FMO DATABASE

FMODB ID: QVKZY

Calculation Name: 4D53-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D53

Chain ID: A

ChEMBL ID:

UniProt ID: O51632

Base Structure: X-ray

Registration Date: 2023-09-22

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1258546.151352
FMO2-HF: Nuclear repulsion	1205184.258136
FMO2-HF: Total energy	-53361.893217
FMO2-MP2: Total energy	-53519.39012

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-29.555	-31.115	37.303	-12.127	-23.617	-0.062

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : 0.012

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	6	HIS	0	0.001	-0.003	2.315	-3.503	-1.010	2.510	-2.393	-2.610	-0.016
4	A	7	LYS	1	0.902	0.924	2.337	-16.414	-24.356	15.574	-3.765	-3.867	0.018
5	A	8	ILE	0	-0.022	0.001	5.663	-0.650	-0.650	0.000	0.000	0.000	0.000
6	A	9	ASP	-1	-0.888	-0.948	9.273	0.888	0.888	0.000	0.000	0.000	0.000
7	A	10	THR	0	-0.025	-0.034	10.633	-0.124	-0.124	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.964	0.983	13.407	-0.390	-0.390	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.801	-0.879	16.230	0.143	0.143	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.790	-0.900	14.088	0.192	0.192	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.035	0.009	14.277	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.812	0.895	17.005	-0.197	-0.197	0.000	0.000	0.000	0.000
13	A	16	ILE	0	-0.006	-0.003	19.880	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.015	0.005	16.189	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	18	TYR	0	-0.038	-0.077	17.858	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	19	SER	0	0.006	0.009	21.857	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.955	-0.978	21.822	0.093	0.093	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.005	-0.009	19.680	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.006	0.008	24.180	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.775	-0.853	26.990	0.080	0.080	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.005	-0.006	25.558	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.814	0.883	26.095	-0.171	-0.171	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.852	0.914	29.764	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.816	0.882	32.181	-0.080	-0.080	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.026	0.000	30.337	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	29	ASN	0	-0.071	-0.029	34.146	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.004	0.019	30.062	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.051	-0.031	29.634	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	32	HIS	0	0.049	0.014	28.123	0.001	0.001	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.031	-0.002	24.368	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.886	-0.913	26.289	0.204	0.204	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.034	0.009	20.456	0.012	0.012	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.743	-0.867	21.226	0.332	0.332	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.844	-0.914	19.648	0.422	0.422	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.055	-0.042	18.286	0.085	0.085	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.004	0.016	17.459	0.059	0.059	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.844	-0.881	15.346	0.589	0.589	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.835	0.946	13.605	-0.430	-0.430	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.000	-0.001	12.783	0.165	0.165	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.030	0.028	12.079	0.087	0.087	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.923	0.970	9.106	-1.427	-1.427	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.784	-0.865	7.896	1.432	1.432	0.000	0.000	0.000	0.000
43	A	46	TYR	0	-0.038	-0.053	8.173	0.204	0.204	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.043	0.014	6.755	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.061	-0.025	3.430	-0.755	-0.183	0.017	-0.173	-0.415	0.000
46	A	49	LYS	1	0.920	0.961	2.941	-3.663	-2.289	0.193	-0.780	-0.787	-0.009
47	A	50	LEU	0	0.002	0.010	5.544	-0.167	-0.167	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.043	0.013	2.327	0.257	-0.258	1.840	-0.498	-0.828	0.000
49	A	52	GLU	-1	-0.890	-0.956	2.379	8.081	7.691	6.413	-0.856	-5.168	-0.016
50	A	53	ASN	0	-0.087	-0.054	3.086	1.472	0.898	0.079	0.835	-0.340	0.000
51	A	54	ARG	1	0.907	0.958	4.677	-2.491	-2.349	-0.001	-0.007	-0.134	0.000
52	A	55	THR	0	0.006	0.006	6.570	-0.060	-0.060	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.033	0.009	8.206	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	57	THR	0	0.031	0.022	10.905	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	58	HIS	0	0.015	0.011	12.692	0.027	0.027	0.000	0.000	0.000	0.000
56	A	59	THR	0	0.006	0.002	15.129	0.020	0.020	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.038	0.030	8.783	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.033	-0.031	10.090	0.003	0.003	0.000	0.000	0.000	0.000
59	A	62	GLY	0	0.027	0.032	14.970	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.065	-0.013	14.748	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.034	0.004	17.286	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	65	PRO	0	0.057	0.018	17.063	0.025	0.025	0.000	0.000	0.000	0.000
63	A	66	MET	0	0.014	0.015	18.099	0.025	0.025	0.000	0.000	0.000	0.000
