FMO DATABASE

FMODB ID: 5J96Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-813504.489142
FMO2-HF: Nuclear repulsion	767882.738159
FMO2-HF: Total energy	-45621.750983
FMO2-MP2: Total energy	-45753.382198

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.
-67.135	-65.281	0.022	-0.807	-1.068	0.006

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 : -0.929 / q_NPA : -0.981

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	0.002	-0.022	3.821	-7.841	-6.173	0.023	-0.775	-0.916	0.006
4	A	11	PRO	0	0.045	0.012	6.381	0.687	0.687	0.000	0.000	0.000	0.000
5	A	12	GLU	-1	-0.809	-0.884	9.388	26.938	26.938	0.000	0.000	0.000	0.000
6	A	13	ALA	0	0.009	0.004	7.312	-1.667	-1.667	0.000	0.000	0.000	0.000
7	A	14	LYS	1	0.875	0.924	4.559	-54.310	-54.124	-0.001	-0.032	-0.152	0.000
8	A	15	ALA	0	-0.006	-0.002	9.408	-2.204	-2.204	0.000	0.000	0.000	0.000
9	A	16	ALA	0	0.015	0.002	11.811	-1.850	-1.850	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.805	0.899	10.205	-25.431	-25.431	0.000	0.000	0.000	0.000
11	A	18	HIS	0	0.033	0.010	12.305	-0.987	-0.987	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.013	0.000	14.783	-1.612	-1.612	0.000	0.000	0.000	0.000
13	A	20	HIS	0	-0.040	-0.001	15.172	-0.187	-0.187	0.000	0.000	0.000	0.000
14	A	21	ASP	-1	-0.818	-0.896	15.178	19.968	19.968	0.000	0.000	0.000	0.000
15	A	22	PHE	0	-0.013	0.000	18.155	-1.214	-1.214	0.000	0.000	0.000	0.000
16	A	23	PHE	0	0.034	0.003	19.869	-0.938	-0.938	0.000	0.000	0.000	0.000
17	A	24	THR	0	-0.023	-0.004	20.112	-0.756	-0.756	0.000	0.000	0.000	0.000
18	A	25	TYR	0	0.008	0.015	22.469	-0.902	-0.902	0.000	0.000	0.000	0.000
19	A	26	VAL	0	0.010	0.006	24.432	-0.638	-0.638	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.003	0.012	25.771	-0.591	-0.591	0.000	0.000	0.000	0.000
21	A	28	VAL	0	0.003	0.000	26.557	-0.494	-0.494	0.000	0.000	0.000	0.000
22	A	29	ARG	1	0.924	0.958	28.708	-11.291	-11.291	0.000	0.000	0.000	0.000
23	A	30	ILE	0	0.002	0.003	29.567	-0.411	-0.411	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.009	-0.012	31.141	-0.391	-0.391	0.000	0.000	0.000	0.000
25	A	32	SER	0	0.014	0.002	32.760	-0.319	-0.319	0.000	0.000	0.000	0.000
26	A	33	ALA	0	0.016	0.009	34.648	-0.291	-0.291	0.000	0.000	0.000	0.000
27	A	34	GLN	0	-0.005	-0.008	35.977	-0.449	-0.449	0.000	0.000	0.000	0.000
28	A	35	LEU	0	-0.039	-0.019	35.598	-0.262	-0.262	0.000	0.000	0.000	0.000
29	A	36	GLU	-1	-0.883	-0.905	38.914	8.041	8.041	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.045	-0.011	40.892	-0.255	-0.255	0.000	0.000	0.000	0.000
31	A	38	TYR	0	-0.065	-0.042	40.734	-0.262	-0.262	0.000	0.000	0.000	0.000
32	A	39	ASN	0	-0.068	-0.037	40.789	-0.171	-0.171	0.000	0.000	0.000	0.000
33	A	40	PRO	0	0.099	0.040	41.493	0.191	0.191	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.877	-0.932	42.532	7.310	7.310	0.000	0.000	0.000	0.000
35	A	42	ALA	0	-0.016	-0.011	38.498	0.170	0.170	0.000	0.000	0.000	0.000
