FMO DATABASE

FMODB ID: NNQ5Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-648030.638249
FMO2-HF: Nuclear repulsion	612155.434998
FMO2-HF: Total energy	-35875.203251
FMO2-MP2: Total energy	-35982.173668

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.
-44.921	-38.697	0.636	-2.731	-4.128	0.005

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 : -0.908 / q_NPA : -0.964

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	9	ASN	0	-0.024	-0.027	2.519	-12.296	-8.440	0.303	-1.873	-2.286	0.006
4	A	10	THR	0	-0.065	-0.045	3.027	3.306	4.523	0.114	-0.489	-0.842	-0.002
5	A	11	VAL	0	0.019	0.025	4.622	-3.357	-3.275	-0.001	-0.016	-0.065	0.000
6	A	12	THR	0	-0.018	-0.020	8.314	0.681	0.681	0.000	0.000	0.000	0.000
7	A	13	LEU	0	-0.012	0.005	10.710	-1.101	-1.101	0.000	0.000	0.000	0.000
8	A	14	VAL	0	-0.007	-0.016	14.305	0.216	0.216	0.000	0.000	0.000	0.000
9	A	15	GLY	0	0.013	0.005	17.591	-0.423	-0.423	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.855	0.918	20.502	-10.550	-10.550	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.009	0.013	21.707	0.207	0.207	0.000	0.000	0.000	0.000
12	A	18	PHE	0	0.012	-0.005	23.459	-0.530	-0.530	0.000	0.000	0.000	0.000
13	A	19	THR	0	0.023	0.008	24.634	-0.302	-0.302	0.000	0.000	0.000	0.000
14	A	20	PRO	0	0.029	0.004	24.724	0.409	0.409	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.026	0.002	20.935	0.222	0.222	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.961	-0.964	23.533	10.592	10.592	0.000	0.000	0.000	0.000
17	A	23	PHE	0	-0.021	-0.006	23.296	0.647	0.647	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.048	-0.029	20.774	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	25	HIS	0	-0.057	-0.065	19.369	-0.254	-0.254	0.000	0.000	0.000	0.000
20	A	26	GLU	-1	-0.921	-0.970	21.805	12.548	12.548	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.006	0.009	16.881	-0.081	-0.081	0.000	0.000	0.000	0.000
22	A	28	TYR	0	-0.025	-0.026	20.253	0.308	0.308	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.036	0.024	23.013	0.024	0.024	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.866	-0.895	16.488	18.820	18.820	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.972	0.991	21.181	-11.977	-11.977	0.000	0.000	0.000	0.000
26	A	32	PHE	0	0.025	0.017	14.591	0.741	0.741	0.000	0.000	0.000	0.000
27	A	33	PHE	0	-0.002	0.004	19.016	-0.979	-0.979	0.000	0.000	0.000	0.000
28	A	34	ASN	0	0.004	0.012	18.638	1.728	1.728	0.000	0.000	0.000	0.000
29	A	35	PHE	0	0.031	0.009	18.085	-0.598	-0.598	0.000	0.000	0.000	0.000
30	A	36	ILE	0	0.005	0.014	19.716	0.715	0.715	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.001	0.006	16.872	-0.366	-0.366	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.876	-0.941	20.496	10.996	10.996	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.016	-0.024	17.555	0.118	0.118	0.000	0.000	0.000	0.000
34	A	40	PRO	0	-0.019	0.001	20.887	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	41	ARG	1	0.844	0.885	21.788	-11.871	-11.871	0.000	0.000	0.000	0.000
36	A	42	LEU	0	0.037	0.013	23.343	-0.318	-0.318	0.000	0.000	0.000	0.000
37	A	43	SER	0	-0.030	-0.017	25.243	-0.203	-0.203	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.871	-0.930	26.870	10.037	10.037	0.000	0.000	0.000	0.000
39	A	45	THR	0	-0.100	-0.055	25.372	-0.140	-0.140	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.900	0.963	24.353	-10.099	-10.099	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.817	-0.864	20.087	12.980	12.980	0.000	0.000	0.000	0.000
42	A	48	TYR	0	-0.018	-0.017	21.801	0.038	0.038	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.028	-0.021	15.943	0.220	0.220	0.000	0.000	0.000	0.000
44	A	50	PRO	0	-0.005	0.016	16.271	-0.240	-0.240	0.000	0.000	0.000	0.000
