FMO DATABASE

FMODB ID: 3JRYL

Calculation Name: 4GS3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GS3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RBI8

Base Structure: X-ray

Registration Date: 2023-09-23

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-648217.1246
FMO2-HF: Nuclear repulsion	612341.04613
FMO2-HF: Total energy	-35876.07847
FMO2-MP2: Total energy	-35983.049107

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:7:GLU)

Summations of interaction energy for fragment #1(A:7: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.
-128.273	-131.227	37.44	-16.487	-17.997	0.158

Interaction energy analysis for fragmet #1(A:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.796 / q_NPA : -0.889

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

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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	9	ASN	0	-0.030	-0.014	2.100	-24.549	-19.783	4.594	-4.015	-5.345	0.039
4	A	10	THR	0	-0.030	-0.042	2.642	12.232	13.391	3.774	-1.248	-3.685	-0.009
5	A	11	VAL	0	0.018	0.015	3.754	-5.205	-5.038	0.018	-0.030	-0.154	0.000
6	A	12	THR	0	-0.019	-0.003	7.562	-0.529	-0.529	0.000	0.000	0.000	0.000
7	A	13	LEU	0	-0.025	-0.009	9.813	-1.085	-1.085	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.001	-0.018	13.327	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	15	GLY	0	0.020	0.012	16.720	-0.323	-0.323	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.802	0.885	19.457	-11.570	-11.570	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.001	0.016	20.526	0.301	0.301	0.000	0.000	0.000	0.000
12	A	18	PHE	0	0.013	-0.004	22.235	-0.623	-0.623	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.035	-0.011	23.523	-0.308	-0.308	0.000	0.000	0.000	0.000
14	A	20	PRO	0	0.035	0.002	23.769	0.360	0.360	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.000	0.003	19.934	0.385	0.385	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.895	-0.936	22.963	12.079	12.079	0.000	0.000	0.000	0.000
17	A	23	PHE	0	-0.020	-0.011	22.366	0.703	0.703	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.042	-0.022	19.496	-0.311	-0.311	0.000	0.000	0.000	0.000
19	A	25	HIS	0	-0.067	-0.044	17.749	-0.078	-0.078	0.000	0.000	0.000	0.000
20	A	26	GLU	-1	-0.808	-0.893	21.037	12.871	12.871	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.021	-0.002	15.794	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	28	TYR	0	-0.035	-0.034	19.509	0.205	0.205	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.066	0.048	22.503	-0.301	-0.301	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.808	-0.829	16.376	18.456	18.456	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.811	0.888	20.374	-12.465	-12.465	0.000	0.000	0.000	0.000
26	A	32	PHE	0	-0.006	-0.009	13.747	0.856	0.856	0.000	0.000	0.000	0.000
27	A	33	PHE	0	0.016	0.004	18.227	-1.031	-1.031	0.000	0.000	0.000	0.000
28	A	34	ASN	0	-0.012	-0.009	17.750	1.153	1.153	0.000	0.000	0.000	0.000
29	A	35	PHE	0	0.057	0.029	16.649	-0.645	-0.645	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.004	0.007	18.860	0.979	0.979	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.001	0.008	15.774	-0.399	-0.399	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.852	-0.915	19.431	11.949	11.949	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.002	-0.010	16.789	0.269	0.269	0.000	0.000	0.000	0.000
34	A	40	PRO	0	0.001	0.009	20.203	-0.219	-0.219	0.000	0.000	0.000	0.000
35	A	41	ARG	1	0.824	0.865	21.173	-12.935	-12.935	0.000	0.000	0.000	0.000
36	A	42	LEU	0	0.014	-0.004	22.638	-0.365	-0.365	0.000	0.000	0.000	0.000
37	A	43	SER	0	-0.021	-0.022	24.792	-0.238	-0.238	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.842	-0.913	26.521	10.750	10.750	0.000	0.000	0.000	0.000
39	A	45	THR	0	-0.057	-0.018	25.578	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.819	0.924	23.686	-10.933	-10.933	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.817	-0.855	19.211	14.448	14.448	0.000	0.000	0.000	0.000
