FMO DATABASE

FMODB ID: VRNR1

Calculation Name: 1X90-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: 1X90

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9LNF2

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1183901.440545
FMO2-HF: Nuclear repulsion	1126449.743367
FMO2-HF: Total energy	-57451.697178
FMO2-MP2: Total energy	-57613.141124

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:3:GLU)

Summations of interaction energy for fragment #1(A:3: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.
-77.459	-73.385	0.076	-1.865	-2.284	0.01

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.920 / q_NPA : -0.971

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	5	SER	0	0.028	0.006	3.327	-13.714	-10.479	0.027	-1.553	-1.708	0.010
4	A	6	THR	0	0.013	0.013	3.143	-6.796	-5.957	0.049	-0.312	-0.576	0.000
5	A	7	ILE	0	-0.004	-0.005	5.295	-6.398	-6.398	0.000	0.000	0.000	0.000
6	A	8	CYS	0	0.013	0.002	7.384	-2.715	-2.715	0.000	0.000	0.000	0.000
7	A	9	ASP	-1	-0.877	-0.931	8.807	29.090	29.090	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.873	0.941	8.740	-27.690	-27.690	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.056	-0.017	12.121	-1.833	-1.833	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.029	0.004	14.437	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	13	ASN	0	0.028	0.005	16.285	0.031	0.031	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.072	0.039	11.914	0.483	0.483	0.000	0.000	0.000	0.000
13	A	15	SER	0	0.025	0.020	11.887	1.733	1.733	0.000	0.000	0.000	0.000
14	A	16	PHE	0	-0.044	-0.020	13.235	0.826	0.826	0.000	0.000	0.000	0.000
15	A	18	LEU	0	0.081	0.043	7.050	1.245	1.245	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.961	1.006	9.327	-18.791	-18.791	0.000	0.000	0.000	0.000
17	A	20	PHE	0	-0.023	-0.018	11.679	-0.652	-0.652	0.000	0.000	0.000	0.000
18	A	21	LEU	0	0.053	-0.004	6.189	-1.309	-1.309	0.000	0.000	0.000	0.000
19	A	22	ASN	0	0.021	0.007	6.071	6.697	6.697	0.000	0.000	0.000	0.000
20	A	23	THR	0	-0.037	-0.027	8.393	-1.801	-1.801	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.918	0.962	10.983	-20.569	-20.569	0.000	0.000	0.000	0.000
22	A	25	PHE	0	0.023	0.033	5.302	-0.658	-0.658	0.000	0.000	0.000	0.000
23	A	26	ALA	0	0.032	0.016	9.004	-0.949	-0.949	0.000	0.000	0.000	0.000
24	A	27	SER	0	-0.022	-0.026	11.257	-1.617	-1.617	0.000	0.000	0.000	0.000
25	A	28	ALA	0	0.008	0.005	10.894	-1.337	-1.337	0.000	0.000	0.000	0.000
26	A	29	ASN	0	-0.023	-0.010	9.830	-2.295	-2.295	0.000	0.000	0.000	0.000
27	A	30	LEU	0	0.023	0.000	12.317	-1.379	-1.379	0.000	0.000	0.000	0.000
28	A	31	GLN	0	0.006	-0.015	15.676	-1.703	-1.703	0.000	0.000	0.000	0.000
29	A	32	ALA	0	0.006	0.010	14.152	-1.040	-1.040	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.001	0.004	14.064	-1.009	-1.009	0.000	0.000	0.000	0.000
31	A	34	ALA	0	0.019	0.028	17.432	-0.979	-0.979	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.870	0.927	19.263	-13.966	-13.966	0.000	0.000	0.000	0.000
33	A	36	THR	0	0.028	0.005	18.235	-0.681	-0.681	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.035	-0.013	20.809	-0.655	-0.655	0.000	0.000	0.000	0.000
35	A	38	LEU	0	0.039	0.033	23.034	-0.652	-0.652	0.000	0.000	0.000	0.000
36	A	39	ASP	-1	-0.798	-0.861	23.448	12.142	12.142	0.000	0.000	0.000	0.000
37	A	40	SER	0	-0.073	-0.042	23.882	-0.522	-0.522	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.038	-0.055	26.522	-0.500	-0.500	0.000	0.000	0.000	0.000
39	A	42	GLN	0	0.056	0.020	28.660	-0.514	-0.514	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.007	0.012	29.340	-0.449	-0.449	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.929	0.947	29.313	-10.534	-10.534	0.000	0.000	0.000	0.000
42	A	45	ALA	0	0.041	0.028	32.733	-0.356	-0.356	0.000	0.000	0.000	0.000
43	A	46	THR	0	0.014	0.000	33.788	-0.339	-0.339	0.000	0.000	0.000	0.000
44	A	47	GLN	0	-0.086	-0.041	33.840	-0.515	-0.515	0.000	0.000	0.000	0.000
