FMO DATABASE

FMODB ID: 1N71Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-765961.762155
FMO2-HF: Nuclear repulsion	727104.814502
FMO2-HF: Total energy	-38856.947653
FMO2-MP2: Total energy	-38972.874411

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.
-53.551	-49.927	34.906	-18.362	-20.166	-0.124

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 : -0.071 / 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

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	-0.049	-0.051	2.910	-4.076	-0.053	0.529	-1.562	-2.991	0.011
4	A	104	ILE	0	-0.047	-0.016	4.809	-0.021	0.128	0.001	-0.038	-0.111	0.000
5	A	105	ASN	0	0.072	0.031	7.795	-0.505	-0.505	0.000	0.000	0.000	0.000
6	A	106	ALA	0	0.051	0.027	9.967	0.035	0.035	0.000	0.000	0.000	0.000
7	A	107	ALA	0	0.020	0.014	12.268	0.041	0.041	0.000	0.000	0.000	0.000
8	A	108	ASP	-1	-0.852	-0.914	12.266	0.271	0.271	0.000	0.000	0.000	0.000
9	A	109	LEU	0	-0.019	-0.010	10.740	0.057	0.057	0.000	0.000	0.000	0.000
10	A	110	TYR	0	-0.010	-0.009	13.488	0.019	0.019	0.000	0.000	0.000	0.000
11	A	111	GLU	-1	-0.969	-0.991	16.899	0.117	0.117	0.000	0.000	0.000	0.000
12	A	112	ASN	0	-0.099	-0.054	15.715	0.066	0.066	0.000	0.000	0.000	0.000
13	A	113	ILE	0	0.015	0.022	16.831	0.043	0.043	0.000	0.000	0.000	0.000
14	A	114	LYS	1	0.922	0.937	17.873	-0.085	-0.085	0.000	0.000	0.000	0.000
15	A	115	ALA	0	-0.050	-0.008	17.431	0.005	0.005	0.000	0.000	0.000	0.000
16	A	116	TYR	0	0.022	0.001	10.696	0.224	0.224	0.000	0.000	0.000	0.000
17	A	117	THR	0	-0.045	-0.020	14.221	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	118	VAL	0	0.035	0.022	12.735	0.028	0.028	0.000	0.000	0.000	0.000
19	A	119	LEU	0	-0.007	-0.007	10.988	0.066	0.066	0.000	0.000	0.000	0.000
20	A	120	ASP	-1	-0.739	-0.848	11.440	-0.888	-0.888	0.000	0.000	0.000	0.000
21	A	121	VAL	0	-0.009	-0.007	9.232	0.093	0.093	0.000	0.000	0.000	0.000
22	A	122	ARG	1	0.757	0.845	12.494	0.549	0.549	0.000	0.000	0.000	0.000
23	A	123	GLU	-1	-0.808	-0.897	14.821	-0.442	-0.442	0.000	0.000	0.000	0.000
24	A	124	PRO	0	0.022	0.009	18.178	0.006	0.006	0.000	0.000	0.000	0.000
25	A	125	PHE	0	-0.033	-0.024	20.592	0.020	0.020	0.000	0.000	0.000	0.000
26	A	126	GLU	-1	-0.723	-0.844	16.224	-0.700	-0.700	0.000	0.000	0.000	0.000
27	A	127	LEU	0	-0.012	-0.004	17.294	0.002	0.002	0.000	0.000	0.000	0.000
28	A	128	ILE	0	-0.013	0.013	20.350	0.022	0.022	0.000	0.000	0.000	0.000
29	A	129	PHE	0	-0.075	-0.034	21.336	0.029	0.029	0.000	0.000	0.000	0.000
30	A	130	GLY	0	-0.006	0.008	20.725	0.006	0.006	0.000	0.000	0.000	0.000
31	A	131	SER	0	0.042	0.027	18.073	-0.059	-0.059	0.000	0.000	0.000	0.000