64	A	67	GLN	0	0.045	0.023	19.517	0.003	0.003	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.759	0.848	13.371	-0.511	-0.511	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.009	0.013	17.051	0.043	0.043	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.045	-0.034	19.237	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.790	0.907	14.474	-0.827	-0.827	0.000	0.000	0.000	0.000
69	A	72	TYR	0	-0.057	-0.062	14.756	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.724	-0.826	21.246	0.282	0.282	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.042	0.017	23.742	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	75	SER	0	-0.050	-0.045	26.085	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	76	PHE	0	0.028	0.016	23.010	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	77	ASN	0	-0.032	-0.030	26.349	0.002	0.002	0.000	0.000	0.000	0.000
75	A	78	LEU	0	-0.020	0.006	26.244	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.022	-0.027	21.133	0.020	0.020	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.740	0.830	21.491	-0.198	-0.198	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.749	-0.862	14.781	0.501	0.501	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.049	-0.004	16.610	-0.035	-0.035	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.017	0.007	11.362	0.057	0.057	0.000	0.000	0.000	0.000
81	A	84	ALA	0	0.000	0.014	12.249	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.018	-0.035	8.525	0.016	0.016	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.027	0.024	10.288	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	87	ILE	0	-0.044	-0.015	12.084	0.004	0.004	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.751	-0.881	13.978	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.049	0.025	15.813	0.024	0.024	0.000	0.000	0.000	0.000
87	A	90	ASN	0	-0.015	-0.007	17.047	0.006	0.006	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.898	0.942	18.629	0.017	0.017	0.000	0.000	0.000	0.000
89	A	92	VAL	0	0.010	0.023	15.244	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.057	0.036	18.119	0.007	0.007	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.015	-0.017	21.210	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	95	ALA	0	-0.002	0.003	18.949	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	96	TRP	0	0.000	-0.029	14.840	0.002	0.002	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.012	-0.014	21.246	0.001	0.001	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.050	-0.017	23.659	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	99	SER	0	-0.008	-0.004	21.199	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	100	PRO	0	0.008	-0.005	23.938	0.013	0.013	0.000	0.000	0.000	0.000
98	A	101	SER	0	0.045	0.023	22.793	0.001	0.001	0.000	0.000	0.000	0.000
99	A	102	HIS	0	0.029	0.022	18.354	0.000	0.000	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.972	0.997	22.073	-0.072	-0.072	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.845	-0.894	25.249	0.160	0.160	0.000	0.000	0.000	0.000
102	A	105	ALA	0	0.018	0.003	22.239	0.004	0.004	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.021	-0.003	21.247	0.008	0.008	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.046	-0.022	24.350	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	108	ASN	0	-0.022	0.028	25.281	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	109	THR	0	0.047	0.023	28.631	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.804	-0.887	28.285	0.169	0.169	0.000	0.000	0.000	0.000
108	A	111	THR	0	-0.091	-0.058	24.797	0.016	0.016	0.000	0.000	0.000	0.000
109	A	112	ASP	-1	-0.768	-0.897	27.484	0.196	0.196	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.784	0.894	23.733	-0.252	-0.252	0.000	0.000	0.000	0.000
111	A	114	ILE	0	0.001	-0.008	19.987	0.000	0.000	0.000	0.000	0.000	0.000
112	A	115	GLY	0	0.027	-0.002	18.194	0.000	0.000	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.029	-0.006	14.434	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	117	TYR	0	-0.017	-0.021	7.305	0.277	0.277	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.809	0.860	9.797	-0.244	-0.244	0.000	0.000	0.000	0.000
116	A	119	LEU	0	-0.011	0.014	2.270	-0.119	-0.639	3.058	-0.389	-2.149	0.001
117	A	120	LYS	1	0.884	0.933	6.672	-0.428	-0.428	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.008	-0.041	2.440	0.821	1.383	1.722	-0.602	-1.682	-0.004
119	A	122	THR	0	0.020	0.000	5.490	-0.316	-0.316	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.854	-0.895	2.437	-13.179	-9.842	2.224	-2.859	-2.701	-0.030
121	A	124	ASN	0	-0.049	-0.026	5.989	0.574	0.574	0.000	0.000	0.000	0.000
122	A	125	ILE	0	0.001	0.020	2.239	-0.168	-0.374	3.676	-0.638	-2.832	-0.006
123	A	126	ASP	-1	-0.776	-0.865	5.128	0.463	0.505	-0.001	-0.001	-0.041	0.000
124	A	127	ILE	0	-0.013	0.007	4.759	-0.162	-0.097	-0.001	-0.001	-0.063	0.000
125	A	128	PHE	0	0.018	0.017	8.050	0.283	0.283	0.000	0.000	0.000	0.000
126	A	129	VAL	0	-0.029	-0.014	9.174	-0.061	-0.061	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.010	0.000	11.947	0.051	0.051	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.029	-0.008	14.899	-0.029	-0.029	0.000	0.000	0.000	0.000
129	A	132	PHE	0	0.056	0.015	17.725	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	133	GLY	0	0.012	-0.007	21.536	0.012	0.012	0.000	0.000	0.000	0.000
131	A	134	LYS	1	0.878	0.947	24.159	-0.193	-0.193	0.000	0.000	0.000	0.000
132	A	135	ARG	1	0.731	0.848	23.782	-0.297	-0.297	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.893	0.941	28.922	-0.242	-0.242	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)