FMO DATABASE

FMODB ID: 661QZ

Calculation Name: 4DJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DJB

Chain ID: A

ChEMBL ID:

UniProt ID: P04489

Base Structure: X-ray

Registration Date: 2023-06-20

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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-980732.450467
FMO2-HF: Nuclear repulsion	933247.31744
FMO2-HF: Total energy	-47485.133028
FMO2-MP2: Total energy	-47622.931473

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:-1:ASP)

Summations of interaction energy for fragment #1(A:-1: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.
110.619	112.022	0.009	-0.77	-0.642	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.978 / q_NPA : -1.005

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	1	MET	0	-0.030	0.009	3.440	-7.237	-5.834	0.009	-0.770	-0.642	0.001
4	A	2	ILE	0	-0.005	-0.004	5.980	-3.246	-3.246	0.000	0.000	0.000	0.000
5	A	3	ARG	1	0.734	0.833	7.398	-26.107	-26.107	0.000	0.000	0.000	0.000
6	A	4	CYS	0	-0.051	-0.012	11.759	-0.478	-0.478	0.000	0.000	0.000	0.000
7	A	5	LEU	0	0.015	0.017	15.443	-0.177	-0.177	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.875	0.920	18.271	-12.591	-12.591	0.000	0.000	0.000	0.000
9	A	7	LEU	0	-0.007	0.015	21.756	-0.137	-0.137	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.851	0.920	25.055	-9.685	-9.685	0.000	0.000	0.000	0.000
11	A	9	VAL	0	0.002	0.006	28.045	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	10	GLU	-1	-0.837	-0.920	31.486	9.003	9.003	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.067	0.021	34.746	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.043	0.017	37.329	-0.076	-0.076	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.005	0.009	34.064	-0.124	-0.124	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.752	-0.865	35.495	8.842	8.842	0.000	0.000	0.000	0.000
17	A	15	GLN	0	-0.075	-0.026	37.555	-0.247	-0.247	0.000	0.000	0.000	0.000
18	A	16	ILE	0	0.020	0.001	40.621	-0.142	-0.142	0.000	0.000	0.000	0.000
19	A	17	PHE	0	0.002	-0.007	37.176	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	18	THR	0	-0.024	-0.019	40.128	-0.076	-0.076	0.000	0.000	0.000	0.000
21	A	19	MET	0	-0.093	-0.048	42.109	-0.149	-0.149	0.000	0.000	0.000	0.000
22	A	20	ALA	0	-0.001	0.020	42.703	-0.159	-0.159	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.013	-0.006	44.310	0.005	0.005	0.000	0.000	0.000	0.000
24	A	22	LEU	0	-0.056	-0.019	38.923	0.135	0.135	0.000	0.000	0.000	0.000
25	A	23	ASN	0	0.007	-0.010	35.980	0.148	0.148	0.000	0.000	0.000	0.000
26	A	24	ILE	0	0.064	0.019	33.152	0.217	0.217	0.000	0.000	0.000	0.000
27	A	25	ARG	1	0.766	0.836	31.673	-8.833	-8.833	0.000	0.000	0.000	0.000
28	A	26	ASP	-1	-0.842	-0.910	31.234	9.585	9.585	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.032	0.024	32.144	0.286	0.286	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.004	0.001	28.310	0.333	0.333	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.757	0.834	27.579	-9.400	-9.400	0.000	0.000	0.000	0.000
32	A	30	ASP	-1	-0.780	-0.866	27.448	10.562	10.562	0.000	0.000	0.000	0.000
33	A	31	ILE	0	-0.023	-0.004	26.743	0.178	0.178	0.000	0.000	0.000	0.000