36	A	43	TYR	0	-0.086	-0.071	37.928	0.312	0.312	0.000	0.000	0.000	0.000
37	A	44	MET	0	0.017	0.009	37.858	0.272	0.272	0.000	0.000	0.000	0.000
38	A	45	GLU	-1	-0.756	-0.836	37.435	8.525	8.525	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.055	-0.036	31.156	0.311	0.311	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.943	0.966	33.623	-8.071	-8.071	0.000	0.000	0.000	0.000
41	A	48	GLU	-1	-0.876	-0.923	35.209	8.287	8.287	0.000	0.000	0.000	0.000
42	A	49	PHE	0	-0.077	-0.039	28.248	0.224	0.224	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.050	-0.039	29.236	0.437	0.437	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.903	-0.928	31.171	9.331	9.331	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.098	-0.051	31.722	0.056	0.056	0.000	0.000	0.000	0.000
46	A	53	ASN	0	-0.093	-0.057	27.457	0.512	0.512	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.056	0.015	23.948	-0.351	-0.351	0.000	0.000	0.000	0.000
48	A	55	VAL	0	0.029	0.008	23.720	0.513	0.513	0.000	0.000	0.000	0.000
49	A	56	SER	0	0.015	0.013	20.782	0.330	0.330	0.000	0.000	0.000	0.000
50	A	57	ASP	-1	-0.872	-0.894	19.339	16.158	16.158	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.035	0.003	18.651	0.698	0.698	0.000	0.000	0.000	0.000
52	A	59	ASP	-1	-0.762	-0.898	17.558	16.873	16.873	0.000	0.000	0.000	0.000
53	A	60	LYS	1	0.844	0.916	17.199	-18.231	-18.231	0.000	0.000	0.000	0.000
54	A	61	PHE	0	0.038	0.030	20.879	-0.751	-0.751	0.000	0.000	0.000	0.000
55	A	62	LEU	0	0.020	0.012	22.278	-0.659	-0.659	0.000	0.000	0.000	0.000
56	A	63	ALA	0	-0.019	-0.008	22.580	-0.604	-0.604	0.000	0.000	0.000	0.000
57	A	64	THR	0	-0.004	-0.013	24.556	-0.578	-0.578	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.012	0.003	26.917	-0.490	-0.490	0.000	0.000	0.000	0.000
59	A	66	MET	0	-0.040	-0.042	26.191	-0.223	-0.223	0.000	0.000	0.000	0.000
60	A	67	ARG	1	0.869	0.935	24.841	-12.755	-12.755	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.907	0.992	30.494	-10.490	-10.490	0.000	0.000	0.000	0.000
62	A	69	SER	0	0.028	-0.019	33.152	-0.401	-0.401	0.000	0.000	0.000	0.000
63	A	70	SER	0	0.035	0.018	34.909	0.225	0.225	0.000	0.000	0.000	0.000
64	A	71	ARG	1	0.878	0.907	36.565	-8.080	-8.080	0.000	0.000	0.000	0.000
65	A	72	HIS	0	0.092	0.061	32.777	0.126	0.126	0.000	0.000	0.000	0.000
66	A	73	MET	0	-0.003	0.012	30.028	0.473	0.473	0.000	0.000	0.000	0.000
67	A	74	ASN	0	-0.052	-0.036	32.179	0.196	0.196	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.019	0.017	32.661	0.156	0.156	0.000	0.000	0.000	0.000
69	A	76	ALA	0	0.000	-0.008	28.157	0.265	0.265	0.000	0.000	0.000	0.000
70	A	77	LEU	0	-0.002	-0.006	28.503	0.404	0.404	0.000	0.000	0.000	0.000
71	A	78	ARG	1	0.831	0.902	30.037	-9.568	-9.568	0.000	0.000	0.000	0.000
72	A	79	ILE	0	0.030	0.008	26.271	0.186	0.186	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.041	-0.016	23.544	0.440	0.440	0.000	0.000	0.000	0.000
