FMO DATABASE

FMODB ID: VQ531

Calculation Name: 3GK5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GK5

Chain ID: A

ChEMBL ID:

UniProt ID: Q97AG6

Base Structure: X-ray

Registration Date: 2023-09-21

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	100
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-764013.152642
FMO2-HF: Nuclear repulsion	725156.575041
FMO2-HF: Total energy	-38856.577602
FMO2-MP2: Total energy	-38972.513339

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:101:TYR)

Summations of interaction energy for fragment #1(A:101:TYR)

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.
-47.78	-42.33	26.678	-15.79	-16.337	-0.1

Interaction energy analysis for fragmet #1(A:101:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.071

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	103	SER	0	-0.038	-0.051	2.888	-3.549	0.215	0.178	-1.537	-2.405	0.008
4	A	104	ILE	0	-0.055	-0.028	4.855	0.243	0.362	0.000	-0.021	-0.098	0.000
5	A	105	ASN	0	0.081	0.037	8.399	-0.448	-0.448	0.000	0.000	0.000	0.000
6	A	106	ALA	0	0.068	0.032	10.591	0.036	0.036	0.000	0.000	0.000	0.000
7	A	107	ALA	0	0.020	0.006	12.722	0.058	0.058	0.000	0.000	0.000	0.000
8	A	108	ASP	-1	-0.847	-0.913	12.481	0.168	0.168	0.000	0.000	0.000	0.000
9	A	109	LEU	0	-0.025	-0.014	11.316	0.078	0.078	0.000	0.000	0.000	0.000
10	A	110	TYR	0	0.006	-0.010	13.914	0.050	0.050	0.000	0.000	0.000	0.000
11	A	111	GLU	-1	-0.959	-0.974	17.261	0.075	0.075	0.000	0.000	0.000	0.000
12	A	112	ASN	0	-0.121	-0.066	16.198	0.092	0.092	0.000	0.000	0.000	0.000
13	A	113	ILE	0	0.019	0.030	17.091	0.052	0.052	0.000	0.000	0.000	0.000
14	A	114	LYS	1	0.923	0.944	18.130	-0.075	-0.075	0.000	0.000	0.000	0.000
15	A	115	ALA	0	-0.057	-0.022	16.572	0.018	0.018	0.000	0.000	0.000	0.000
16	A	116	TYR	0	-0.016	-0.009	10.393	0.254	0.254	0.000	0.000	0.000	0.000
17	A	117	THR	0	-0.018	-0.003	14.353	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	118	VAL	0	0.010	-0.005	12.722	0.013	0.013	0.000	0.000	0.000	0.000
19	A	119	LEU	0	-0.003	-0.004	11.040	0.076	0.076	0.000	0.000	0.000	0.000
20	A	120	ASP	-1	-0.757	-0.864	11.643	-1.049	-1.049	0.000	0.000	0.000	0.000
21	A	121	VAL	0	0.016	-0.007	9.414	0.101	0.101	0.000	0.000	0.000	0.000
22	A	122	ARG	1	0.759	0.879	12.692	0.668	0.668	0.000	0.000	0.000	0.000
23	A	123	GLU	-1	-0.846	-0.944	14.874	-0.493	-0.493	0.000	0.000	0.000	0.000
24	A	124	PRO	0	0.045	0.017	18.388	0.004	0.004	0.000	0.000	0.000	0.000
25	A	125	PHE	0	-0.045	-0.026	20.609	0.019	0.019	0.000	0.000	0.000	0.000
26	A	126	GLU	-1	-0.727	-0.847	16.364	-0.772	-0.772	0.000	0.000	0.000	0.000
27	A	127	LEU	0	-0.003	-0.001	17.263	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	128	ILE	0	-0.025	0.017	20.414	0.029	0.029	0.000	0.000	0.000	0.000
