FMO DATABASE

FMODB ID: 4JQJN

Calculation Name: 5V50-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5V50

Chain ID: A

ChEMBL ID:
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UniProt ID: H6U756

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1198066.629529
FMO2-HF: Nuclear repulsion	1144231.335235
FMO2-HF: Total energy	-53835.294294
FMO2-MP2: Total energy	-53990.86738

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:31:GLN)

Summations of interaction energy for fragment #1(A:31:GLN)

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.
0.465	2.596	-0.025	-1.016	-1.09	0

Interaction energy analysis for fragmet #1(A:31:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.036

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].
3	A	33	ASP	-1	-0.762	-0.843	3.863	3.291	5.422	-0.025	-1.016	-1.090
4	A	34	PRO	0	0.019	0.007	6.903	-0.871	-0.871	0.000	0.000	0.000
5	A	35	ASP	-1	-0.832	-0.906	10.236	0.831	0.831	0.000	0.000	0.000
6	A	36	SER	0	-0.036	-0.041	8.967	-0.431	-0.431	0.000	0.000	0.000
7	A	37	PHE	0	-0.035	-0.007	9.612	-0.294	-0.294	0.000	0.000	0.000
8	A	38	LYS	1	0.849	0.904	11.457	-1.251	-1.251	0.000	0.000	0.000
9	A	39	ASN	0	-0.027	-0.028	14.839	-0.218	-0.218	0.000	0.000	0.000
10	A	40	LYS	1	0.835	0.917	13.421	-0.175	-0.175	0.000	0.000	0.000
11	A	41	TRP	0	0.036	0.000	13.360	-0.130	-0.130	0.000	0.000	0.000
12	A	42	LEU	0	-0.005	0.007	16.869	-0.051	-0.051	0.000	0.000	0.000
13	A	43	GLU	-1	-0.881	-0.933	18.369	0.146	0.146	0.000	0.000	0.000
14	A	44	LEU	0	-0.050	-0.017	16.775	-0.038	-0.038	0.000	0.000	0.000
15	A	45	HIS	0	0.021	0.006	19.642	-0.049	-0.049	0.000	0.000	0.000
16	A	46	ASN	0	0.052	0.020	23.019	-0.037	-0.037	0.000	0.000	0.000
17	A	47	ASN	0	-0.021	0.010	22.445	-0.013	-0.013	0.000	0.000	0.000
18	A	48	GLU	-1	-0.805	-0.868	25.246	0.005	0.005	0.000	0.000	0.000
19	A	49	ARG	1	0.818	0.902	27.119	-0.145	-0.145	0.000	0.000	0.000
20	A	50	THR	0	0.018	-0.003	28.015	-0.004	-0.004	0.000	0.000	0.000
21	A	51	THR	0	-0.082	-0.056	28.937	-0.010	-0.010	0.000	0.000	0.000
22	A	52	ARG	1	0.747	0.850	29.165	-0.039	-0.039	0.000	0.000	0.000
23	A	53	GLN	0	-0.076	-0.028	33.697	0.003	0.003	0.000	0.000	0.000
24	A	54	LEU	0	0.018	0.024	31.875	0.000	0.000	0.000	0.000	0.000
25	A	55	ASP	-1	-0.873	-0.933	31.487	0.162	0.162	0.000	0.000	0.000
26	A	56	SER	0	-0.076	-0.042	26.535	0.000	0.000	0.000	0.000	0.000
