FMO DATABASE

FMODB ID: YVQG2

Calculation Name: 4GR2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GR2

Chain ID: A

ChEMBL ID:

UniProt ID: Q94AU9

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816588.715653
FMO2-HF: Nuclear repulsion	770966.808421
FMO2-HF: Total energy	-45621.907232
FMO2-MP2: Total energy	-45753.518446

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:GLU)

Summations of interaction energy for fragment #1(A:8: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.
-77.335	-74.43	0.052	-1.492	-1.464	0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.890 / q_NPA : -0.950

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	10	SER	0	0.004	-0.017	3.815	-6.088	-4.205	0.037	-0.988	-0.931	0.009
4	A	11	PRO	0	0.032	0.003	6.404	1.365	1.365	0.000	0.000	0.000	0.000
5	A	12	GLU	-1	-0.808	-0.882	9.427	27.278	27.278	0.000	0.000	0.000	0.000
6	A	13	ALA	0	0.005	0.009	7.174	-1.552	-1.552	0.000	0.000	0.000	0.000
7	A	14	LYS	1	0.874	0.925	3.535	-66.988	-65.966	0.015	-0.504	-0.533	0.005
8	A	15	ALA	0	0.014	0.009	9.062	-2.357	-2.357	0.000	0.000	0.000	0.000
9	A	16	ALA	0	0.010	0.003	11.815	-1.945	-1.945	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.811	0.904	9.884	-26.121	-26.121	0.000	0.000	0.000	0.000
11	A	18	HIS	0	0.042	0.020	12.135	-1.033	-1.033	0.000	0.000	0.000	0.000
12	A	19	LEU	0	-0.002	-0.009	14.445	-1.683	-1.683	0.000	0.000	0.000	0.000
13	A	20	HIS	0	-0.052	-0.013	14.908	-0.162	-0.162	0.000	0.000	0.000	0.000
14	A	21	ASP	-1	-0.816	-0.889	14.807	20.473	20.473	0.000	0.000	0.000	0.000
15	A	22	PHE	0	-0.023	-0.010	17.884	-1.301	-1.301	0.000	0.000	0.000	0.000
16	A	23	PHE	0	0.036	-0.003	19.609	-0.918	-0.918	0.000	0.000	0.000	0.000
17	A	24	THR	0	-0.030	-0.012	19.873	-0.740	-0.740	0.000	0.000	0.000	0.000
18	A	25	TYR	0	0.014	0.013	22.239	-0.905	-0.905	0.000	0.000	0.000	0.000
19	A	26	VAL	0	-0.004	0.000	24.203	-0.659	-0.659	0.000	0.000	0.000	0.000
20	A	27	ALA	0	0.009	0.014	25.531	-0.583	-0.583	0.000	0.000	0.000	0.000
21	A	28	VAL	0	-0.008	-0.004	26.036	-0.510	-0.510	0.000	0.000	0.000	0.000
22	A	29	ARG	1	0.930	0.959	28.362	-11.389	-11.389	0.000	0.000	0.000	0.000
23	A	30	ILE	0	-0.001	0.008	29.236	-0.426	-0.426	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.009	-0.012	30.879	-0.402	-0.402	0.000	0.000	0.000	0.000
25	A	32	SER	0	0.025	0.009	32.452	-0.323	-0.323	0.000	0.000	0.000	0.000
26	A	33	ALA	0	0.033	0.020	34.347	-0.288	-0.288	0.000	0.000	0.000	0.000
27	A	34	GLN	0	-0.003	-0.001	35.578	-0.489	-0.489	0.000	0.000	0.000	0.000
28	A	35	LEU	0	-0.044	-0.025	35.312	-0.253	-0.253	0.000	0.000	0.000	0.000
29	A	36	GLU	-1	-0.884	-0.919	38.403	8.216	8.216	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.060	-0.017	40.347	-0.267	-0.267	0.000	0.000	0.000	0.000
31	A	38	TYR	0	-0.060	-0.031	40.608	-0.284	-0.284	0.000	0.000	0.000	0.000
32	A	39	ASN	0	-0.068	-0.040	40.574	-0.178	-0.178	0.000	0.000	0.000	0.000