74	A	81	GLU	-1	-0.828	-0.888	26.042	10.250	10.250	0.000	0.000	0.000	0.000
75	A	82	VAL	0	0.007	-0.004	28.461	0.060	0.060	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.839	0.901	20.309	-15.404	-15.404	0.000	0.000	0.000	0.000
77	A	84	SER	0	-0.065	-0.034	23.813	0.567	0.567	0.000	0.000	0.000	0.000
78	A	85	ALA	0	0.005	0.004	24.818	0.118	0.118	0.000	0.000	0.000	0.000
79	A	86	TYR	0	0.055	0.030	25.870	0.141	0.141	0.000	0.000	0.000	0.000
80	A	87	ALA	0	-0.028	-0.012	22.311	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	88	LYS	1	0.896	0.948	22.664	-13.390	-13.390	0.000	0.000	0.000	0.000
82	A	89	ASN	0	-0.041	-0.014	25.703	0.013	0.013	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.866	-0.929	28.828	10.197	10.197	0.000	0.000	0.000	0.000
84	A	91	PHE	0	-0.046	-0.030	22.749	-0.040	-0.040	0.000	0.000	0.000	0.000
85	A	92	GLU	-1	-0.822	-0.900	27.262	10.387	10.387	0.000	0.000	0.000	0.000
86	A	93	TRP	0	-0.008	-0.023	19.115	0.574	0.574	0.000	0.000	0.000	0.000
87	A	94	ASP	-1	-0.827	-0.911	24.990	12.649	12.649	0.000	0.000	0.000	0.000
88	A	95	ASN	0	-0.003	-0.008	27.165	-0.118	-0.118	0.000	0.000	0.000	0.000
89	A	96	MET	0	0.002	0.018	20.901	0.047	0.047	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.893	0.944	22.782	-12.802	-12.802	0.000	0.000	0.000	0.000
91	A	98	ARG	1	0.902	0.939	24.512	-10.070	-10.070	0.000	0.000	0.000	0.000
92	A	99	LEU	0	-0.016	-0.016	27.310	-0.247	-0.247	0.000	0.000	0.000	0.000
93	A	100	ALA	0	-0.023	-0.008	22.208	-0.037	-0.037	0.000	0.000	0.000	0.000
94	A	101	PHE	0	-0.018	-0.020	21.784	0.032	0.032	0.000	0.000	0.000	0.000
95	A	102	LYS	1	0.901	0.940	25.594	-9.907	-9.907	0.000	0.000	0.000	0.000
96	A	103	ASN	0	-0.008	0.002	25.546	-0.626	-0.626	0.000	0.000	0.000	0.000
97	A	104	VAL	0	-0.004	-0.002	22.168	-0.128	-0.128	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.887	-0.938	25.418	10.868	10.868	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.857	-0.926	28.637	9.520	9.520	0.000	0.000	0.000	0.000
100	A	107	SER	0	-0.049	-0.034	26.596	-0.261	-0.261	0.000	0.000	0.000	0.000
101	A	108	ASN	0	-0.007	0.004	25.470	-0.020	-0.020	0.000	0.000	0.000	0.000
102	A	109	THR	0	-0.024	-0.014	28.822	-0.345	-0.345	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.905	0.963	29.664	-10.472	-10.472	0.000	0.000	0.000	0.000
104	A	111	LEU	0	0.019	0.010	26.845	-0.174	-0.174	0.000	0.000	0.000	0.000
105	A	112	MET	0	-0.014	-0.001	31.078	-0.123	-0.123	0.000	0.000	0.000	0.000
106	A	113	ARG	1	0.930	0.955	33.307	-8.291	-8.291	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.880	-0.961	34.197	8.988	8.988	0.000	0.000	0.000	0.000
108	A	115	TYR	0	-0.032	0.005	33.446	-0.129	-0.129	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.037	-0.016	35.583	-0.152	-0.152	0.000	0.000	0.000	0.000
110	A	117	LEU	0	-0.108	-0.035	38.567	-0.425	-0.425	0.000	0.000	0.000	0.000

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