FMO DATABASE

FMODB ID: 6N64Z

Calculation Name: 3EUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EUD

Chain ID: A

ChEMBL ID:

UniProt ID: P40486

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-800357.58502
FMO2-HF: Nuclear repulsion	759454.81257
FMO2-HF: Total energy	-40902.77245
FMO2-MP2: Total energy	-41022.920746

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:0:LYS)

Summations of interaction energy for fragment #1(A:0: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.
-40.775	-38.354	0.116	-0.98	-1.557	-0.002

Interaction energy analysis for fragmet #1(A:0:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.966 / q_NPA : 0.963

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	2	ILE	0	0.005	0.007	3.797	0.694	2.492	-0.007	-0.804	-0.988	-0.001
4	A	3	THR	0	0.035	0.021	6.192	0.547	0.547	0.000	0.000	0.000	0.000
5	A	4	PRO	0	-0.010	-0.002	9.999	0.939	0.939	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.906	0.974	11.978	15.489	15.489	0.000	0.000	0.000	0.000
7	A	6	PHE	0	-0.010	-0.013	15.245	0.042	0.042	0.000	0.000	0.000	0.000
8	A	7	SER	0	-0.013	-0.003	17.807	0.367	0.367	0.000	0.000	0.000	0.000
9	A	8	ILE	0	-0.008	-0.003	21.243	-0.208	-0.208	0.000	0.000	0.000	0.000
10	A	9	THR	0	0.004	0.017	24.338	0.436	0.436	0.000	0.000	0.000	0.000
11	A	10	GLN	0	0.045	0.003	28.043	-0.221	-0.221	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.782	-0.869	30.811	-9.175	-9.175	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.827	-0.918	33.920	-8.512	-8.512	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.823	-0.892	33.753	-8.651	-8.651	0.000	0.000	0.000	0.000
15	A	14	PHE	0	0.008	0.007	29.728	-0.281	-0.281	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.003	-0.001	23.929	0.110	0.110	0.000	0.000	0.000	0.000
17	A	16	PHE	0	-0.037	-0.021	25.823	-0.256	-0.256	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.007	0.009	18.515	-0.058	-0.058	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.830	0.900	20.426	12.018	12.018	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.008	-0.007	14.484	-0.423	-0.423	0.000	0.000	0.000	0.000
21	A	20	PHE	0	0.005	-0.011	16.034	0.134	0.134	0.000	0.000	0.000	0.000
22	A	21	ILE	0	-0.064	-0.030	12.004	-1.299	-1.299	0.000	0.000	0.000	0.000
23	A	22	SER	0	0.035	0.000	12.128	0.897	0.897	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.069	-0.035	11.610	-0.706	-0.706	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.011	0.027	9.065	-1.042	-1.042	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.934	0.953	11.085	19.849	19.849	0.000	0.000	0.000	0.000
27	A	26	PHE	0	0.058	0.031	13.148	-0.768	-0.768	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.015	-0.020	14.291	0.345	0.345	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.012	-0.003	16.941	-0.283	-0.283	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.014	0.012	15.009	0.318	0.318	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.026	0.001	12.622	-0.959	-0.959	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.045	-0.030	11.981	-1.346	-1.346	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.916	-0.948	12.451	-22.199	-22.199	0.000	0.000	0.000	0.000
34	A	33	ILE	0	-0.008	-0.032	14.806	-0.589	-0.589	0.000	0.000	0.000	0.000
35	A	34	ILE	0	0.004	0.016	15.934	0.466	0.466	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.004	0.004	18.883	-0.522	-0.522	0.000	0.000	0.000	0.000
37	A	36	GLN	0	-0.050	-0.035	21.075	-0.204	-0.204	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.811	-0.888	23.327	-12.897	-12.897	0.000	0.000	0.000	0.000
39	A	38	ASN	0	-0.007	0.003	24.467	-0.076	-0.076	0.000	0.000	0.000	0.000
40	A	39	MET	0	-0.001	0.023	18.232	-0.990	-0.990	0.000	0.000	0.000	0.000
41	A	40	ILE	0	0.017	0.010	17.545	0.350	0.350	0.000	0.000	0.000	0.000
42	A	41	ILE	0	-0.049	-0.023	12.887	-1.069	-1.069	0.000	0.000	0.000	0.000
43	A	42	PHE	0	0.028	0.009	11.955	1.005	1.005	0.000	0.000	0.000	0.000
44	A	43	HIS	0	-0.034	-0.037	5.995	-4.032	-4.032	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.021	0.017	9.793	1.626	1.626	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.005	0.020	4.739	-1.923	-1.857	-0.001	-0.005	-0.060	0.000
47	A	46	PRO	0	0.011	-0.005	2.940	1.365	1.925	0.125	-0.158	-0.526	-0.001