32	A	132	ILE	0	0.064	0.037	13.971	0.034	0.034	0.000	0.000	0.000	0.000
33	A	133	ALA	0	0.044	0.020	18.133	0.012	0.012	0.000	0.000	0.000	0.000
34	A	134	ASN	0	-0.069	-0.043	19.679	0.001	0.001	0.000	0.000	0.000	0.000
35	A	135	SER	0	-0.029	-0.005	16.244	0.012	0.012	0.000	0.000	0.000	0.000
36	A	136	ILE	0	-0.006	0.002	15.951	0.010	0.010	0.000	0.000	0.000	0.000
37	A	137	ASN	0	-0.049	-0.045	15.960	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	138	ILE	0	-0.041	-0.028	14.977	0.078	0.078	0.000	0.000	0.000	0.000
39	A	139	PRO	0	0.048	0.049	14.277	-0.095	-0.095	0.000	0.000	0.000	0.000
40	A	140	ILE	0	0.039	0.007	10.799	0.045	0.045	0.000	0.000	0.000	0.000
41	A	141	SER	0	-0.083	-0.059	13.626	0.042	0.042	0.000	0.000	0.000	0.000
42	A	142	GLU	-1	-0.827	-0.903	16.692	-0.184	-0.184	0.000	0.000	0.000	0.000
43	A	143	LEU	0	-0.021	-0.004	10.488	0.072	0.072	0.000	0.000	0.000	0.000
44	A	144	ARG	1	0.904	0.951	14.605	0.308	0.308	0.000	0.000	0.000	0.000
45	A	145	GLU	-1	-0.862	-0.937	15.445	-0.167	-0.167	0.000	0.000	0.000	0.000
46	A	146	LYS	1	0.768	0.855	17.748	0.261	0.261	0.000	0.000	0.000	0.000
47	A	147	TRP	0	0.049	0.026	13.396	0.067	0.067	0.000	0.000	0.000	0.000
48	A	148	LYS	1	0.864	0.933	15.312	0.058	0.058	0.000	0.000	0.000	0.000
49	A	149	ILE	0	-0.029	-0.007	17.831	0.019	0.019	0.000	0.000	0.000	0.000
50	A	150	LEU	0	-0.016	0.008	11.951	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	151	GLU	-1	-0.812	-0.883	16.090	0.247	0.247	0.000	0.000	0.000	0.000
52	A	152	ARG	1	0.907	0.936	12.952	-0.756	-0.756	0.000	0.000	0.000	0.000
53	A	153	ASP	-1	-0.931	-0.971	14.212	0.549	0.549	0.000	0.000	0.000	0.000
54	A	154	LYS	1	0.823	0.916	15.264	-0.193	-0.193	0.000	0.000	0.000	0.000
55	A	155	LYS	1	0.869	0.960	9.570	-1.129	-1.129	0.000	0.000	0.000	0.000
56	A	156	TYR	0	0.011	-0.008	10.087	-0.177	-0.177	0.000	0.000	0.000	0.000
57	A	157	ALA	0	-0.005	-0.006	9.483	0.298	0.298	0.000	0.000	0.000	0.000
58	A	158	VAL	0	-0.042	-0.011	6.636	-0.054	-0.054	0.000	0.000	0.000	0.000
59	A	159	ILE	0	0.033	0.016	7.363	-0.615	-0.615	0.000	0.000	0.000	0.000
60	A	160	CYM	-1	-0.875	-0.792	8.364	-1.525	-1.525	0.000	0.000	0.000	0.000
61	A	161	ALA	0	0.022	-0.010	10.249	0.147	0.147	0.000	0.000	0.000	0.000
62	A	162	HIS	0	-0.029	-0.072	10.385	0.139	0.139	0.000	0.000	0.000	0.000
63	A	163	GLY	0	0.079	0.019	6.245	0.100	0.100	0.000	0.000	0.000	0.000
64	A	164	ASN	0	-0.052	-0.032	5.498	-1.234	-1.234	0.000	0.000	0.000	0.000
65	A	165	ARG	1	0.831	0.826	7.480	0.974	0.974	0.000	0.000	0.000	0.000
66	A	166	SER	0	-0.009	-0.021	5.063	0.796	0.796	0.000	0.000	0.000	0.000
