FMO DATABASE

FMODB ID: N9M9Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-706525.977991
FMO2-HF: Nuclear repulsion	664607.086135
FMO2-HF: Total energy	-41918.891857
FMO2-MP2: Total energy	-42036.729436

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.
0.278	3.119	0.167	-1.079	-1.93	-0.001

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 : 0.019 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	-11	ASP	-1	-0.902	-0.934	3.582	-1.732	-0.089	0.000	-0.680	-0.963	0.000
4	A	-10	LEU	0	-0.015	-0.011	2.910	0.211	1.228	0.168	-0.357	-0.829	-0.001
5	A	-9	GLY	0	0.019	0.023	4.637	0.637	0.818	-0.001	-0.042	-0.138	0.000
6	A	-8	THR	0	0.014	-0.019	5.780	0.363	0.363	0.000	0.000	0.000	0.000
7	A	-7	GLU	-1	-0.921	-0.940	9.266	-0.277	-0.277	0.000	0.000	0.000	0.000
8	A	-6	ASN	0	0.012	-0.001	7.682	0.418	0.418	0.000	0.000	0.000	0.000
9	A	-5	LEU	0	-0.016	-0.008	7.605	0.184	0.184	0.000	0.000	0.000	0.000
10	A	-4	TYR	0	0.008	0.002	10.590	0.142	0.142	0.000	0.000	0.000	0.000
11	A	-3	PHE	0	0.038	0.021	13.418	0.076	0.076	0.000	0.000	0.000	0.000
12	A	-2	GLN	0	-0.008	-0.020	10.791	0.144	0.144	0.000	0.000	0.000	0.000
13	A	-1	SER	0	-0.084	-0.039	13.989	0.068	0.068	0.000	0.000	0.000	0.000
14	A	0	MET	0	0.013	0.002	16.285	0.043	0.043	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.867	0.956	14.633	0.278	0.278	0.000	0.000	0.000	0.000
16	A	27	PHE	0	0.052	0.015	19.097	0.023	0.023	0.000	0.000	0.000	0.000
17	A	28	HIS	0	0.012	0.012	21.924	0.016	0.016	0.000	0.000	0.000	0.000
18	A	29	LEU	0	-0.005	-0.010	19.883	0.017	0.017	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.924	-0.969	20.700	-0.130	-0.130	0.000	0.000	0.000	0.000
20	A	31	ILE	0	-0.004	-0.011	24.788	0.015	0.015	0.000	0.000	0.000	0.000
21	A	32	GLN	0	0.052	0.045	26.997	0.002	0.002	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.870	-0.927	27.428	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.852	-0.918	29.154	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.886	-0.948	31.082	-0.086	-0.086	0.000	0.000	0.000	0.000
25	A	36	THR	0	-0.037	-0.022	31.647	0.006	0.006	0.000	0.000	0.000	0.000
26	A	37	LYS	1	0.850	0.913	29.776	0.070	0.070	0.000	0.000	0.000	0.000
27	A	38	CYS	0	-0.089	-0.019	34.943	0.008	0.008	0.000	0.000	0.000	0.000
28	A	39	ALA	0	0.007	-0.009	36.848	0.004	0.004	0.000	0.000	0.000	0.000
29	A	40	GLU	-1	-0.911	-0.960	37.278	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	41	LEU	0	-0.046	-0.015	39.178	0.004	0.004	0.000	0.000	0.000	0.000
31	A	42	LEU	0	-0.038	-0.025	41.049	0.004	0.004	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.967	0.991	42.568	0.043	0.043	0.000	0.000	0.000	0.000
33	A	44	SER	0	-0.053	-0.013	43.630	0.003	0.003	0.000	0.000	0.000	0.000
34	A	45	GLN	0	0.021	-0.008	45.112	0.003	0.003	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.034	-0.026	46.838	0.001	0.001	0.000	0.000	0.000	0.000
36	A	47	GLU	-1	-0.840	-0.904	49.311	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	48	LYS	1	0.752	0.866	49.551	0.026	0.026	0.000	0.000	0.000	0.000
38	A	49	HIS	0	-0.024	0.000	52.516	0.000	0.000	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.904	0.958	48.640	0.027	0.027	0.000	0.000	0.000	0.000
40	A	51	ALA	0	-0.003	0.006	52.588	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	52	CYS	0	-0.004	0.040	48.130	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	53	SER	0	0.054	0.021	47.391	0.001	0.001	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.014	-0.003	43.895	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	55	VAL	0	-0.024	-0.007	41.891	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	56	TRP	0	0.010	-0.005	31.809	0.004	0.004	0.000	0.000	0.000	0.000
46	A	57	ASP	-1	-0.781	-0.890	37.652	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	58	ASN	0	-0.049	-0.037	34.883	0.001	0.001	0.000	0.000	0.000	0.000
48	A	59	ILE	0	-0.016	0.008	29.324	0.000	0.000	0.000	0.000	0.000	0.000
49	A	60	THR	0	0.034	0.013	32.246	0.000	0.000	0.000	0.000	0.000	0.000