27	A	57	LEU	0	-0.038	0.002	24.874	0.007	0.007	0.000	0.000	0.000
28	A	58	GLU	-1	-0.860	-0.923	24.678	0.329	0.329	0.000	0.000	0.000
29	A	59	TRP	0	0.010	-0.012	15.672	-0.003	-0.003	0.000	0.000	0.000
30	A	60	ASP	-1	-0.834	-0.928	21.121	0.368	0.368	0.000	0.000	0.000
31	A	61	GLY	0	-0.012	-0.011	18.523	0.020	0.020	0.000	0.000	0.000
32	A	62	ASP	-1	-0.886	-0.938	18.603	0.442	0.442	0.000	0.000	0.000
33	A	63	LEU	0	-0.036	-0.015	20.627	-0.027	-0.027	0.000	0.000	0.000
34	A	64	ALA	0	0.008	0.009	15.842	-0.031	-0.031	0.000	0.000	0.000
35	A	65	TRP	0	-0.014	0.001	15.663	-0.060	-0.060	0.000	0.000	0.000
36	A	66	LYS	1	0.796	0.896	16.899	-0.218	-0.218	0.000	0.000	0.000
37	A	67	ALA	0	0.017	0.009	17.064	-0.050	-0.050	0.000	0.000	0.000
38	A	68	GLN	0	-0.007	-0.007	9.897	-0.024	-0.024	0.000	0.000	0.000
39	A	69	GLN	0	-0.068	-0.017	14.582	-0.106	-0.106	0.000	0.000	0.000
40	A	70	VAL	0	0.014	0.017	17.087	-0.044	-0.044	0.000	0.000	0.000
41	A	71	ALA	0	0.002	-0.005	14.037	-0.046	-0.046	0.000	0.000	0.000
42	A	72	THR	0	-0.041	-0.053	12.876	-0.080	-0.080	0.000	0.000	0.000
43	A	73	GLN	0	-0.065	-0.025	14.324	-0.055	-0.055	0.000	0.000	0.000
44	A	74	CYS	0	-0.061	-0.020	10.163	0.099	0.099	0.000	0.000	0.000
45	A	75	ASN	0	-0.006	0.003	17.166	-0.027	-0.027	0.000	0.000	0.000
46	A	76	VAL	0	0.013	-0.013	19.767	0.021	0.021	0.000	0.000	0.000
47	A	77	ASP	-1	-0.935	-0.959	22.180	-0.152	-0.152	0.000	0.000	0.000
48	A	78	ASN	0	-0.076	-0.042	25.045	0.028	0.028	0.000	0.000	0.000
49	A	79	PRO	0	0.020	0.030	21.868	0.002	0.002	0.000	0.000	0.000
50	A	80	GLN	0	-0.027	-0.018	23.418	0.002	0.002	0.000	0.000	0.000
51	A	81	LEU	0	-0.004	0.004	23.387	0.015	0.015	0.000	0.000	0.000
52	A	82	TRP	0	0.056	0.005	21.994	-0.005	-0.005	0.000	0.000	0.000
53	A	83	GLY	0	0.036	0.016	27.005	0.011	0.011	0.000	0.000	0.000
54	A	84	ASP	-1	-0.872	-0.926	29.394	0.118	0.118	0.000	0.000	0.000
55	A	85	ASN	0	0.001	-0.001	26.455	-0.016	-0.016	0.000	0.000	0.000
56	A	86	GLY	0	0.020	0.010	26.502	0.002	0.002	0.000	0.000	0.000
57	A	87	ALA	0	0.024	0.012	26.186	-0.007	-0.007	0.000	0.000	0.000
58	A	88	SER	0	-0.064	-0.048	27.382	-0.022	-0.022	0.000	0.000	0.000
59	A	89	PHE	0	-0.005	-0.009	22.262	0.021	0.021	0.000	0.000	0.000
60	A	90	ASN	0	-0.031	-0.004	22.803	-0.022	-0.022	0.000	0.000	0.000
61	A	91	ILE	0	0.044	0.006	19.388	0.019	0.019	0.000	0.000	0.000
62	A	92	GLY	0	0.042	0.043	19.182	0.003	0.003	0.000	0.000	0.000
