FMO DATABASE

FMODB ID: 6Y31Z

Calculation Name: 4ID3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ID3

Chain ID: A

ChEMBL ID:

UniProt ID: P12689

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	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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-641774.806917
FMO2-HF: Nuclear repulsion	607065.221675
FMO2-HF: Total energy	-34709.585242
FMO2-MP2: Total energy	-34812.811166

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:164:LYS)

Summations of interaction energy for fragment #1(A:164: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.
70.907	67.376	21.974	-4.811	-13.633	-0.106

Interaction energy analysis for fragmet #1(A:164:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.962

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	166	PHE	0	0.012	0.008	3.832	2.288	3.991	-0.013	-0.762	-0.928	0.001
4	A	167	LYS	1	0.900	0.966	3.343	38.626	39.547	0.022	-0.269	-0.674	0.001
5	A	168	ASN	0	-0.013	-0.021	4.798	2.573	2.660	-0.001	-0.008	-0.077	0.000
6	A	169	CYS	0	-0.037	0.010	7.711	3.898	3.898	0.000	0.000	0.000	0.000
7	A	170	VAL	0	-0.012	-0.024	9.050	-2.933	-2.933	0.000	0.000	0.000	0.000
8	A	171	ILE	0	0.003	0.010	10.459	2.185	2.185	0.000	0.000	0.000	0.000
9	A	172	TYR	0	0.025	0.018	13.737	-0.324	-0.324	0.000	0.000	0.000	0.000
10	A	173	ILE	0	0.016	0.005	14.195	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	174	ASN	0	0.022	0.021	18.275	0.690	0.690	0.000	0.000	0.000	0.000
12	A	175	GLY	0	0.018	0.009	22.103	0.211	0.211	0.000	0.000	0.000	0.000
13	A	176	TYR	0	0.055	0.027	22.198	-0.632	-0.632	0.000	0.000	0.000	0.000
14	A	177	THR	0	-0.027	-0.021	19.071	0.080	0.080	0.000	0.000	0.000	0.000
15	A	178	LYS	1	0.932	0.968	20.822	12.697	12.697	0.000	0.000	0.000	0.000
16	A	179	PRO	0	0.122	0.057	15.685	0.205	0.205	0.000	0.000	0.000	0.000
17	A	180	GLY	0	0.054	0.052	18.480	0.179	0.179	0.000	0.000	0.000	0.000
18	A	181	ARG	1	0.876	0.910	16.629	14.646	14.646	0.000	0.000	0.000	0.000
19	A	182	LEU	0	0.001	0.016	14.088	-1.065	-1.065	0.000	0.000	0.000	0.000
20	A	183	GLN	0	0.132	0.065	13.162	-0.828	-0.828	0.000	0.000	0.000	0.000
21	A	184	LEU	0	-0.017	-0.010	12.179	-2.039	-2.039	0.000	0.000	0.000	0.000
22	A	185	HIS	1	0.828	0.914	10.868	20.055	20.055	0.000	0.000	0.000	0.000
23	A	186	GLU	-1	-0.851	-0.929	8.832	-27.356	-27.356	0.000	0.000	0.000	0.000
24	A	187	MET	0	-0.014	-0.007	7.312	-4.798	-4.798	0.000	0.000	0.000	0.000
25	A	188	ILE	0	0.011	0.016	6.860	-4.403	-4.403	0.000	0.000	0.000	0.000
26	A	189	VAL	0	0.003	0.003	4.567	-6.135	-6.028	-0.001	-0.022	-0.084	0.000
27	A	190	LEU	0	0.011	0.023	2.441	-31.554	-28.678	0.685	-1.756	-1.806	-0.023
28	A	191	HIS	0	-0.019	-0.030	1.969	-39.171	-36.248	6.738	-4.786	-4.875	-0.060
29	A	192	GLY	0	-0.041	-0.047	1.954	-0.977	-4.003	14.483	-6.908	-4.550	-0.016
30	A	193	GLY	0	0.031	0.039	2.453	17.450	8.328	0.061	9.700	-0.639	-0.009
31	A	194	LYS	1	0.920	0.946	5.777	32.307	32.307	0.000	0.000	0.000	0.000
32	A	195	PHE	0	0.029	0.017	8.592	1.793	1.793	0.000	0.000	0.000	0.000
33	A	196	LEU	0	-0.008	-0.002	11.654	0.371	0.371	0.000	0.000	0.000	0.000
34	A	197	HIS	0	0.042	0.004	15.228	0.152	0.152	0.000	0.000	0.000	0.000
35	A	198	TYR	0	0.017	0.007	17.940	0.839	0.839	0.000	0.000	0.000	0.000
36	A	199	LEU	0	-0.018	0.001	19.525	-0.793	-0.793	0.000	0.000	0.000	0.000
37	A	200	SER	0	0.035	0.015	19.220	0.593	0.593	0.000	0.000	0.000	0.000
38	A	201	SER	0	0.041	0.011	20.947	0.666	0.666	0.000	0.000	0.000	0.000
39	A	202	LYS	1	0.887	0.946	20.253	11.667	11.667	0.000	0.000	0.000	0.000
