FMO DATABASE

FMODB ID: LZ2K9

Calculation Name: 3O6U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O6U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XI95

Base Structure: X-ray

Registration Date: 2023-09-20

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-989639.67703
FMO2-HF: Nuclear repulsion	942301.144968
FMO2-HF: Total energy	-47338.532063
FMO2-MP2: Total energy	-47476.495378

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:28:MET)

Summations of interaction energy for fragment #1(A:28:MET)

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.
-6.326	-4.655	3.605	-1.551	-3.723	0.009

Interaction energy analysis for fragmet #1(A:28:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.040

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	30	LYS	1	0.925	0.971	2.698	-4.326	-3.423	3.605	-1.441	-3.066	0.009
4	A	31	ASP	-1	-0.749	-0.828	4.589	-0.223	-0.130	-0.001	-0.013	-0.079	0.000
5	A	32	GLY	0	-0.023	-0.006	7.857	0.141	0.141	0.000	0.000	0.000	0.000
6	A	33	ASP	-1	-0.888	-0.925	11.076	-0.141	-0.141	0.000	0.000	0.000	0.000
7	A	34	TYR	0	-0.036	-0.037	7.824	0.044	0.044	0.000	0.000	0.000	0.000
8	A	35	THR	0	-0.036	-0.040	14.070	0.025	0.025	0.000	0.000	0.000	0.000
9	A	36	VAL	0	-0.045	-0.012	16.466	0.000	0.000	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.905	-0.967	18.492	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	38	THR	0	0.019	0.031	22.058	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	39	ALA	0	-0.024	-0.031	24.198	0.008	0.008	0.000	0.000	0.000	0.000
13	A	40	LYS	1	0.865	0.930	26.031	0.058	0.058	0.000	0.000	0.000	0.000
14	A	41	ALA	0	0.000	0.003	28.885	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	42	ASP	-1	-0.791	-0.892	30.126	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	43	ASP	-1	-0.940	-0.983	31.796	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	44	HIS	0	-0.091	-0.048	34.475	0.003	0.003	0.000	0.000	0.000	0.000
18	A	45	GLY	0	-0.017	0.004	34.834	0.002	0.002	0.000	0.000	0.000	0.000
19	A	46	TYR	0	-0.050	-0.038	30.758	0.001	0.001	0.000	0.000	0.000	0.000
20	A	47	LYS	1	0.955	0.999	27.296	0.041	0.041	0.000	0.000	0.000	0.000
21	A	48	ALA	0	0.004	-0.006	24.317	0.003	0.003	0.000	0.000	0.000	0.000
22	A	49	LYS	1	0.943	0.977	22.103	0.053	0.053	0.000	0.000	0.000	0.000
23	A	50	LEU	0	0.015	0.015	15.834	0.009	0.009	0.000	0.000	0.000	0.000
24	A	51	SER	0	-0.012	-0.006	17.535	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	52	ILE	0	-0.008	0.009	11.122	0.022	0.022	0.000	0.000	0.000	0.000
26	A	53	LYS	1	0.898	0.939	13.449	0.073	0.073	0.000	0.000	0.000	0.000
27	A	54	VAL	0	-0.015	-0.002	6.957	0.057	0.057	0.000	0.000	0.000	0.000
28	A	55	SER	0	-0.003	-0.014	10.101	0.000	0.000	0.000	0.000	0.000	0.000
29	A	56	ASP	-1	-1.000	-1.007	8.444	0.067	0.067	0.000	0.000	0.000	0.000
30	A	57	GLY	0	-0.039	-0.024	4.858	0.079	0.079	0.000	0.000	0.000	0.000
31	A	58	LYS	1	0.899	0.948	5.566	0.402	0.402	0.000	0.000	0.000	0.000
32	A	59	ILE	0	-0.004	0.001	8.484	-0.151	-0.151	0.000	0.000	0.000	0.000
33	A	60	THR	0	-0.023	-0.019	11.074	0.071	0.071	0.000	0.000	0.000	0.000
34	A	61	GLU	-1	-0.935	-0.970	13.911	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	62	ALA	0	0.006	-0.003	15.532	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	63	LYS	1	0.866	0.946	17.718	0.060	0.060	0.000	0.000	0.000	0.000
