FMO DATABASE

FMODB ID: YVZ52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-764894.89576
FMO2-HF: Nuclear repulsion	726038.90892
FMO2-HF: Total energy	-38855.98684
FMO2-MP2: Total energy	-38972.010284

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.
-27.612	-14.249	8.542	-8.772	-13.135	-0.049

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 : -0.037 / q_NPA : -0.024

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	103	SER	0	-0.028	-0.030	3.192	-3.311	0.421	0.080	-1.560	-2.253	0.007
4	A	104	ILE	0	-0.056	-0.021	5.101	0.117	0.229	-0.001	-0.014	-0.096	0.000
5	A	105	ASN	0	0.126	0.076	8.343	-0.393	-0.393	0.000	0.000	0.000	0.000
6	A	106	ALA	0	0.052	0.022	10.574	0.030	0.030	0.000	0.000	0.000	0.000
7	A	107	ALA	0	0.009	0.000	12.697	0.048	0.048	0.000	0.000	0.000	0.000
8	A	108	ASP	-1	-0.859	-0.928	12.478	0.150	0.150	0.000	0.000	0.000	0.000
9	A	109	LEU	0	-0.043	-0.037	11.316	0.065	0.065	0.000	0.000	0.000	0.000
10	A	110	TYR	0	-0.001	-0.018	13.841	0.043	0.043	0.000	0.000	0.000	0.000
11	A	111	GLU	-1	-0.950	-0.972	17.197	0.072	0.072	0.000	0.000	0.000	0.000
12	A	112	ASN	0	-0.106	-0.051	16.147	0.066	0.066	0.000	0.000	0.000	0.000
13	A	113	ILE	0	0.020	0.031	17.002	0.048	0.048	0.000	0.000	0.000	0.000
14	A	114	LYS	1	0.921	0.941	18.035	-0.076	-0.076	0.000	0.000	0.000	0.000
15	A	115	ALA	0	-0.051	-0.018	16.555	0.016	0.016	0.000	0.000	0.000	0.000
16	A	116	TYR	0	-0.008	-0.006	10.461	0.226	0.226	0.000	0.000	0.000	0.000
17	A	117	THR	0	-0.018	-0.004	14.371	-0.044	-0.044	0.000	0.000	0.000	0.000
18	A	118	VAL	0	0.014	-0.003	12.776	0.018	0.018	0.000	0.000	0.000	0.000
19	A	119	LEU	0	-0.005	-0.009	10.941	0.070	0.070	0.000	0.000	0.000	0.000
20	A	120	ASP	-1	-0.763	-0.885	11.506	-0.868	-0.868	0.000	0.000	0.000	0.000
21	A	121	VAL	0	0.011	-0.008	9.555	0.099	0.099	0.000	0.000	0.000	0.000
22	A	122	ARG	1	0.782	0.912	12.660	0.557	0.557	0.000	0.000	0.000	0.000
23	A	123	GLU	-1	-0.864	-0.955	14.834	-0.400	-0.400	0.000	0.000	0.000	0.000
24	A	124	PRO	0	0.045	0.015	18.415	0.002	0.002	0.000	0.000	0.000	0.000
25	A	125	PHE	0	-0.046	-0.025	20.610	0.015	0.015	0.000	0.000	0.000	0.000
26	A	126	GLU	-1	-0.756	-0.890	16.624	-0.595	-0.595	0.000	0.000	0.000	0.000
27	A	127	LEU	0	-0.005	-0.001	17.145	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	128	ILE	0	-0.023	0.018	20.371	0.025	0.025	0.000	0.000	0.000	0.000
29	A	129	PHE	0	-0.076	-0.041	21.428	0.027	0.027	0.000	0.000	0.000	0.000
30	A	130	GLY	0	-0.001	0.013	21.139	0.006	0.006	0.000	0.000	0.000	0.000
