FMO DATABASE

FMODB ID: 76G6K

Calculation Name: 5X5L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X5L

Chain ID: A

ChEMBL ID:

UniProt ID: E1A0Z5

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-806440.511951
FMO2-HF: Nuclear repulsion	764867.910279
FMO2-HF: Total energy	-41572.601672
FMO2-MP2: Total energy	-41692.443192

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:141:LYS)

Summations of interaction energy for fragment #1(A:141: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.
-225.44	-225.487	39.936	-18.869	-21.017	-0.202

Interaction energy analysis for fragmet #1(A:141:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.898

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	143	TYR	0	-0.021	-0.055	3.823	-0.510	1.082	-0.022	-0.727	-0.842	0.002
4	A	144	LYS	1	0.874	0.925	6.731	20.993	20.993	0.000	0.000	0.000	0.000
5	A	145	ASN	0	0.039	0.003	10.116	-0.373	-0.373	0.000	0.000	0.000	0.000
6	A	146	ILE	0	0.027	0.025	6.423	0.941	0.941	0.000	0.000	0.000	0.000
7	A	147	GLU	-1	-0.824	-0.891	3.882	-27.559	-27.246	0.000	-0.053	-0.260	0.000
8	A	148	ILE	0	-0.027	-0.013	2.798	2.156	4.063	0.255	-0.469	-1.692	0.000
9	A	149	ASP	-1	-0.864	-0.929	2.367	-42.516	-39.721	2.100	-2.287	-2.608	-0.032
10	A	150	THR	0	-0.048	-0.073	3.066	-2.247	-1.554	0.068	-0.154	-0.607	-0.001
11	A	151	ASP	-1	-0.933	-0.924	5.820	-30.395	-30.395	0.000	0.000	0.000	0.000
12	A	152	THR	0	0.012	-0.004	8.610	1.742	1.742	0.000	0.000	0.000	0.000
13	A	153	HIS	0	-0.050	-0.021	8.534	1.801	1.801	0.000	0.000	0.000	0.000
14	A	154	SER	0	-0.015	0.014	8.409	2.184	2.184	0.000	0.000	0.000	0.000
15	A	155	VAL	0	-0.011	-0.017	6.962	-3.751	-3.751	0.000	0.000	0.000	0.000
16	A	156	TYR	0	0.003	-0.017	6.964	3.832	3.832	0.000	0.000	0.000	0.000
17	A	157	ILE	0	-0.001	0.001	8.991	-1.742	-1.742	0.000	0.000	0.000	0.000
18	A	158	HIS	0	-0.003	0.003	7.628	2.414	2.414	0.000	0.000	0.000	0.000
19	A	159	SER	0	-0.019	-0.029	12.549	1.449	1.449	0.000	0.000	0.000	0.000
20	A	160	GLU	-1	-0.858	-0.913	14.472	-16.869	-16.869	0.000	0.000	0.000	0.000
21	A	161	ASN	0	-0.075	-0.026	15.779	0.857	0.857	0.000	0.000	0.000	0.000
22	A	162	LYS	1	0.874	0.922	15.577	14.573	14.573	0.000	0.000	0.000	0.000
23	A	163	LYS	1	0.843	0.926	7.606	21.142	21.142	0.000	0.000	0.000	0.000
24	A	164	ILE	0	-0.017	-0.009	12.918	0.663	0.663	0.000	0.000	0.000	0.000
25	A	165	LEU	0	-0.003	0.006	11.384	-1.378	-1.378	0.000	0.000	0.000	0.000
26	A	166	LEU	0	0.003	0.000	11.645	1.146	1.146	0.000	0.000	0.000	0.000
27	A	167	ASN	0	-0.002	0.009	13.877	-1.141	-1.141	0.000	0.000	0.000	0.000
28	A	168	LEU	0	-0.005	0.000	9.831	0.547	0.547	0.000	0.000	0.000	0.000
29	A	169	THR	0	-0.017	-0.026	13.880	0.718	0.718	0.000	0.000	0.000	0.000