63	A	93	ARG	1	0.923	0.973	17.407	0.287	0.287	0.000	0.000	0.000
64	A	94	TYR	0	0.009	0.006	14.580	0.031	0.031	0.000	0.000	0.000
65	A	95	THR	0	-0.003	-0.018	12.135	0.025	0.025	0.000	0.000	0.000
66	A	96	LYS	1	0.870	0.920	9.398	0.266	0.266	0.000	0.000	0.000
67	A	97	GLU	-1	-0.845	-0.915	14.655	-0.054	-0.054	0.000	0.000	0.000
68	A	98	GLN	0	0.010	0.027	16.326	-0.036	-0.036	0.000	0.000	0.000
69	A	99	ALA	0	0.028	0.028	17.304	0.031	0.031	0.000	0.000	0.000
70	A	100	PHE	0	0.034	0.005	18.734	0.033	0.033	0.000	0.000	0.000
71	A	101	ALA	0	0.001	0.002	20.635	0.018	0.018	0.000	0.000	0.000
72	A	102	GLU	-1	-0.921	-0.965	21.411	-0.207	-0.207	0.000	0.000	0.000
73	A	103	TRP	0	-0.019	-0.028	18.796	0.028	0.028	0.000	0.000	0.000
74	A	104	THR	0	0.036	0.018	24.641	0.003	0.003	0.000	0.000	0.000
75	A	105	ALA	0	0.006	0.015	26.643	0.008	0.008	0.000	0.000	0.000
76	A	106	THR	0	-0.062	-0.041	28.300	0.006	0.006	0.000	0.000	0.000
77	A	107	SER	0	-0.008	-0.022	30.595	0.006	0.006	0.000	0.000	0.000
78	A	108	GLY	0	-0.048	-0.017	32.518	0.006	0.006	0.000	0.000	0.000
79	A	109	SER	0	-0.062	-0.049	34.981	-0.002	-0.002	0.000	0.000	0.000
80	A	110	PHE	0	0.022	0.035	35.465	0.004	0.004	0.000	0.000	0.000
81	A	111	PRO	0	-0.063	-0.032	37.182	-0.002	-0.002	0.000	0.000	0.000
82	A	112	ASP	-1	-0.769	-0.871	36.798	-0.028	-0.028	0.000	0.000	0.000
83	A	113	ASP	-1	-0.799	-0.893	36.100	-0.013	-0.013	0.000	0.000	0.000
84	A	114	ARG	1	0.763	0.860	33.414	0.031	0.031	0.000	0.000	0.000
85	A	115	SER	0	0.006	-0.004	31.976	-0.002	-0.002	0.000	0.000	0.000
86	A	116	ILE	0	0.006	0.008	30.250	0.008	0.008	0.000	0.000	0.000
87	A	117	PRO	0	-0.005	-0.003	26.310	0.013	0.013	0.000	0.000	0.000
88	A	118	TRP	0	0.001	0.008	27.315	0.013	0.013	0.000	0.000	0.000
89	A	119	GLN	0	-0.033	-0.036	29.128	0.022	0.022	0.000	0.000	0.000
90	A	120	ARG	1	0.837	0.934	26.575	-0.032	-0.032	0.000	0.000	0.000
91	A	121	ILE	0	-0.022	0.001	24.395	0.018	0.018	0.000	0.000	0.000
92	A	122	VAL	0	-0.037	-0.015	27.303	0.017	0.017	0.000	0.000	0.000
93	A	123	ALA	0	0.005	0.013	30.757	0.000	0.000	0.000	0.000	0.000
94	A	124	ASN	0	-0.029	-0.031	32.347	0.021	0.021	0.000	0.000	0.000
95	A	125	SER	0	0.009	0.027	34.851	0.009	0.009	0.000	0.000	0.000
96	A	126	ALA	0	-0.018	-0.003	29.327	0.012	0.012	0.000	0.000	0.000
97	A	127	GLN	0	0.001	-0.023	29.994	0.012	0.012	0.000	0.000	0.000
98	A	128	LYS	1	0.844	0.918	25.159	-0.269	-0.269	0.000	0.000	0.000
