FMO DATABASE

FMODB ID: 2JJQR

Calculation Name: 5DPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H492

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	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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1107213.469412
FMO2-HF: Nuclear repulsion	1056288.945413
FMO2-HF: Total energy	-50924.524
FMO2-MP2: Total energy	-51073.510916

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:6:GLU)

Summations of interaction energy for fragment #1(A:6:GLU)

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.
-44.049	-42.724	-0.009	-0.549	-0.768	0.002

Interaction energy analysis for fragmet #1(A:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.925 / q_NPA : -0.973

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	8	VAL	0	-0.003	-0.002	3.868	-6.614	-5.289	-0.009	-0.549	-0.768	0.002
4	A	9	ASN	0	-0.039	-0.010	6.135	-3.958	-3.958	0.000	0.000	0.000	0.000
5	A	10	VAL	0	-0.009	-0.007	9.128	-1.412	-1.412	0.000	0.000	0.000	0.000
6	A	11	GLY	0	0.029	0.020	12.367	-0.530	-0.530	0.000	0.000	0.000	0.000
7	A	12	SER	0	0.027	-0.006	15.802	0.545	0.545	0.000	0.000	0.000	0.000
8	A	13	PRO	0	-0.044	-0.025	18.867	-0.382	-0.382	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.009	-0.018	22.032	-0.393	-0.393	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.823	-0.886	20.104	13.437	13.437	0.000	0.000	0.000	0.000
11	A	16	ARG	1	0.967	1.005	19.355	-13.522	-13.522	0.000	0.000	0.000	0.000
12	A	17	PRO	0	0.030	0.015	22.779	-0.351	-0.351	0.000	0.000	0.000	0.000
13	A	18	PHE	0	0.053	0.007	26.325	0.094	0.094	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.789	0.871	29.263	-8.731	-8.731	0.000	0.000	0.000	0.000
15	A	20	GLN	0	-0.018	-0.015	23.693	0.248	0.248	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.763	0.874	25.608	-10.834	-10.834	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.865	0.931	27.596	-8.891	-8.891	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.023	-0.007	31.190	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	24	PHE	0	0.092	0.030	32.808	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.088	0.042	35.642	-0.168	-0.168	0.000	0.000	0.000	0.000
21	A	26	ASP	-1	-0.865	-0.899	34.504	8.368	8.368	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.758	0.868	32.213	-8.999	-8.999	0.000	0.000	0.000	0.000
23	A	28	CYS	0	0.022	0.029	37.279	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	29	LYS	1	0.842	0.919	37.861	-8.015	-8.015	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.780	-0.869	36.099	8.436	8.436	0.000	0.000	0.000	0.000
26	A	31	VAL	0	-0.002	-0.002	39.897	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	32	GLN	0	-0.029	-0.016	42.147	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	33	GLN	0	-0.003	-0.017	41.925	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.052	-0.020	41.059	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.976	0.978	44.464	-6.577	-6.577	0.000	0.000	0.000	0.000
31	A	36	ASP	-1	-0.841	-0.901	47.296	6.115	6.115	0.000	0.000	0.000	0.000
32	A	37	GLN	0	-0.065	-0.023	45.799	0.019	0.019	0.000	0.000	0.000	0.000
33	A	38	HIS	0	-0.048	-0.026	45.542	-0.138	-0.138	0.000	0.000	0.000	0.000
34	A	39	PRO	0	0.041	0.018	48.846	0.063	0.063	0.000	0.000	0.000	0.000
35	A	40	SER	0	-0.023	0.014	51.174	0.005	0.005	0.000	0.000	0.000	0.000
36	A	41	LYS	1	0.847	0.901	46.254	-6.561	-6.561	0.000	0.000	0.000	0.000