33	A	40	PRO	0	0.097	0.037	41.089	0.196	0.196	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.877	-0.924	41.940	7.367	7.367	0.000	0.000	0.000	0.000
35	A	42	ALA	0	-0.003	-0.013	38.065	0.174	0.174	0.000	0.000	0.000	0.000
36	A	43	TYR	0	-0.074	-0.060	37.331	0.325	0.325	0.000	0.000	0.000	0.000
37	A	44	MET	0	0.023	0.017	37.395	0.279	0.279	0.000	0.000	0.000	0.000
38	A	45	GLU	-1	-0.785	-0.858	37.059	8.636	8.636	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.036	-0.030	30.820	0.330	0.330	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.921	0.965	33.227	-8.208	-8.208	0.000	0.000	0.000	0.000
41	A	48	GLU	-1	-0.867	-0.932	34.556	8.438	8.438	0.000	0.000	0.000	0.000
42	A	49	PHE	0	-0.068	-0.026	27.706	0.223	0.223	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.022	-0.023	28.818	0.437	0.437	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.926	-0.953	30.521	9.497	9.497	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.077	-0.046	31.620	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	53	ASN	0	-0.060	-0.022	27.361	0.406	0.406	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.041	0.004	23.350	-0.291	-0.291	0.000	0.000	0.000	0.000
48	A	55	VAL	0	0.018	0.000	23.452	0.575	0.575	0.000	0.000	0.000	0.000
49	A	56	SER	0	0.001	0.002	20.150	0.282	0.282	0.000	0.000	0.000	0.000
50	A	57	ASP	-1	-0.853	-0.883	18.761	16.746	16.746	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.071	0.022	18.609	0.544	0.544	0.000	0.000	0.000	0.000
52	A	59	ASP	-1	-0.739	-0.871	17.591	16.754	16.754	0.000	0.000	0.000	0.000
53	A	60	LYS	1	0.851	0.931	16.810	-18.669	-18.669	0.000	0.000	0.000	0.000
54	A	61	PHE	0	0.037	0.033	20.676	-0.778	-0.778	0.000	0.000	0.000	0.000
55	A	62	LEU	0	0.014	0.006	22.223	-0.675	-0.675	0.000	0.000	0.000	0.000
56	A	63	ALA	0	-0.018	-0.012	22.264	-0.621	-0.621	0.000	0.000	0.000	0.000
57	A	64	THR	0	-0.003	-0.010	24.264	-0.566	-0.566	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.018	0.005	26.636	-0.507	-0.507	0.000	0.000	0.000	0.000
59	A	66	MET	0	-0.048	-0.050	25.856	-0.213	-0.213	0.000	0.000	0.000	0.000
60	A	67	ARG	1	0.850	0.920	24.988	-12.688	-12.688	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.864	0.956	29.848	-10.686	-10.686	0.000	0.000	0.000	0.000
62	A	69	SER	0	0.034	-0.016	32.933	-0.386	-0.386	0.000	0.000	0.000	0.000
63	A	70	SER	0	0.029	0.014	34.504	0.249	0.249	0.000	0.000	0.000	0.000
64	A	71	ARG	1	0.876	0.913	36.221	-8.122	-8.122	0.000	0.000	0.000	0.000
65	A	72	HIS	0	0.063	0.054	32.356	0.137	0.137	0.000	0.000	0.000	0.000
66	A	73	MET	0	0.013	0.019	29.757	0.482	0.482	0.000	0.000	0.000	0.000
67	A	74	ASN	0	-0.049	-0.031	31.653	0.185	0.185	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.016	0.016	32.201	0.165	0.165	0.000	0.000	0.000	0.000
69	A	76	ALA	0	0.005	-0.005	27.628	0.273	0.273	0.000	0.000	0.000	0.000
70	A	77	LEU	0	-0.009	-0.008	28.028	0.401	0.401	0.000	0.000	0.000	0.000
71	A	78	ARG	1	0.820	0.889	29.435	-9.658	-9.658	0.000	0.000	0.000	0.000
