FMO DATABASE

FMODB ID: LNY89

Calculation Name: 1R7J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R7J

Chain ID: A

ChEMBL ID:

UniProt ID: Q5W1E8

Base Structure: X-ray

Registration Date: 2023-09-23

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-622423.012159
FMO2-HF: Nuclear repulsion	584685.108764
FMO2-HF: Total energy	-37737.903396
FMO2-MP2: Total energy	-37844.028672

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
59.471	62.535	0.402	-1.532	-1.933	-0.009

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.967

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	5	SER	0	0.009	-0.001	2.783	-10.813	-7.887	0.404	-1.526	-1.804	-0.009
4	A	6	LYS	1	1.001	0.980	5.025	29.145	29.210	-0.001	-0.002	-0.061	0.000
5	A	7	LEU	0	0.050	0.022	7.448	1.978	1.978	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.794	-0.885	5.796	-33.466	-33.466	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.060	-0.019	5.206	2.049	2.049	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.006	-0.010	8.666	2.137	2.137	0.000	0.000	0.000	0.000
9	A	11	GLN	0	0.029	0.022	11.699	0.601	0.601	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.018	-0.007	10.221	1.337	1.337	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.036	-0.023	12.274	1.268	1.268	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.010	-0.002	14.579	1.114	1.114	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.739	-0.863	15.027	-14.317	-14.317	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.065	-0.020	16.031	0.804	0.804	0.000	0.000	0.000	0.000
15	A	17	CYS	0	-0.050	-0.035	17.823	0.760	0.760	0.000	0.000	0.000	0.000
16	A	18	LYS	1	0.967	0.999	20.251	12.800	12.800	0.000	0.000	0.000	0.000
17	A	19	SER	0	-0.023	-0.009	22.277	0.546	0.546	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.036	0.032	23.338	0.399	0.399	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.032	-0.038	19.366	-0.118	-0.118	0.000	0.000	0.000	0.000
20	A	22	PRO	0	0.014	0.035	20.805	-0.128	-0.128	0.000	0.000	0.000	0.000
21	A	23	LYS	1	1.001	0.983	17.822	15.221	15.221	0.000	0.000	0.000	0.000
22	A	24	THR	0	0.009	-0.003	17.230	-0.883	-0.883	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.991	1.009	16.212	12.230	12.230	0.000	0.000	0.000	0.000
24	A	26	ILE	0	0.011	0.014	14.416	-0.722	-0.722	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.053	-0.010	12.988	-1.095	-1.095	0.000	0.000	0.000	0.000
26	A	28	TYR	0	0.007	-0.010	11.308	-1.352	-1.352	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.013	0.024	10.743	-0.710	-0.710	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.008	-0.019	9.082	-0.851	-0.851	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.049	-0.017	4.434	-1.458	-1.385	-0.001	-0.004	-0.068	0.000
30	A	32	LEU	0	-0.008	0.001	6.953	-3.794	-3.794	0.000	0.000	0.000	0.000
31	A	33	SER	0	0.082	0.042	9.101	2.519	2.519	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.106	0.024	11.403	0.213	0.213	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.006	-0.004	13.602	0.401	0.401	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.028	-0.011	7.205	0.552	0.552	0.000	0.000	0.000	0.000
35	A	37	THR	0	0.034	0.005	11.652	0.023	0.023	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.027	-0.019	13.503	0.820	0.820	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.958	0.982	10.987	25.016	25.016	0.000	0.000	0.000	0.000
38	A	40	TYR	0	0.022	0.008	7.481	0.414	0.414	0.000	0.000	0.000	0.000
39	A	41	ILE	0	0.017	0.014	14.120	0.687	0.687	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.968	0.981	17.500	14.836	14.836	0.000	0.000	0.000	0.000
41	A	43	MET	0	-0.003	0.008	13.054	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.002	-0.013	15.339	0.469	0.469	0.000	0.000	0.000	0.000
43	A	45	MET	0	-0.033	-0.015	18.776	0.638	0.638	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.873	-0.923	21.114	-13.454	-13.454	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.068	-0.025	18.411	0.377	0.377	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.893	-0.942	22.391	-10.831	-10.831	0.000	0.000	0.000	0.000
47	A	49	ILE	0	-0.036	0.004	19.064	0.188	0.188	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.029	-0.019	19.160	0.003	0.003	0.000	0.000	0.000	0.000
49	A	51	ARG	1	0.879	0.921	22.679	10.713	10.713	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.028	-0.030	25.089	-0.414	-0.414	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.810	-0.881	26.659	-9.527	-9.527	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.016	0.008	28.965	0.002	0.002	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.940	0.959	26.286	9.892	9.892	0.000	0.000	0.000	0.000
54	A	56	GLN	0	-0.003	-0.003	24.482	-0.725	-0.725	0.000	0.000	0.000	0.000
55	A	57	TYR	0	-0.010	-0.005	21.319	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	58	MET	0	0.020	-0.001	22.956	-0.062	-0.062	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.004	0.022	20.113	-0.349	-0.349	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.023	-0.013	23.915	0.492	0.492	0.000	0.000	0.000	0.000
59	A	61	LYS	1	1.038	1.008	25.582	9.928	9.928	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.937	0.965	23.036	12.635	12.635	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.033	0.000	21.721	-0.467	-0.467	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-1.005	-1.001	21.560	-11.406	-11.406	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.928	-0.967	23.373	-11.159	-11.159	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.012	0.021	17.491	-0.422	-0.422	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.068	-0.040	17.481	-0.683	-0.683	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.928	-0.971	19.448	-12.557	-12.557	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.877	-0.931	20.688	-13.134	-13.134	0.000	0.000	0.000	0.000
68	A	70	ILE	0	-0.075	-0.040	14.432	-0.587	-0.587	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.807	0.872	17.102	13.336	13.336	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.991	1.005	18.501	11.929	11.929	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.013	-0.009	14.145	-0.051	-0.051	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.004	-0.021	13.564	-0.869	-0.869	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.904	-0.935	15.978	-13.130	-13.130	0.000	0.000	0.000	0.000
74	A	76	MET	0	-0.050	-0.031	18.970	0.356	0.356	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.927	0.968	11.648	20.358	20.358	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.982	1.007	16.621	13.051	13.051	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.009	-0.017	17.454	0.451	0.451	0.000	0.000	0.000	0.000
78	A	80	MET	0	-0.045	-0.015	19.161	0.306	0.306	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.883	-0.950	14.936	-16.654	-16.654	0.000	0.000	0.000	0.000
80	A	82	GLN	0	-0.010	-0.002	18.532	0.142	0.142	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.025	-0.013	21.132	0.503	0.503	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.928	0.961	20.352	13.773	13.773	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.865	-0.930	18.923	-13.085	-13.085	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.915	0.971	22.677	9.929	9.929	0.000	0.000	0.000	0.000
85	A	87	ILE	0	-0.027	-0.007	25.643	0.353	0.353	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.051	0.006	21.953	0.492	0.492	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.075	-0.031	25.899	0.331	0.331	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.051	-0.025	27.710	0.294	0.294	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.031	-0.017	28.663	0.252	0.252	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.060	-0.017	27.143	-0.235	-0.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)