31	A	131	SER	0	0.011	-0.009	17.928	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	132	ILE	0	0.061	0.037	14.013	0.043	0.043	0.000	0.000	0.000	0.000
33	A	133	ALA	0	0.027	0.000	18.066	0.006	0.006	0.000	0.000	0.000	0.000
34	A	134	ASN	0	-0.073	-0.044	19.646	0.007	0.007	0.000	0.000	0.000	0.000
35	A	135	SER	0	-0.021	0.015	15.881	0.008	0.008	0.000	0.000	0.000	0.000
36	A	136	ILE	0	0.009	0.018	15.594	0.003	0.003	0.000	0.000	0.000	0.000
37	A	137	ASN	0	-0.024	-0.038	15.998	-0.025	-0.025	0.000	0.000	0.000	0.000
38	A	138	ILE	0	-0.056	-0.034	14.448	0.072	0.072	0.000	0.000	0.000	0.000
39	A	139	PRO	0	0.062	0.065	14.129	-0.109	-0.109	0.000	0.000	0.000	0.000
40	A	140	ILE	0	0.061	0.016	10.644	0.041	0.041	0.000	0.000	0.000	0.000
41	A	141	SER	0	-0.057	-0.024	13.463	0.030	0.030	0.000	0.000	0.000	0.000
42	A	142	GLU	-1	-0.912	-0.960	16.369	-0.196	-0.196	0.000	0.000	0.000	0.000
43	A	143	LEU	0	-0.031	-0.008	10.075	0.065	0.065	0.000	0.000	0.000	0.000
44	A	144	ARG	1	0.946	0.974	14.601	0.258	0.258	0.000	0.000	0.000	0.000
45	A	145	GLU	-1	-0.920	-0.977	15.488	-0.160	-0.160	0.000	0.000	0.000	0.000
46	A	146	LYS	1	0.858	0.924	17.751	0.214	0.214	0.000	0.000	0.000	0.000
47	A	147	TRP	0	0.047	0.034	13.524	0.030	0.030	0.000	0.000	0.000	0.000
48	A	148	LYS	1	0.901	0.937	15.492	0.029	0.029	0.000	0.000	0.000	0.000
49	A	149	ILE	0	-0.062	-0.025	18.093	0.031	0.031	0.000	0.000	0.000	0.000
50	A	150	LEU	0	-0.016	0.013	12.633	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	151	GLU	-1	-0.818	-0.904	16.322	0.203	0.203	0.000	0.000	0.000	0.000
52	A	152	ARG	1	0.930	0.949	14.117	-0.602	-0.602	0.000	0.000	0.000	0.000
53	A	153	ASP	-1	-0.975	-0.989	14.401	0.501	0.501	0.000	0.000	0.000	0.000
54	A	154	LYS	1	0.895	0.958	14.875	-0.235	-0.235	0.000	0.000	0.000	0.000
55	A	155	LYS	1	0.848	0.950	9.304	-1.031	-1.031	0.000	0.000	0.000	0.000
56	A	156	TYR	0	0.034	0.009	10.239	-0.168	-0.168	0.000	0.000	0.000	0.000
57	A	157	ALA	0	0.001	0.000	9.411	0.270	0.270	0.000	0.000	0.000	0.000
58	A	158	VAL	0	-0.040	-0.016	6.433	0.051	0.051	0.000	0.000	0.000	0.000
59	A	159	ILE	0	0.037	0.027	7.197	-0.626	-0.626	0.000	0.000	0.000	0.000
60	A	160	CYM	-1	-0.795	-0.780	8.232	-1.511	-1.511	0.000	0.000	0.000	0.000
61	A	161	ALA	0	-0.053	-0.062	10.035	0.165	0.165	0.000	0.000	0.000	0.000
62	A	162	HIS	0	-0.050	-0.062	10.643	0.127	0.127	0.000	0.000	0.000	0.000
63	A	163	GLY	0	0.082	0.030	6.620	0.086	0.086	0.000	0.000	0.000	0.000
64	A	164	ASN	0	-0.046	-0.027	5.525	-0.875	-0.875	0.000	0.000	0.000	0.000
65	A	165	ARG	1	0.858	0.871	7.665	0.852	0.852	0.000	0.000	0.000	0.000
66	A	166	SER	0	0.021	-0.013	4.752	0.771	0.820	-0.001	-0.004	-0.044	0.000