29	A	129	PHE	0	-0.075	-0.039	21.389	0.033	0.033	0.000	0.000	0.000	0.000
30	A	130	GLY	0	0.000	0.010	21.168	0.007	0.007	0.000	0.000	0.000	0.000
31	A	131	SER	0	0.025	-0.002	17.971	-0.062	-0.062	0.000	0.000	0.000	0.000
32	A	132	ILE	0	0.054	0.039	14.061	0.053	0.053	0.000	0.000	0.000	0.000
33	A	133	ALA	0	0.038	0.014	18.135	0.004	0.004	0.000	0.000	0.000	0.000
34	A	134	ASN	0	-0.070	-0.042	19.741	0.004	0.004	0.000	0.000	0.000	0.000
35	A	135	SER	0	-0.022	0.001	16.037	0.012	0.012	0.000	0.000	0.000	0.000
36	A	136	ILE	0	-0.004	0.009	15.918	0.000	0.000	0.000	0.000	0.000	0.000
37	A	137	ASN	0	-0.024	-0.034	16.139	-0.030	-0.030	0.000	0.000	0.000	0.000
38	A	138	ILE	0	-0.048	-0.030	14.626	0.081	0.081	0.000	0.000	0.000	0.000
39	A	139	PRO	0	0.061	0.064	14.175	-0.132	-0.132	0.000	0.000	0.000	0.000
40	A	140	ILE	0	0.066	0.015	10.485	0.052	0.052	0.000	0.000	0.000	0.000
41	A	141	SER	0	-0.082	-0.035	13.420	0.025	0.025	0.000	0.000	0.000	0.000
42	A	142	GLU	-1	-0.837	-0.911	16.324	-0.236	-0.236	0.000	0.000	0.000	0.000
43	A	143	LEU	0	-0.023	-0.002	10.229	0.075	0.075	0.000	0.000	0.000	0.000
44	A	144	ARG	1	0.943	0.977	14.516	0.354	0.354	0.000	0.000	0.000	0.000
45	A	145	GLU	-1	-0.897	-0.968	15.418	-0.232	-0.232	0.000	0.000	0.000	0.000
46	A	146	LYS	1	0.754	0.852	17.700	0.322	0.322	0.000	0.000	0.000	0.000
47	A	147	TRP	0	0.058	0.040	13.582	0.049	0.049	0.000	0.000	0.000	0.000
48	A	148	LYS	1	0.882	0.930	15.527	0.081	0.081	0.000	0.000	0.000	0.000
49	A	149	ILE	0	-0.053	-0.021	18.102	0.040	0.040	0.000	0.000	0.000	0.000
50	A	150	LEU	0	0.023	0.033	12.274	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	151	GLU	-1	-0.858	-0.898	16.304	0.199	0.199	0.000	0.000	0.000	0.000
52	A	152	ARG	1	0.942	0.959	13.573	-0.706	-0.706	0.000	0.000	0.000	0.000
53	A	153	ASP	-1	-0.967	-0.982	14.360	0.542	0.542	0.000	0.000	0.000	0.000
54	A	154	LYS	1	0.866	0.922	14.836	-0.239	-0.239	0.000	0.000	0.000	0.000
55	A	155	LYS	1	0.873	0.963	9.276	-1.213	-1.213	0.000	0.000	0.000	0.000
56	A	156	TYR	0	0.040	-0.003	10.286	-0.222	-0.222	0.000	0.000	0.000	0.000
57	A	157	ALA	0	-0.004	0.000	9.399	0.299	0.299	0.000	0.000	0.000	0.000
58	A	158	VAL	0	-0.038	-0.015	6.601	0.025	0.025	0.000	0.000	0.000	0.000
59	A	159	ILE	0	0.033	0.021	7.289	-0.685	-0.685	0.000	0.000	0.000	0.000
60	A	160	CYM	-1	-0.834	-0.780	8.115	-1.892	-1.892	0.000	0.000	0.000	0.000
61	A	161	ALA	0	-0.016	-0.039	10.061	0.191	0.191	0.000	0.000	0.000	0.000
62	A	162	HIS	0	-0.041	-0.071	10.596	0.155	0.155	0.000	0.000	0.000	0.000
63	A	163	GLY	0	0.066	0.006	6.563	0.087	0.087	0.000	0.000	0.000	0.000
64	A	164	ASN	0	-0.048	-0.031	5.476	-1.115	-1.115	0.000	0.000	0.000	0.000
