FMO DATABASE

FMODB ID: 39MRL

Calculation Name: 5TUV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TUV

Chain ID: B

ChEMBL ID:

UniProt ID: Q15329

Base Structure: X-ray

Registration Date: 2023-06-22

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-630266.608168
FMO2-HF: Nuclear repulsion	586693.811711
FMO2-HF: Total energy	-43572.796456
FMO2-MP2: Total energy	-43698.835602

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(B:124:LYS)

Summations of interaction energy for fragment #1(B:124:LYS)

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.
-11.974	-7.269	4.311	-2.59	-6.426	-0.004

Interaction energy analysis for fragmet #1(B:124:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.967

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	B	126	VAL	0	0.002	-0.003	2.637	2.404	5.231	0.477	-1.358	-1.946	0.004
4	B	127	ILE	0	-0.018	-0.026	2.267	-1.957	-0.395	3.831	-1.187	-4.207	-0.008
5	B	128	ASP	-1	-0.900	-0.953	3.936	-36.998	-36.682	0.003	-0.045	-0.273	0.000
6	B	129	ARG	1	0.972	0.987	5.912	31.822	31.822	0.000	0.000	0.000	0.000
7	B	130	LEU	0	-0.031	-0.010	6.757	2.749	2.749	0.000	0.000	0.000	0.000
8	B	131	ARG	1	0.893	0.946	8.241	24.781	24.781	0.000	0.000	0.000	0.000
9	B	132	TYR	0	-0.008	0.003	9.955	1.252	1.252	0.000	0.000	0.000	0.000
10	B	133	LEU	0	0.091	0.044	11.549	1.419	1.419	0.000	0.000	0.000	0.000
11	B	134	LYS	1	0.752	0.846	12.506	18.730	18.730	0.000	0.000	0.000	0.000
12	B	135	ALA	0	-0.066	-0.041	14.298	0.443	0.443	0.000	0.000	0.000	0.000
13	B	136	GLU	-1	-0.849	-0.898	15.952	-14.986	-14.986	0.000	0.000	0.000	0.000
14	B	137	ILE	0	0.014	-0.005	17.054	0.710	0.710	0.000	0.000	0.000	0.000
15	B	138	GLU	-1	-0.782	-0.880	18.717	-15.882	-15.882	0.000	0.000	0.000	0.000
16	B	139	ASP	-1	-0.942	-0.958	21.360	-11.749	-11.749	0.000	0.000	0.000	0.000
17	B	140	LEU	0	-0.014	-0.018	20.572	0.603	0.603	0.000	0.000	0.000	0.000
18	B	141	GLU	-1	-0.882	-0.916	23.323	-11.299	-11.299	0.000	0.000	0.000	0.000
19	B	142	LEU	0	-0.020	-0.025	24.962	0.580	0.580	0.000	0.000	0.000	0.000
20	B	143	LYS	1	0.836	0.918	26.838	10.249	10.249	0.000	0.000	0.000	0.000
21	B	144	GLU	-1	-0.904	-0.950	27.605	-10.412	-10.412	0.000	0.000	0.000	0.000
22	B	145	ARG	1	0.876	0.924	28.466	10.995	10.995	0.000	0.000	0.000	0.000
23	B	146	GLU	-1	-0.840	-0.892	31.285	-9.012	-9.012	0.000	0.000	0.000	0.000
24	B	147	LEU	0	-0.002	-0.009	30.844	0.375	0.375	0.000	0.000	0.000	0.000
25	B	148	ASP	-1	-0.900	-0.951	33.464	-8.761	-8.761	0.000	0.000	0.000	0.000
26	B	149	GLN	0	-0.136	-0.074	35.104	0.455	0.455	0.000	0.000	0.000	0.000
27	B	150	GLN	0	-0.058	-0.044	35.821	0.242	0.242	0.000	0.000	0.000	0.000
28	B	151	LYS	1	0.954	0.974	37.529	8.233	8.233	0.000	0.000	0.000	0.000
29	B	152	LEU	0	-0.023	-0.010	39.666	0.248	0.248	0.000	0.000	0.000	0.000
30	B	153	TRP	0	0.000	-0.022	41.461	0.333	0.333	0.000	0.000	0.000	0.000
