FMO DATABASE

FMODB ID: R84Z8

Calculation Name: 5T8L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T8L

Chain ID: A

ChEMBL ID:

UniProt ID: P39929

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-785250.542902
FMO2-HF: Nuclear repulsion	734252.418322
FMO2-HF: Total energy	-50998.12458
FMO2-MP2: Total energy	-51143.210352

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:18:SER)

Summations of interaction energy for fragment #1(A:18:SER)

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.
-13.492	-12.431	14.605	-7.051	-8.616	0.036

Interaction energy analysis for fragmet #1(A:18:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.025

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	20	THR	0	0.082	0.037	2.085	-6.797	-4.992	4.004	-2.616	-3.193	0.016
4	A	21	LYS	1	0.903	0.956	1.883	-5.846	-7.279	10.565	-4.244	-4.888	0.019
5	A	22	ALA	0	0.026	0.013	3.500	-0.975	-0.286	0.036	-0.191	-0.535	0.001
6	A	23	ILE	0	0.037	0.027	5.646	0.281	0.281	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.008	0.001	6.371	-0.204	-0.204	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.961	0.991	6.767	0.158	0.158	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.019	0.025	9.474	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.923	0.954	10.949	-0.439	-0.439	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.918	-0.956	11.254	0.268	0.268	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.090	-0.060	12.263	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.039	0.016	14.951	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	31	ASN	0	-0.002	-0.006	16.915	0.000	0.000	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.027	-0.019	18.239	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.012	-0.020	18.513	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	34	SER	0	0.059	0.039	21.338	0.001	0.001	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.924	0.963	21.111	-0.103	-0.103	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.942	0.972	21.567	0.035	0.035	0.000	0.000	0.000	0.000
20	A	37	GLN	0	0.003	-0.012	25.660	0.006	0.006	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.021	-0.007	27.547	0.000	0.000	0.000	0.000	0.000	0.000
22	A	39	HIS	0	-0.011	-0.005	28.979	0.002	0.002	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.011	-0.016	28.554	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.927	0.948	29.121	0.002	0.002	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.008	0.017	33.524	0.001	0.001	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.005	-0.004	33.510	0.001	0.001	0.000	0.000	0.000	0.000
27	A	44	ILE	0	-0.004	0.006	34.277	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.003	0.001	37.841	0.000	0.000	0.000	0.000	0.000	0.000
29	A	46	ASN	0	-0.010	-0.014	39.015	0.001	0.001	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.036	-0.013	39.883	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.869	-0.923	42.233	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	49	ASN	0	-0.007	-0.023	43.625	0.000	0.000	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.854	-0.917	43.784	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.020	-0.003	46.591	0.000	0.000	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.965	0.976	48.172	0.000	0.000	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.044	0.032	48.769	0.000	0.000	0.000	0.000	0.000	0.000
37	A	54	PHE	0	-0.029	-0.023	48.040	0.000	0.000	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.014	-0.002	52.320	0.000	0.000	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.037	-0.005	54.674	0.000	0.000	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.932	0.968	54.120	0.003	0.003	0.000	0.000	0.000	0.000
41	A	58	GLY	0	0.029	0.017	57.692	0.000	0.000	0.000	0.000	0.000	0.000
42	A	59	ASN	0	-0.016	-0.003	54.728	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.026	0.991	54.194	0.012	0.012	0.000	0.000	0.000	0.000
44	A	61	VAL	0	0.009	0.007	52.631	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.032	0.011	48.897	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.033	0.029	49.185	0.000	0.000	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.957	0.981	48.419	0.021	0.021	0.000	0.000	0.000	0.000
48	A	65	ASN	0	-0.029	-0.030	47.095	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.023	0.021	44.777	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.045	0.017	43.512	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.953	0.982	42.813	0.031	0.031	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.908	0.940	39.646	0.011	0.011	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.899	0.949	38.967	0.012	0.012	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.932	0.971	38.225	0.039	0.039	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.050	-0.026	35.607	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	73	ILE	0	-0.005	-0.002	33.769	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.853	-0.936	33.173	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	75	GLN	0	-0.011	-0.001	33.020	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.017	-0.006	28.387	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.007	-0.004	28.617	