FMO DATABASE

FMODB ID: V52J1

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	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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-956394.90563
FMO2-HF: Nuclear repulsion	909996.725659
FMO2-HF: Total energy	-46398.179971
FMO2-MP2: Total energy	-46530.537103

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.
-2.344	2.35	0.433	-2.082	-3.044	-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 : 0.046 / 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

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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	0.011	-0.006	2.611	-1.389	1.413	0.146	-1.361	-1.586	0.001
4	A	5	SER	0	-0.011	-0.016	2.722	-0.268	1.447	0.288	-0.691	-1.313	-0.003
5	A	6	ALA	0	0.119	0.073	4.666	0.237	0.414	-0.001	-0.030	-0.145	0.000
6	A	7	MET	0	0.008	0.010	6.581	0.418	0.418	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.765	0.843	5.979	-0.136	-0.136	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.927	-0.966	7.714	0.185	0.185	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.013	-0.001	10.481	0.050	0.050	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.093	-0.067	12.259	0.059	0.059	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.028	-0.021	12.516	0.034	0.034	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.023	0.022	14.826	0.015	0.015	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.823	-0.919	16.385	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.872	-0.964	18.347	-0.182	-0.182	0.000	0.000	0.000	0.000
15	A	16	TYR	0	-0.107	-0.073	16.798	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.030	-0.008	18.923	0.004	0.004	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.940	-0.955	21.209	-0.064	-0.064	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.017	0.000	21.234	0.008	0.008	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.908	0.939	23.912	0.060	0.060	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.876	0.940	26.026	0.072	0.072	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.046	0.021	23.922	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.009	-0.014	23.115	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	24	ASN	0	0.015	0.025	23.052	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.995	0.978	19.698	0.082	0.082	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.016	-0.019	18.756	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.065	-0.041	19.107	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.068	0.043	17.184	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.001	0.008	14.019	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.010	0.007	14.146	-0.071	-0.071	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.017	-0.050	14.923	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.014	-0.005	10.873	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	33	LEU	0	0.000	-0.019	9.634	-0.129	-0.129	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.037	-0.008	10.882	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.059	-0.036	11.555	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.045	-0.017	5.840	-0.111	-0.111	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.779	-0.911	7.376	-0.883	-0.883	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.024	-0.011	9.271	0.094	0.094	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.040	-0.013	11.960	0.047	0.047	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.099	0.046	9.842	0.051	0.051	0.000	0.000	0.000	0.000
40	A	41	PHE	0	-0.078	-0.032	11.833	0.066	0.066	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.013	-0.004	13.444	0.051	0.051	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.882	-0.930	14.822	-0.274	-0.274	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.059	-0.027	13.688	0.032	0.032	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.046	-0.030	15.833	0.038	0.038	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-1.000	-0.982	18.608	-0.188	-0.188	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.037	-0.007	18.811	0.019	0.019	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.072	-0.013	19.501	0.016	0.016	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.042	-0.042	21.917	0.002	0.002	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.021	-0.013	25.557	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.932	0.960	28.454	0.075	0.075	0.000	0.000	0.000	0.000
51	A	52	THR	0	0.006	-0.011	31.546	0.003	0.003	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.831	0.917	30.282	0.090	0.090	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.085	0.054	27.174	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.043	-0.038	23.620	0.011	0.011	0.000	0.000	0.000	0.000
55	A	56	PHE	0	0.108	0.033	19.543	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.018	-0.016	23.872	0.006	0.006	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.051	0.031	25.003	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.888	-0.924	25.912	-0.121	-0.121	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.871	-0.957	29.397	-0.102	-0.102	0.000	0.000	0.000	0.000
60	A	61	GLN	0	0.026	-0.004	30.961	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	THR	0	0.012	0.004	29.848	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.047	-0.014	26.829	0.003	0.003	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.087	-0.045	31.005	0.005	0.005	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.929	0.977	34.264	0.094	0.094	0.000	0.000	0.000	0.000
65	A	66	ASN	0	-0.046	-0.017	32.269	0.007	0.007	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.027	0.004	34.000	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.017	0.015	35.214	0.000	0.000	0.000	0.000	0.000	0.000
68	A	69	GLN	0	0.029	0.005	35.991	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	THR	0	0.044	0.026	31.043	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.879	0.927	31.063	0.079	0.079	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.033	0.017	28.957	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.912	0.967	26.307	0.118	0.118	0.000	0.000	0.000	0.000
73	A	74	HIS	0	0.038	0.021	23.817	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.002	0.003	18.901	0.006	0.006	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.047	0.036	20.954	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.053	0.047	18.664	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.024	-0.017	17.217	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.015	0.000	19.093	0.023	0.023	0.000	0.000	0.000	0.000
79	A	80	TYR	0	0.043	0.014	18.286	0.021	0.021	0.000	0.000	0.000	0.000
80	A	81	TRP	0	0.016	0.022	22.592	0.004	0.004	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.036	0.016	21.515	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.041	0.000	24.751	0.015	0.015	0.000	0.000	0.000	0.000
83	A	84	THR	0	0.027	-0.009	26.152	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	85	ASN	0	-0.095	-0.016	28.350	0.006	0.006	0.000	0.000	0.000	0.000
85	A	86	THR	0	0.042	0.025	26.634	0.002	0.002	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.042	0.023	28.518	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	88	THR	0	0.067	0.005	25.002	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.068	0.051	24.057	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.940	0.968	24.217	0.102	0.102	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.862	0.943	22.201	0.110	0.110	0.000	0.000	0.000	0.000
91	A	92	CYS	0	0.110	0.033	19.447	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.004	0.014	19.321	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	94	MET	0	-0.061	-0.030	19.966	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.029	0.012	14.890	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.947	-0.982	15.159	-0.181	-0.181	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.003	0.002	15.543	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.004	-0.004	12.636	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	99	MET	0	-0.042	-0.021	9.774	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	100	GLN	0	0.014	-0.004	10.673	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	101	SER	0	0.046	0.038	12.370	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	102	MET	0	-0.087	-0.027	8.136	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	103	GLN	0	-0.042	-0.041	7.605	-0.133	-0.133	0.000	0.000	0.000	0.000
103	A	104	PHE	0	0.000	0.017	6.190	-0.150	-0.150	0.000	0.000	0.000	0.000
104	A	105	PRO	0	-0.061	-0.022	6.611	0.107	0.107	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.117	0.031	9.552	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.697	-0.823	10.163	0.149	0.149	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.071	-0.025	7.216	0.012	0.012	0.000	0.000	0.000	0.000
108	A	109	ILE	0	0.062	0.022	11.005	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.953	-0.984	13.009	-0.034	-0.034	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.824	0.916	11.739	-0.073	-0.073	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.056	0.035	12.043	0.007	0.007	0.000	0.000	0.000	0.000
112	A	113	CYS	0	-0.002	0.038	14.853	0.012	0.012	0.000	0.000	0.000	0.000
113	A	114	GLY	0	-0.004	0.018	18.204	0.008	0.008	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.042	-0.023	16.446	0.004	0.004	0.000	0.000	0.000	0.000
115	A	116	ILE	0	-0.080	-0.004	18.331	0.008	0.008	0.000	0.000	0.000	0.000

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