FMO DATABASE

FMODB ID: LJQ89

Calculation Name: 1JNP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JNP

Chain ID: A

ChEMBL ID:

UniProt ID: P56280

Base Structure: X-ray

Registration Date: 2023-03-13

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-887457.900987
FMO2-HF: Nuclear repulsion	844191.899254
FMO2-HF: Total energy	-43266.001733
FMO2-MP2: Total energy	-43393.133573

3D Structure Molmil

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:8:ARG)

Summations of interaction energy for fragment #1(A:8: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.
-57.892	-60.774	21.511	-9.923	-8.706	-0.041

Interaction energy analysis for fragmet #1(A:8:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.894 / q_NPA : 0.901

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	10	GLU	-1	-0.829	-0.960	3.813	-28.035	-26.198	-0.029	-0.851	-0.957	-0.002
4	A	11	THR	0	-0.042	0.007	7.027	0.880	0.880	0.000	0.000	0.000	0.000
5	A	12	PRO	0	-0.035	-0.023	9.736	1.025	1.025	0.000	0.000	0.000	0.000
6	A	13	ALA	0	-0.013	-0.010	12.964	0.543	0.543	0.000	0.000	0.000	0.000
7	A	14	HIS	1	0.852	0.906	12.987	17.234	17.234	0.000	0.000	0.000	0.000
8	A	15	PRO	0	0.077	0.052	15.513	0.705	0.705	0.000	0.000	0.000	0.000
9	A	16	ASN	0	-0.028	0.012	18.723	0.466	0.466	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.855	0.904	22.348	10.643	10.643	0.000	0.000	0.000	0.000
11	A	18	LEU	0	0.032	0.018	18.656	-0.266	-0.266	0.000	0.000	0.000	0.000
12	A	19	TRP	0	-0.008	-0.016	22.607	0.245	0.245	0.000	0.000	0.000	0.000
13	A	20	ILE	0	0.019	0.009	24.271	-0.368	-0.368	0.000	0.000	0.000	0.000
14	A	21	TRP	0	-0.093	-0.043	25.343	0.291	0.291	0.000	0.000	0.000	0.000
15	A	22	GLU	-1	-0.843	-0.958	26.096	-10.742	-10.742	0.000	0.000	0.000	0.000
16	A	23	LYS	1	0.876	0.922	26.374	9.829	9.829	0.000	0.000	0.000	0.000
17	A	24	HIS	0	0.052	0.047	23.362	0.073	0.073	0.000	0.000	0.000	0.000
18	A	25	VAL	0	0.003	0.021	21.516	-0.661	-0.661	0.000	0.000	0.000	0.000
19	A	26	TYR	0	0.014	-0.046	20.490	0.425	0.425	0.000	0.000	0.000	0.000
20	A	27	LEU	0	-0.016	0.011	20.827	-0.468	-0.468	0.000	0.000	0.000	0.000
21	A	28	ASP	-1	-0.721	-0.857	18.452	-13.748	-13.748	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.868	-0.932	21.688	-12.308	-12.308	0.000	0.000	0.000	0.000
23	A	30	PHE	0	-0.071	-0.014	18.396	0.414	0.414	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.915	0.957	21.043	11.344	11.344	0.000	0.000	0.000	0.000
25	A	32	ARG	1	0.824	0.885	15.856	15.553	15.553	0.000	0.000	0.000	0.000
26	A	33	SER	0	0.003	-0.009	18.940	-0.052	-0.052	0.000	0.000	0.000	0.000
27	A	34	TRP	0	0.009	-0.012	12.395	-1.186	-1.186	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.028	0.000	16.647	0.978	0.978	0.000	0.000	0.000	0.000
