FMO DATABASE

FMODB ID: 4JNZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-813100.416611
FMO2-HF: Nuclear repulsion	767479.162
FMO2-HF: Total energy	-45621.25461
FMO2-MP2: Total energy	-45752.860961

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.
-63.24	-61.687	0.012	-0.731	-0.834	0.005

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 : -0.933 / 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	0.032	0.007	3.821	-7.063	-5.510	0.012	-0.731	-0.834	0.005
4	A	11	PRO	0	0.031	0.003	6.358	0.492	0.492	0.000	0.000	0.000	0.000
5	A	12	GLU	-1	-0.849	-0.927	9.369	25.445	25.445	0.000	0.000	0.000	0.000
6	A	13	ALA	0	0.010	0.008	7.494	-1.640	-1.640	0.000	0.000	0.000	0.000
7	A	14	LYS	1	0.911	0.952	5.539	-46.203	-46.203	0.000	0.000	0.000	0.000
8	A	15	ALA	0	-0.009	-0.003	9.515	-2.102	-2.102	0.000	0.000	0.000	0.000
9	A	16	ALA	0	0.019	0.005	12.072	-1.772	-1.772	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.904	0.965	10.363	-27.403	-27.403	0.000	0.000	0.000	0.000
11	A	18	HIS	0	0.022	0.003	12.404	-0.843	-0.843	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.010	-0.003	14.892	-1.543	-1.543	0.000	0.000	0.000	0.000
13	A	20	HIS	0	-0.077	-0.010	15.291	-0.334	-0.334	0.000	0.000	0.000	0.000
14	A	21	ASP	-1	-0.859	-0.943	15.508	19.233	19.233	0.000	0.000	0.000	0.000
15	A	22	PHE	0	-0.041	-0.009	18.255	-1.217	-1.217	0.000	0.000	0.000	0.000
16	A	23	PHE	0	0.036	0.004	20.066	-0.938	-0.938	0.000	0.000	0.000	0.000
17	A	24	THR	0	-0.006	0.002	20.172	-0.859	-0.859	0.000	0.000	0.000	0.000
18	A	25	TYR	0	0.014	0.020	22.569	-0.888	-0.888	0.000	0.000	0.000	0.000
19	A	26	VAL	0	0.005	0.004	24.535	-0.640	-0.640	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.001	0.012	25.868	-0.583	-0.583	0.000	0.000	0.000	0.000
21	A	28	VAL	0	0.008	0.002	26.675	-0.499	-0.499	0.000	0.000	0.000	0.000
22	A	29	ARG	1	0.924	0.952	28.812	-11.158	-11.158	0.000	0.000	0.000	0.000
23	A	30	ILE	0	0.006	0.006	29.561	-0.402	-0.402	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.011	-0.014	31.135	-0.390	-0.390	0.000	0.000	0.000	0.000
25	A	32	SER	0	-0.017	-0.011	32.859	-0.427	-0.427	0.000	0.000	0.000	0.000
26	A	33	ALA	0	0.058	0.027	34.745	-0.278	-0.278	0.000	0.000	0.000	0.000
27	A	34	GLN	0	-0.013	-0.011	35.999	-0.440	-0.440	0.000	0.000	0.000	0.000
28	A	35	LEU	0	-0.053	-0.025	35.648	-0.261	-0.261	0.000	0.000	0.000	0.000
29	A	36	GLU	-1	-0.955	-0.960	39.004	7.903	7.903	0.000	0.000	0.000	0.000
30	A	37	SER	0	-0.048	-0.013	40.990	-0.252	-0.252	0.000	0.000	0.000	0.000
31	A	38	TYR	0	-0.059	-0.040	41.001	-0.258	-0.258	0.000	0.000	0.000	0.000
32	A	39	ASN	0	-0.080	-0.045	40.840	-0.186	-0.186	0.000	0.000	0.000	0.000
33	A	40	PRO	0	0.095	0.038	41.582	0.190	0.190	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.879	-0.931	42.623	7.327	7.327	0.000	0.000	0.000	0.000
35	A	42	ALA	0	-0.004	-0.004	38.518	0.167	0.167	0.000	0.000	0.000	0.000