34	A	32	LEU	0	0.030	0.005	22.041	0.424	0.424	0.000	0.000	0.000	0.000
35	A	33	ARG	1	0.795	0.900	23.578	-10.322	-10.322	0.000	0.000	0.000	0.000
36	A	34	ARG	1	0.962	0.974	25.073	-10.202	-10.202	0.000	0.000	0.000	0.000
37	A	35	TRP	0	0.053	0.037	16.918	0.242	0.242	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.823	0.872	20.532	-12.377	-12.377	0.000	0.000	0.000	0.000
39	A	37	ASP	-1	-0.865	-0.907	21.452	12.739	12.739	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.933	-0.967	22.814	12.759	12.759	0.000	0.000	0.000	0.000
41	A	39	ASN	0	-0.039	-0.029	17.080	0.034	0.034	0.000	0.000	0.000	0.000
42	A	40	TYR	0	0.028	0.018	16.660	1.044	1.044	0.000	0.000	0.000	0.000
43	A	41	LEU	0	-0.011	-0.004	17.890	0.648	0.648	0.000	0.000	0.000	0.000
44	A	42	GLY	0	-0.026	-0.006	15.787	0.227	0.227	0.000	0.000	0.000	0.000
45	A	43	MET	0	-0.049	-0.007	13.850	1.901	1.901	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.002	-0.003	11.746	2.105	2.105	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.821	-0.894	10.030	25.494	25.494	0.000	0.000	0.000	0.000
48	A	46	GLY	0	-0.024	-0.016	12.886	-1.621	-1.621	0.000	0.000	0.000	0.000
49	A	47	ALA	0	-0.036	-0.014	14.084	1.243	1.243	0.000	0.000	0.000	0.000
50	A	48	GLY	0	-0.028	0.003	16.581	-0.887	-0.887	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.027	-0.018	19.232	0.123	0.123	0.000	0.000	0.000	0.000
52	A	50	PHE	0	-0.045	-0.015	19.578	-0.212	-0.212	0.000	0.000	0.000	0.000
53	A	51	ILE	0	0.005	-0.011	24.331	0.104	0.104	0.000	0.000	0.000	0.000
54	A	52	GLU	-1	-0.924	-0.942	25.364	11.116	11.116	0.000	0.000	0.000	0.000
55	A	53	GLU	-1	-0.820	-0.897	28.075	9.172	9.172	0.000	0.000	0.000	0.000
56	A	54	ILE	0	-0.084	-0.030	29.664	0.201	0.201	0.000	0.000	0.000	0.000
57	A	55	HIS	0	-0.003	0.018	32.688	-0.419	-0.419	0.000	0.000	0.000	0.000
58	A	56	PRO	0	-0.059	-0.049	35.946	0.032	0.032	0.000	0.000	0.000	0.000
59	A	57	GLU	-1	-0.859	-0.930	37.262	7.542	7.542	0.000	0.000	0.000	0.000
60	A	58	GLY	0	0.066	0.036	34.445	0.077	0.077	0.000	0.000	0.000	0.000
61	A	59	PHE	0	-0.049	-0.021	29.146	0.066	0.066	0.000	0.000	0.000	0.000
62	A	60	SER	0	-0.019	-0.016	25.449	0.092	0.092	0.000	0.000	0.000	0.000
63	A	61	LEU	0	0.015	0.016	24.230	0.066	0.066	0.000	0.000	0.000	0.000
64	A	62	TYR	0	-0.003	-0.009	20.331	0.294	0.294	0.000	0.000	0.000	0.000
65	A	63	VAL	0	0.029	0.009	18.101	-0.160	-0.160	0.000	0.000	0.000	0.000
66	A	64	HIS	0	-0.010	-0.015	15.147	-0.340	-0.340	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.018	0.002	13.394	-0.435	-0.435	0.000	0.000	0.000	0.000
68	A	66	ASP	-1	-0.805	-0.894	6.663	42.581	42.581	0.000	0.000	0.000	0.000
69	A	67	VAL	0	0.001	-0.006	9.756	-0.784	-0.784	0.000	0.000	0.000	0.000
70	A	68	ARG	1	0.780	0.876	6.790	-32.154	-32.154	0.000	0.000	0.000	0.000
71	A	69	ALA	0	-0.016	-0.025	6.478	3.524	3.524	0.000	0.000	0.000	0.000
72	A	70	VAL	0	0.033	0.013	8.953	-1.935	-1.935	0.000	0.000	0.000	0.000
73	A	71	SER	0	0.037	0.020	11.957	-0.475	-0.475	0.000	0.000	0.000	0.000
74	A	72	LEU	0	-0.040	-0.011	10.902	-1.393	-1.393	0.000	0.000	0.000	0.000
75	A	73	LEU	0	0.023	0.008	12.565	-0.989	-0.989	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.906	-0.964	14.216	16.219	16.219	0.000	0.000	0.000	0.000