42	A	48	TYR	0	-0.033	-0.049	21.037	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	49	LEU	0	0.003	0.004	14.755	0.215	0.215	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.016	0.016	16.028	-0.200	-0.200	0.000	0.000	0.000	0.000
45	A	51	ILE	0	0.010	0.024	13.465	2.004	2.004	0.000	0.000	0.000	0.000
46	A	52	THR	0	-0.024	-0.034	13.480	-1.675	-1.675	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.018	-0.005	13.117	2.138	2.138	0.000	0.000	0.000	0.000
48	A	54	SER	0	0.017	-0.024	14.826	-1.439	-1.439	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.026	-0.020	16.597	0.348	0.348	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.843	0.897	15.190	-17.912	-17.912	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.063	-0.030	11.981	0.340	0.340	0.000	0.000	0.000	0.000
52	A	58	PHE	0	0.005	-0.003	16.096	0.158	0.158	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.879	-0.929	19.099	12.772	12.772	0.000	0.000	0.000	0.000
54	A	60	GLY	0	0.004	0.010	21.833	0.040	0.040	0.000	0.000	0.000	0.000
55	A	61	MET	0	-0.097	-0.030	18.370	-0.274	-0.274	0.000	0.000	0.000	0.000
56	A	62	ASN	0	-0.048	-0.044	23.358	0.349	0.349	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.025	-0.002	19.021	0.491	0.491	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.842	-0.894	23.229	10.495	10.495	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.022	-0.009	25.427	0.295	0.295	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.002	0.008	25.682	-0.448	-0.448	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.060	-0.041	22.312	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.866	0.931	21.465	-11.882	-11.882	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.017	-0.002	17.166	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.897	0.955	10.813	-22.057	-22.057	0.000	0.000	0.000	0.000
65	A	71	ILE	0	0.008	-0.005	10.871	-0.199	-0.199	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.741	-0.832	4.790	45.642	45.715	-0.001	-0.004	-0.068	0.000
67	A	73	GLY	0	0.067	0.026	6.976	-1.513	-1.513	0.000	0.000	0.000	0.000
68	A	74	GLN	0	-0.022	0.012	1.776	-31.261	-34.538	11.739	-4.734	-3.728	0.062
69	A	75	LEU	0	0.015	0.012	5.487	-6.891	-6.885	-0.001	-0.001	-0.003	0.000
70	A	76	ARG	1	0.834	0.918	6.017	-38.083	-38.083	0.000	0.000	0.000	0.000
71	A	77	SER	0	0.020	0.002	9.836	-2.245	-2.245	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.011	-0.003	13.282	0.171	0.171	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.009	-0.002	15.590	-1.112	-1.112	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.995	1.010	19.327	-14.816	-14.816	0.000	0.000	0.000	0.000
75	A	89	LYS	1	1.000	1.002	22.691	-12.680	-12.680	0.000	0.000	0.000	0.000
76	A	90	LEU	0	0.000	-0.006	16.610	0.451	0.451	0.000	0.000	0.000	0.000
77	A	91	ILE	0	-0.082	-0.030	17.221	-0.875	-0.875	0.000	0.000	0.000	0.000
78	A	92	LEU	0	0.025	0.006	14.071	1.110	1.110	0.000	0.000	0.000	0.000
79	A	93	THR	0	-0.073	-0.036	12.136	-1.375	-1.375	0.000	0.000	0.000	0.000
80	A	94	VAL	0	0.039	0.028	9.185	2.542	2.542	0.000	0.000	0.000	0.000
81	A	95	PHE	0	0.011	-0.003	8.358	-2.444	-2.444	0.000	0.000	0.000	0.000
82	A	96	ALA	0	0.014	0.001	8.321	4.512	4.512	0.000	0.000	0.000	0.000
83	A	97	ARG	1	0.663	0.771	1.706	-87.750	-93.598	17.317	-6.455	-5.014	0.066
84	A	98	ASP	-1	-0.855	-0.925	8.949	20.538	20.538	0.000	0.000	0.000	0.000
85	A	99	ILE	0	0.009	0.006	11.029	0.452	0.452	0.000	0.000	0.000	0.000
86	A	100	SER	0	0.001	0.003	14.308	-0.941	-0.941	0.000	0.000	0.000	0.000
87	A	101	VAL	0	0.014	0.011	16.853	-0.063	-0.063	0.000	0.000	0.000	0.000
88	A	102	VAL	0	-0.040	-0.013	19.374	-0.125	-0.125	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.027	0.020	22.063	-0.233	-0.233	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.804	-0.878	24.853	11.497	11.497	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLU)