FMO DATABASE

FMODB ID: 85Z5Y

Calculation Name: 2X57-A-Xray372

Preferred Name: Vasoactive intestinal polypeptide receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2X57

Chain ID: A

ChEMBL ID: CHEMBL4532

UniProt ID: P41587

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	OptH
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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-705077.654565
FMO2-HF: Nuclear repulsion	663159.310644
FMO2-HF: Total energy	-41918.343921
FMO2-MP2: Total energy	-42036.096037

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:-13:GLY)

Summations of interaction energy for fragment #1(A:-13: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.
-0.3	2.798	0.512	-1.365	-2.247	0

Interaction energy analysis for fragmet #1(A:-13:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.005

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	-11	ASP	-1	-0.903	-0.938	3.587	-1.902	-0.276	0.000	-0.681	-0.946
4	A	-10	LEU	0	-0.021	-0.010	2.641	-0.176	1.117	0.513	-0.643	-1.163
5	A	-9	GLY	0	0.019	0.025	4.649	0.599	0.778	-0.001	-0.041	-0.138
6	A	-8	THR	0	0.017	-0.019	5.780	0.371	0.371	0.000	0.000	0.000
7	A	-7	GLU	-1	-0.920	-0.942	9.267	-0.272	-0.272	0.000	0.000	0.000
8	A	-6	ASN	0	0.016	0.001	7.684	0.419	0.419	0.000	0.000	0.000
9	A	-5	LEU	0	-0.020	-0.012	7.601	0.183	0.183	0.000	0.000	0.000
10	A	-4	TYR	0	0.011	0.007	10.592	0.145	0.145	0.000	0.000	0.000
11	A	-3	PHE	0	0.044	0.023	13.466	0.074	0.074	0.000	0.000	0.000
12	A	-2	GLN	0	-0.018	-0.018	10.627	0.139	0.139	0.000	0.000	0.000
13	A	-1	SER	0	-0.087	-0.042	13.991	0.068	0.068	0.000	0.000	0.000
14	A	0	MET	0	0.023	0.006	16.286	0.042	0.042	0.000	0.000	0.000
15	A	26	ARG	1	0.871	0.949	14.324	0.282	0.282	0.000	0.000	0.000
16	A	27	PHE	0	0.063	0.020	19.100	0.022	0.022	0.000	0.000	0.000
17	A	28	HIS	0	0.031	0.017	21.927	0.019	0.019	0.000	0.000	0.000
18	A	29	LEU	0	-0.009	-0.008	19.840	0.015	0.015	0.000	0.000	0.000
19	A	30	GLU	-1	-0.932	-0.971	21.204	-0.120	-0.120	0.000	0.000	0.000
20	A	31	ILE	0	-0.026	-0.021	24.792	0.014	0.014	0.000	0.000	0.000
21	A	32	GLN	0	0.042	0.040	27.002	0.006	0.006	0.000	0.000	0.000
22	A	33	GLU	-1	-0.893	-0.944	27.525	-0.060	-0.060	0.000	0.000	0.000
23	A	34	GLU	-1	-0.941	-0.986	29.148	-0.055	-0.055	0.000	0.000	0.000
24	A	35	GLU	-1	-0.921	-0.974	31.086	-0.086	-0.086	0.000	0.000	0.000
25	A	36	THR	0	-0.025	-0.001	31.713	0.006	0.006	0.000	0.000	0.000
26	A	37	LYS	1	0.922	0.956	30.044	0.063	0.063	0.000	0.000	0.000
