FMO DATABASE

FMODB ID: ZV7KN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1253519.817944
FMO2-HF: Nuclear repulsion	1200159.38948
FMO2-HF: Total energy	-53360.428464
FMO2-MP2: Total energy	-53517.941119

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.
9.762	-23.609	54.221	0.333	-21.185	-0.045

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 : -0.058 / q_NPA : -0.001

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	-0.009	-0.010	2.632	-3.650	-1.781	0.772	-1.270	-1.371	-0.008
4	A	7	LYS	1	0.961	0.975	4.562	0.415	0.641	-0.001	-0.019	-0.206	0.000
5	A	8	ILE	0	-0.005	-0.016	6.054	-0.099	-0.099	0.000	0.000	0.000	0.000
6	A	9	ASP	-1	-0.940	-0.947	9.572	0.171	0.171	0.000	0.000	0.000	0.000
7	A	10	THR	0	0.016	-0.008	11.124	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.953	0.971	13.764	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	12	GLU	-1	-0.906	-0.969	16.707	0.043	0.043	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.837	-0.923	14.913	0.105	0.105	0.000	0.000	0.000	0.000
11	A	14	MET	0	-0.010	-0.001	15.030	0.026	0.026	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.920	0.980	17.776	-0.054	-0.054	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.016	0.000	20.788	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	17	LEU	0	0.016	0.009	17.095	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	TYR	0	-0.044	-0.072	18.844	0.007	0.007	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.003	-0.003	22.666	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.949	-0.965	22.912	0.104	0.104	0.000	0.000	0.000	0.000
18	A	21	ILE	0	-0.005	-0.011	20.683	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.017	-0.006	25.124	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.876	-0.954	28.066	0.054	0.054	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.001	-0.001	26.544	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	25	ARG	1	0.807	0.876	27.010	-0.125	-0.125	0.000	0.000	0.000	0.000
23	A	26	LYS	1	0.961	1.002	30.655	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.845	0.927	33.118	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.024	-0.005	31.479	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	29	ASN	0	-0.061	-0.021	35.046	0.000	0.000	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.016	0.014	31.009	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	ASN	0	-0.013	-0.018	31.161	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	32	HIS	0	0.020	-0.002	29.974	0.007	0.007	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.035	0.004	25.425	0.001	0.001	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.957	-0.971	27.586	0.085	0.085	0.000	0.000	0.000	0.000
32	A	35	ILE	0	0.024	-0.006	21.504	0.010	0.010	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.767	-0.893	22.498	0.155	0.155	0.000	0.000	0.000	0.000
34	A	37	ASP	-1	-0.857	-0.926	20.708	0.159	0.159	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.085	-0.050	19.486	0.024	0.024	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.036	-0.011	18.756	0.039	0.039	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.807	-0.867	16.665	0.280	0.280	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.863	0.956	14.830	-0.135	-0.135	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.000	-0.006	13.934	0.090	0.090	0.000	0.000	0.000	0.000
40	A	43	ALA	0	0.033	0.023	13.395	0.100	0.100	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.937	0.973	9.929	-0.252	-0.252	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.922	-0.941	8.949	0.784	0.784	0.000	0.000	0.000	0.000
43	A	46	TYR	0	-0.039	-0.049	9.016	0.253	0.253	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.067	0.028	8.012	0.139	0.139	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.047	-0.025	4.350	-0.057	0.394	0.017	-0.098	-0.371	0.000
46	A	49	LYS	1	0.982	1.008	4.265	-0.254	0.366	0.037	-0.254	-0.403	-0.002
47	A	50	LEU	0	-0.005	0.008	5.830	-0.282	-0.282	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.032	-0.003	2.260	2.311	-1.185	2.132	2.841	-1.476	0.005
49	A	52	GLU	-1	-1.010	-1.026	1.823	10.049	-12.336	36.484	-6.044	-8.055	-0.010
50	A	53	ASN	0	-0.065	-0.051	2.460	8.077	-0.706	-0.127	9.437	-0.528	-0.006
51	A	54	ARG	1	0.897	0.974	4.489	-1.393	-1.213	-0.001	-0.029	-0.150	0.000
52	A	55	THR	0	0.008	0.001	6.068	-0.074	-0.074	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.035	0.019	7.697	0.131	0.131	0.000	0.000	0.000	0.000
54	A	57	THR	0	0.028	0.012	10.363	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	58	HIS	0	0.000	-0.003	12.824	0.048	0.048	0.000	0.000	0.000	0.000
56	A	59	THR	0	-0.021	-0.016	15.436	0.005	0.005	0.000	0.000	0.000	0.000
57	A	60	LEU	0	0.036	0.023	9.130	-0.032	-0.032	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.046	-0.037	9.918	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	62	GLY	0	0.063	0.046	15.062	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.080	-0.010	15.527	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.040	0.017	17.981	0.016	0.016	0.000	0.000	0.000	0.000
62	A	65	PRO	0	0.066	0.022	17.752	0.009	0.009	0.000	0.000	0.000	0.000
63	A	66	MET	0	0.037	0.015	18.924	0.002	0.002	0.000	0.000	0.000	0.000
64	A	67	GLN	0	0.010	0.008	20.544	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.770	0.876	14.516	-0.463	-0.463	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.029	0.021	18.428	0.003	0.003	0.000	0.000	0.000	0.000
