FMO DATABASE

FMODB ID: JQGJ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-648578.96567
FMO2-HF: Nuclear repulsion	612703.161328
FMO2-HF: Total energy	-35875.804342
FMO2-MP2: Total energy	-35982.757994

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.
-106.965	-105.645	26.48	-13.047	-14.755	0.107

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 : -0.813 / q_NPA : -0.906

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	-0.004	-0.014	1.638	-15.181	-13.852	5.964	-3.361	-3.932	0.010
4	A	10	THR	0	-0.053	-0.045	2.496	9.248	9.959	2.786	-0.936	-2.562	-0.013
5	A	11	VAL	0	0.010	0.018	4.198	-4.782	-4.599	0.003	-0.055	-0.132	0.000
6	A	12	THR	0	-0.009	-0.009	7.913	0.192	0.192	0.000	0.000	0.000	0.000
7	A	13	LEU	0	-0.018	0.002	10.396	-1.188	-1.188	0.000	0.000	0.000	0.000
8	A	14	VAL	0	0.000	-0.011	13.843	0.101	0.101	0.000	0.000	0.000	0.000
9	A	15	GLY	0	0.011	0.003	17.095	-0.411	-0.411	0.000	0.000	0.000	0.000
10	A	16	LYS	1	0.844	0.915	19.870	-11.104	-11.104	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.014	0.012	20.704	0.306	0.306	0.000	0.000	0.000	0.000
12	A	18	PHE	0	0.012	-0.003	22.428	-0.607	-0.607	0.000	0.000	0.000	0.000
13	A	19	THR	0	0.018	0.007	23.676	-0.342	-0.342	0.000	0.000	0.000	0.000
14	A	20	PRO	0	0.019	-0.001	23.834	0.417	0.417	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.024	0.001	20.178	0.288	0.288	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.949	-0.958	22.938	11.507	11.507	0.000	0.000	0.000	0.000
17	A	23	PHE	0	-0.020	-0.018	22.613	0.752	0.752	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.037	-0.026	19.116	-0.227	-0.227	0.000	0.000	0.000	0.000
19	A	25	HIS	0	-0.042	-0.034	18.043	-0.349	-0.349	0.000	0.000	0.000	0.000
20	A	26	GLU	-1	-0.844	-0.921	20.932	12.993	12.993	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.010	0.005	15.822	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	28	TYR	0	-0.006	-0.016	19.405	0.263	0.263	0.000	0.000	0.000	0.000
23	A	29	GLY	0	0.038	0.033	22.287	-0.063	-0.063	0.000	0.000	0.000	0.000
24	A	30	GLU	-1	-0.802	-0.833	16.141	18.507	18.507	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.849	0.908	20.343	-12.577	-12.577	0.000	0.000	0.000	0.000
26	A	32	PHE	0	-0.007	-0.005	13.694	0.939	0.939	0.000	0.000	0.000	0.000
27	A	33	PHE	0	0.027	0.019	18.347	-1.004	-1.004	0.000	0.000	0.000	0.000
28	A	34	ASN	0	-0.007	0.002	18.006	2.043	2.043	0.000	0.000	0.000	0.000
29	A	35	PHE	0	0.049	0.022	16.985	-0.711	-0.711	0.000	0.000	0.000	0.000
30	A	36	ILE	0	0.004	0.008	18.937	0.898	0.898	0.000	0.000	0.000	0.000
31	A	37	LEU	0	0.002	0.007	16.023	-0.475	-0.475	0.000	0.000	0.000	0.000
32	A	38	GLU	-1	-0.852	-0.910	19.614	11.693	11.693	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.009	-0.023	17.034	0.072	0.072	0.000	0.000	0.000	0.000
34	A	40	PRO	0	-0.001	0.006	20.449	-0.121	-0.121	0.000	0.000	0.000	0.000
35	A	41	ARG	1	0.828	0.869	21.398	-12.872	-12.872	0.000	0.000	0.000	0.000
36	A	42	LEU	0	0.020	0.002	23.049	-0.389	-0.389	0.000	0.000	0.000	0.000
37	A	43	SER	0	-0.029	-0.023	25.079	-0.199	-0.199	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.820	-0.897	26.581	10.533	10.533	0.000	0.000	0.000	0.000
39	A	45	THR	0	-0.082	-0.037	25.556	-0.105	-0.105	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.833	0.925	23.899	-10.723	-10.723	0.000	0.000	0.000	0.000
41	A	47	ASP	-1	-0.813	-0.850	19.388	14.200	14.200	0.000	0.000	0.000	0.000
42	A	48	TYR	0	-0.039	-0.050	21.242	0.048	0.048	0.000	0.000	0.000	0.000
43	A	49	LEU	0	-0.023	-0.016	15.266	0.306	0.306	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.000	0.014	15.809	-0.308	-0.308	0.000	0.000	0.000	0.000