27	A	38	CYS	0	-0.068	-0.007	34.946	0.008	0.008	0.000	0.000	0.000
28	A	39	ALA	0	0.010	-0.008	36.852	0.004	0.004	0.000	0.000	0.000
29	A	40	GLU	-1	-0.917	-0.961	36.954	-0.042	-0.042	0.000	0.000	0.000
30	A	41	LEU	0	-0.043	-0.014	39.177	0.004	0.004	0.000	0.000	0.000
31	A	42	LEU	0	-0.040	-0.033	41.053	0.004	0.004	0.000	0.000	0.000
32	A	43	ARG	1	0.976	0.993	42.571	0.043	0.043	0.000	0.000	0.000
33	A	44	SER	0	-0.037	0.002	43.658	0.003	0.003	0.000	0.000	0.000
34	A	45	GLN	0	-0.050	-0.037	44.870	0.005	0.005	0.000	0.000	0.000
35	A	46	THR	0	-0.043	-0.042	46.893	0.001	0.001	0.000	0.000	0.000
36	A	47	GLU	-1	-0.968	-0.968	49.314	-0.023	-0.023	0.000	0.000	0.000
37	A	48	LYS	1	0.884	0.936	49.661	0.024	0.024	0.000	0.000	0.000
38	A	49	HIS	0	-0.016	0.001	52.569	0.000	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.923	0.968	49.219	0.026	0.026	0.000	0.000	0.000
40	A	51	ALA	0	0.001	0.011	52.591	-0.001	-0.001	0.000	0.000	0.000
41	A	52	CYS	0	0.006	0.045	48.133	-0.002	-0.002	0.000	0.000	0.000
42	A	53	SER	0	0.028	0.005	47.750	0.000	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.026	0.006	43.896	-0.001	-0.001	0.000	0.000	0.000
44	A	55	VAL	0	-0.012	0.000	41.809	-0.001	-0.001	0.000	0.000	0.000
45	A	56	TRP	0	0.048	0.015	31.867	0.003	0.003	0.000	0.000	0.000
46	A	57	ASP	-1	-0.809	-0.908	37.653	-0.058	-0.058	0.000	0.000	0.000
47	A	58	ASN	0	-0.007	0.004	34.873	0.004	0.004	0.000	0.000	0.000
48	A	59	ILE	0	-0.010	0.007	29.384	0.000	0.000	0.000	0.000	0.000
49	A	60	THR	0	0.039	0.020	32.249	0.000	0.000	0.000	0.000	0.000
50	A	62	TRP	0	-0.028	-0.006	37.505	0.005	0.005	0.000	0.000	0.000
51	A	63	ARG	1	0.851	0.904	40.984	0.028	0.028	0.000	0.000	0.000
52	A	64	PRO	0	0.018	-0.006	43.170	0.001	0.001	0.000	0.000	0.000
53	A	65	ALA	0	-0.055	-0.019	46.746	0.001	0.001	0.000	0.000	0.000
54	A	66	ASN	0	-0.026	-0.033	49.189	-0.001	-0.001	0.000	0.000	0.000
55	A	67	VAL	0	0.062	0.008	52.262	0.000	0.000	0.000	0.000	0.000
56	A	68	GLY	0	-0.028	-0.008	53.544	0.001	0.001	0.000	0.000	0.000
57	A	69	GLU	-1	-0.847	-0.888	49.182	-0.024	-0.024	0.000	0.000	0.000
58	A	70	THR	0	0.010	-0.045	45.637	-0.001	-0.001	0.000	0.000	0.000
59	A	71	VAL	0	-0.080	-0.026	41.777	0.001	0.001	0.000	0.000	0.000
60	A	72	THR	0	0.017	-0.015	40.219	-0.001	-0.001	0.000	0.000	0.000
61	A	73	VAL	0	-0.026	-0.014	36.202	0.002	0.002	0.000	0.000	0.000
62	A	74	PRO	0	0.015	0.005	32.786	-0.001	-0.001	0.000	0.000	0.000
63	A	75	CYS	0	-0.055	-0.031	31.061	0.002	0.002	0.000	0.000	0.000