40	A	203	LYS	1	0.965	1.006	19.979	13.244	13.244	0.000	0.000	0.000	0.000
41	A	204	THR	0	0.004	-0.005	16.021	-0.150	-0.150	0.000	0.000	0.000	0.000
42	A	205	VAL	0	-0.057	-0.016	15.388	-1.257	-1.257	0.000	0.000	0.000	0.000
43	A	206	THR	0	0.015	0.001	12.720	0.405	0.405	0.000	0.000	0.000	0.000
44	A	207	HIS	0	0.021	0.022	12.616	0.473	0.473	0.000	0.000	0.000	0.000
45	A	208	ILE	0	-0.029	-0.006	16.309	-0.503	-0.503	0.000	0.000	0.000	0.000
46	A	209	VAL	0	-0.003	0.013	15.018	0.173	0.173	0.000	0.000	0.000	0.000
47	A	210	ALA	0	0.008	-0.009	18.342	0.285	0.285	0.000	0.000	0.000	0.000
48	A	211	SER	0	0.019	-0.018	21.714	-0.159	-0.159	0.000	0.000	0.000	0.000
49	A	212	ASN	0	-0.023	-0.013	23.620	0.087	0.087	0.000	0.000	0.000	0.000
50	A	213	LEU	0	0.007	-0.001	24.667	-0.285	-0.285	0.000	0.000	0.000	0.000
51	A	214	PRO	0	0.050	0.033	28.273	0.317	0.317	0.000	0.000	0.000	0.000
52	A	215	LEU	0	0.074	0.025	31.344	-0.269	-0.269	0.000	0.000	0.000	0.000
53	A	216	LYS	1	0.945	0.959	31.347	9.853	9.853	0.000	0.000	0.000	0.000
54	A	217	LYS	1	0.816	0.898	27.071	11.355	11.355	0.000	0.000	0.000	0.000
55	A	218	ARG	1	0.903	0.955	28.111	9.876	9.876	0.000	0.000	0.000	0.000
56	A	219	ILE	0	0.026	0.027	29.693	-0.091	-0.091	0.000	0.000	0.000	0.000
57	A	220	GLU	-1	-0.805	-0.889	27.518	-11.355	-11.355	0.000	0.000	0.000	0.000
58	A	221	PHE	0	-0.018	-0.022	24.213	-0.433	-0.433	0.000	0.000	0.000	0.000
59	A	222	ALA	0	0.077	0.047	25.285	-0.351	-0.351	0.000	0.000	0.000	0.000
60	A	223	ASN	0	0.001	-0.016	25.219	-0.267	-0.267	0.000	0.000	0.000	0.000
61	A	224	TYR	0	0.032	0.014	20.448	-0.527	-0.527	0.000	0.000	0.000	0.000
62	A	225	LYS	1	0.867	0.946	16.423	17.113	17.113	0.000	0.000	0.000	0.000
63	A	226	VAL	0	-0.004	-0.006	18.830	-0.806	-0.806	0.000	0.000	0.000	0.000
64	A	227	VAL	0	0.006	0.006	15.760	0.555	0.555	0.000	0.000	0.000	0.000
65	A	228	SER	0	0.017	-0.026	19.183	-0.263	-0.263	0.000	0.000	0.000	0.000
66	A	229	PRO	0	-0.039	-0.048	16.495	-0.821	-0.821	0.000	0.000	0.000	0.000
67	A	230	ASP	-1	-0.802	-0.872	15.148	-16.003	-16.003	0.000	0.000	0.000	0.000
68	A	231	TRP	0	-0.001	0.013	11.481	-1.129	-1.129	0.000	0.000	0.000	0.000
69	A	232	ILE	0	-0.050	-0.022	9.871	-1.153	-1.153	0.000	0.000	0.000	0.000
70	A	233	VAL	0	0.002	-0.012	10.473	-1.482	-1.482	0.000	0.000	0.000	0.000
71	A	234	ASP	-1	-0.787	-0.865	12.225	-16.821	-16.821	0.000	0.000	0.000	0.000
72	A	235	SER	0	-0.031	-0.026	8.771	-0.134	-0.134	0.000	0.000	0.000	0.000
73	A	236	VAL	0	-0.052	-0.032	6.818	-1.203	-1.203	0.000	0.000	0.000	0.000
74	A	237	LYS	1	0.903	0.951	8.515	17.269	17.269	0.000	0.000	0.000	0.000
75	A	238	GLU	-1	-0.816	-0.895	11.252	-16.250	-16.250	0.000	0.000	0.000	0.000
76	A	239	ALA	0	-0.045	-0.009	7.065	0.102	0.102	0.000	0.000	0.000	0.000
77	A	240	ARG	1	0.849	0.906	6.864	17.802	17.802	0.000	0.000	0.000	0.000
78	A	241	LEU	0	-0.037	-0.023	7.511	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	242	LEU	0	0.048	0.039	9.050	1.194	1.194	0.000	0.000	0.000	0.000
80	A	243	PRO	0	0.022	0.007	12.694	-0.568	-0.568	0.000	0.000	0.000	0.000
81	A	244	TRP	0	0.021	0.009	14.850	0.477	0.477	0.000	0.000	0.000	0.000
82	A	245	GLN	0	0.035	-0.003	16.182	-0.127	-0.127	0.000	0.000	0.000	0.000
83	A	246	ASN	0	0.011	0.008	18.103	0.806	0.806	0.000	0.000	0.000	0.000
84	A	247	TYR	0	-0.014	-0.036	15.795	0.059	0.059	0.000	0.000	0.000	0.000
85	A	248	SER	0	-0.010	-0.005	19.619	-0.216	-0.216	0.000	0.000	0.000	0.000
86	A	249	LEU	0	0.000	0.017	21.695	0.525	0.525	0.000	0.000	0.000	0.000
87	A	250	THR	0	-0.044	-0.010	24.327	0.439	0.439	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:164:LYS)