45	A	51	ILE	0	0.012	0.016	13.586	1.729	1.729	0.000	0.000	0.000	0.000
46	A	52	THR	0	-0.028	-0.020	13.579	-1.040	-1.040	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.010	0.001	13.463	1.928	1.928	0.000	0.000	0.000	0.000
48	A	54	SER	0	0.018	-0.019	14.677	-1.525	-1.525	0.000	0.000	0.000	0.000
49	A	55	ASN	0	0.035	-0.002	16.365	0.207	0.207	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.833	0.886	15.198	-17.883	-17.883	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.038	-0.027	12.055	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	58	PHE	0	0.027	0.019	16.366	0.115	0.115	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.920	-0.948	19.119	12.532	12.532	0.000	0.000	0.000	0.000
54	A	60	GLY	0	-0.028	-0.009	21.457	0.250	0.250	0.000	0.000	0.000	0.000
55	A	61	MET	0	-0.091	-0.025	18.475	-0.272	-0.272	0.000	0.000	0.000	0.000
56	A	62	ASN	0	-0.049	-0.034	23.300	0.213	0.213	0.000	0.000	0.000	0.000
57	A	63	LEU	0	0.012	-0.011	18.916	0.319	0.319	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.838	-0.899	23.246	10.314	10.314	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.002	-0.009	25.444	0.332	0.332	0.000	0.000	0.000	0.000
60	A	66	GLY	0	-0.028	-0.008	25.791	-0.389	-0.389	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.040	-0.020	22.456	-0.101	-0.101	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.850	0.924	21.469	-12.041	-12.041	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.031	0.007	17.237	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.965	0.987	11.434	-20.876	-20.876	0.000	0.000	0.000	0.000
65	A	71	ILE	0	0.005	-0.004	10.984	0.073	0.073	0.000	0.000	0.000	0.000
66	A	72	GLU	-1	-0.731	-0.823	4.851	44.196	44.267	-0.001	-0.003	-0.066	0.000
67	A	73	GLY	0	0.046	0.014	6.636	-0.979	-0.979	0.000	0.000	0.000	0.000
68	A	74	GLN	0	0.003	0.036	2.027	-25.079	-23.972	4.572	-2.900	-2.780	0.046
69	A	75	LEU	0	0.007	0.001	6.016	-5.631	-5.631	0.000	0.000	0.000	0.000
70	A	76	ARG	1	0.855	0.930	6.215	-36.681	-36.681	0.000	0.000	0.000	0.000
71	A	77	SER	0	0.014	0.005	10.100	-2.052	-2.052	0.000	0.000	0.000	0.000
72	A	78	TYR	0	0.017	0.001	12.866	0.449	0.449	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.002	0.003	15.350	-1.275	-1.275	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.993	1.007	19.017	-14.384	-14.384	0.000	0.000	0.000	0.000
75	A	89	LYS	1	1.005	1.000	22.655	-12.568	-12.568	0.000	0.000	0.000	0.000
76	A	90	LEU	0	-0.012	-0.011	16.638	0.456	0.456	0.000	0.000	0.000	0.000
77	A	91	ILE	0	-0.082	-0.036	17.235	-0.822	-0.822	0.000	0.000	0.000	0.000
78	A	92	LEU	0	0.037	0.013	13.982	1.058	1.058	0.000	0.000	0.000	0.000
79	A	93	THR	0	-0.026	-0.042	12.363	-1.339	-1.339	0.000	0.000	0.000	0.000
80	A	94	VAL	0	0.023	0.023	9.510	2.616	2.616	0.000	0.000	0.000	0.000
81	A	95	PHE	0	-0.010	-0.016	8.372	-2.227	-2.227	0.000	0.000	0.000	0.000
82	A	96	ALA	0	0.000	-0.008	8.551	3.898	3.898	0.000	0.000	0.000	0.000
83	A	97	ARG	1	0.692	0.795	1.853	-83.072	-85.153	13.156	-5.792	-5.283	0.064
84	A	98	ASP	-1	-0.930	-0.968	8.815	20.750	20.750	0.000	0.000	0.000	0.000
85	A	99	ILE	0	0.001	-0.005	11.131	0.165	0.165	0.000	0.000	0.000	0.000
86	A	100	SER	0	0.010	0.015	14.327	-0.813	-0.813	0.000	0.000	0.000	0.000
87	A	101	VAL	0	0.019	0.010	17.200	0.046	0.046	0.000	0.000	0.000	0.000
88	A	102	VAL	0	-0.045	-0.020	19.471	-0.154	-0.154	0.000	0.000	0.000	0.000
89	A	103	PRO	0	0.026	0.019	22.220	-0.252	-0.252	0.000	0.000	0.000	0.000
90	A	104	GLU	-1	-0.803	-0.891	24.832	11.332	11.332	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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