FMO DATABASE

FMODB ID: MVK9Z

Calculation Name: 4NXJ-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: 4NXJ

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8IK82

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1083224.39871
FMO2-HF: Nuclear repulsion	1033415.423222
FMO2-HF: Total energy	-49808.975488
FMO2-MP2: Total energy	-49955.183521

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:GLY)

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

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.
-12.629	-12.455	9.981	-5.246	-4.909	-0.051

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.006

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	3	ASP	-1	-0.844	-0.930	3.859	-3.830	-2.127	-0.005	-0.816	-0.882	0.003
4	A	4	GLU	-1	-0.833	-0.908	1.905	-14.890	-16.612	9.987	-4.383	-3.882	-0.054
5	A	5	ILE	0	-0.024	-0.014	4.338	2.233	2.426	-0.001	-0.047	-0.145	0.000
6	A	6	GLU	-1	-0.725	-0.836	6.026	-0.674	-0.674	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.790	-0.852	7.839	-0.784	-0.784	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.005	-0.007	6.848	0.583	0.583	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.795	0.873	9.810	1.970	1.970	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.041	-0.025	12.024	0.307	0.307	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.858	0.911	11.378	1.217	1.217	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.000	-0.017	14.055	0.177	0.177	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.806	-0.859	15.915	-0.399	-0.399	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.023	-0.007	18.027	0.095	0.095	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.000	0.004	17.595	0.064	0.064	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.009	-0.020	19.246	0.069	0.069	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.068	-0.037	21.777	0.086	0.086	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.006	0.006	23.795	0.035	0.035	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.027	0.017	23.817	0.028	0.028	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.023	0.006	25.059	0.033	0.033	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.895	0.951	27.541	0.298	0.298	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.006	0.017	27.596	0.019	0.019	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.013	0.004	27.881	0.016	0.016	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.020	-0.005	31.583	0.013	0.013	0.000	0.000	0.000	0.000
25	A	25	PHE	0	0.015	0.009	33.523	0.013	0.013	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.715	-0.841	34.479	-0.122	-0.122	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.820	0.896	36.203	0.138	0.138	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.910	0.944	39.009	0.102	0.102	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.869	0.952	35.491	0.125	0.125	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.025	-0.007	36.991	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.034	0.007	33.409	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.021	-0.006	30.556	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.025	0.016	31.316	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.009	0.012	31.327	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.013	0.016	33.871	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.038	0.022	37.468	0.007	0.007	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.060	0.027	38.965	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.059	-0.037	41.224	0.006	0.006	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.053	-0.025	43.559	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.027	-0.005	42.078	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.021	0.001	43.538	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.832	-0.892	44.550	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.046	0.022	36.388	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.016	-0.003	36.343	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.006	0.013	39.685	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.020	0.034	41.229	0.002	0.002	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.029	0.001	35.512	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.788	0.859	35.372	0.054	0.054	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.824	-0.881	27.562	-0.116	-0.116	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.015	0.019	32.000	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.016	-0.011	26.706	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.719	-0.831	29.025	-0.146	-0.146	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.045	-0.018	27.732	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.034	-0.018	26.758	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.042	-0.054	25.493	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.036	-0.005	23.486	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.880	0.937	22.060	0.255	0.255	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.031	0.015	21.471	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.826	0.914	19.580	0.184	0.184	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.019	-0.001	17.646	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.022	0.008	16.619	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.075	-0.047	16.030	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.010	0.008	11.980	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.953	0.984	13.215	0.138	0.138	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.062	-0.063	15.241	0.016	0.016	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.854	0.917	10.395	0.491	0.491	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.043	-0.035	14.002	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.010	-0.002	16.852	0.008	0.008	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.014	-0.027	19.913	0.043	0.043	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.766	-0.853	17.354	-0.335	-0.335	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.022	0.008	20.716	0.019	0.019	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.741	-0.836	22.474	-0.209	-0.209	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.863	0.911	24.612	0.155	0.155	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.750	-0.853	23.824	-0.199	-0.199	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.002	-0.008	26.255	0.014	0.014	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.007	0.004	28.671	0.014	0.014	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.022	0.018	28.710	0.012	0.012	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.044	-0.019	28.795	0.010	0.010	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.024	-0.006	32.421	0.008	0.008	0.000	0.000	0.000	0.000
80	A	80	ASN	0	0.000	-0.022	34.001	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.007	-0.005	33.000	0.014	0.014	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.087	-0.026	36.596	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.033	-0.062	37.973	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.042	-0.022	38.669	0.006	0.006	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.072	-0.058	41.035	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.044	-0.020	41.687	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.732	-0.842	44.313	-0.059	-0.059	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.019	0.008	46.596	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.084	-0.050	47.592	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.056	-0.044	46.387	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.012	-0.017	45.247	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.017	-0.008	41.499	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.089	0.054	41.521	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.833	0.919	42.176	0.091	0.091	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.024	-0.026	39.987	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.026	0.017	37.851	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.768	-0.875	37.856	-0.096	-0.096	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.908	-0.941	39.299	-0.111	-0.111	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.062	-0.037	33.193	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.766	-0.858	34.417	-0.138	-0.138	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.034	-0.033	35.065	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.133	-0.083	32.132	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.005	-0.042	26.900	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.902	0.948	31.184	0.117	0.117	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.913	0.983	33.266	0.142	0.142	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.075	-0.037	29.190	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	ASN	0	0.029	-0.008	27.059	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.046	0.033	26.084	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.903	0.954	26.093	0.193	0.193	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.021	-0.012	22.631	-0.024	-0.024	0.000	0.000	0.000	0.000
111	A	111	GLN	0	0.025	0.017	21.879	-0.048	-0.048	0.000	0.000	0.000	0.000
112	A	112	THR	0	0.016	-0.007	21.026	-0.027	-0.027	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.814	0.893	20.690	0.455	0.455	0.000	0.000	0.000	0.000
114	A	114	TYR	0	0.009	0.001	15.377	-0.067	-0.067	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.024	-0.020	16.315	-0.068	-0.068	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.009	-0.013	16.473	-0.029	-0.029	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.063	-0.010	12.430	0.001	0.001	0.000	0.000	0.000	0.000
118	A	118	HIS	0	-0.078	-0.039	10.142	0.096	0.096	0.000	0.000	0.000	0.000

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