48	A	47	TYR	0	-0.021	-0.026	4.551	-2.984	-2.987	-0.001	-0.013	0.017	0.000
49	A	48	TYR	0	0.006	0.007	7.341	-0.304	-0.304	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.004	-0.006	9.301	0.393	0.393	0.000	0.000	0.000	0.000
51	A	50	ARG	1	0.902	0.940	12.518	20.433	20.433	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.033	-0.010	14.443	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	52	ARG	1	0.900	0.943	18.008	14.886	14.886	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.011	0.007	21.120	0.115	0.115	0.000	0.000	0.000	0.000
55	A	54	PRO	0	-0.031	-0.006	24.674	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	55	HIS	1	0.836	0.920	27.934	10.254	10.254	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.884	-0.952	27.635	-11.145	-11.145	0.000	0.000	0.000	0.000
58	A	57	LEU	0	-0.057	-0.023	23.946	0.301	0.301	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.026	-0.016	27.780	0.080	0.080	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.863	-0.904	23.843	-12.840	-12.840	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.800	-0.881	26.908	-9.629	-9.629	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.952	-0.978	28.919	-9.148	-9.148	0.000	0.000	0.000	0.000
63	A	62	ARG	1	0.785	0.861	30.646	9.472	9.472	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.028	-0.033	25.275	0.012	0.012	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.031	-0.020	25.465	0.284	0.284	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.008	0.002	20.100	-0.372	-0.372	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.032	-0.010	22.249	0.226	0.226	0.000	0.000	0.000	0.000
68	A	67	TYR	0	-0.006	-0.007	16.962	0.052	0.052	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.842	-0.910	20.615	-10.781	-10.781	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.002	-0.009	20.878	-0.421	-0.421	0.000	0.000	0.000	0.000
71	A	70	LYS	1	0.911	0.956	22.150	9.728	9.728	0.000	0.000	0.000	0.000
72	A	71	ASP	-1	-0.809	-0.902	21.800	-11.689	-11.689	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.918	-0.931	16.579	-15.433	-15.433	0.000	0.000	0.000	0.000
74	A	73	CYS	0	-0.072	-0.014	17.319	-0.590	-0.590	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.014	0.005	15.291	0.415	0.415	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.008	-0.004	18.886	-0.089	-0.089	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.031	-0.001	18.975	0.253	0.253	0.000	0.000	0.000	0.000
78	A	77	LYS	1	0.806	0.907	22.273	10.674	10.674	0.000	0.000	0.000	0.000
79	A	78	VAL	0	0.025	0.013	22.895	0.113	0.113	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.044	0.028	26.232	0.249	0.249	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.769	0.865	28.623	9.411	9.411	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.037	-0.013	30.686	0.234	0.234	0.000	0.000	0.000	0.000
83	A	82	ASN	0	-0.050	-0.034	32.199	0.474	0.474	0.000	0.000	0.000	0.000
84	A	83	LYS	1	0.820	0.890	35.037	8.173	8.173	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.069	-0.058	36.876	0.245	0.245	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.868	-0.904	33.303	-9.363	-9.363	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.007	-0.005	33.566	-0.176	-0.176	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.010	-0.011	27.222	-0.158	-0.158	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.793	-0.906	30.427	-9.967	-9.967	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.898	-0.960	27.512	-11.129	-11.129	0.000	0.000	0.000	0.000
91	A	90	LEU	0	-0.038	-0.017	25.616	-0.541	-0.541	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.905	-0.949	25.341	-11.102	-11.102	0.000	0.000	0.000	0.000
93	A	92	LEU	0	-0.031	-0.009	25.092	-0.216	-0.216	0.000	0.000	0.000	0.000
94	A	93	PRO	0	0.046	0.010	20.123	-0.449	-0.449	0.000	0.000	0.000	0.000
95	A	94	THR	0	-0.012	-0.010	19.358	-0.496	-0.496	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.840	0.903	19.962	13.841	13.841	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.080	0.058	20.791	-0.150	-0.150	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.016	0.012	14.434	-0.552	-0.552	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.026	-0.007	15.987	0.443	0.443	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:LYS)