64	A	76	PRO	0	0.049	0.034	29.086	0.001	0.001	0.000	0.000	0.000
65	A	77	LYS	1	0.964	0.999	26.318	0.058	0.058	0.000	0.000	0.000
66	A	78	VAL	0	0.041	0.080	23.159	-0.001	-0.001	0.000	0.000	0.000
67	A	79	PHE	0	-0.018	-0.007	22.985	-0.013	-0.013	0.000	0.000	0.000
68	A	80	SER	0	-0.018	-0.072	23.169	0.007	0.007	0.000	0.000	0.000
69	A	81	ASN	0	-0.075	-0.040	18.487	0.021	0.021	0.000	0.000	0.000
70	A	82	PHE	0	-0.016	0.011	19.924	-0.003	-0.003	0.000	0.000	0.000
71	A	83	TYR	0	-0.039	-0.036	24.078	0.003	0.003	0.000	0.000	0.000
72	A	84	SER	0	-0.019	-0.005	26.417	0.004	0.004	0.000	0.000	0.000
73	A	85	LYS	1	0.887	0.936	28.778	0.048	0.048	0.000	0.000	0.000
74	A	86	ALA	0	-0.004	0.016	30.639	-0.005	-0.005	0.000	0.000	0.000
75	A	87	GLY	0	0.023	0.014	31.921	0.003	0.003	0.000	0.000	0.000
76	A	88	ASN	0	-0.045	-0.037	34.154	-0.002	-0.002	0.000	0.000	0.000
77	A	89	ILE	0	0.023	0.017	35.161	0.000	0.000	0.000	0.000	0.000
78	A	90	SER	0	0.001	0.005	38.432	0.002	0.002	0.000	0.000	0.000
79	A	91	LYS	1	0.868	0.944	40.950	0.046	0.046	0.000	0.000	0.000
80	A	92	ASN	0	0.035	0.057	44.420	0.002	0.002	0.000	0.000	0.000
81	A	94	THR	0	0.016	-0.013	50.139	0.002	0.002	0.000	0.000	0.000
82	A	95	SER	0	-0.012	-0.033	53.439	0.000	0.000	0.000	0.000	0.000
83	A	96	ASP	-1	-0.917	-0.946	54.051	-0.027	-0.027	0.000	0.000	0.000
84	A	97	GLY	0	-0.025	-0.003	51.091	-0.001	-0.001	0.000	0.000	0.000
85	A	98	TRP	0	-0.066	-0.045	45.615	0.001	0.001	0.000	0.000	0.000
86	A	99	SER	0	-0.014	0.003	45.811	0.000	0.000	0.000	0.000	0.000
87	A	100	GLU	-1	-0.864	-0.942	43.460	-0.049	-0.049	0.000	0.000	0.000
88	A	101	THR	0	-0.058	-0.032	38.353	0.003	0.003	0.000	0.000	0.000
89	A	102	PHE	0	-0.059	0.003	41.678	0.000	0.000	0.000	0.000	0.000
90	A	103	PRO	0	0.043	-0.018	39.332	0.001	0.001	0.000	0.000	0.000
91	A	104	ASH	0	-0.046	-0.048	37.748	-0.003	-0.003	0.000	0.000	0.000
92	A	105	PHE	0	0.087	0.021	29.509	0.002	0.002	0.000	0.000	0.000
93	A	106	VAL	0	0.031	0.017	32.474	-0.001	-0.001	0.000	0.000	0.000
94	A	107	ASP	-1	-0.815	-0.868	33.577	-0.050	-0.050	0.000	0.000	0.000
95	A	108	ALA	0	-0.111	-0.060	35.944	0.003	0.003	0.000	0.000	0.000
96	A	110	GLY	0	0.000	0.015	30.912	0.000	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.017	-0.004	25.074	0.001	0.001	0.000	0.000	0.000
98	A	112	SER	0	-0.043	-0.025	27.138	0.005	0.005	0.000	0.000	0.000
99	A	113	ASP	-1	-0.906	-0.962	22.666	-0.177	-0.177	0.000	0.000	0.000
100	A	114	PRO	0	-0.020	0.007	20.801	0.009	0.009	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-13:GLY)