67	A	70	HIS	0	-0.068	-0.060	20.435	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.902	0.976	15.776	-0.319	-0.319	0.000	0.000	0.000	0.000
69	A	72	TYR	0	-0.096	-0.084	15.713	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.758	-0.842	21.989	0.116	0.116	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.023	-0.003	24.910	0.002	0.002	0.000	0.000	0.000	0.000
72	A	75	SER	0	-0.078	-0.076	27.252	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	76	PHE	0	-0.019	0.015	24.127	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	77	ASN	0	-0.012	-0.003	27.450	0.007	0.007	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.026	0.018	27.293	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.043	-0.032	22.372	0.012	0.012	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.809	0.904	22.374	-0.159	-0.159	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.753	-0.878	15.346	0.478	0.478	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.040	-0.006	17.415	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.006	0.004	11.862	0.052	0.052	0.000	0.000	0.000	0.000
81	A	84	ALA	0	-0.016	0.001	12.407	-0.072	-0.072	0.000	0.000	0.000	0.000
82	A	85	SER	0	0.004	-0.012	8.721	0.100	0.100	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.033	0.031	10.243	-0.060	-0.060	0.000	0.000	0.000	0.000
84	A	87	ILE	0	-0.044	-0.018	11.812	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.873	-0.944	14.481	0.053	0.053	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.012	0.001	16.544	0.017	0.017	0.000	0.000	0.000	0.000
87	A	90	ASN	0	0.004	0.008	17.709	0.011	0.011	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.926	0.949	19.246	-0.072	-0.072	0.000	0.000	0.000	0.000
89	A	92	VAL	0	0.024	0.026	15.875	0.000	0.000	0.000	0.000	0.000	0.000
90	A	93	VAL	0	0.047	0.034	18.753	0.010	0.010	0.000	0.000	0.000	0.000
91	A	94	ASN	0	0.025	-0.010	21.797	0.001	0.001	0.000	0.000	0.000	0.000
92	A	95	ALA	0	-0.009	0.006	19.152	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	96	TRP	0	-0.023	-0.031	15.496	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.021	-0.025	21.291	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.064	-0.025	23.350	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	99	SER	0	0.021	0.029	21.716	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	100	PRO	0	0.022	-0.003	24.078	0.004	0.004	0.000	0.000	0.000	0.000
98	A	101	SER	0	0.014	0.008	22.586	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	102	HIS	0	0.025	0.004	18.829	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	103	LYS	1	0.981	0.995	22.496	-0.098	-0.098	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.876	-0.932	25.611	0.142	0.142	0.000	0.000	0.000	0.000
102	A	105	ALA	0	0.031	0.015	22.671	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.021	0.000	21.748	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.040	-0.019	24.981	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	108	ASN	0	-0.017	0.005	26.051	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	109	THR	0	0.077	0.029	29.206	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.869	-0.908	29.457	0.116	0.116	0.000	0.000	0.000	0.000
108	A	111	THR	0	-0.143	-0.073	25.835	0.005	0.005	0.000	0.000	0.000	0.000
109	A	112	ASP	-1	-0.822	-0.944	28.861	0.107	0.107	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.863	0.953	25.044	-0.115	-0.115	0.000	0.000	0.000	0.000
111	A	114	ILE	0	0.020	0.004	21.065	0.010	0.010	0.000	0.000	0.000	0.000
112	A	115	GLY	0	0.017	0.002	19.419	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	116	GLY	0	0.022	0.001	15.761	0.024	0.024	0.000	0.000	0.000	0.000
114	A	117	TYR	0	-0.006	-0.011	7.830	0.055	0.055	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.822	0.882	10.808	-0.206	-0.206	0.000	0.000	0.000	0.000
116	A	119	LEU	0	-0.023	0.003	3.085	-1.181	-0.670	1.191	-0.401	-1.302	0.005
117	A	120	LYS	1	1.025	1.012	7.506	-0.092	-0.092	0.000	0.000	0.000	0.000
118	A	121	THR	0	-0.042	-0.062	2.499	-0.056	0.684	0.871	-0.308	-1.303	-0.001
119	A	122	THR	0	0.003	0.000	5.532	-0.076	-0.076	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.852	-0.886	2.802	-8.269	-5.028	0.603	-1.933	-1.911	-0.018
121	A	124	ASN	0	-0.031	-0.016	6.235	0.209	0.209	0.000	0.000	0.000	0.000
122	A	125	ILE	0	0.035	0.026	1.972	2.687	-3.858	12.243	-1.589	-4.109	-0.010
123	A	126	ASP	-1	-0.818	-0.895	5.706	0.434	0.434	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.006	0.014	4.934	-0.089	-0.089	0.000	0.000	0.000	0.000
125	A	128	PHE	0	-0.003	-0.014	8.524	0.109	0.109	0.000	0.000	0.000	0.000
126	A	129	VAL	0	-0.009	0.004	10.192	0.001	0.001	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.001	-0.010	12.936	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.029	-0.003	16.146	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	132	PHE	0	0.062	0.022	19.073	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	133	GLY	0	-0.010	-0.012	22.859	0.009	0.009	0.000	0.000	0.000	0.000
131	A	134	LYS	1	0.983	1.009	25.298	-0.109	-0.109	0.000	0.000	0.000	0.000
132	A	135	ARG	1	0.799	0.900	25.146	-0.134	-0.134	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.943	0.968	30.056	-0.118	-0.118	0.000	0.000	0.000	0.000

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