FMO DATABASE

FMODB ID: QV5RY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-787536.017147
FMO2-HF: Nuclear repulsion	736537.60993
FMO2-HF: Total energy	-50998.407217
FMO2-MP2: Total energy	-51143.409143

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.
-14.359	-12.437	11.16	-5.523	-7.558	0.031

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 : 0.062 / q_NPA : 0.037

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	0.088	0.033	1.909	-7.601	-8.262	7.312	-3.089	-3.562	0.014
4	A	21	LYS	1	0.913	0.959	2.217	-5.620	-3.559	3.825	-2.258	-3.628	0.016
5	A	22	ALA	0	0.017	0.008	3.964	-1.229	-0.707	0.023	-0.176	-0.368	0.001
6	A	23	ILE	0	0.022	0.017	6.197	0.287	0.287	0.000	0.000	0.000	0.000
7	A	24	VAL	0	-0.018	-0.003	6.451	-0.156	-0.156	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.980	0.998	7.041	0.173	0.173	0.000	0.000	0.000	0.000
9	A	26	LEU	0	0.011	0.018	9.989	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.871	0.894	11.140	-0.384	-0.384	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.933	-0.974	10.550	0.353	0.353	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.075	-0.044	12.856	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.046	0.026	15.535	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	31	ASN	0	0.010	0.010	17.436	0.001	0.001	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.042	-0.026	18.595	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.019	-0.018	18.961	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	34	SER	0	0.064	0.022	21.929	0.001	0.001	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.912	0.966	20.922	-0.119	-0.119	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.951	0.979	21.813	0.031	0.031	0.000	0.000	0.000	0.000
20	A	37	GLN	0	0.036	-0.001	26.045	0.007	0.007	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.017	-0.011	27.824	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	39	HIS	0	-0.006	0.009	29.503	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.008	-0.010	28.886	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.913	0.937	29.936	0.004	0.004	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.017	0.017	33.795	0.001	0.001	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.015	-0.013	33.933	0.001	0.001	0.000	0.000	0.000	0.000
27	A	44	ILE	0	-0.008	-0.005	34.684	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.003	-0.002	38.069	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	46	ASN	0	0.005	-0.005	39.364	0.001	0.001	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.047	-0.020	40.158	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.858	-0.920	42.728	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	49	ASN	0	-0.002	-0.016	44.100	0.000	0.000	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.779	-0.878	43.816	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.013	-0.002	46.799	0.000	0.000	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.936	0.966	48.389	0.001	0.001	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.047	0.030	48.888	0.000	0.000	0.000	0.000	0.000	0.000
37	A	54	PHE	0	-0.051	-0.032	48.168	0.000	0.000	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.017	-0.011	52.527	0.000	0.000	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.053	-0.026	54.754	0.001	0.001	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.938	0.974	53.559	0.003	0.003	0.000	0.000	0.000	0.000
41	A	58	GLY	0	0.056	0.036	58.013	0.000	0.000	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.011	0.016	54.864	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.015	0.981	54.168	0.014	0.014	0.000	0.000	0.000	0.000
44	A	61	VAL	0	0.005	0.012	52.950	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.044	0.024	48.881	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.017	0.024	49.320	0.000	0.000	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.960	0.984	48.596	0.023	0.023	0.000	0.000	0.000	0.000
48	A	65	ASN	0	-0.029	-0.031	47.139	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.023	0.020	44.942	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.041	0.015	43.753	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.966	0.987	42.997	0.033	0.033	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.836	0.916	40.464	0.009	0.009	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.895	0.946	39.307	0.014	0.014	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.828	0.914	38.030	0.039	0.039	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.019	-0.013	36.268	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	73	ILE	0	-0.011	-0.004	34.178	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.809	-0.911	33.543	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	75	GLN	0	-0.017	-0.014	33.316	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.006	0.000	28.900	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.014	-0.004	28.971	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	78	SER	0	0.009	0.011	28.456	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.959	0.982	26.441	