45	A	48	THR	0	-0.036	-0.043	36.528	-0.311	-0.311	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.033	0.037	38.451	-0.186	-0.186	0.000	0.000	0.000	0.000
47	A	50	LYS	1	0.946	0.976	37.772	-8.291	-8.291	0.000	0.000	0.000	0.000
48	A	51	LYS	1	0.833	0.921	39.201	-8.149	-8.149	0.000	0.000	0.000	0.000
49	A	52	LEU	0	-0.023	0.002	41.860	-0.176	-0.176	0.000	0.000	0.000	0.000
50	A	53	GLN	0	0.023	0.001	43.846	-0.147	-0.147	0.000	0.000	0.000	0.000
51	A	54	SER	0	-0.016	-0.003	45.365	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.049	-0.017	45.299	-0.159	-0.159	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.066	-0.037	48.290	-0.188	-0.188	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.920	-0.957	50.223	6.111	6.111	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.092	-0.043	51.300	-0.130	-0.130	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.019	0.006	53.074	-0.119	-0.119	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.038	-0.029	51.750	0.054	0.054	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.823	-0.873	55.112	5.732	5.732	0.000	0.000	0.000	0.000
59	A	62	PRO	0	0.041	-0.004	55.856	0.100	0.100	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.901	0.964	52.847	-5.892	-5.892	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.008	-0.058	51.729	0.135	0.135	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.909	0.964	51.246	-5.743	-5.743	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.014	-0.009	51.617	0.083	0.083	0.000	0.000	0.000	0.000
64	A	67	ALA	0	0.063	0.044	48.635	0.077	0.077	0.000	0.000	0.000	0.000
65	A	68	TYR	0	0.036	-0.015	46.067	0.209	0.209	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.936	0.967	47.100	-5.954	-5.954	0.000	0.000	0.000	0.000
67	A	70	SER	0	0.045	0.043	47.382	0.011	0.011	0.000	0.000	0.000	0.000
68	A	71	CYS	0	-0.046	0.001	40.554	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	72	VAL	0	-0.036	-0.013	42.765	0.209	0.209	0.000	0.000	0.000	0.000
70	A	73	ASP	-1	-0.881	-0.936	43.185	6.863	6.863	0.000	0.000	0.000	0.000
71	A	74	GLU	-1	-0.878	-0.940	40.959	7.719	7.719	0.000	0.000	0.000	0.000
72	A	75	TYR	0	-0.066	-0.077	36.021	0.410	0.410	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.877	-0.938	38.351	7.428	7.428	0.000	0.000	0.000	0.000
74	A	77	SER	0	0.000	0.009	39.227	0.198	0.198	0.000	0.000	0.000	0.000
75	A	78	ALA	0	0.003	0.007	35.579	0.217	0.217	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.031	-0.023	34.414	0.330	0.330	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.018	0.021	34.267	0.239	0.239	0.000	0.000	0.000	0.000
78	A	81	ASN	0	0.037	0.000	34.485	0.324	0.324	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.035	-0.017	29.557	0.387	0.387	0.000	0.000	0.000	0.000
80	A	83	GLH	0	-0.103	-0.087	29.581	0.573	0.573	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.766	-0.875	30.331	9.095	9.095	0.000	0.000	0.000	0.000
82	A	85	ALA	0	-0.008	-0.012	28.313	0.270	0.270	0.000	0.000	0.000	0.000
83	A	86	PHE	0	-0.043	-0.030	23.499	0.691	0.691	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.846	-0.886	26.069	10.142	10.142	0.000	0.000	0.000	0.000
85	A	88	HIS	0	-0.079	-0.044	27.420	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	89	LEU	0	-0.023	-0.013	20.585	0.438	0.438	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.037	-0.013	22.726	0.648	0.648	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.045	-0.019	23.697	0.211	0.211	0.000	0.000	0.000	0.000
89	A	92	GLY	0	-0.016	-0.014	22.783	0.064	0.064	0.000	0.000	0.000	0.000
90	A	93	ASP	-1	-0.866	-0.934	23.532	10.839	10.839	0.000	0.000	0.000	0.000
91	A	94	GLY	0	0.030	0.005	24.974	-0.231	-0.231	0.000	0.000	0.000	0.000
92	A	95	MET	0	-0.031	-0.033	25.850	-0.203	-0.203	0.000	0.000	0.000	0.000
93	A	96	GLY	0	0.054	0.060	29.277	-0.337	-0.337	0.000	0.000	0.000	0.000
94	A	97	MET	0	-0.013	0.011	23.061	0.020	0.020	0.000	0.000	0.000	0.000
