FMO DATABASE

FMODB ID: 8N27Y

Calculation Name: 3DA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA7

Chain ID: A

ChEMBL ID:

UniProt ID: P11540

Base Structure: X-ray

Registration Date: 2023-09-26

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	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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864781.04269
FMO2-HF: Nuclear repulsion	822094.9319
FMO2-HF: Total energy	-42686.11079
FMO2-MP2: Total energy	-42813.234548

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:4:ARG)

Summations of interaction energy for fragment #1(A:4: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.
-92.144	-84.776	43.282	-22.223	-28.429	-0.226

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.897

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	6	TRP	0	0.055	0.015	2.532	-5.844	-1.522	0.797	-1.817	-3.303	-0.005
4	A	7	ARG	1	0.890	0.946	5.794	25.226	25.226	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.755	-0.838	9.351	-19.162	-19.162	0.000	0.000	0.000	0.000
6	A	9	ALA	0	0.027	0.001	12.399	0.728	0.728	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.745	-0.822	15.696	-14.939	-14.939	0.000	0.000	0.000	0.000
8	A	11	ILE	0	-0.016	-0.001	17.273	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	12	ASN	0	-0.006	0.007	20.086	0.466	0.466	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.014	-0.002	23.210	0.369	0.369	0.000	0.000	0.000	0.000
11	A	14	THR	0	-0.037	-0.028	24.977	0.162	0.162	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.002	0.000	28.464	0.299	0.299	0.000	0.000	0.000	0.000
13	A	16	GLY	0	0.060	0.051	29.904	-0.094	-0.094	0.000	0.000	0.000	0.000
14	A	17	PHE	0	-0.014	-0.010	28.454	-0.270	-0.270	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.779	0.865	18.015	14.422	14.422	0.000	0.000	0.000	0.000
16	A	19	ASN	0	0.055	0.025	22.220	-0.102	-0.102	0.000	0.000	0.000	0.000
17	A	20	SER	0	-0.008	-0.016	21.207	-0.155	-0.155	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.851	-0.906	19.042	-14.417	-14.417	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.764	0.864	14.516	15.362	15.362	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.022	0.007	12.420	-0.635	-0.635	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.021	-0.015	8.356	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	25	TYR	0	0.025	0.006	7.648	-0.723	-0.723	0.000	0.000	0.000	0.000
23	A	26	SER	0	0.004	-0.034	2.502	2.960	3.805	0.414	-0.367	-0.892	0.000
24	A	27	SER	0	0.006	0.000	2.664	0.918	2.584	0.637	-0.985	-1.318	-0.007
25	A	28	ASP	-1	-0.824	-0.880	1.731	-108.777	-110.333	17.518	-8.003	-7.959	-0.106
26	A	29	TRP	0	-0.013	-0.001	4.731	1.469	1.542	-0.001	-0.009	-0.063	0.000
27	A	30	LEU	0	0.033	0.034	2.677	3.396	4.299	0.191	-0.217	-0.877	0.000
28	A	31	ILE	0	-0.007	-0.018	5.774	0.736	0.736	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.014	-0.022	6.450	1.112	1.112	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.907	0.970	10.432	17.277	17.277	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.018	-0.005	13.685	-0.152	-0.152	0.000	0.000	0.000	0.000
32	A	35	THR	0	0.091	0.028	15.691	0.076	0.076	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.812	-0.855	17.729	-15.857	-15.857	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.022	0.009	18.255	0.018	0.018	0.000	0.000	0.000	0.000
35	A	38	TYR	0	-0.080	-0.073	13.357	0.286	0.286	0.000	0.000	0.000	0.000
36	A	39	GLN	0	0.040	0.032	15.252	-1.104	-1.104	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.063	-0.055	15.400	-0.738	-0.738	0.000	0.000	0.000	0.000
38	A	41	PHE	0	0.036	0.005	10.760	-0.561	-0.561	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.002	0.002	12.619	-0.946	-0.946	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.874	0.945	10.099	25.012	25.012	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.008	-0.008	11.313	1.827	1.827	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.884	0.927	12.153	18.951	18.951	0.000	0.000	0.000	0.000
43	A	46	CYM	-1	-0.753	-0.837	14.796	-15.201	-15.201	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.118	-0.076	17.573	-0.102	-0.102	0.000	0.000	0.000	0.000
45	A	48	GLN	0	0.011	-0.010	21.048	0.648	0.648	0.000	0.000	0.000	0.000
46	A	49	VAL	0	0.017	0.017	20.134	-0.090	-0.090	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.027	0.007	22.365	0.636	0.636	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.073	-0.061	20.664	0.082	0.082	0.000	0.000	0.000	0.000
49	A	52	THR	0	0.035	-0.016	21.568	-0.600	-0.600	0.000	0.000	0.000	0.000
50	A	53	PHE	0	-0.018	-0.015	16.158	-0.604	-0.604	0.000	0.000	0.000	0.000