99	A	129	VAL	0	0.022	0.003	21.024	-0.029	-0.029	0.000	0.000	0.000
100	A	130	GLY	0	0.008	0.012	19.331	0.055	0.055	0.000	0.000	0.000
101	A	131	CYS	0	-0.050	-0.012	16.237	-0.002	-0.002	0.000	0.000	0.000
102	A	132	GLY	0	0.012	-0.007	13.164	0.134	0.134	0.000	0.000	0.000
103	A	133	GLU	-1	-0.831	-0.917	9.450	-0.466	-0.466	0.000	0.000	0.000
104	A	134	ALA	0	0.005	0.016	9.747	0.110	0.110	0.000	0.000	0.000
105	A	135	THR	0	-0.031	-0.009	7.377	-0.003	-0.003	0.000	0.000	0.000
106	A	137	VAL	0	0.027	-0.001	13.231	-0.131	-0.131	0.000	0.000	0.000
107	A	138	LEU	0	0.001	0.006	15.403	0.100	0.100	0.000	0.000	0.000
108	A	139	GLU	-1	-0.909	-0.955	18.335	-0.525	-0.525	0.000	0.000	0.000
109	A	140	GLY	0	-0.044	-0.024	20.035	0.022	0.022	0.000	0.000	0.000
110	A	141	ASP	-1	-0.907	-0.943	18.791	-0.621	-0.621	0.000	0.000	0.000
111	A	142	MET	0	-0.092	-0.048	14.606	-0.103	-0.103	0.000	0.000	0.000
112	A	143	ALA	0	-0.010	-0.009	10.847	0.073	0.073	0.000	0.000	0.000
113	A	144	TYR	0	-0.059	-0.032	12.848	-0.016	-0.016	0.000	0.000	0.000
114	A	145	THR	0	-0.001	0.003	10.119	-0.072	-0.072	0.000	0.000	0.000
115	A	146	VAL	0	-0.011	0.005	12.405	0.095	0.095	0.000	0.000	0.000
116	A	147	ASN	0	-0.033	-0.045	13.696	0.041	0.041	0.000	0.000	0.000
117	A	148	VAL	0	0.010	0.000	15.674	-0.004	-0.004	0.000	0.000	0.000
118	A	150	TYR	0	0.012	-0.010	19.951	-0.031	-0.031	0.000	0.000	0.000
119	A	151	TYR	0	-0.027	-0.046	22.559	0.018	0.018	0.000	0.000	0.000
120	A	152	ASP	-1	-0.816	-0.892	25.696	0.167	0.167	0.000	0.000	0.000
121	A	153	PRO	0	0.056	0.025	28.450	0.012	0.012	0.000	0.000	0.000
122	A	154	PRO	0	-0.041	-0.013	30.449	-0.006	-0.006	0.000	0.000	0.000
123	A	155	LEU	0	-0.049	0.001	30.981	-0.004	-0.004	0.000	0.000	0.000
124	A	156	SER	0	-0.017	-0.014	32.816	-0.003	-0.003	0.000	0.000	0.000
125	A	157	ASP	-1	-0.826	-0.885	36.538	0.048	0.048	0.000	0.000	0.000
126	A	158	TYR	0	0.001	-0.008	39.170	0.004	0.004	0.000	0.000	0.000
127	A	159	TYR	0	-0.034	-0.016	40.123	0.000	0.000	0.000	0.000	0.000
128	A	160	THR	0	-0.024	-0.045	37.952	0.005	0.005	0.000	0.000	0.000
129	A	161	ASN	0	-0.027	-0.019	35.772	0.015	0.015	0.000	0.000	0.000
130	A	162	ALA	0	0.011	0.003	36.379	0.004	0.004	0.000	0.000	0.000
131	A	163	GLY	0	-0.031	0.001	38.952	0.001	0.001	0.000	0.000	0.000
132	A	164	ASP	-1	-0.940	-0.953	37.214	0.100	0.100	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:GLN)