FMO DATABASE

FMODB ID: YZZM2

Calculation Name: 4XS5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XS5

Chain ID: A

ChEMBL ID:

UniProt ID: C6VVE1

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	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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002313.541735
FMO2-HF: Nuclear repulsion	955215.652933
FMO2-HF: Total energy	-47097.888803
FMO2-MP2: Total energy	-47234.988215

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
83.693	86.759	6.61	-4.896	-4.781	0.061

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.985

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	4	LYS	1	0.820	0.922	1.962	-106.375	-103.563	6.612	-4.846	-4.577	0.061
4	A	5	LEU	0	0.015	0.007	6.075	-4.207	-4.207	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.856	-0.911	9.451	20.706	20.706	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.787	0.873	12.417	-21.216	-21.216	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.899	0.959	15.285	-16.495	-16.495	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.922	-0.962	18.941	12.727	12.727	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.007	0.010	21.651	-0.066	-0.066	0.000	0.000	0.000	0.000
10	A	11	TYR	0	0.065	0.029	17.147	-0.257	-0.257	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.003	-0.003	12.191	0.366	0.366	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.053	-0.065	12.244	-0.947	-0.947	0.000	0.000	0.000	0.000
13	A	14	ILE	0	0.001	-0.008	7.749	1.976	1.976	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.823	-0.877	7.681	28.113	28.113	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.003	-0.024	4.540	4.786	4.777	-0.001	-0.014	0.023	0.000
16	A	17	ASP	-1	-0.831	-0.929	4.295	60.976	61.239	-0.001	-0.036	-0.227	0.000
17	A	18	ALA	0	-0.031	-0.006	5.718	-3.262	-3.262	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.034	0.018	7.161	-2.304	-2.304	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.014	-0.009	10.046	-2.284	-2.284	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.003	0.017	9.071	2.075	2.075	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.056	0.001	10.619	-2.065	-2.065	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.006	-0.003	10.519	1.981	1.981	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.898	-0.957	8.324	22.835	22.835	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.015	-0.004	5.820	1.681	1.681	0.000	0.000	0.000	0.000
25	A	26	PRO	0	-0.015	0.007	7.663	1.007	1.007	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.038	0.017	10.554	-0.681	-0.681	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.001	0.010	5.319	-0.478	-0.478	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.012	0.005	7.267	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.784	-0.881	8.183	15.716	15.716	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.887	-0.942	9.026	18.605	18.605	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.020	-0.021	6.371	0.217	0.217	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.027	0.015	8.765	-1.244	-1.244	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.868	0.916	11.923	-17.978	-17.978	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.139	-0.049	10.930	-1.103	-1.103	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.028	0.014	10.606	-0.728	-0.728	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.038	0.011	14.203	-0.692	-0.692	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.789	0.879	14.278	-18.012	-18.012	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.847	-0.900	14.400	18.663	18.663	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.033	-0.012	18.479	-0.342	-0.342	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.084	-0.037	16.021	0.087	0.087	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.084	0.050	18.917	0.833	0.833	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.005	-0.002	19.255	-0.283	-0.283	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.065	-0.031	13.141	0.873	0.873	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.017	0.020	15.067	-0.605	-0.605	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.004	0.010	10.278	1.647	1.647	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.008	-0.013	11.579	-1.915	-1.915	0.000	0.000	0.000	0.000
47	A	48	MET	0	-0.001	-0.009	10.825	1.898	1.898	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.113	0.068	12.497	-1.248	-1.248	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.115	-0.051	9.105	-2.076	-2.076	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.045	-0.006	10.239	0.092	0.092	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.820	0.891	12.612	-19.391	-19.391	0.000	0.000	0.000	0.000
52	A	53	SER	0	-0.034	-0.016	14.701	-1.033	-1.033	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.023	0.016	14.482	1.311	1.311	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.747	-0.868	15.098	17.134	17.134	0.000	0.000	0.000	0.000
55	A	56	ALA	0	-0.021	-0.013	17.376	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.012	-0.023	15.061	-0.492	-0.492	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.037	0.013	14.056	0.290	0.290	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.032	0.024	14.921	0.086	0.086	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.009	0.000	18.132	-0.394	-0.394	0.000	0.000	0.000	0.000