50	A	62	TRP	0	-0.020	-0.008	37.502	0.004	0.004	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.825	0.879	40.980	0.029	0.029	0.000	0.000	0.000	0.000
52	A	64	PRO	0	0.028	0.002	43.166	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	ALA	0	-0.061	-0.022	46.742	0.001	0.001	0.000	0.000	0.000	0.000
54	A	66	ASN	0	-0.045	-0.039	49.185	0.000	0.000	0.000	0.000	0.000	0.000
55	A	67	VAL	0	0.068	0.010	52.258	0.000	0.000	0.000	0.000	0.000	0.000
56	A	68	GLY	0	-0.028	-0.006	53.561	0.001	0.001	0.000	0.000	0.000	0.000
57	A	69	GLU	-1	-0.811	-0.861	49.143	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	70	THR	0	0.011	-0.014	45.614	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	71	VAL	0	-0.076	-0.026	41.801	0.001	0.001	0.000	0.000	0.000	0.000
60	A	72	THR	0	0.021	-0.015	40.287	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	73	VAL	0	-0.026	-0.014	36.580	0.002	0.002	0.000	0.000	0.000	0.000
62	A	74	PRO	0	0.022	0.013	32.792	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	75	CYS	0	-0.033	-0.023	31.078	0.003	0.003	0.000	0.000	0.000	0.000
64	A	76	PRO	0	0.040	0.031	29.172	0.001	0.001	0.000	0.000	0.000	0.000
65	A	77	LYS	1	0.920	0.960	26.443	0.062	0.062	0.000	0.000	0.000	0.000
66	A	78	VAL	0	0.031	0.048	23.243	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	79	PHE	0	-0.008	-0.006	22.982	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	80	SER	0	-0.001	-0.035	23.208	0.007	0.007	0.000	0.000	0.000	0.000
69	A	81	ASN	0	-0.085	-0.041	18.722	0.021	0.021	0.000	0.000	0.000	0.000
70	A	82	PHE	0	-0.015	0.008	20.106	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	83	TYR	0	-0.038	-0.033	24.075	0.004	0.004	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.012	-0.003	26.413	0.004	0.004	0.000	0.000	0.000	0.000
73	A	85	LYS	1	0.797	0.884	28.774	0.053	0.053	0.000	0.000	0.000	0.000
74	A	86	ALA	0	-0.009	0.011	30.634	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	87	GLY	0	0.030	0.018	31.916	0.003	0.003	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.050	-0.042	34.149	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	89	ILE	0	0.028	0.022	35.050	0.000	0.000	0.000	0.000	0.000	0.000
78	A	90	SER	0	-0.001	0.003	38.428	0.002	0.002	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.865	0.942	40.901	0.047	0.047	0.000	0.000	0.000	0.000
80	A	92	ASN	0	0.024	0.025	44.417	0.002	0.002	0.000	0.000	0.000	0.000
81	A	94	THR	0	0.014	-0.009	50.135	0.002	0.002	0.000	0.000	0.000	0.000
82	A	95	SER	0	-0.006	-0.023	53.435	0.000	0.000	0.000	0.000	0.000	0.000
83	A	96	ASP	-1	-0.921	-0.950	54.390	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	97	GLY	0	-0.010	0.001	51.089	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	98	TRP	0	-0.065	-0.051	45.608	0.001	0.001	0.000	0.000	0.000	0.000
86	A	99	SER	0	-0.015	0.002	45.874	0.000	0.000	0.000	0.000	0.000	0.000
87	A	100	GLU	-1	-0.840	-0.932	43.270	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	101	THR	0	-0.058	-0.017	38.291	0.003	0.003	0.000	0.000	0.000	0.000
89	A	102	PHE	0	-0.057	0.003	41.675	0.000	0.000	0.000	0.000	0.000	0.000
90	A	103	PRO	0	0.046	-0.017	39.376	0.001	0.001	0.000	0.000	0.000	0.000
91	A	104	ASH	0	-0.044	-0.053	37.455	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	105	PHE	0	0.102	0.034	29.287	0.002	0.002	0.000	0.000	0.000	0.000
93	A	106	VAL	0	0.021	0.012	32.367	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	107	ASP	-1	-0.805	-0.854	33.574	-0.051	-0.051	0.000	0.000	0.000	0.000
95	A	108	ALA	0	-0.080	-0.037	35.941	0.003	0.003	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.004	0.016	30.908	0.000	0.000	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.020	-0.003	24.954	0.001	0.001	0.000	0.000	0.000	0.000
98	A	112	SER	0	-0.031	-0.016	27.224	0.005	0.005	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.864	-0.938	22.358	-0.181	-0.181	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.069	-0.023	20.788	0.009	0.009	0.000	0.000	0.000	0.000

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