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	78	SER	0	0.012	0.021	28.347	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.965	0.976	26.491	0.084	0.084	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.035	-0.010	23.847	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.762	-0.875	23.313	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.068	0.046	23.703	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.070	-0.041	18.969	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.033	-0.024	19.205	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.904	-0.940	19.139	-0.089	-0.089	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.028	-0.015	18.707	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.078	-0.043	14.938	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.871	-0.940	14.989	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	89	GLN	0	-0.008	0.001	16.773	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.014	-0.002	11.716	-0.095	-0.095	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.013	-0.009	11.271	-0.065	-0.065	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.067	0.034	12.860	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	93	SER	0	-0.009	-0.008	13.810	0.011	0.011	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.037	-0.018	7.795	-0.091	-0.091	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.848	-0.913	10.433	0.260	0.260	0.000	0.000	0.000	0.000
79	A	96	SER	0	0.019	0.011	11.877	0.041	0.041	0.000	0.000	0.000	0.000
80	A	97	ALA	0	-0.009	0.002	11.202	0.016	0.016	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.092	-0.066	7.053	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.058	0.046	10.384	0.039	0.039	0.000	0.000	0.000	0.000
83	A	100	ASN	0	-0.002	-0.003	13.807	0.035	0.035	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.019	-0.020	8.930	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.948	-0.976	12.633	0.162	0.162	0.000	0.000	0.000	0.000
86	A	103	THR	0	0.003	0.002	13.784	0.022	0.022	0.000	0.000	0.000	0.000
87	A	104	MET	0	-0.015	-0.004	15.511	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.957	0.973	11.714	0.067	0.067	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.026	0.030	16.143	0.017	0.017	0.000	0.000	0.000	0.000
90	A	107	MET	0	0.004	-0.001	18.831	0.005	0.005	0.000	0.000	0.000	0.000
91	A	108	GLN	0	-0.026	-0.011	17.207	0.006	0.006	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-0.902	-0.945	19.362	0.032	0.032	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.028	0.012	21.262	0.008	0.008	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.013	-0.001	23.929	0.003	0.003	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.821	0.897	20.794	0.013	0.013	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.006	0.011	25.623	0.003	0.003	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.029	0.002	27.441	0.004	0.004	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.963	0.994	29.107	0.033	0.033	0.000	0.000	0.000	0.000
99	A	116	THR	0	-0.049	-0.031	28.890	0.001	0.001	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.027	-0.016	31.221	0.002	0.002	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.030	-0.001	33.513	0.001	0.001	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.001	-0.005	34.860	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	120	GLY	0	-0.049	-0.011	36.706	0.001	0.001	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.035	-0.018	37.489	0.003	0.003	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.938	-0.960	39.403	0.004	0.004	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.076	-0.050	41.746	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.914	-0.951	45.471	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.834	0.889	43.851	0.015	0.015	0.000	0.000	0.000	0.000
109	A	126	VAL	0	0.036	0.020	44.072	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.935	-0.972	39.822	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.810	-0.899	42.751	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.020	0.013	44.913	0.000	0.000	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.100	-0.049	43.332	0.000	0.000	0.000	0.000	0.000	0.000
114	A	131	ASP	-1	-0.819	-0.894	41.597	-0.029	-0.029	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.883	-0.932	44.915	-0.017	-0.017	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.048	-0.034	48.655	0.000	0.000	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.789	0.874	41.768	0.026	0.026	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.896	-0.940	46.516	-0.030	-0.030	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.099	-0.050	48.421	0.001	0.001	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.084	-0.041	48.982	0.000	0.000	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.898	-0.946	44.655	-0.032	-0.032	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.028	0.000	49.511	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.054	-0.037	52.294	0.001	0.001	0.000	0.000	0.000	0.000
124	A	141	ASP	-1	-1.007	-0.989	47.986	-0.032	-0.032	0.000	0.000	0.000	0.000
125	A	142	GLU	-1	-1.047	-1.020	48.037	-0.032	-0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:SER)