FMO DATABASE

FMODB ID: JLZL9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-708739.497239
FMO2-HF: Nuclear repulsion	666820.413338
FMO2-HF: Total energy	-41919.0839
FMO2-MP2: Total energy	-42036.983255

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.
-2.394	0.677	0.17	-1.282	-1.957	-0.004

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 : 0.036 / q_NPA : 0.000

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	-0.903	-0.943	3.218	-4.925	-2.752	0.032	-0.991	-1.214	-0.004
4	A	-10	LEU	0	-0.019	-0.011	3.058	0.862	1.651	0.139	-0.277	-0.650	0.000
5	A	-9	GLY	0	0.028	0.024	4.669	0.720	0.829	-0.001	-0.014	-0.093	0.000
6	A	-8	THR	0	-0.011	-0.025	6.499	0.232	0.232	0.000	0.000	0.000	0.000
7	A	-7	GLU	-1	-0.914	-0.944	10.006	-0.281	-0.281	0.000	0.000	0.000	0.000
8	A	-6	ASN	0	0.026	0.010	7.790	0.397	0.397	0.000	0.000	0.000	0.000
9	A	-5	LEU	0	-0.016	-0.004	7.609	0.153	0.153	0.000	0.000	0.000	0.000
10	A	-4	TYR	0	0.006	0.008	10.600	0.133	0.133	0.000	0.000	0.000	0.000
11	A	-3	PHE	0	0.036	0.024	13.039	0.071	0.071	0.000	0.000	0.000	0.000
12	A	-2	GLN	0	-0.009	-0.034	11.056	0.143	0.143	0.000	0.000	0.000	0.000
13	A	-1	SER	0	-0.082	-0.041	14.204	0.072	0.072	0.000	0.000	0.000	0.000
14	A	0	MET	0	0.000	-0.002	16.222	0.052	0.052	0.000	0.000	0.000	0.000
15	A	26	ARG	1	0.813	0.913	14.800	0.377	0.377	0.000	0.000	0.000	0.000
16	A	27	PHE	0	0.037	0.014	18.837	0.027	0.027	0.000	0.000	0.000	0.000
17	A	28	HIS	0	0.004	0.006	21.691	0.019	0.019	0.000	0.000	0.000	0.000
18	A	29	LEU	0	-0.007	-0.010	19.774	0.020	0.020	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.844	-0.925	19.890	-0.208	-0.208	0.000	0.000	0.000	0.000
20	A	31	ILE	0	-0.005	0.006	24.217	0.016	0.016	0.000	0.000	0.000	0.000
21	A	32	GLN	0	0.050	0.036	26.812	0.003	0.003	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.842	-0.915	26.677	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.826	-0.881	28.605	-0.092	-0.092	0.000	0.000	0.000	0.000
24	A	35	GLU	-1	-0.874	-0.941	30.583	-0.102	-0.102	0.000	0.000	0.000	0.000
25	A	36	THR	0	-0.033	-0.029	31.244	0.009	0.009	0.000	0.000	0.000	0.000
26	A	37	LYS	1	0.798	0.880	29.248	0.101	0.101	0.000	0.000	0.000	0.000
27	A	38	CYS	0	-0.066	-0.014	34.709	0.011	0.011	0.000	0.000	0.000	0.000
28	A	39	ALA	0	0.030	0.011	36.583	0.005	0.005	0.000	0.000	0.000	0.000
29	A	40	GLU	-1	-0.875	-0.942	37.182	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	41	LEU	0	-0.044	0.000	38.897	0.005	0.005	0.000	0.000	0.000	0.000
31	A	42	LEU	0	-0.007	-0.001	40.665	0.004	0.004	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.948	0.986	42.259	0.051	0.051	0.000	0.000	0.000	0.000
33	A	44	SER	0	-0.029	-0.026	42.515	0.003	0.003	0.000	0.000	0.000	0.000
34	A	45	GLN	0	0.001	-0.020	44.041	0.004	0.004	0.000	0.000	0.000	0.000
35	A	46	THR	0	-0.050	-0.026	46.316	0.001	0.001	0.000	0.000	0.000	0.000
36	A	47	GLU	-1	-0.828	-0.898	48.874	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	48	LYS	1	0.753	0.850	48.579	0.036	0.036	0.000	0.000	0.000	0.000
38	A	49	HIS	0	-0.054	-0.018	52.386	0.000	0.000	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.871	0.945	47.757	0.040	0.040	0.000	0.000	0.000	0.000
40	A	51	ALA	0	-0.011	0.001	52.096	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	52	CYS	0	-0.010	0.041	47.857	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	53	SER	0	0.057	0.025	47.460	0.000	0.000	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.027	-0.003	43.721	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	55	VAL	0	-0.032	-0.014	41.621	0.000	0.000	0.000	0.000	0.000	0.000
45	A	56	TRP	0	-0.018	-0.020	31.477	0.003	0.003	0.000	0.000	0.000	0.000
46	A	57	ASP	-1	-0.763	-0.886	37.370	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	58	ASN	0	-0.046	-0.027	35.069	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	59	ILE	0	-0.016	0.011	29.152	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	60	THR	0	0.036	0.010	32.001	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	62	TRP	0	-0.018	-0.010	37.232	0.005	0.005	0.000	0.000	0.000	0.000