77	A	75	ALA	0	0.001	0.008	16.899	-0.973	-0.973	0.000	0.000	0.000	0.000
78	A	76	ILE	0	-0.004	-0.003	13.976	-0.932	-0.932	0.000	0.000	0.000	0.000
79	A	77	VAL	0	-0.003	-0.005	17.640	-0.925	-0.925	0.000	0.000	0.000	0.000
80	A	78	GLN	0	-0.065	-0.024	20.044	-0.358	-0.358	0.000	0.000	0.000	0.000
81	A	79	HIS	0	0.019	0.007	20.988	-0.793	-0.793	0.000	0.000	0.000	0.000
82	A	80	LEU	0	0.005	-0.001	19.911	-0.683	-0.683	0.000	0.000	0.000	0.000
83	A	81	THR	0	-0.033	-0.033	23.582	-0.645	-0.645	0.000	0.000	0.000	0.000
84	A	82	GLU	-1	-0.870	-0.926	25.830	11.326	11.326	0.000	0.000	0.000	0.000
85	A	83	ALA	0	-0.008	0.019	26.045	-0.538	-0.538	0.000	0.000	0.000	0.000
86	A	84	ILE	0	-0.013	-0.012	25.760	-0.432	-0.432	0.000	0.000	0.000	0.000
87	A	85	ILE	0	-0.018	-0.002	29.286	-0.463	-0.463	0.000	0.000	0.000	0.000
88	A	86	SER	0	-0.049	-0.046	30.663	-0.393	-0.393	0.000	0.000	0.000	0.000
89	A	87	SER	0	0.022	0.015	31.463	-0.274	-0.274	0.000	0.000	0.000	0.000
90	A	88	LEU	0	-0.011	-0.011	31.992	-0.299	-0.299	0.000	0.000	0.000	0.000
91	A	89	ALA	0	0.003	0.003	35.025	-0.308	-0.308	0.000	0.000	0.000	0.000
92	A	90	VAL	0	-0.013	-0.001	36.764	-0.261	-0.261	0.000	0.000	0.000	0.000
93	A	91	GLU	-1	-0.919	-0.964	35.590	8.638	8.638	0.000	0.000	0.000	0.000
94	A	92	PHE	0	0.013	-0.007	38.739	-0.230	-0.230	0.000	0.000	0.000	0.000
95	A	93	ASP	-1	-0.878	-0.912	41.006	7.188	7.188	0.000	0.000	0.000	0.000
96	A	94	HIS	0	-0.075	-0.068	41.569	-0.133	-0.133	0.000	0.000	0.000	0.000
97	A	95	ALA	0	-0.048	-0.012	42.626	-0.165	-0.165	0.000	0.000	0.000	0.000
98	A	96	THR	0	-0.030	-0.028	44.490	-0.182	-0.182	0.000	0.000	0.000	0.000
99	A	97	GLY	0	-0.060	-0.018	46.715	-0.183	-0.183	0.000	0.000	0.000	0.000
100	A	98	GLY	0	-0.032	-0.006	46.184	-0.135	-0.135	0.000	0.000	0.000	0.000
101	A	99	GLU	-1	-0.995	-0.988	46.109	6.652	6.652	0.000	0.000	0.000	0.000
102	A	100	ARG	1	0.903	0.932	42.711	-6.956	-6.956	0.000	0.000	0.000	0.000
103	A	101	VAL	0	0.016	0.016	38.605	-0.124	-0.124	0.000	0.000	0.000	0.000
104	A	102	HIS	0	-0.092	-0.052	36.332	0.043	0.043	0.000	0.000	0.000	0.000
105	A	103	LEU	0	0.045	0.007	33.927	0.093	0.093	0.000	0.000	0.000	0.000
106	A	104	ILE	0	-0.011	-0.010	32.630	0.274	0.274	0.000	0.000	0.000	0.000
107	A	105	ASP	-1	-0.824	-0.887	31.438	9.171	9.171	0.000	0.000	0.000	0.000
108	A	106	LEU	0	-0.058	-0.011	29.139	0.265	0.265	0.000	0.000	0.000	0.000
109	A	107	HIS	1	0.836	0.879	24.381	-11.111	-11.111	0.000	0.000	0.000	0.000
110	A	108	PHE	0	0.025	0.005	20.473	-0.093	-0.093	0.000	0.000	0.000	0.000
111	A	109	GLU	-1	-0.837	-0.885	21.105	11.867	11.867	0.000	0.000	0.000	0.000
112	A	110	VAL	0	0.019	0.000	14.507	0.354	0.354	0.000	0.000	0.000	0.000
113	A	111	LEU	0	-0.040	-0.019	15.878	-0.623	-0.623	0.000	0.000	0.000	0.000
114	A	112	ASP	-1	-0.823	-0.923	11.780	20.763	20.763	0.000	0.000	0.000	0.000
115	A	113	ASN	0	-0.024	-0.025	6.997	-2.915	-2.915	0.000	0.000	0.000	0.000
116	A	114	LEU	0	-0.025	-0.022	9.780	0.753	0.753	0.000	0.000	0.000	0.000
117	A	115	LEU	0	-0.040	-0.009	9.078	-0.772	-0.772	0.000	0.000	0.000	0.000
118	A	116	GLU	-1	-0.843	-0.867	4.955	29.492	29.492	0.000	0.000	0.000	0.000

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