60	A	61	THR	0	-0.068	-0.039	12.680	-0.184	-0.184	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.003	0.000	14.635	0.007	0.007	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.870	0.931	16.713	-12.889	-12.889	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.882	0.949	17.809	-14.865	-14.865	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.017	0.001	13.651	-0.369	-0.369	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.075	0.032	17.030	0.018	0.018	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.055	-0.021	19.733	-0.533	-0.533	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.050	-0.043	18.214	-0.445	-0.445	0.000	0.000	0.000	0.000
68	A	69	CYS	0	-0.028	0.011	18.040	0.178	0.178	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.051	0.037	20.714	-0.355	-0.355	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.098	-0.041	24.012	-0.776	-0.776	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.918	-0.958	22.596	12.225	12.225	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.065	-0.034	24.763	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	74	GLY	0	0.030	0.019	22.653	-0.112	-0.112	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.015	-0.004	21.531	-0.358	-0.358	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.029	-0.028	14.968	0.829	0.829	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.005	0.008	18.032	-0.463	-0.463	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.002	-0.011	15.188	1.386	1.386	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.017	-0.010	15.725	-0.821	-0.821	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.023	-0.016	15.662	1.608	1.608	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.934	0.947	17.814	-15.170	-15.170	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.858	-0.899	18.886	14.777	14.777	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.869	-0.936	20.851	12.391	12.391	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.906	-0.953	21.915	13.520	13.520	0.000	0.000	0.000	0.000
84	A	85	PHE	0	0.023	-0.006	15.082	0.192	0.192	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.014	-0.011	20.505	0.232	0.232	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.901	-0.944	22.325	11.103	11.103	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.074	-0.029	19.489	-0.183	-0.183	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.030	-0.035	17.245	-0.096	-0.096	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.848	-0.895	21.430	10.536	10.536	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.859	-0.931	24.782	10.274	10.274	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.098	-0.044	19.808	-0.184	-0.184	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.712	0.837	24.466	-10.777	-10.777	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.052	-0.025	20.884	-0.225	-0.225	0.000	0.000	0.000	0.000
94	A	95	PRO	0	-0.021	0.001	25.037	0.123	0.123	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.869	-0.935	24.462	11.193	11.193	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.056	-0.020	18.683	0.472	0.472	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.013	0.015	21.589	-0.570	-0.570	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.027	-0.017	19.250	0.880	0.880	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.002	0.007	20.475	-0.648	-0.648	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.021	0.024	20.279	0.925	0.925	0.000	0.000	0.000	0.000
101	A	102	THR	0	-0.079	-0.076	20.045	0.623	0.623	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.876	0.930	14.386	-20.455	-20.455	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.887	-0.946	18.967	15.218	15.218	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.856	-0.930	22.231	11.989	11.989	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.012	0.000	19.558	-0.291	-0.291	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.056	-0.039	18.887	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.902	-0.944	22.182	11.554	11.554	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.020	-0.008	23.679	-0.439	-0.439	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.015	-0.004	20.264	-0.237	-0.237	0.000	0.000	0.000	0.000
110	A	111	PHE	0	-0.031	-0.026	23.719	-0.218	-0.218	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.016	-0.005	26.592	-0.498	-0.498	0.000	0.000	0.000	0.000
112	A	113	HIS	0	0.025	0.016	25.558	-0.497	-0.497	0.000	0.000	0.000	0.000
113	A	114	SER	0	-0.011	-0.008	26.819	-0.207	-0.207	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.062	-0.039	28.547	-0.355	-0.355	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.922	-0.967	30.890	8.864	8.864	0.000	0.000	0.000	0.000
116	A	117	ASN	0	-0.079	-0.025	28.280	-0.392	-0.392	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-1.009	-0.994	32.612	8.562	8.562	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.109	-0.061	35.282	-0.361	-0.361	0.000	0.000	0.000	0.000
119	A	121	GLY	0	-0.034	0.009	35.935	-0.266	-0.266	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)