36	A	43	TYR	0	-0.019	-0.020	37.648	0.231	0.231	0.000	0.000	0.000	0.000
37	A	44	MET	0	0.012	0.004	37.951	0.238	0.238	0.000	0.000	0.000	0.000
38	A	45	GLU	-1	-0.733	-0.809	37.628	8.443	8.443	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.054	-0.031	31.241	0.311	0.311	0.000	0.000	0.000	0.000
40	A	47	ARG	1	0.941	0.964	33.714	-8.020	-8.020	0.000	0.000	0.000	0.000
41	A	48	GLU	-1	-0.873	-0.923	35.303	8.266	8.266	0.000	0.000	0.000	0.000
42	A	49	PHE	0	-0.081	-0.040	28.332	0.214	0.214	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.053	-0.049	29.488	0.424	0.424	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.894	-0.922	31.266	9.314	9.314	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.110	-0.055	31.808	0.042	0.042	0.000	0.000	0.000	0.000
46	A	53	ASN	0	-0.097	-0.047	27.480	0.564	0.564	0.000	0.000	0.000	0.000
47	A	54	SER	0	0.075	0.034	24.057	-0.352	-0.352	0.000	0.000	0.000	0.000
48	A	55	VAL	0	0.045	0.020	23.808	0.503	0.503	0.000	0.000	0.000	0.000
49	A	56	SER	0	0.001	0.005	20.917	0.306	0.306	0.000	0.000	0.000	0.000
50	A	57	ASP	-1	-0.904	-0.945	19.438	16.067	16.067	0.000	0.000	0.000	0.000
51	A	58	GLY	0	-0.005	-0.013	18.741	0.693	0.693	0.000	0.000	0.000	0.000
52	A	59	ASP	-1	-0.765	-0.914	17.796	16.909	16.909	0.000	0.000	0.000	0.000
53	A	60	LYS	1	0.858	0.935	16.964	-18.462	-18.462	0.000	0.000	0.000	0.000
54	A	61	PHE	0	0.033	0.026	20.948	-0.756	-0.756	0.000	0.000	0.000	0.000
55	A	62	LEU	0	0.017	0.009	22.103	-0.654	-0.654	0.000	0.000	0.000	0.000
56	A	63	ALA	0	-0.019	-0.007	22.637	-0.598	-0.598	0.000	0.000	0.000	0.000
57	A	64	THR	0	0.000	-0.008	24.615	-0.589	-0.589	0.000	0.000	0.000	0.000
58	A	65	LEU	0	-0.018	0.005	26.980	-0.492	-0.492	0.000	0.000	0.000	0.000
59	A	66	MET	0	-0.036	-0.039	26.155	-0.234	-0.234	0.000	0.000	0.000	0.000
60	A	67	ARG	1	0.886	0.943	24.787	-12.746	-12.746	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.926	0.996	30.851	-10.371	-10.371	0.000	0.000	0.000	0.000
62	A	69	SER	0	0.018	-0.025	33.213	-0.399	-0.399	0.000	0.000	0.000	0.000
63	A	70	SER	0	0.031	0.016	34.968	0.227	0.227	0.000	0.000	0.000	0.000
64	A	71	ARG	1	0.853	0.874	36.625	-8.086	-8.086	0.000	0.000	0.000	0.000
65	A	72	HIS	0	0.088	0.056	32.830	0.084	0.084	0.000	0.000	0.000	0.000
66	A	73	MET	0	-0.004	0.010	29.791	0.458	0.458	0.000	0.000	0.000	0.000
67	A	74	ASN	0	-0.001	-0.003	32.254	0.326	0.326	0.000	0.000	0.000	0.000
68	A	75	LEU	0	0.004	0.008	32.708	0.150	0.150	0.000	0.000	0.000	0.000
69	A	76	ALA	0	-0.004	-0.011	28.224	0.258	0.258	0.000	0.000	0.000	0.000
70	A	77	LEU	0	-0.003	-0.005	28.605	0.407	0.407	0.000	0.000	0.000	0.000
71	A	78	ARG	1	0.883	0.943	30.149	-9.449	-9.449	0.000	0.000	0.000	0.000
72	A	79	ILE	0	0.036	0.009	26.355	0.177	0.177	0.000	0.000	0.000	0.000
73	A	80	LEU	0	-0.048	-0.020	23.659	0.436	0.436	0.000	0.000	0.000	0.000