37	A	42	ILE	0	0.071	0.056	43.315	0.041	0.041	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.032	-0.002	40.894	0.143	0.143	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.009	-0.009	37.960	0.033	0.033	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.039	-0.015	32.937	0.192	0.192	0.000	0.000	0.000	0.000
41	A	46	ILE	0	0.010	0.004	33.279	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	47	GLU	-1	-0.849	-0.917	27.925	10.874	10.874	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.873	0.939	21.787	-13.116	-13.116	0.000	0.000	0.000	0.000
44	A	49	TYR	0	0.054	0.013	27.198	0.302	0.302	0.000	0.000	0.000	0.000
45	A	50	LYS	1	0.882	0.925	23.330	-11.923	-11.923	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.051	0.033	23.334	0.589	0.589	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.750	-0.852	24.534	11.225	11.225	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.780	0.871	20.327	-13.060	-13.060	0.000	0.000	0.000	0.000
49	A	54	GLN	0	0.018	0.033	24.094	0.271	0.271	0.000	0.000	0.000	0.000
50	A	55	LEU	0	-0.027	0.004	26.717	-0.168	-0.168	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.044	0.028	25.840	0.514	0.514	0.000	0.000	0.000	0.000
52	A	57	VAL	0	0.003	0.006	23.723	-0.336	-0.336	0.000	0.000	0.000	0.000
53	A	58	LEU	0	0.016	0.008	26.787	-0.212	-0.212	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.801	-0.865	28.458	9.699	9.699	0.000	0.000	0.000	0.000
55	A	60	LYS	1	0.803	0.893	29.948	-8.664	-8.664	0.000	0.000	0.000	0.000
56	A	61	THR	0	0.010	0.016	29.493	-0.111	-0.111	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.927	0.968	31.837	-8.790	-8.790	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.003	-0.009	34.504	0.006	0.006	0.000	0.000	0.000	0.000
59	A	64	LEU	0	0.030	0.022	38.693	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.029	-0.008	42.028	0.005	0.005	0.000	0.000	0.000	0.000
61	A	66	PRO	0	-0.004	-0.003	44.749	-0.050	-0.050	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.803	-0.913	48.613	6.269	6.269	0.000	0.000	0.000	0.000
63	A	68	HIS	0	0.005	-0.008	50.265	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.065	-0.018	46.119	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.016	0.001	48.318	0.016	0.016	0.000	0.000	0.000	0.000
66	A	71	MET	0	0.065	0.038	43.255	0.165	0.165	0.000	0.000	0.000	0.000
67	A	72	SER	0	0.007	0.009	44.261	0.181	0.181	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.893	-0.945	45.345	6.458	6.458	0.000	0.000	0.000	0.000
69	A	74	LEU	0	0.038	0.019	40.537	0.137	0.137	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.004	0.000	39.980	0.227	0.227	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.926	0.952	40.347	-6.601	-6.601	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.043	-0.004	40.226	0.083	0.083	0.000	0.000	0.000	0.000
73	A	78	ILE	0	0.020	0.010	35.448	0.165	0.165	0.000	0.000	0.000	0.000
74	A	79	ARG	1	0.852	0.935	36.458	-8.054	-8.054	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.904	0.935	37.083	-7.148	-7.148	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.821	0.881	34.729	-8.702	-8.702	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.022	-0.019	30.916	0.202	0.202	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.058	-0.021	32.981	0.201	0.201	0.000	0.000	0.000	0.000
79	A	84	LEU	0	-0.028	0.006	32.132	0.095	0.095	0.000	0.000	0.000	0.000