31	B	154	LEU	0	0.034	0.050	42.297	0.137	0.137	0.000	0.000	0.000	0.000
32	B	155	GLN	0	0.041	0.023	42.052	0.078	0.078	0.000	0.000	0.000	0.000
33	B	156	GLN	0	-0.009	0.011	45.614	0.082	0.082	0.000	0.000	0.000	0.000
34	B	157	SER	0	-0.040	-0.029	47.360	0.161	0.161	0.000	0.000	0.000	0.000
35	B	158	ILE	0	0.035	0.009	46.430	0.126	0.126	0.000	0.000	0.000	0.000
36	B	159	LYS	1	0.866	0.914	48.467	6.587	6.587	0.000	0.000	0.000	0.000
37	B	160	ASN	0	0.010	0.011	51.823	0.069	0.069	0.000	0.000	0.000	0.000
38	B	161	VAL	0	-0.010	0.013	53.225	0.108	0.108	0.000	0.000	0.000	0.000
39	B	162	MET	0	-0.036	-0.030	51.919	0.100	0.100	0.000	0.000	0.000	0.000
40	B	163	ASP	-1	-0.956	-0.959	56.316	-5.306	-5.306	0.000	0.000	0.000	0.000
41	B	164	ASP	-1	-0.753	-0.860	58.313	-5.126	-5.126	0.000	0.000	0.000	0.000
42	B	165	SER	0	-0.069	-0.046	60.488	0.042	0.042	0.000	0.000	0.000	0.000
43	B	166	ILE	0	-0.029	-0.025	63.805	0.083	0.083	0.000	0.000	0.000	0.000
44	B	167	ASN	0	-0.042	-0.040	58.339	0.083	0.083	0.000	0.000	0.000	0.000
45	B	168	ASN	0	-0.005	0.003	61.305	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	169	ARG	1	0.883	0.959	62.163	4.649	4.649	0.000	0.000	0.000	0.000
47	B	170	PHE	0	-0.038	-0.036	63.688	0.109	0.109	0.000	0.000	0.000	0.000
48	B	171	SER	0	0.016	0.032	59.311	-0.042	-0.042	0.000	0.000	0.000	0.000
49	B	172	TYR	0	-0.071	-0.029	61.168	0.010	0.010	0.000	0.000	0.000	0.000
50	B	173	VAL	0	0.012	0.004	59.528	-0.026	-0.026	0.000	0.000	0.000	0.000
51	B	174	THR	0	-0.064	-0.058	62.833	0.087	0.087	0.000	0.000	0.000	0.000
52	B	175	HIS	0	0.056	-0.002	64.575	-0.095	-0.095	0.000	0.000	0.000	0.000
53	B	176	GLU	-1	-0.898	-0.947	65.586	-4.610	-4.610	0.000	0.000	0.000	0.000
54	B	177	ASP	-1	-0.847	-0.894	61.393	-5.012	-5.012	0.000	0.000	0.000	0.000
55	B	178	ILE	0	-0.018	-0.010	60.150	-0.092	-0.092	0.000	0.000	0.000	0.000
56	B	179	CYS	0	-0.004	-0.011	61.422	-0.053	-0.053	0.000	0.000	0.000	0.000
57	B	180	ASN	0	-0.021	-0.002	61.794	0.013	0.013	0.000	0.000	0.000	0.000
58	B	181	CYS	0	-0.100	-0.041	57.049	-0.079	-0.079	0.000	0.000	0.000	0.000
59	B	182	PHE	0	-0.062	-0.029	55.634	-0.124	-0.124	0.000	0.000	0.000	0.000
60	B	183	ASN	0	-0.023	-0.008	59.824	0.118	0.118	0.000	0.000	0.000	0.000
61	B	184	GLY	0	0.006	0.011	61.682	-0.027	-0.027	0.000	0.000	0.000	0.000
62	B	185	ASP	-1	-0.904	-0.952	61.310	-5.072	-5.072	0.000	0.000	0.000	0.000
63	B	186	THR	0	-0.066	-0.033	64.091	0.084	0.084	0.000	0.000	0.000	0.000
64	B	187	LEU	0	0.028	0.022	60.565	-0.088	-0.088	0.000	0.000	0.000	0.000
65	B	188	LEU	0	-0.020	-0.019	61.898	0.086	0.086	0.000	0.000	0.000	0.000
66	B	189	ALA	0	0.018	0.018	61.064	-0.101	-0.101	0.000	0.000	0.000	0.000
67	B	190	ILE	0	-0.023	-0.014	59.575	0.082	0.082	0.000	0.000	0.000	0.000
68	B	191	GLN	0	0.011	0.009	59.707	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	192	ALA	0	0.009	-0.004	58.465	0.087	0.087	0.000	0.000	0.000	0.000
70	B	193	PRO	0	0.045	0.036	58.868	-0.053	-0.053	0.000	0.000	0.000	0.000
71	B	194	SER	0	0.053	0.027	54.149	-0.054	-0.054	0.000	0.000	0.000	0.000
72	B	195	GLY	0	-0.024	-0.012	52.429	0.029	0.029	0.000	0.000	0.000	0.000
73	B	196	THR	0	-0.038	-0.026	53.515	0.021	0.021	0.000	0.000	0.000	0.000
74	B	197	GLN	0	0.010	0.014	49.692	0.001	0.001	0.000	0.000	0.000	0.000
75	B	198	LEU	0	0.010	-0.002	51.988	0.124	0.124	0.000	0.000	0.000	0.000
76	B	199	GLU	-1	-0.904	-0.937	50.936	-6.154	-6.154	0.000	0.000	0.000	0.000
77	B	200	VAL	0	0.018	0.005	51.033	0.136	0.136	0.000	0.000	0.000	0.000
78	B	201	PRO	0	-0.020	0.012	50.549	-0.134	-0.134	0.000	0.000	0.000	0.000
79	B	202	ILE	0	0.047	0.015	47.713	0.016	0.016	0.000	0.000	0.000	0.000
80	B	203	PRO	0	-0.002	0.003	50.710	0.110	0.110	0.000	0.000	0.000	0.000
81	B	204	GLU	-1	-0.887	-0.947	52.267	-5.915	-5.915	0.000	0.000	0.000	0.000
82	B	205	MET	0	-0.051	-0.034	54.228	0.050	0.050	0.000	0.000	0.000	0.000
83	B	206	GLY	0	0.015	0.018	57.542	-0.049	-0.049	0.000	0.000	0.000	0.000
84	B	207	GLN	0	-0.031	-0.007	60.403	-0.028	-0.028	0.000	0.000	0.000	0.000
85	B	208	ASN	0	0.037	0.004	63.449	-0.064	-0.064	0.000	0.000	0.000	0.000
86	B	209	GLY	0	0.013	0.006	64.972	0.031	0.031	0.000	0.000	0.000	0.000
87	B	210	GLN	0	-0.004	0.000	61.866	0.021	0.021	0.000	0.000	0.000	0.000
88	B	211	LYS	1	0.908	0.957	53.419	5.691	5.691	0.000	0.000	0.000	0.000
89	B	212	LYS	1	0.866	0.939	54.923	5.777	5.777	0.000	0.000	0.000	0.000
90	B	213	TYR	0	0.047	0.016	54.512	-0.157	-0.157	0.000	0.000	0.000	0.000
91	B	214	GLN	0	-0.001	-0.002	56.633	0.080	0.080	0.000	0.000	0.000	0.000
92	B	215	ILE	0	0.060	0.020	55.465	-0.110	-0.110	0.000	0.000	0.000	0.000
93	B	216	ASN	0	-0.038	-0.021	55.643	0.057	0.057	0.000	0.000	0.000	0.000
94	B	217	LEU	0	0.029	0.020	55.833	-0.113	-0.113	0.000	0.000	0.000	0.000
95	B	218	LYS	1	0.823	0.889	53.449	5.956	5.956	0.000	0.000	0.000	0.000
96	B	219	SER	0	-0.002	-0.014	57.099	-0.115	-0.115	0.000	0.000	0.000	0.000
97	B	220	HIS	0	0.018	0.011	55.830	0.135	0.135	0.000	0.000	0.000	0.000
98	B	221	SER	0	-0.002	-0.009	58.549	0.046	0.046	0.000	0.000	0.000	0.000
99	B	222	GLY	0	0.011	0.007	61.075	0.059	0.059	0.000	0.000	0.000	0.000
100	B	223	PRO	0	-0.027	0.014	63.532	-0.049	-0.049	0.000	0.000	0.000	0.000
101	B	224	ILE	0	0.001	-0.009	61.286	-0.049	-0.049	0.000	0.000	0.000	0.000
102	B	225	HIS	0	-0.006	0.001	64.079	0.089	0.089	0.000	0.000	0.000	0.000
103	B	226	VAL	0	0.004	-0.010	63.949	-0.087	-0.087	0.000	0.000	0.000	0.000
104	B	227	LEU	0	-0.018	0.004	65.301	0.093	0.093	0.000	0.000	0.000	0.000
105	B	228	LEU	0	-0.013	-0.014	65.758	-0.072	-0.072	0.000	0.000	0.000	0.000
106	B	229	ILE	0	-0.020	-0.007	64.016	0.067	0.067	0.000	0.000	0.000	0.000
107	B	230	ASN	0	0.017	0.018	67.225	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:124:LYS)