65	A	165	ARG	1	0.848	0.844	7.627	0.987	0.987	0.000	0.000	0.000	0.000
66	A	166	SER	0	0.018	-0.023	4.827	0.812	0.812	0.000	0.000	0.000	0.000
67	A	167	ALA	0	0.050	0.038	2.514	-1.156	-0.174	0.395	-0.470	-0.907	-0.002
68	A	168	ALA	0	-0.024	-0.020	3.185	-0.483	0.753	0.065	-0.470	-0.831	-0.006
69	A	169	ALA	0	-0.014	-0.004	5.906	0.603	0.603	0.000	0.000	0.000	0.000
70	A	170	VAL	0	-0.012	-0.012	2.288	-0.254	0.870	2.517	-0.857	-2.783	0.005
71	A	171	GLU	-1	-0.853	-0.939	2.477	-8.211	-3.643	1.209	-2.349	-3.428	-0.026
72	A	172	PHE	0	-0.049	-0.004	3.906	0.913	1.065	0.003	-0.028	-0.127	0.000
73	A	173	LEU	0	0.000	-0.017	7.073	0.400	0.400	0.000	0.000	0.000	0.000
74	A	174	SER	0	-0.008	-0.001	3.287	0.282	0.806	0.018	-0.150	-0.392	0.000
75	A	175	GLN	0	-0.035	-0.024	5.497	0.652	0.652	0.000	0.000	0.000	0.000
76	A	176	LEU	0	-0.072	-0.023	7.249	-0.063	-0.063	0.000	0.000	0.000	0.000
77	A	177	GLY	0	-0.041	-0.015	8.595	-0.092	-0.092	0.000	0.000	0.000	0.000
78	A	178	LEU	0	-0.020	-0.002	8.807	-0.100	-0.100	0.000	0.000	0.000	0.000
79	A	179	ASN	0	0.022	0.017	7.450	1.256	1.256	0.000	0.000	0.000	0.000
80	A	180	ILE	0	-0.009	0.006	4.982	-0.479	-0.479	0.000	0.000	0.000	0.000
81	A	181	VAL	0	-0.028	-0.011	5.107	1.996	1.996	0.000	0.000	0.000	0.000
82	A	182	ASP	-1	-0.727	-0.817	1.585	-36.945	-44.037	22.294	-9.894	-5.308	-0.079
83	A	183	VAL	0	0.008	0.004	4.502	1.313	1.386	-0.001	-0.014	-0.058	0.000
84	A	184	GLU	-1	-0.848	-0.891	5.591	-0.826	-0.826	0.000	0.000	0.000	0.000
85	A	185	GLY	0	0.035	0.007	6.806	0.322	0.322	0.000	0.000	0.000	0.000
86	A	186	GLY	0	-0.026	-0.003	8.312	0.133	0.133	0.000	0.000	0.000	0.000
87	A	187	ILE	0	-0.027	-0.035	9.801	0.197	0.197	0.000	0.000	0.000	0.000
88	A	188	GLN	0	-0.037	-0.009	13.038	0.054	0.054	0.000	0.000	0.000	0.000
89	A	189	SER	0	-0.038	-0.014	11.711	0.083	0.083	0.000	0.000	0.000	0.000
90	A	190	TRP	0	0.002	-0.008	13.334	0.100	0.100	0.000	0.000	0.000	0.000
91	A	191	ILE	0	-0.012	-0.023	14.913	0.083	0.083	0.000	0.000	0.000	0.000
92	A	192	GLU	-1	-0.905	-0.936	16.636	-0.352	-0.352	0.000	0.000	0.000	0.000
93	A	193	GLU	-1	-0.933	-0.958	15.124	-0.353	-0.353	0.000	0.000	0.000	0.000
94	A	194	GLY	0	-0.073	-0.020	18.713	0.042	0.042	0.000	0.000	0.000	0.000
95	A	195	TYR	0	-0.018	-0.010	16.613	0.042	0.042	0.000	0.000	0.000	0.000
96	A	196	PRO	0	-0.070	-0.034	20.023	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	197	VAL	0	-0.015	0.012	19.356	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	198	VAL	0	-0.052	-0.034	21.354	0.036	0.036	0.000	0.000	0.000	0.000
99	A	199	LEU	0	0.031	0.004	23.018	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	200	GLU	-1	-0.965	-0.968	24.179	-0.215	-0.215	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:101:TYR)