74	A	81	GLU	-1	-0.883	-0.920	26.177	10.351	10.351	0.000	0.000	0.000	0.000
75	A	82	VAL	0	-0.005	-0.015	28.612	0.058	0.058	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.875	0.938	20.317	-15.221	-15.221	0.000	0.000	0.000	0.000
77	A	84	SER	0	-0.062	-0.036	23.861	0.565	0.565	0.000	0.000	0.000	0.000
78	A	85	ALA	0	0.013	0.010	24.980	0.117	0.117	0.000	0.000	0.000	0.000
79	A	86	TYR	0	0.057	0.033	25.845	0.135	0.135	0.000	0.000	0.000	0.000
80	A	87	ALA	0	-0.022	-0.010	22.524	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	88	LYS	1	0.887	0.939	22.582	-13.457	-13.457	0.000	0.000	0.000	0.000
82	A	89	ASN	0	-0.030	-0.006	25.899	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	90	ASP	-1	-0.876	-0.931	29.064	10.104	10.104	0.000	0.000	0.000	0.000
84	A	91	PHE	0	-0.050	-0.033	23.199	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	92	GLU	-1	-0.881	-0.948	27.494	10.304	10.304	0.000	0.000	0.000	0.000
86	A	93	TRP	0	0.002	-0.018	19.425	0.549	0.549	0.000	0.000	0.000	0.000
87	A	94	ASP	-1	-0.896	-0.945	24.990	12.460	12.460	0.000	0.000	0.000	0.000
88	A	95	ASN	0	0.014	0.006	27.165	-0.179	-0.179	0.000	0.000	0.000	0.000
89	A	96	MET	0	0.010	0.022	21.025	0.056	0.056	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.960	0.993	22.170	-13.419	-13.419	0.000	0.000	0.000	0.000
91	A	98	ARG	1	0.906	0.945	24.492	-9.975	-9.975	0.000	0.000	0.000	0.000
92	A	99	LEU	0	-0.010	-0.013	27.248	-0.243	-0.243	0.000	0.000	0.000	0.000
93	A	100	ALA	0	-0.021	-0.005	22.195	-0.032	-0.032	0.000	0.000	0.000	0.000
94	A	101	PHE	0	-0.011	-0.021	21.742	0.072	0.072	0.000	0.000	0.000	0.000
95	A	102	LYS	1	0.934	0.958	25.577	-9.904	-9.904	0.000	0.000	0.000	0.000
96	A	103	ASN	0	-0.015	-0.004	25.316	-0.628	-0.628	0.000	0.000	0.000	0.000
97	A	104	VAL	0	-0.018	-0.012	22.324	-0.113	-0.113	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.891	-0.935	25.404	10.837	10.837	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.863	-0.936	28.623	9.525	9.525	0.000	0.000	0.000	0.000
100	A	107	SER	0	-0.076	-0.042	26.428	-0.264	-0.264	0.000	0.000	0.000	0.000
101	A	108	ASN	0	0.012	0.010	25.720	0.028	0.028	0.000	0.000	0.000	0.000
102	A	109	THR	0	-0.010	-0.003	28.812	-0.335	-0.335	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.935	0.970	29.797	-10.337	-10.337	0.000	0.000	0.000	0.000
104	A	111	LEU	0	0.013	0.007	26.763	-0.188	-0.188	0.000	0.000	0.000	0.000
105	A	112	MET	0	-0.012	0.003	31.174	-0.112	-0.112	0.000	0.000	0.000	0.000
106	A	113	ARG	1	0.913	0.945	33.300	-8.238	-8.238	0.000	0.000	0.000	0.000
107	A	114	GLU	-1	-0.921	-0.983	34.515	8.879	8.879	0.000	0.000	0.000	0.000
108	A	115	TYR	0	-0.036	0.003	33.463	-0.097	-0.097	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.041	-0.015	35.579	-0.146	-0.146	0.000	0.000	0.000	0.000
110	A	117	LEU	0	-0.072	-0.015	38.562	-0.346	-0.346	0.000	0.000	0.000	0.000

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