95	A	98	ASN	0	-0.054	-0.027	27.351	-0.460	-0.460	0.000	0.000	0.000	0.000
96	A	99	MET	0	0.015	0.011	29.175	-0.273	-0.273	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.840	0.907	31.517	-9.187	-9.187	0.000	0.000	0.000	0.000
98	A	101	VAL	0	-0.017	-0.016	27.294	-0.121	-0.121	0.000	0.000	0.000	0.000
99	A	102	SER	0	-0.051	-0.026	30.750	-0.119	-0.119	0.000	0.000	0.000	0.000
100	A	103	ALA	0	0.065	0.041	33.165	-0.147	-0.147	0.000	0.000	0.000	0.000
101	A	104	ALA	0	0.005	0.003	32.746	-0.200	-0.200	0.000	0.000	0.000	0.000
102	A	105	LEU	0	-0.074	-0.039	31.094	-0.124	-0.124	0.000	0.000	0.000	0.000
103	A	106	ASP	-1	-0.875	-0.951	34.259	8.473	8.473	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.069	0.066	37.569	-0.253	-0.253	0.000	0.000	0.000	0.000
105	A	108	ALA	0	-0.072	-0.044	35.590	-0.170	-0.170	0.000	0.000	0.000	0.000
106	A	109	ASP	-1	-0.858	-0.927	37.447	8.162	8.162	0.000	0.000	0.000	0.000
107	A	110	THR	0	0.027	0.012	38.858	-0.226	-0.226	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.029	-0.046	37.238	-0.148	-0.148	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.856	-0.924	41.525	7.042	7.042	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.874	-0.925	44.388	6.655	6.655	0.000	0.000	0.000	0.000
111	A	115	VAL	0	-0.072	-0.056	43.665	-0.191	-0.191	0.000	0.000	0.000	0.000
112	A	116	LYS	1	0.769	0.886	43.645	-7.283	-7.283	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.933	0.966	45.517	-6.187	-6.187	0.000	0.000	0.000	0.000
114	A	118	LEU	0	-0.028	-0.006	48.743	-0.215	-0.215	0.000	0.000	0.000	0.000
115	A	119	ARG	1	0.912	0.954	49.919	-6.009	-6.009	0.000	0.000	0.000	0.000
116	A	120	SER	0	-0.009	-0.015	49.848	0.059	0.059	0.000	0.000	0.000	0.000
117	A	121	VAL	0	0.038	0.032	45.466	-0.039	-0.039	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.724	-0.862	42.895	7.383	7.383	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.005	-0.013	41.404	0.105	0.105	0.000	0.000	0.000	0.000
120	A	124	SER	0	0.057	0.033	38.717	0.239	0.239	0.000	0.000	0.000	0.000
121	A	125	VAL	0	0.011	0.016	38.583	0.284	0.284	0.000	0.000	0.000	0.000
122	A	126	VAL	0	0.035	0.045	39.190	0.211	0.211	0.000	0.000	0.000	0.000
123	A	127	ASN	0	-0.029	-0.026	35.741	0.142	0.142	0.000	0.000	0.000	0.000
124	A	128	ASN	0	-0.033	-0.009	34.232	0.589	0.589	0.000	0.000	0.000	0.000
125	A	129	SER	0	0.106	0.050	34.225	0.247	0.247	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.951	0.985	34.580	-8.493	-8.493	0.000	0.000	0.000	0.000
127	A	131	THR	0	-0.083	-0.057	29.624	0.312	0.312	0.000	0.000	0.000	0.000
128	A	132	ILE	0	0.039	0.009	29.887	0.458	0.458	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.868	0.938	30.901	-8.647	-8.647	0.000	0.000	0.000	0.000
130	A	134	ASN	0	-0.040	-0.027	27.961	0.088	0.088	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.043	-0.014	25.170	0.398	0.398	0.000	0.000	0.000	0.000
132	A	136	CYS	0	0.008	0.012	26.109	0.398	0.398	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.049	0.026	27.368	0.202	0.202	0.000	0.000	0.000	0.000
134	A	138	ILE	0	-0.015	-0.013	21.149	0.312	0.312	0.000	0.000	0.000	0.000
135	A	139	ALA	0	0.027	0.011	23.036	0.483	0.483	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.001	0.013	24.290	0.241	0.241	0.000	0.000	0.000	0.000
137	A	141	VAL	0	0.012	0.020	21.047	0.172	0.172	0.000	0.000	0.000	0.000
138	A	142	ILE	0	0.030	0.003	18.800	0.282	0.282	0.000	0.000	0.000	0.000
139	A	143	SER	0	-0.029	-0.028	20.986	0.147	0.147	0.000	0.000	0.000	0.000
140	A	144	ASN	0	-0.022	-0.031	23.566	-0.299	-0.299	0.000	0.000	0.000	0.000
141	A	145	MET	0	-0.064	-0.015	16.050	0.076	0.076	0.000	0.000	0.000	0.000
142	A	146	LEU	0	-0.050	-0.002	19.751	0.673	0.673	0.000	0.000	0.000	0.000
143	A	147	PRO	0	-0.025	-0.011	19.050	-0.462	-0.462	0.000	0.000	0.000	0.000
144	A	148	ARG	1	0.892	0.945	21.828	-13.052	-13.052	0.000	0.000	0.000	0.000
145	A	149	ASN	0	0.005	0.011	25.029	0.294	0.294	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)