37	A	64	TYR	0	-0.027	-0.033	20.731	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	65	ASN	0	-0.027	-0.017	22.323	0.007	0.007	0.000	0.000	0.000	0.000
39	A	66	GLU	-1	-0.694	-0.799	25.737	-0.051	-0.051	0.000	0.000	0.000	0.000
40	A	67	PHE	0	-0.034	-0.035	26.106	0.004	0.004	0.000	0.000	0.000	0.000
41	A	68	ASN	0	0.029	0.046	30.650	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	69	GLY	0	0.007	0.005	31.565	0.001	0.001	0.000	0.000	0.000	0.000
43	A	70	GLU	-1	-0.930	-0.961	32.597	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	71	THR	0	-0.057	-0.047	35.813	0.002	0.002	0.000	0.000	0.000	0.000
45	A	72	ASN	0	-0.027	-0.022	30.285	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	73	ALA	0	0.009	0.017	32.796	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	74	MET	0	0.005	0.001	29.104	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	75	LYS	1	0.954	0.980	30.525	0.040	0.040	0.000	0.000	0.000	0.000
49	A	76	ARG	1	0.805	0.911	25.337	0.036	0.036	0.000	0.000	0.000	0.000
50	A	77	GLU	-1	-0.972	-0.982	32.213	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	78	ASP	-1	-0.872	-0.911	35.065	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	79	LYS	1	0.901	0.952	37.435	0.011	0.011	0.000	0.000	0.000	0.000
53	A	80	ASP	-1	-0.850	-0.919	39.880	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	81	TYR	0	-0.053	-0.038	34.276	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	82	ASN	0	-0.040	-0.064	34.599	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	83	GLU	-1	-0.825	-0.891	37.336	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	84	LYS	1	0.872	0.965	36.964	0.024	0.024	0.000	0.000	0.000	0.000
58	A	85	MET	0	-0.027	-0.024	33.032	0.000	0.000	0.000	0.000	0.000	0.000
59	A	86	THR	0	0.039	-0.004	37.078	0.000	0.000	0.000	0.000	0.000	0.000
60	A	87	GLY	0	-0.024	0.006	37.990	0.000	0.000	0.000	0.000	0.000	0.000
61	A	88	VAL	0	-0.115	-0.048	37.916	0.000	0.000	0.000	0.000	0.000	0.000
62	A	89	SER	0	-0.069	-0.042	34.294	0.001	0.001	0.000	0.000	0.000	0.000
63	A	90	GLY	0	0.056	0.009	36.489	0.000	0.000	0.000	0.000	0.000	0.000
64	A	91	ILE	0	-0.078	-0.023	30.109	0.000	0.000	0.000	0.000	0.000	0.000
65	A	92	GLY	0	0.031	0.021	33.237	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	93	PRO	0	-0.015	-0.005	29.736	0.000	0.000	0.000	0.000	0.000	0.000
67	A	94	ALA	0	0.000	0.000	29.376	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	95	GLU	-1	-0.887	-0.947	30.574	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	96	TYR	0	-0.022	-0.058	26.703	0.001	0.001	0.000	0.000	0.000	0.000
70	A	97	GLU	-1	-0.812	-0.917	25.070	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	98	PRO	0	0.013	0.008	23.885	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	99	GLN	0	-0.067	-0.031	23.707	0.004	0.004	0.000	0.000	0.000	0.000
73	A	100	LEU	0	0.007	0.005	21.241	0.004	0.004	0.000	0.000	0.000	0.000
74	A	101	GLU	-1	-0.817	-0.906	19.473	-0.044	-0.044	0.000	0.000	0.000	0.000
75	A	102	LYS	1	0.919	0.948	18.568	0.015	0.015	0.000	0.000	0.000	0.000
76	A	103	ALA	0	0.024	0.020	18.652	0.012	0.012	0.000	0.000	0.000	0.000
77	A	104	LEU	0	-0.006	0.006	13.255	0.012	0.012	0.000	0.000	0.000	0.000
78	A	105	ILE	0	-0.024	-0.013	14.243	0.027	0.027	0.000	0.000	0.000	0.000
79	A	106	GLU	-1	-0.987	-0.974	14.613	0.101	0.101	0.000	0.000	0.000	0.000
80	A	107	LYS	1	0.916	0.957	14.426	0.000	0.000	0.000	0.000	0.000	0.000