80	A	85	ASN	0	0.044	0.016	34.078	-0.465	-0.465	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.009	-0.006	37.115	0.054	0.054	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.028	0.006	36.586	-0.120	-0.120	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.069	-0.017	31.995	0.165	0.165	0.000	0.000	0.000	0.000
84	A	89	ALA	0	0.055	0.034	34.569	-0.204	-0.204	0.000	0.000	0.000	0.000
85	A	90	PHE	0	-0.016	-0.031	34.020	0.298	0.298	0.000	0.000	0.000	0.000
86	A	91	PHE	0	0.014	0.028	35.316	-0.286	-0.286	0.000	0.000	0.000	0.000
87	A	92	LEU	0	-0.009	-0.013	35.349	0.298	0.298	0.000	0.000	0.000	0.000
88	A	93	LEU	0	-0.008	0.001	34.523	-0.244	-0.244	0.000	0.000	0.000	0.000
89	A	94	VAL	0	0.055	0.016	37.275	0.178	0.178	0.000	0.000	0.000	0.000
90	A	95	ASN	0	-0.027	-0.026	38.672	0.108	0.108	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.008	0.003	33.657	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	97	HIS	0	0.011	0.014	38.204	-0.218	-0.218	0.000	0.000	0.000	0.000
93	A	98	SER	0	-0.006	-0.019	40.297	0.087	0.087	0.000	0.000	0.000	0.000
94	A	99	MET	0	0.008	0.008	41.054	-0.256	-0.256	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.051	-0.023	42.347	-0.139	-0.139	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.004	-0.007	44.124	-0.138	-0.138	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.009	0.006	45.914	-0.158	-0.158	0.000	0.000	0.000	0.000
98	A	103	SER	0	-0.043	-0.027	48.055	0.089	0.089	0.000	0.000	0.000	0.000
99	A	104	THR	0	0.051	0.027	49.560	-0.064	-0.064	0.000	0.000	0.000	0.000
100	A	105	PRO	0	0.030	0.019	49.288	0.173	0.173	0.000	0.000	0.000	0.000
101	A	106	ILE	0	0.004	-0.010	43.104	0.056	0.056	0.000	0.000	0.000	0.000
102	A	107	ALA	0	0.001	0.000	47.241	0.082	0.082	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.870	-0.933	49.556	5.894	5.894	0.000	0.000	0.000	0.000
104	A	109	ILE	0	-0.029	-0.007	44.788	0.026	0.026	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.060	-0.049	43.362	0.047	0.047	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.834	-0.932	46.099	6.351	6.351	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.090	-0.043	47.773	-0.090	-0.090	0.000	0.000	0.000	0.000
108	A	113	GLU	-1	-0.852	-0.930	42.603	7.090	7.090	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.723	0.878	41.749	-6.239	-6.239	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.813	-0.902	37.284	8.254	8.254	0.000	0.000	0.000	0.000
111	A	116	GLU	-1	-0.920	-0.954	39.379	7.407	7.407	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.772	-0.877	36.236	8.227	8.227	0.000	0.000	0.000	0.000
113	A	118	GLY	0	0.060	0.036	39.675	-0.050	-0.050	0.000	0.000	0.000	0.000
114	A	119	PHE	0	-0.024	-0.011	37.109	-0.082	-0.082	0.000	0.000	0.000	0.000
115	A	120	LEU	0	0.053	0.036	39.912	-0.039	-0.039	0.000	0.000	0.000	0.000
116	A	121	TYR	0	-0.089	-0.079	32.921	0.324	0.324	0.000	0.000	0.000	0.000
117	A	122	MET	0	-0.012	0.005	35.518	-0.143	-0.143	0.000	0.000	0.000	0.000
118	A	123	VAL	0	-0.007	-0.002	30.884	0.327	0.327	0.000	0.000	0.000	0.000
119	A	124	TYR	0	-0.024	-0.031	28.941	-0.238	-0.238	0.000	0.000	0.000	0.000
120	A	125	ALA	0	-0.018	-0.020	30.715	0.456	0.456	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.003	-0.021	29.701	-0.343	-0.343	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.045	-0.034	29.975	-0.150	-0.150	0.000	0.000	0.000	0.000
123	A	128	GLU	-1	-0.813	-0.909	34.101	7.807	7.807	0.000	0.000	0.000	0.000
124	A	129	THR	0	-0.045	-0.014	33.054	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLU)