FMO DATABASE

FMODB ID: VRLR1

Calculation Name: 1XG8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XG8

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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	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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-941493.032976
FMO2-HF: Nuclear repulsion	895954.806915
FMO2-HF: Total energy	-45538.226062
FMO2-MP2: Total energy	-45671.80456

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:-8:ALA)

Summations of interaction energy for fragment #1(A:-8:ALA)

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.
-3.347	-0.371	-0.018	-1.309	-1.649	0.005

Interaction energy analysis for fragmet #1(A:-8:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.018

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	-6	LEU	0	0.049	0.032	3.827	-0.228	1.933	-0.020	-1.154	-0.987	0.005
4	A	-5	TYR	0	-0.019	-0.013	6.202	0.566	0.566	0.000	0.000	0.000	0.000
5	A	-4	PHE	0	-0.048	-0.010	3.802	-0.051	0.122	0.001	-0.025	-0.149	0.000
6	A	-3	GLN	0	-0.044	-0.021	4.792	0.582	0.740	-0.001	-0.006	-0.151	0.000
7	A	-2	SER	0	-0.063	-0.038	8.529	-0.132	-0.132	0.000	0.000	0.000	0.000
8	A	-1	ASN	0	-0.037	-0.036	6.670	-0.030	-0.030	0.000	0.000	0.000	0.000
9	A	0	ALA	0	0.029	0.013	9.060	0.017	0.017	0.000	0.000	0.000	0.000
10	A	1	VAL	0	-0.015	0.007	10.991	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	2	VAL	0	0.032	0.015	13.400	0.025	0.025	0.000	0.000	0.000	0.000
12	A	3	VAL	0	-0.031	-0.021	16.097	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	4	TYR	0	0.022	-0.012	16.360	0.009	0.009	0.000	0.000	0.000	0.000
14	A	5	GLY	0	0.049	-0.016	21.356	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	6	ALA	0	0.025	0.044	24.988	0.010	0.010	0.000	0.000	0.000	0.000
16	A	7	ASP	-1	-0.848	-0.916	28.464	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	8	VAL	0	0.003	0.004	31.181	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	9	ILE	0	-0.003	0.003	31.079	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	10	CYS	0	0.025	0.048	28.527	0.007	0.007	0.000	0.000	0.000	0.000
20	A	11	ALA	0	0.024	-0.004	31.077	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	12	SER	0	0.018	0.009	30.149	0.000	0.000	0.000	0.000	0.000	0.000
22	A	13	CYS	0	-0.092	-0.048	28.983	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	14	VAL	0	0.028	0.024	31.488	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	15	ASN	0	-0.036	-0.029	34.341	0.003	0.003	0.000	0.000	0.000	0.000
25	A	16	ALA	0	-0.052	-0.003	28.676	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	17	PRO	0	-0.014	-0.014	27.348	0.005	0.005	0.000	0.000	0.000	0.000
27	A	18	THR	0	0.086	0.049	28.087	0.001	0.001	0.000	0.000	0.000	0.000
28	A	19	SER	0	0.049	0.004	24.999	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	20	LYS	1	0.850	0.902	24.769	0.022	0.022	0.000	0.000	0.000	0.000
30	A	21	ASP	-1	-0.835	-0.904	26.320	-0.079	-0.079	0.000	0.000	0.000	0.000
31	A	22	ILE	0	-0.003	-0.002	21.688	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	23	TYR	0	0.020	0.008	19.618	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	24	ASP	-1	-0.885	-0.937	22.180	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	25	TRP	0	-0.099	-0.049	20.971	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	26	LEU	0	-0.006	-0.017	16.774	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	27	GLN	0	-0.012	-0.011	19.315	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	28	PRO	0	-0.050	-0.029	20.124	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	29	LEU	0	-0.049	-0.017	19.703	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	30	LEU	0	0.011	0.008	14.327	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	31	LYS	1	0.984	1.011	17.662	0.156	0.156	0.000	0.000	0.000	0.000
41	A	32	ARG	1	0.881	0.939	19.430	0.193	0.193	0.000	0.000	0.000	0.000
42	A	33	LYS	1	0.910	0.955	18.676	0.310	0.310	0.000	0.000	0.000	0.000
43	A	34	TYR	0	-0.040	-0.053	14.385	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	35	PRO	0	0.006	0.004	16.001	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	36	ASN	0	-0.024	-0.014	15.597	0.064	0.064	0.000	0.000	0.000	0.000
46	A	37	ILE	0	-0.001	0.024	10.297	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	38	SER	0	0.010	0.020	11.842	0.099	0.099	0.000	0.000	0.000	0.000
48	A	39	PHE	0	0.035	0.013	11.246	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	40	LYS	1	0.907	0.961	11.687	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	41	TYR	0	0.027	0.002	14.430	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	42	THR	0	-0.003	0.001	17.104	0.029	0.029	0.000	0.000	0.000	0.000