81	A	108	GLN	0	-0.094	-0.048	9.496	0.103	0.103	0.000	0.000	0.000	0.000
82	A	109	SER	0	0.009	0.000	9.435	0.071	0.071	0.000	0.000	0.000	0.000
83	A	110	SER	0	0.011	-0.006	11.251	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	111	ASP	-1	-0.957	-0.970	13.554	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	112	ILE	0	-0.014	0.009	15.589	0.022	0.022	0.000	0.000	0.000	0.000
86	A	113	ASP	-1	-0.901	-0.960	18.367	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	114	VAL	0	-0.071	-0.043	22.063	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	115	ILE	0	0.039	0.012	24.392	0.005	0.005	0.000	0.000	0.000	0.000
89	A	116	THR	0	-0.009	-0.023	26.996	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	117	GLY	0	0.047	0.031	30.515	0.001	0.001	0.000	0.000	0.000	0.000
91	A	118	ALA	0	0.032	0.021	28.817	0.000	0.000	0.000	0.000	0.000	0.000
92	A	119	THR	0	0.018	0.015	27.401	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	120	SER	0	0.004	0.002	26.615	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	121	SER	0	0.052	-0.002	26.116	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	122	SER	0	-0.013	0.010	23.268	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	123	ASN	0	0.015	-0.001	21.792	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	124	GLN	0	-0.033	-0.011	21.663	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	125	PHE	0	0.005	-0.015	17.773	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	126	LYS	1	0.896	0.943	17.656	0.051	0.051	0.000	0.000	0.000	0.000
100	A	127	LYS	1	1.010	1.008	16.634	0.073	0.073	0.000	0.000	0.000	0.000
101	A	128	LEU	0	-0.004	0.002	16.707	-0.026	-0.026	0.000	0.000	0.000	0.000
102	A	129	ALA	0	0.039	0.012	14.066	-0.035	-0.035	0.000	0.000	0.000	0.000
103	A	130	GLU	-1	-0.951	-0.979	12.364	-0.231	-0.231	0.000	0.000	0.000	0.000
104	A	131	LYN	0	0.003	0.002	11.767	-0.099	-0.099	0.000	0.000	0.000	0.000
105	A	132	VAL	0	-0.024	-0.016	12.397	-0.051	-0.051	0.000	0.000	0.000	0.000
106	A	133	LEU	0	0.022	0.000	8.345	-0.092	-0.092	0.000	0.000	0.000	0.000
107	A	134	LYS	1	0.931	0.975	7.507	0.035	0.035	0.000	0.000	0.000	0.000
108	A	135	ASN	0	-0.001	-0.005	8.481	-0.165	-0.165	0.000	0.000	0.000	0.000
109	A	136	ALA	0	0.054	0.030	7.469	0.101	0.101	0.000	0.000	0.000	0.000
110	A	137	GLU	-1	-0.982	-0.979	3.508	-3.206	-2.724	0.002	-0.087	-0.397	0.000
111	A	138	GLU	-1	-1.023	-1.019	4.856	0.435	0.628	-0.001	-0.010	-0.181	0.000
112	A	139	GLY	0	-0.058	-0.020	7.365	0.480	0.480	0.000	0.000	0.000	0.000
113	A	140	LYS	1	0.872	0.951	8.007	0.315	0.315	0.000	0.000	0.000	0.000
114	A	141	THR	0	-0.001	-0.010	11.721	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	142	GLU	-1	-0.946	-0.967	13.864	0.001	0.001	0.000	0.000	0.000	0.000
116	A	143	ALA	0	0.023	0.013	16.337	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	144	THR	0	-0.044	-0.031	16.755	0.006	0.006	0.000	0.000	0.000	0.000
118	A	145	LEU	0	0.012	-0.001	19.276	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	146	VAL	0	0.001	-0.010	18.173	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	147	ASP	-1	-0.949	-0.982	21.100	-0.057	-0.057	0.000	0.000	0.000	0.000
121	A	148	LEU	0	-0.046	-0.022	21.711	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	149	GLU	-1	-0.953	-0.961	24.950	-0.053	-0.053	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:28:MET)