29	A	36	PRO	0	-0.033	0.016	16.864	-1.175	-1.175	0.000	0.000	0.000	0.000
30	A	37	VAL	0	-0.011	-0.002	14.935	0.411	0.411	0.000	0.000	0.000	0.000
31	A	38	VAL	0	-0.061	-0.036	15.973	0.185	0.185	0.000	0.000	0.000	0.000
32	A	39	ILE	0	0.031	0.004	18.632	-0.200	-0.200	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.887	0.953	18.560	14.885	14.885	0.000	0.000	0.000	0.000
34	A	41	SER	0	0.117	0.043	20.468	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	42	ASN	0	-0.146	-0.072	23.186	-0.431	-0.431	0.000	0.000	0.000	0.000
36	A	43	GLU	-1	-0.855	-0.907	25.056	-10.189	-10.189	0.000	0.000	0.000	0.000
37	A	44	LYS	1	0.802	0.909	20.113	15.277	15.277	0.000	0.000	0.000	0.000
38	A	45	PHE	0	0.007	-0.012	22.860	-0.520	-0.520	0.000	0.000	0.000	0.000
39	A	46	GLN	0	0.022	0.003	17.353	0.827	0.827	0.000	0.000	0.000	0.000
40	A	47	VAL	0	0.031	0.028	18.185	-0.115	-0.115	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.024	-0.017	12.429	-0.313	-0.313	0.000	0.000	0.000	0.000
42	A	49	LEU	0	0.000	-0.016	14.911	0.517	0.517	0.000	0.000	0.000	0.000
43	A	50	ARG	1	0.859	0.885	9.929	25.534	25.534	0.000	0.000	0.000	0.000
44	A	51	GLN	0	-0.003	0.024	12.190	1.857	1.857	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.940	-0.975	13.482	-17.593	-17.593	0.000	0.000	0.000	0.000
46	A	53	ASP	-1	-0.917	-0.950	16.138	-13.507	-13.507	0.000	0.000	0.000	0.000
47	A	54	VAL	0	-0.043	-0.007	18.674	0.325	0.325	0.000	0.000	0.000	0.000
48	A	55	THR	0	-0.074	-0.049	22.352	0.275	0.275	0.000	0.000	0.000	0.000
49	A	56	LEU	0	0.039	0.007	24.225	-0.171	-0.171	0.000	0.000	0.000	0.000
50	A	57	GLY	0	-0.038	-0.018	26.613	0.052	0.052	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.957	-0.969	29.287	-8.928	-8.928	0.000	0.000	0.000	0.000
52	A	59	ALA	0	-0.031	-0.018	30.452	-0.135	-0.135	0.000	0.000	0.000	0.000
53	A	60	MET	0	0.014	0.046	30.115	0.287	0.287	0.000	0.000	0.000	0.000
54	A	61	SER	0	-0.037	-0.053	31.872	-0.084	-0.084	0.000	0.000	0.000	0.000
55	A	62	PRO	0	0.031	-0.006	33.322	-0.111	-0.111	0.000	0.000	0.000	0.000
56	A	63	SER	0	0.051	0.021	34.347	-0.131	-0.131	0.000	0.000	0.000	0.000
57	A	64	GLN	0	0.005	0.038	35.500	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	65	LEU	0	0.023	0.047	28.969	-0.210	-0.210	0.000	0.000	0.000	0.000
59	A	66	VAL	0	-0.009	-0.043	33.170	-0.075	-0.075	0.000	0.000	0.000	0.000
60	A	67	PRO	0	-0.076	-0.026	33.331	-0.089	-0.089	0.000	0.000	0.000	0.000
61	A	68	TYR	0	-0.058	-0.061	25.365	-0.258	-0.258	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.889	-0.941	26.187	-11.375	-11.375	0.000	0.000	0.000	0.000
63	A	70	LEU	0	-0.043	-0.022	22.727	-0.408	-0.408	0.000	0.000	0.000	0.000
64	A	71	PRO	0	0.018	0.042	24.749	0.453	0.453	0.000	0.000	0.000	0.000