30	A	170	LEU	0	0.058	0.024	11.467	-1.810	-1.810	0.000	0.000	0.000	0.000
31	A	171	THR	0	0.030	0.004	11.471	-2.274	-2.274	0.000	0.000	0.000	0.000
32	A	172	GLU	-1	-0.788	-0.868	11.148	-21.700	-21.700	0.000	0.000	0.000	0.000
33	A	173	TYR	0	0.037	0.022	5.972	-3.796	-3.796	0.000	0.000	0.000	0.000
34	A	174	LYS	1	0.881	0.950	7.075	21.329	21.329	0.000	0.000	0.000	0.000
35	A	175	ILE	0	0.001	-0.006	6.396	-4.717	-4.717	0.000	0.000	0.000	0.000
36	A	176	ILE	0	0.005	0.000	6.219	-2.682	-2.682	0.000	0.000	0.000	0.000
37	A	177	SER	0	0.013	-0.001	2.900	-14.858	-13.237	0.191	-0.794	-1.017	-0.005
38	A	178	PHE	0	0.006	0.016	1.806	-35.000	-37.629	9.705	-3.837	-3.240	-0.044
39	A	179	MET	0	-0.051	-0.036	4.244	0.580	0.698	-0.001	-0.004	-0.113	0.000
40	A	180	ILE	0	-0.039	-0.015	2.089	4.837	1.823	7.066	-1.132	-2.919	-0.002
41	A	181	ASP	-1	-0.814	-0.885	1.811	-140.614	-144.212	20.569	-9.370	-7.601	-0.120
42	A	182	GLN	0	-0.049	-0.028	3.838	9.649	9.804	0.005	-0.042	-0.118	0.000
43	A	183	PRO	0	0.047	0.029	6.494	3.098	3.098	0.000	0.000	0.000	0.000
44	A	184	HIS	0	-0.003	-0.018	8.573	1.397	1.397	0.000	0.000	0.000	0.000
45	A	185	LYS	1	0.744	0.886	10.455	28.085	28.085	0.000	0.000	0.000	0.000
46	A	186	VAL	0	-0.039	-0.032	12.340	-0.514	-0.514	0.000	0.000	0.000	0.000
47	A	187	PHE	0	0.029	0.016	7.610	1.072	1.072	0.000	0.000	0.000	0.000
48	A	188	THR	0	0.011	-0.018	13.108	1.269	1.269	0.000	0.000	0.000	0.000
49	A	189	ARG	1	0.845	0.892	14.675	14.544	14.544	0.000	0.000	0.000	0.000
50	A	190	GLY	0	0.092	0.046	16.183	-0.502	-0.502	0.000	0.000	0.000	0.000
51	A	191	GLU	-1	-0.774	-0.841	12.104	-23.601	-23.601	0.000	0.000	0.000	0.000
52	A	192	LEU	0	0.027	-0.005	10.227	-1.548	-1.548	0.000	0.000	0.000	0.000
53	A	193	MET	0	-0.033	-0.009	12.404	-0.808	-0.808	0.000	0.000	0.000	0.000
54	A	194	ASN	0	0.028	0.007	14.527	0.162	0.162	0.000	0.000	0.000	0.000
55	A	195	HIS	0	-0.010	0.008	8.955	-0.531	-0.531	0.000	0.000	0.000	0.000
56	A	196	CYS	0	-0.066	-0.030	9.197	-3.191	-3.191	0.000	0.000	0.000	0.000
57	A	197	MET	0	-0.140	-0.069	11.124	0.539	0.539	0.000	0.000	0.000	0.000
58	A	198	ASN	0	-0.129	0.171	14.897	0.582	0.582	0.000	0.000	0.000	0.000
59	A	199	ASP	-1	-0.645	-1.026	17.689	-17.452	-17.452	0.000	0.000	0.000	0.000
60	A	200	SER	0	-0.074	-0.048	17.928	0.059	0.059	0.000	0.000	0.000	0.000
61	A	201	ASP	-1	-0.889	-0.955	19.180	-14.190	-14.190	0.000	0.000	0.000	0.000
62	A	202	ALA	0	-0.071	-0.024	20.939	0.642	0.642	0.000	0.000	0.000	0.000
63	A	203	LEU	0	0.010	-0.011	22.716	0.002	0.002	0.000	0.000	0.000	0.000
64	A	204	GLU	-1	-0.815	-0.935	20.412	-15.777	-15.777	0.000	0.000	0.000	0.000
65	A	205	ARG	1	0.856	0.910	20.408	12.494	12.494	0.000	0.000	0.000	0.000