51	A	63	ARG	1	0.855	0.901	40.767	0.046	0.046	0.000	0.000	0.000	0.000
52	A	64	PRO	0	0.019	0.007	42.612	0.001	0.001	0.000	0.000	0.000	0.000
53	A	65	ALA	0	-0.051	-0.011	46.242	0.001	0.001	0.000	0.000	0.000	0.000
54	A	66	ASN	0	0.001	-0.024	48.646	0.001	0.001	0.000	0.000	0.000	0.000
55	A	67	VAL	0	0.034	0.003	51.957	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	68	GLY	0	-0.002	0.004	53.042	0.002	0.002	0.000	0.000	0.000	0.000
57	A	69	GLU	-1	-0.816	-0.882	48.655	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	70	THR	0	0.003	-0.004	45.300	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	71	VAL	0	-0.087	-0.040	41.709	0.001	0.001	0.000	0.000	0.000	0.000
60	A	72	THR	0	0.027	-0.009	39.886	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	73	VAL	0	-0.025	-0.008	36.092	0.002	0.002	0.000	0.000	0.000	0.000
62	A	74	PRO	0	0.030	0.011	32.227	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	75	CYS	0	-0.069	-0.032	30.681	0.004	0.004	0.000	0.000	0.000	0.000
64	A	76	PRO	0	0.045	0.029	28.924	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	77	LYS	1	0.873	0.929	25.721	0.100	0.100	0.000	0.000	0.000	0.000
66	A	78	VAL	0	0.018	0.038	22.701	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	79	PHE	0	-0.004	-0.007	22.518	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	80	SER	0	0.003	-0.027	22.960	0.009	0.009	0.000	0.000	0.000	0.000
69	A	81	ASN	0	-0.081	-0.040	18.678	0.013	0.013	0.000	0.000	0.000	0.000
70	A	82	PHE	0	-0.006	0.014	20.227	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	83	TYR	0	-0.048	-0.033	24.119	0.012	0.012	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.040	-0.027	26.494	0.002	0.002	0.000	0.000	0.000	0.000
73	A	85	LYS	1	0.806	0.894	28.544	0.085	0.085	0.000	0.000	0.000	0.000
74	A	86	ALA	0	0.021	0.019	29.843	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	87	GLY	0	0.014	0.001	31.276	0.004	0.004	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.045	-0.033	33.647	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	89	ILE	0	0.023	0.022	34.533	0.001	0.001	0.000	0.000	0.000	0.000
78	A	90	SER	0	-0.001	0.004	37.973	0.002	0.002	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.855	0.942	40.813	0.062	0.062	0.000	0.000	0.000	0.000
80	A	92	ASN	0	0.038	0.023	44.152	0.002	0.002	0.000	0.000	0.000	0.000
81	A	94	THR	0	-0.026	-0.034	49.888	0.002	0.002	0.000	0.000	0.000	0.000
82	A	95	SER	0	-0.023	-0.054	53.257	0.000	0.000	0.000	0.000	0.000	0.000
83	A	96	ASP	-1	-0.892	-0.912	54.472	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	97	GLY	0	0.010	0.016	50.977	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	98	TRP	0	-0.059	-0.044	45.040	0.001	0.001	0.000	0.000	0.000	0.000
86	A	99	SER	0	-0.029	-0.012	45.679	0.001	0.001	0.000	0.000	0.000	0.000
87	A	100	GLU	-1	-0.833	-0.935	42.782	-0.065	-0.065	0.000	0.000	0.000	0.000
88	A	101	THR	0	-0.070	-0.017	38.086	0.003	0.003	0.000	0.000	0.000	0.000
89	A	102	PHE	0	-0.055	-0.004	41.539	0.000	0.000	0.000	0.000	0.000	0.000
90	A	103	PRO	0	0.013	-0.022	38.989	0.001	0.001	0.000	0.000	0.000	0.000
91	A	104	ASH	0	-0.003	-0.041	37.289	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	105	PHE	0	0.065	0.019	28.871	0.001	0.001	0.000	0.000	0.000	0.000
93	A	106	VAL	0	0.026	0.021	32.482	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	107	ASP	-1	-0.809	-0.863	33.581	-0.075	-0.075	0.000	0.000	0.000	0.000
95	A	108	ALA	0	-0.052	-0.019	35.776	0.002	0.002	0.000	0.000	0.000	0.000
96	A	110	GLY	0	0.017	0.016	30.813	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	111	TYR	0	-0.024	0.005	25.128	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	112	SER	0	-0.049	-0.023	27.205	0.007	0.007	0.000	0.000	0.000	0.000
99	A	113	ASP	-1	-0.827	-0.906	22.568	-0.225	-0.225	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.095	-0.054	20.805	0.020	0.020	0.000	0.000	0.000	0.000

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