65	A	72	LEU	0	0.057	0.068	26.496	-0.240	-0.240	0.000	0.000	0.000	0.000
66	A	73	MET	0	0.006	-0.016	26.782	-0.139	-0.139	0.000	0.000	0.000	0.000
67	A	74	TRP	0	0.103	0.034	21.577	-0.073	-0.073	0.000	0.000	0.000	0.000
68	A	75	GLN	0	-0.065	-0.030	24.048	0.071	0.071	0.000	0.000	0.000	0.000
69	A	76	LEU	0	0.022	0.034	20.493	0.180	0.180	0.000	0.000	0.000	0.000
70	A	77	TYR	0	-0.016	-0.005	23.626	0.584	0.584	0.000	0.000	0.000	0.000
71	A	78	PRO	0	-0.005	-0.019	24.756	-0.362	-0.362	0.000	0.000	0.000	0.000
72	A	79	LYS	1	0.854	0.941	24.498	10.837	10.837	0.000	0.000	0.000	0.000
73	A	80	ASP	-1	-0.838	-0.926	18.521	-15.408	-15.408	0.000	0.000	0.000	0.000
74	A	81	ARG	1	0.900	0.962	20.552	11.022	11.022	0.000	0.000	0.000	0.000
75	A	82	TYR	0	0.036	-0.030	18.077	0.255	0.255	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.841	0.935	23.041	9.663	9.663	0.000	0.000	0.000	0.000
77	A	84	SER	0	0.004	0.010	26.573	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	85	ALA	0	-0.008	-0.015	27.519	0.316	0.316	0.000	0.000	0.000	0.000
79	A	86	ASP	-1	-0.836	-0.895	30.296	-9.708	-9.708	0.000	0.000	0.000	0.000
80	A	87	SER	0	-0.039	-0.051	31.602	0.075	0.075	0.000	0.000	0.000	0.000
81	A	88	MET	0	0.006	0.031	28.213	0.051	0.051	0.000	0.000	0.000	0.000
82	A	89	TYR	0	-0.067	-0.073	26.206	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	90	TRP	0	0.062	0.027	21.122	-0.119	-0.119	0.000	0.000	0.000	0.000
84	A	91	GLN	0	-0.060	-0.025	17.728	0.489	0.489	0.000	0.000	0.000	0.000
85	A	92	ILE	0	0.032	0.027	14.004	-0.277	-0.277	0.000	0.000	0.000	0.000
86	A	93	LEU	0	-0.053	-0.018	14.288	-0.061	-0.061	0.000	0.000	0.000	0.000
87	A	94	TYR	0	-0.014	-0.016	9.802	-1.539	-1.539	0.000	0.000	0.000	0.000
88	A	95	HIS	0	0.029	0.031	10.472	1.540	1.540	0.000	0.000	0.000	0.000
89	A	96	ILE	0	0.104	0.084	5.109	0.027	0.027	0.000	0.000	0.000	0.000
90	A	97	LYN	0	-0.016	0.008	4.436	1.401	1.834	0.000	-0.182	-0.251	0.000
91	A	98	PHE	0	-0.127	-0.044	1.832	-13.412	-18.480	21.508	-9.689	-6.751	-0.038
92	A	99	ARG	1	0.882	0.938	3.026	37.017	36.884	0.033	0.806	-0.706	-0.001
93	A	100	ASP	-1	-0.901	-0.950	5.036	-24.510	-24.461	-0.001	-0.007	-0.041	0.000
94	A	101	VAL	0	0.065	0.029	6.323	2.086	2.086	0.000	0.000	0.000	0.000
95	A	102	GLU	-1	-0.882	-0.925	6.200	-23.701	-23.701	0.000	0.000	0.000	0.000
96	A	103	ASP	-1	-0.754	-0.830	8.082	-25.535	-25.535	0.000	0.000	0.000	0.000
97	A	104	MET	0	-0.006	-0.006	9.669	-0.821	-0.821	0.000	0.000	0.000	0.000
98	A	105	LEU	0	-0.040	0.006	12.505	0.558	0.558	0.000	0.000	0.000	0.000
99	A	106	LEU	0	-0.017	0.004	14.318	0.165	0.165	0.000	0.000	0.000	0.000
100	A	107	GLU	-1	-0.848	-0.950	17.846	-16.457	-16.457	0.000	0.000	0.000	0.000
101	A	108	LEU	0	-0.022	0.001	20.298	0.555	0.555	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:ARG)