67	A	167	ALA	0	0.057	0.040	2.174	-0.903	-0.098	1.378	-0.946	-1.237	-0.002
68	A	168	ALA	0	-0.011	-0.011	3.097	1.024	1.297	0.003	0.352	-0.627	-0.003
69	A	169	ALA	0	-0.014	-0.007	6.123	0.470	0.470	0.000	0.000	0.000	0.000
70	A	170	VAL	0	-0.007	-0.012	2.351	-0.306	0.789	2.158	-0.945	-2.309	0.001
71	A	171	GLU	-1	-0.800	-0.889	1.956	-15.271	-13.468	8.154	-4.333	-5.624	-0.054
72	A	172	PHE	0	-0.066	-0.011	4.360	0.667	0.782	0.000	-0.031	-0.083	0.000
73	A	173	LEU	0	-0.007	-0.015	7.119	0.329	0.329	0.000	0.000	0.000	0.000
74	A	174	SER	0	-0.029	-0.038	2.456	0.309	1.723	0.390	-0.817	-0.987	0.002
75	A	175	GLN	0	-0.037	-0.031	4.831	0.150	0.157	-0.001	-0.007	0.001	0.000
76	A	176	LEU	0	-0.042	-0.004	6.975	-0.114	-0.114	0.000	0.000	0.000	0.000
77	A	177	GLY	0	-0.037	-0.008	8.248	-0.125	-0.125	0.000	0.000	0.000	0.000
78	A	178	LEU	0	0.002	0.002	8.710	-0.274	-0.274	0.000	0.000	0.000	0.000
79	A	179	ASN	0	0.014	0.016	7.990	1.088	1.088	0.000	0.000	0.000	0.000
80	A	180	ILE	0	-0.015	-0.009	4.587	-0.385	-0.283	-0.001	-0.007	-0.094	0.000
81	A	181	VAL	0	-0.042	-0.009	5.062	1.593	1.593	0.000	0.000	0.000	0.000
82	A	182	ASP	-1	-0.726	-0.827	1.600	-36.498	-42.782	22.296	-10.008	-6.004	-0.079
83	A	183	VAL	0	0.024	-0.006	4.462	1.579	1.701	-0.001	-0.020	-0.100	0.000
84	A	184	GLU	-1	-0.840	-0.888	5.210	-0.141	-0.141	0.000	0.000	0.000	0.000
85	A	185	GLY	0	0.030	0.009	6.485	0.261	0.261	0.000	0.000	0.000	0.000
86	A	186	GLY	0	-0.029	-0.003	7.971	0.138	0.138	0.000	0.000	0.000	0.000
87	A	187	ILE	0	-0.016	-0.030	9.552	0.230	0.230	0.000	0.000	0.000	0.000
88	A	188	GLN	0	-0.035	-0.008	12.929	0.040	0.040	0.000	0.000	0.000	0.000
89	A	189	SER	0	-0.037	-0.029	11.329	0.093	0.093	0.000	0.000	0.000	0.000
90	A	190	TRP	0	-0.026	-0.033	13.051	0.100	0.100	0.000	0.000	0.000	0.000
91	A	191	ILE	0	-0.016	-0.016	14.760	0.076	0.076	0.000	0.000	0.000	0.000
92	A	192	GLU	-1	-0.934	-0.962	16.821	-0.309	-0.309	0.000	0.000	0.000	0.000
93	A	193	GLU	-1	-0.893	-0.926	14.671	-0.260	-0.260	0.000	0.000	0.000	0.000
94	A	194	GLY	0	-0.050	-0.008	18.142	0.039	0.039	0.000	0.000	0.000	0.000
95	A	195	TYR	0	-0.026	-0.016	16.278	0.040	0.040	0.000	0.000	0.000	0.000
96	A	196	PRO	0	-0.054	-0.020	19.536	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	197	VAL	0	-0.005	0.013	19.250	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	198	VAL	0	-0.045	-0.027	21.174	0.031	0.031	0.000	0.000	0.000	0.000
99	A	199	LEU	0	0.010	0.004	22.865	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	200	GLU	-1	-0.951	-0.971	23.713	-0.159	-0.159	0.000	0.000	0.000	0.000

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