66	A	206	THR	0	0.032	0.016	19.844	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	207	VAL	0	0.073	0.049	15.147	-0.518	-0.518	0.000	0.000	0.000	0.000
68	A	208	ASP	-1	-0.742	-0.814	16.925	-16.064	-16.064	0.000	0.000	0.000	0.000
69	A	209	SER	0	-0.096	-0.046	18.844	-0.156	-0.156	0.000	0.000	0.000	0.000
70	A	210	HIS	0	0.006	-0.007	15.020	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	211	VAL	0	0.034	0.025	13.498	-0.756	-0.756	0.000	0.000	0.000	0.000
72	A	212	SER	0	-0.051	-0.026	15.545	-0.122	-0.122	0.000	0.000	0.000	0.000
73	A	213	LYS	1	0.965	0.976	17.748	15.170	15.170	0.000	0.000	0.000	0.000
74	A	214	LEU	0	0.019	0.024	10.280	0.252	0.252	0.000	0.000	0.000	0.000
75	A	215	ARG	1	0.884	0.940	14.640	17.271	17.271	0.000	0.000	0.000	0.000
76	A	216	LYS	1	0.887	0.951	16.062	14.157	14.157	0.000	0.000	0.000	0.000
77	A	217	LYS	1	0.857	0.901	15.367	18.860	18.860	0.000	0.000	0.000	0.000
78	A	218	LEU	0	-0.007	-0.002	11.111	-0.173	-0.173	0.000	0.000	0.000	0.000
79	A	219	GLU	-1	-0.904	-0.964	15.276	-14.593	-14.593	0.000	0.000	0.000	0.000
80	A	220	GLU	-1	-1.013	-0.998	18.799	-14.468	-14.468	0.000	0.000	0.000	0.000
81	A	221	GLN	0	-0.015	-0.006	15.798	0.664	0.664	0.000	0.000	0.000	0.000
82	A	222	GLY	0	-0.023	-0.012	17.252	-0.243	-0.243	0.000	0.000	0.000	0.000
83	A	223	ILE	0	-0.038	-0.011	12.667	-0.114	-0.114	0.000	0.000	0.000	0.000
84	A	224	PHE	0	0.051	0.014	16.530	-0.212	-0.212	0.000	0.000	0.000	0.000
85	A	225	GLN	0	-0.103	-0.069	17.399	-0.481	-0.481	0.000	0.000	0.000	0.000
86	A	226	MET	0	0.107	0.082	11.230	-0.975	-0.975	0.000	0.000	0.000	0.000
87	A	227	LEU	0	-0.034	-0.028	10.919	1.045	1.045	0.000	0.000	0.000	0.000
88	A	228	ILE	0	0.015	0.039	14.370	1.393	1.393	0.000	0.000	0.000	0.000
89	A	229	ASN	0	0.013	-0.011	16.828	-0.821	-0.821	0.000	0.000	0.000	0.000
90	A	230	VAL	0	-0.023	-0.005	17.931	0.592	0.592	0.000	0.000	0.000	0.000
91	A	231	ARG	1	0.984	0.966	20.312	11.245	11.245	0.000	0.000	0.000	0.000
92	A	232	GLY	0	-0.008	-0.005	23.436	0.250	0.250	0.000	0.000	0.000	0.000
93	A	233	VAL	0	0.002	0.021	18.575	0.114	0.114	0.000	0.000	0.000	0.000
94	A	234	GLY	0	-0.003	-0.020	17.105	-0.386	-0.386	0.000	0.000	0.000	0.000
95	A	235	TYR	0	-0.078	-0.061	14.114	1.141	1.141	0.000	0.000	0.000	0.000
96	A	236	ARG	1	0.984	1.014	12.995	16.885	16.885	0.000	0.000	0.000	0.000
97	A	237	LEU	0	-0.012	0.011	8.117	1.555	1.555	0.000	0.000	0.000	0.000
98	A	238	ASP	-1	-0.737	-0.848	11.366	-19.883	-19.883	0.000	0.000	0.000	0.000
99	A	239	ASN	0	-0.073	-0.037	13.402	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	240	PRO	0	0.053	0.035	15.917	0.559	0.559	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:141:LYS)