0.088	0.088	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.027	0.007	24.172	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.749	-0.869	23.558	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.081	0.050	23.979	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.063	-0.043	19.372	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.054	-0.025	19.525	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.874	-0.933	19.524	-0.102	-0.102	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.035	-0.016	19.131	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.075	-0.038	15.272	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.850	-0.940	15.290	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	89	GLN	0	-0.016	-0.009	16.928	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.011	0.009	12.013	-0.113	-0.113	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.036	-0.015	11.344	-0.075	-0.075	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.067	0.029	12.449	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	93	SER	0	-0.005	-0.003	14.043	0.007	0.007	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.019	-0.012	7.664	-0.109	-0.109	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.807	-0.868	10.024	0.196	0.196	0.000	0.000	0.000	0.000
79	A	96	SER	0	0.013	0.002	11.262	0.035	0.035	0.000	0.000	0.000	0.000
80	A	97	ALA	0	-0.010	-0.005	10.887	0.017	0.017	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.101	-0.068	6.670	-0.104	-0.104	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.078	0.051	9.958	0.044	0.044	0.000	0.000	0.000	0.000
83	A	100	ASN	0	-0.003	0.013	13.394	0.060	0.060	0.000	0.000	0.000	0.000
84	A	101	LEU	0	-0.010	-0.012	8.719	0.016	0.016	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.953	-0.981	12.076	0.092	0.092	0.000	0.000	0.000	0.000
86	A	103	THR	0	0.013	-0.004	13.387	0.039	0.039	0.000	0.000	0.000	0.000
87	A	104	MET	0	-0.025	-0.019	15.409	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.942	0.971	11.709	0.137	0.137	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.022	0.020	16.102	0.024	0.024	0.000	0.000	0.000	0.000
90	A	107	MET	0	-0.005	-0.001	18.706	0.014	0.014	0.000	0.000	0.000	0.000
91	A	108	GLN	0	-0.015	-0.010	16.988	0.007	0.007	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-0.887	-0.929	19.133	0.011	0.011	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.030	0.013	21.174	0.009	0.009	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.017	0.006	23.883	0.005	0.005	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.813	0.895	20.719	0.032	0.032	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.008	0.021	25.540	0.006	0.006	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.026	0.002	27.390	0.005	0.005	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.958	0.985	29.045	0.045	0.045	0.000	0.000	0.000	0.000
99	A	116	THR	0	-0.037	-0.029	28.753	0.002	0.002	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.027	-0.020	30.904	0.003	0.003	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.074	-0.030	33.574	0.001	0.001	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.023	-0.016	34.326	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	120	GLY	0	-0.045	-0.006	36.453	0.002	0.002	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.031	-0.031	37.490	0.003	0.003	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.944	-0.963	39.680	0.001	0.001	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.081	-0.049	41.884	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.908	-0.950	45.598	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.855	0.913	43.474	0.018	0.018	0.000	0.000	0.000	0.000
109	A	126	VAL	0	0.018	0.000	44.467	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.868	-0.928	39.819	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.808	-0.892	42.875	-0.023	-0.023	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.017	-0.003	44.701	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.096	-0.052	43.731	0.000	0.000	0.000	0.000	0.000	0.000
114	A	131	ASP	-1	-0.833	-0.897	41.663	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.882	-0.929	45.007	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.060	-0.028	48.452	0.000	0.000	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.801	0.898	41.689	0.034	0.034	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.899	-0.953	46.562	-0.035	-0.035	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.101	-0.058	48.416	0.001	0.001	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.090	-0.041	48.894	0.001	0.001	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.911	-0.957	44.442	-0.040	-0.040	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.049	-0.011	49.117	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.049	-0.037	51.775	0.001	0.001	0.000	0.000	0.000	0.000
124	A	141	ASP	-1	-0.955	-0.971	48.080	-0.038	-0.038	0.000	0.000	0.000	0.000
125	A	142	GLU	-1	-1.062	-1.019	47.966	-0.038	-0.038	0.000	0.000	0.000	0.000

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