67	A	167	ALA	0	0.049	0.033	2.646	-1.447	-0.527	0.267	-0.363	-0.825	-0.001
68	A	168	ALA	0	-0.004	-0.012	3.337	-0.130	0.897	0.039	-0.392	-0.675	-0.004
69	A	169	ALA	0	-0.007	0.003	6.078	0.491	0.491	0.000	0.000	0.000	0.000
70	A	170	VAL	0	-0.006	-0.007	2.177	-0.032	0.363	3.754	-1.001	-3.148	0.003
71	A	171	GLU	-1	-0.878	-0.954	3.054	-2.563	-0.698	0.112	-0.639	-1.338	-0.003
72	A	172	PHE	0	-0.060	-0.004	4.015	0.633	0.757	0.001	-0.022	-0.104	0.000
73	A	173	LEU	0	0.004	-0.019	7.084	0.313	0.313	0.000	0.000	0.000	0.000
74	A	174	SER	0	-0.032	-0.009	3.459	-0.276	0.208	0.014	-0.142	-0.355	0.000
75	A	175	GLN	0	-0.030	-0.024	5.487	0.479	0.479	0.000	0.000	0.000	0.000
76	A	176	LEU	0	-0.078	-0.026	7.237	-0.073	-0.073	0.000	0.000	0.000	0.000
77	A	177	GLY	0	-0.043	-0.015	8.579	-0.090	-0.090	0.000	0.000	0.000	0.000
78	A	178	LEU	0	-0.014	0.001	8.790	-0.097	-0.097	0.000	0.000	0.000	0.000
79	A	179	ASN	0	0.032	0.017	7.489	1.177	1.177	0.000	0.000	0.000	0.000
80	A	180	ILE	0	-0.002	0.010	4.631	-0.605	-0.481	-0.001	-0.010	-0.113	0.000
81	A	181	VAL	0	-0.051	-0.023	5.125	1.779	1.779	0.000	0.000	0.000	0.000
82	A	182	ASP	-1	-0.750	-0.869	2.089	-22.247	-17.794	4.279	-4.607	-4.125	-0.051
83	A	183	VAL	0	-0.006	0.002	4.383	1.281	1.359	-0.001	-0.018	-0.059	0.000
84	A	184	GLU	-1	-0.861	-0.915	5.746	-0.625	-0.625	0.000	0.000	0.000	0.000
85	A	185	GLY	0	0.044	0.012	6.828	0.251	0.251	0.000	0.000	0.000	0.000
86	A	186	GLY	0	-0.024	-0.007	8.334	0.106	0.106	0.000	0.000	0.000	0.000
87	A	187	ILE	0	-0.018	-0.033	9.806	0.161	0.161	0.000	0.000	0.000	0.000
88	A	188	GLN	0	0.015	0.011	13.046	0.059	0.059	0.000	0.000	0.000	0.000
89	A	189	SER	0	-0.023	0.009	11.758	0.073	0.073	0.000	0.000	0.000	0.000
90	A	190	TRP	0	-0.007	-0.005	13.339	0.076	0.076	0.000	0.000	0.000	0.000
91	A	191	ILE	0	-0.006	-0.019	14.906	0.067	0.067	0.000	0.000	0.000	0.000
92	A	192	GLU	-1	-0.960	-0.965	16.912	-0.256	-0.256	0.000	0.000	0.000	0.000
93	A	193	GLU	-1	-0.953	-0.989	15.647	-0.260	-0.260	0.000	0.000	0.000	0.000
94	A	194	GLY	0	-0.083	-0.022	18.729	0.034	0.034	0.000	0.000	0.000	0.000
95	A	195	TYR	0	-0.026	-0.008	16.440	0.037	0.037	0.000	0.000	0.000	0.000
96	A	196	PRO	0	-0.068	-0.029	19.998	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	197	VAL	0	-0.006	0.005	18.866	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	198	VAL	0	-0.034	-0.029	21.309	0.030	0.030	0.000	0.000	0.000	0.000
99	A	199	LEU	0	0.026	-0.002	22.967	-0.021	-0.021	0.000	0.000	0.000	0.000
100	A	200	GLU	-1	-0.984	-0.973	24.110	-0.172	-0.172	0.000	0.000	0.000	0.000

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