51	A	54	ASP	-1	-0.741	-0.874	16.803	-16.101	-16.101	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.052	0.031	17.781	-0.442	-0.442	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.015	-0.013	15.793	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	57	ALA	0	-0.005	-0.011	13.551	-0.887	-0.887	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.886	-0.938	14.325	-16.546	-16.546	0.000	0.000	0.000	0.000
56	A	59	TYR	0	0.006	0.012	16.914	-0.125	-0.125	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.020	-0.016	11.692	-0.343	-0.343	0.000	0.000	0.000	0.000
58	A	61	GLN	0	-0.060	-0.037	9.582	-1.018	-1.018	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.022	-0.003	13.843	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	63	TYR	0	-0.014	-0.015	16.628	0.603	0.603	0.000	0.000	0.000	0.000
61	A	64	HIS	1	0.773	0.893	11.878	22.857	22.857	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.845	0.929	13.136	13.354	13.354	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.003	0.000	14.164	-0.245	-0.245	0.000	0.000	0.000	0.000
64	A	67	PRO	0	0.044	0.018	16.170	0.519	0.519	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.782	-0.882	19.834	-12.977	-12.977	0.000	0.000	0.000	0.000
66	A	69	ASN	0	0.015	0.020	21.784	0.242	0.242	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.048	-0.052	18.771	0.152	0.152	0.000	0.000	0.000	0.000
68	A	71	ILE	0	0.002	0.014	20.674	0.440	0.440	0.000	0.000	0.000	0.000
69	A	72	THR	0	-0.043	-0.041	16.977	-0.296	-0.296	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.819	0.868	16.634	16.794	16.794	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.017	-0.003	20.798	0.609	0.609	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.772	-0.853	20.658	-12.980	-12.980	0.000	0.000	0.000	0.000
73	A	76	ALA	0	0.023	0.015	23.623	0.503	0.503	0.000	0.000	0.000	0.000
74	A	77	GLN	0	-0.044	-0.038	24.134	0.069	0.069	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.023	0.000	26.680	0.391	0.391	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.015	0.000	27.568	0.326	0.326	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.034	0.024	30.114	0.300	0.300	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.055	-0.029	23.252	-0.132	-0.132	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.001	-0.017	29.224	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.028	0.014	26.354	0.147	0.147	0.000	0.000	0.000	0.000
81	A	84	SER	0	0.004	-0.014	28.303	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	85	LYS	1	0.852	0.932	31.239	8.767	8.767	0.000	0.000	0.000	0.000
83	A	86	GLY	0	-0.005	-0.002	30.144	0.202	0.202	0.000	0.000	0.000	0.000
84	A	87	ASN	0	-0.006	-0.002	31.206	-0.273	-0.273	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.011	0.003	24.620	0.048	0.048	0.000	0.000	0.000	0.000
86	A	89	ALA	0	0.026	0.005	29.146	0.025	0.025	0.000	0.000	0.000	0.000
87	A	90	ASP	-1	-0.832	-0.920	31.218	-8.540	-8.540	0.000	0.000	0.000	0.000
88	A	91	VAL	0	-0.051	-0.020	29.888	0.180	0.180	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.020	-0.010	27.949	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.019	0.013	29.115	-0.302	-0.302	0.000	0.000	0.000	0.000
91	A	94	GLY	0	-0.010	-0.001	29.086	-0.053	-0.053	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.809	0.905	23.558	11.528	11.528	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.003	-0.007	21.855	0.315	0.315	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.021	0.014	18.654	-0.287	-0.287	0.000	0.000	0.000	0.000
95	A	98	GLY	0	-0.025	-0.030	16.421	-0.508	-0.508	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.055	0.038	13.964	0.608	0.608	0.000	0.000	0.000	0.000
97	A	100	ASP	-1	-0.835	-0.907	13.270	-16.756	-16.756	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.015	-0.010	9.187	-1.316	-1.316	0.000	0.000	0.000	0.000
99	A	102	PHE	0	0.029	0.017	7.969	1.137	1.137	0.000	0.000	0.000	0.000
100	A	103	SER	0	-0.063	-0.055	8.477	-2.095	-2.095	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.031	-0.019	5.932	2.895	2.895	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.982	0.982	9.125	18.272	18.272	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.823	-0.882	11.992	-17.713	-17.713	0.000	0.000	0.000	0.000
104	A	107	GLY	0	-0.028	-0.012	8.446	0.403	0.403	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.785	0.888	8.746	17.127	17.127	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.027	0.008	5.410	0.285	0.285	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.018	0.005	3.109	-2.417	-1.154	0.363	-0.441	-1.185	0.002
108	A	111	GLY	0	0.069	0.043	2.425	-15.576	-12.373	1.547	-2.050	-2.701	-0.026
109	A	112	LYS	1	0.986	1.013	1.884	-14.212	-17.563	21.816	-8.334	-10.131	-0.084

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)