45	A	51	ILE	0	0.020	0.018	14.468	1.328	1.328	0.000	0.000	0.000	0.000
46	A	52	THR	0	-0.015	-0.014	14.285	-0.879	-0.879	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.012	0.002	14.017	1.564	1.564	0.000	0.000	0.000	0.000
48	A	54	SER	0	0.004	-0.024	15.235	-1.406	-1.406	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.028	-0.007	16.963	0.501	0.501	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.928	0.956	16.457	-17.153	-17.153	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.027	-0.017	12.448	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	58	PHE	0	0.007	0.005	16.913	0.070	0.070	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.931	-0.951	19.866	12.371	12.371	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.034	-0.012	22.019	0.288	0.288	0.000	0.000	0.000	0.000
55	A	61	MET	0	-0.072	-0.018	19.753	-0.244	-0.244	0.000	0.000	0.000	0.000
56	A	62	ASN	0	0.010	0.002	24.236	0.093	0.093	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.011	-0.008	19.877	0.292	0.292	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.912	-0.951	24.235	9.783	9.783	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.002	0.001	26.533	0.318	0.318	0.000	0.000	0.000	0.000
60	A	66	GLY	0	-0.029	-0.007	26.820	-0.333	-0.333	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.035	-0.019	23.350	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.876	0.939	22.073	-11.909	-11.909	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.026	0.005	18.103	0.040	0.040	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.958	0.984	13.062	-19.178	-19.178	0.000	0.000	0.000	0.000
65	A	71	ILE	0	0.019	0.005	11.949	0.166	0.166	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.734	-0.832	5.465	39.657	39.657	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.049	0.016	7.615	-0.441	-0.441	0.000	0.000	0.000	0.000
68	A	74	GLN	0	0.027	0.051	4.150	-2.662	-2.570	-0.001	-0.015	-0.075	0.000
69	A	75	LEU	0	-0.004	-0.007	6.554	-3.189	-3.189	0.000	0.000	0.000	0.000
70	A	76	ARG	1	0.892	0.942	7.853	-28.795	-28.795	0.000	0.000	0.000	0.000
71	A	77	SER	0	0.007	0.005	10.933	-1.417	-1.417	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.015	0.000	13.862	0.520	0.520	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.000	0.000	16.360	-1.194	-1.194	0.000	0.000	0.000	0.000
74	A	80	ARG	1	1.014	1.017	20.051	-12.975	-12.975	0.000	0.000	0.000	0.000
75	A	89	LYS	1	1.002	0.987	23.356	-11.623	-11.623	0.000	0.000	0.000	0.000
76	A	90	LEU	0	-0.025	-0.004	17.631	0.390	0.390	0.000	0.000	0.000	0.000
77	A	91	ILE	0	-0.077	-0.034	18.065	-0.684	-0.684	0.000	0.000	0.000	0.000
78	A	92	LEU	0	0.039	0.011	14.576	0.831	0.831	0.000	0.000	0.000	0.000
79	A	93	THR	0	-0.024	-0.042	13.137	-1.020	-1.020	0.000	0.000	0.000	0.000
80	A	94	VAL	0	0.019	0.017	10.421	1.801	1.801	0.000	0.000	0.000	0.000
81	A	95	PHE	0	-0.018	-0.015	9.121	-1.423	-1.423	0.000	0.000	0.000	0.000
82	A	96	ALA	0	-0.005	-0.009	9.139	2.816	2.816	0.000	0.000	0.000	0.000
83	A	97	ARG	1	0.761	0.852	2.542	-51.216	-50.239	0.221	-0.338	-0.860	0.001
84	A	98	ASP	-1	-0.901	-0.957	9.533	21.108	21.108	0.000	0.000	0.000	0.000
85	A	99	ILE	0	-0.012	-0.012	12.158	-0.341	-0.341	0.000	0.000	0.000	0.000
86	A	100	SER	0	0.003	0.015	15.465	-0.559	-0.559	0.000	0.000	0.000	0.000
87	A	101	VAL	0	0.023	0.008	18.154	-0.073	-0.073	0.000	0.000	0.000	0.000
88	A	102	VAL	0	-0.055	-0.023	20.212	-0.077	-0.077	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.032	0.019	22.997	-0.268	-0.268	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.840	-0.908	25.444	10.579	10.579	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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