52	A	43	TYR	0	-0.040	-0.012	18.712	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	44	ILE	0	0.019	0.016	19.005	0.010	0.010	0.000	0.000	0.000	0.000
54	A	45	ASP	-1	-0.818	-0.905	22.586	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	46	ILE	0	0.007	-0.011	24.117	0.006	0.006	0.000	0.000	0.000	0.000
56	A	47	THR	0	-0.014	0.002	26.452	0.003	0.003	0.000	0.000	0.000	0.000
57	A	48	LYS	1	0.796	0.868	28.329	0.004	0.004	0.000	0.000	0.000	0.000
58	A	49	ASP	-1	-0.835	-0.893	26.778	0.054	0.054	0.000	0.000	0.000	0.000
59	A	50	ASN	0	-0.146	-0.083	24.280	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	51	ASP	-1	-0.863	-0.925	26.069	0.072	0.072	0.000	0.000	0.000	0.000
61	A	52	ASN	0	-0.190	-0.103	20.915	0.020	0.020	0.000	0.000	0.000	0.000
62	A	53	LEU	0	0.052	0.025	20.684	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	54	THR	0	-0.043	-0.036	15.523	0.025	0.025	0.000	0.000	0.000	0.000
64	A	55	ASP	-1	-0.922	-0.973	16.477	0.238	0.238	0.000	0.000	0.000	0.000
65	A	56	HIS	0	-0.032	-0.043	10.910	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	57	ASP	-1	-0.783	-0.841	16.078	0.082	0.082	0.000	0.000	0.000	0.000
67	A	58	LEU	0	0.013	0.005	18.360	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	59	GLN	0	0.010	0.014	15.851	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	60	PHE	0	-0.057	-0.045	13.901	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	61	ILE	0	0.007	-0.009	19.637	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	62	GLU	-1	-0.888	-0.931	22.763	0.066	0.066	0.000	0.000	0.000	0.000
72	A	63	ARG	1	0.779	0.846	17.591	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	64	ILE	0	-0.061	-0.020	21.898	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	65	GLU	-1	-0.921	-0.958	25.257	0.013	0.013	0.000	0.000	0.000	0.000
75	A	66	GLN	0	-0.169	-0.077	26.927	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	67	ASP	-1	-0.985	-1.006	28.531	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	68	GLU	-1	-0.837	-0.847	22.350	0.001	0.001	0.000	0.000	0.000	0.000
78	A	69	LEU	0	-0.069	-0.033	19.630	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	70	PHE	0	0.012	-0.021	23.938	0.004	0.004	0.000	0.000	0.000	0.000
80	A	71	TYR	0	0.005	-0.026	23.579	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	72	PRO	0	-0.012	-0.034	22.630	0.002	0.002	0.000	0.000	0.000	0.000
82	A	73	LEU	0	-0.003	0.046	17.841	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	74	ILE	0	-0.097	-0.045	15.267	0.002	0.002	0.000	0.000	0.000	0.000
84	A	75	THR	0	0.051	0.024	12.980	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	76	MET	0	-0.046	-0.028	7.859	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	77	ASN	0	-0.056	-0.058	5.491	0.104	0.104	0.000	0.000	0.000	0.000
87	A	78	ASP	-1	-0.820	-0.888	8.019	0.338	0.338	0.000	0.000	0.000	0.000
88	A	79	GLU	-1	-0.890	-0.938	6.357	-0.898	-0.898	0.000	0.000	0.000	0.000
89	A	80	TYR	0	-0.043	-0.065	10.616	-0.051	-0.051	0.000	0.000	0.000	0.000
90	A	81	VAL	0	-0.077	-0.025	12.262	-0.061	-0.061	0.000	0.000	0.000	0.000
91	A	82	ALA	0	-0.052	-0.046	14.712	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	83	ASP	-1	-0.765	-0.847	18.535	-0.081	-0.081	0.000	0.000	0.000	0.000
93	A	84	GLY	0	0.059	0.040	21.638	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	85	TYR	0	-0.040	-0.015	25.311	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	86	ILE	0	0.001	0.005	20.544	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	87	GLN	0	-0.025	-0.014	22.527	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	88	THR	0	0.032	-0.012	21.133	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	89	LYS	1	0.922	0.957	19.930	0.217	0.217	0.000	0.000	0.000	0.000
99	A	90	GLN	0	0.068	0.052	18.207	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	91	ILE	0	0.056	0.038	15.924	-0.041	-0.041	0.000	0.000	0.000	0.000
101	A	92	THR	0	0.001	-0.019	14.989	-0.034	-0.034	0.000	0.000	0.000	0.000
102	A	93	ARG	1	0.916	0.959	15.091	0.256	0.256	0.000	0.000	0.000	0.000
103	A	94	PHE	0	0.026	0.036	8.935	-0.088	-0.088	0.000	0.000	0.000	0.000
104	A	95	ILE	0	0.042	0.014	10.542	-0.153	-0.153	0.000	0.000	0.000	0.000
105	A	96	ASP	-1	-0.858	-0.922	10.826	-0.737	-0.737	0.000	0.000	0.000	0.000
106	A	97	GLN	0	-0.001	0.013	8.453	-0.105	-0.105	0.000	0.000	0.000	0.000
107	A	98	LYS	1	0.832	0.919	4.484	2.060	2.124	-0.001	-0.003	-0.060	0.000
108	A	99	LEU	0	-0.046	-0.015	8.380	-0.276	-0.276	0.000	0.000	0.000	0.000
109	A	100	VAL	0	-0.073	-0.033	10.537	0.008	0.008	0.000	0.000	0.000	0.000
110	A	101	ASN	0	-0.057	-0.031	9.289	0.203	0.203	0.000	0.000	0.000	0.000
111	A	102	GLU	-1	-0.878	-0.926	4.091	-5.309	-4.889	0.003	-0.121	-0.302	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-8:ALA)