014	20.550	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.046	0.033	18.621	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.011	0.009	17.023	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.004	0.011	18.963	0.022	0.022	0.000	0.000	0.000	0.000
79	A	80	TYR	0	0.046	0.019	17.879	0.007	0.007	0.000	0.000	0.000	0.000
80	A	81	TRP	0	-0.009	-0.002	22.510	0.010	0.010	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.038	0.014	22.311	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.039	-0.011	25.272	0.008	0.008	0.000	0.000	0.000	0.000
83	A	84	THR	0	0.020	-0.011	27.045	0.004	0.004	0.000	0.000	0.000	0.000
84	A	85	ASN	0	-0.057	-0.008	28.237	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	THR	0	0.071	0.033	26.917	0.002	0.002	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.026	0.020	28.367	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	THR	0	0.074	0.022	25.377	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.058	0.044	24.037	0.002	0.002	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.937	0.963	23.930	0.005	0.005	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.799	0.896	22.374	0.006	0.006	0.000	0.000	0.000	0.000
91	A	92	CYS	0	0.006	-0.018	19.650	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.006	-0.016	19.133	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	94	MET	0	-0.089	-0.036	19.876	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.017	0.013	14.685	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.844	-0.927	15.025	0.046	0.046	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.040	0.002	15.628	0.020	0.020	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.019	0.003	13.167	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	99	MET	0	-0.030	-0.012	9.494	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.031	-0.022	10.867	0.021	0.021	0.000	0.000	0.000	0.000
100	A	101	SER	0	0.000	0.011	12.854	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	102	MET	0	-0.063	-0.032	9.044	0.007	0.007	0.000	0.000	0.000	0.000
102	A	103	GLN	0	-0.043	-0.013	8.126	-0.121	-0.121	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.017	0.008	6.274	0.103	0.103	0.000	0.000	0.000	0.000
104	A	105	PRO	0	-0.014	-0.005	6.945	-0.042	-0.042	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.079	0.021	9.974	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.695	-0.795	10.934	0.930	0.930	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.063	-0.019	7.609	0.009	0.009	0.000	0.000	0.000	0.000
108	A	109	ILE	0	0.028	0.020	11.540	-0.087	-0.087	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.920	-0.970	13.347	0.215	0.215	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.808	0.888	13.343	-0.560	-0.560	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.062	0.034	12.152	-0.030	-0.030	0.000	0.000	0.000	0.000
112	A	113	CYS	0	0.003	0.026	15.201	-0.045	-0.045	0.000	0.000	0.000	0.000
113	A	114	GLY	0	0.006	0.009	18.325	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.019	0.006	17.917	-0.015	-0.015	0.000	0.000	0.000	0.000
115	A	116	ILE	0	-0.065	-0.022	18.029	-0.027	-0.027	0.000	0.000	0.000	0.000

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