72	A	79	ILE	0	0.034	0.008	25.900	0.125	0.125	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.029	-0.014	23.196	0.462	0.462	0.000	0.000	0.000	0.000
74	A	81	GLU	-1	-0.818	-0.862	25.447	10.421	10.421	0.000	0.000	0.000	0.000
75	A	82	VAL	0	0.022	0.004	27.819	0.119	0.119	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.805	0.873	20.011	-15.720	-15.720	0.000	0.000	0.000	0.000
77	A	84	SER	0	-0.085	-0.051	23.632	0.635	0.635	0.000	0.000	0.000	0.000
78	A	85	ALA	0	-0.008	0.003	24.654	0.074	0.074	0.000	0.000	0.000	0.000
79	A	86	TYR	0	0.071	0.032	25.625	0.243	0.243	0.000	0.000	0.000	0.000
80	A	87	ALA	0	-0.029	-0.020	21.933	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	88	LYS	1	0.876	0.945	22.491	-13.185	-13.185	0.000	0.000	0.000	0.000
82	A	89	ASN	0	-0.024	-0.003	25.766	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.862	-0.933	28.752	10.289	10.289	0.000	0.000	0.000	0.000
84	A	91	PHE	0	-0.024	-0.015	22.579	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	92	GLU	-1	-0.816	-0.893	26.783	10.607	10.607	0.000	0.000	0.000	0.000
86	A	93	TRP	0	-0.017	-0.029	18.496	0.511	0.511	0.000	0.000	0.000	0.000
87	A	94	ASP	-1	-0.804	-0.896	24.646	12.733	12.733	0.000	0.000	0.000	0.000
88	A	95	ASN	0	0.005	-0.007	26.732	-0.165	-0.165	0.000	0.000	0.000	0.000
89	A	96	MET	0	-0.015	0.014	20.430	0.028	0.028	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.828	0.903	23.040	-12.695	-12.695	0.000	0.000	0.000	0.000
91	A	98	ARG	1	0.899	0.938	24.158	-10.244	-10.244	0.000	0.000	0.000	0.000
92	A	99	LEU	0	0.000	-0.006	27.241	-0.278	-0.278	0.000	0.000	0.000	0.000
93	A	100	ALA	0	-0.023	-0.005	22.115	-0.058	-0.058	0.000	0.000	0.000	0.000
94	A	101	PHE	0	-0.002	-0.008	21.751	0.095	0.095	0.000	0.000	0.000	0.000
95	A	102	LYS	1	0.876	0.925	25.454	-9.993	-9.993	0.000	0.000	0.000	0.000
96	A	103	ASN	0	-0.005	-0.008	25.247	-0.630	-0.630	0.000	0.000	0.000	0.000
97	A	104	VAL	0	-0.012	0.004	22.257	-0.072	-0.072	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.846	-0.922	25.500	11.068	11.068	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.844	-0.906	28.684	9.582	9.582	0.000	0.000	0.000	0.000
100	A	107	SER	0	-0.033	-0.027	26.548	-0.294	-0.294	0.000	0.000	0.000	0.000
101	A	108	ASN	0	-0.026	-0.010	25.599	0.015	0.015	0.000	0.000	0.000	0.000
102	A	109	THR	0	-0.037	-0.032	28.913	-0.366	-0.366	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.880	0.958	28.803	-10.753	-10.753	0.000	0.000	0.000	0.000
104	A	111	LEU	0	0.024	0.016	26.856	-0.215	-0.215	0.000	0.000	0.000	0.000
105	A	112	MET	0	0.006	0.006	30.825	-0.124	-0.124	0.000	0.000	0.000	0.000
106	A	113	ARG	1	0.923	0.961	33.151	-8.451	-8.451	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.874	-0.957	33.197	9.263	9.263	0.000	0.000	0.000	0.000
108	A	115	TYR	0	-0.046	-0.008	33.105	-0.188	-0.188	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.035	-0.011	35.229	-0.145	-0.145	0.000	0.000	0.000	0.000
110	A	117	LEU	0	-0.102	-0.042	38.499	-0.439	-0.439	0.000	0.000	0.000	0.000

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