FMO DATABASE

FMODB ID: JLVG9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-630447.537836
FMO2-HF: Nuclear repulsion	586875.223221
FMO2-HF: Total energy	-43572.314614
FMO2-MP2: Total energy	-43698.377603

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.
-14.952	-10.868	6.314	-3.03	-7.368	-0.007

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 : 0.956 / q_NPA : 0.958

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	-0.005	2.670	2.095	4.969	0.525	-1.373	-2.026	0.003
4	B	127	ILE	0	-0.014	-0.028	1.933	-3.297	-2.444	5.786	-1.587	-5.053	-0.010
5	B	128	ASP	-1	-0.890	-0.949	3.986	-39.386	-39.029	0.003	-0.070	-0.289	0.000
6	B	129	ARG	1	0.969	0.987	5.897	32.020	32.020	0.000	0.000	0.000	0.000
7	B	130	LEU	0	-0.027	-0.009	6.847	2.829	2.829	0.000	0.000	0.000	0.000
8	B	131	ARG	1	0.886	0.943	8.308	25.781	25.781	0.000	0.000	0.000	0.000
9	B	132	TYR	0	0.046	0.040	9.947	1.684	1.684	0.000	0.000	0.000	0.000
10	B	133	LEU	0	0.097	0.049	11.557	1.393	1.393	0.000	0.000	0.000	0.000
11	B	134	LYS	1	0.749	0.854	12.499	19.671	19.671	0.000	0.000	0.000	0.000
12	B	135	ALA	0	-0.060	-0.035	14.339	0.360	0.360	0.000	0.000	0.000	0.000
13	B	136	GLU	-1	-0.896	-0.930	15.959	-15.105	-15.105	0.000	0.000	0.000	0.000
14	B	137	ILE	0	-0.003	-0.014	16.996	0.748	0.748	0.000	0.000	0.000	0.000
15	B	138	GLU	-1	-0.762	-0.890	18.303	-16.452	-16.452	0.000	0.000	0.000	0.000
16	B	139	ASP	-1	-0.938	-0.955	21.400	-11.905	-11.905	0.000	0.000	0.000	0.000
17	B	140	LEU	0	-0.023	-0.022	20.269	0.635	0.635	0.000	0.000	0.000	0.000
18	B	141	GLU	-1	-0.889	-0.907	23.348	-11.710	-11.710	0.000	0.000	0.000	0.000
19	B	142	LEU	0	-0.013	-0.034	24.984	0.614	0.614	0.000	0.000	0.000	0.000
20	B	143	LYS	1	0.865	0.943	26.866	10.434	10.434	0.000	0.000	0.000	0.000
21	B	144	GLU	-1	-0.907	-0.953	27.551	-10.564	-10.564	0.000	0.000	0.000	0.000
22	B	145	ARG	1	0.862	0.917	28.302	11.223	11.223	0.000	0.000	0.000	0.000
23	B	146	GLU	-1	-0.902	-0.936	31.314	-9.162	-9.162	0.000	0.000	0.000	0.000
24	B	147	LEU	0	-0.022	-0.021	31.259	0.417	0.417	0.000	0.000	0.000	0.000
25	B	148	ASP	-1	-0.894	-0.944	32.758	-9.114	-9.114	0.000	0.000	0.000	0.000
26	B	149	GLN	0	-0.126	-0.069	35.268	0.507	0.507	0.000	0.000	0.000	0.000
27	B	150	GLN	0	-0.025	-0.018	35.904	0.108	0.108	0.000	0.000	0.000	0.000
28	B	151	LYS	1	0.994	1.005	37.691	8.261	8.261	0.000	0.000	0.000	0.000
29	B	152	LEU	0	-0.026	-0.015	39.665	0.252	0.252	0.000	0.000	0.000	0.000
30	B	153	TRP	0	0.027	-0.008	41.466	0.330	0.330	0.000	0.000	0.000	0.000
31	B	154	LEU	0	0.025	0.043	42.468	0.139	0.139	0.000	0.000	0.000	0.000
32	B	155	GLN	0	0.010	-0.014	42.767	0.162	0.162	0.000	0.000	0.000	0.000
33	B	156	GLN	0	-0.023	0.010	45.605	0.069	0.069	0.000	0.000	0.000	0.000
34	B	157	SER	0	-0.036	-0.022	47.365	0.176	0.176	0.000	0.000	0.000	0.000
35	B	158	ILE	0	0.032	0.012	46.490	0.125	0.125	0.000	0.000	0.000	0.000
36	B	159	LYS	1	0.864	0.918	48.288	6.683	6.683	0.000	0.000	0.000	0.000
37	B	160	ASN	0	0.021	0.006	51.815	0.076	0.076	0.000	0.000	0.000	0.000
38	B	161	VAL	0	-0.012	0.015	52.927	0.110	0.110	0.000	0.000	0.000	0.000
39	B	162	MET	0	-0.041	-0.036	51.860	0.109	0.109	0.000	0.000	0.000	0.000
40	B	163	ASP	-1	-0.970	-0.968	56.299	-5.346	-5.346	0.000	0.000	0.000	0.000
41	B	164	ASP	-1	-0.789	-0.871	58.305	-5.208	-5.208	0.000	0.000	0.000	0.000
42	B	165	SER	0	-0.065	-0.051	60.486	0.045	0.045	0.000	0.000	0.000	0.000
43	B	166	ILE	0	-0.026	-0.020	63.834	0.080	0.080	0.000	0.000	0.000	0.000
44	B	167	ASN	0	-0.007	-0.021	58.336	0.094	0.094	0.000	0.000	0.000	0.000
45	B	168	ASN	0	0.017	0.012	61.307	-0.029	-0.029	0.000	0.000	0.000	0.000
46	B	169	ARG	1	0.877	0.957	62.140	4.676	4.676	0.000	0.000	0.000	0.000
47	B	170	PHE	0	-0.041	-0.041	63.520	0.107	0.107	0.000	0.000	0.000	0.000
48	B	171	SER	0	0.004	0.010	59.253	-0.041	-0.041	0.000	0.000	0.000	0.000
49	B	172	TYR	0	-0.074	-0.009	61.131	0.003	0.003	0.000	0.000	0.000	0.000
50	B	173	VAL	0	0.028	0.013	59.432	-0.027	-0.027	0.000	0.000	0.000	0.000
51	B	174	THR	0	-0.064	-0.064	62.773	0.084	0.084	0.000	0.000	0.000	0.000
52	B	175	HIS	0	0.061	0.002	64.502	-0.092	-0.092	0.000	0.000	0.000	0.000
53	B	176	GLU	-1	-0.890	-0.937	65.504	-4.630	-4.630	0.000	0.000	0.000	0.000
54	B	177	ASP	-1	-0.838	-0.886	61.315	-5.050	-5.050	0.000	0.000	0.000	0.000
55	B	178	ILE	0	-0.025	-0.008	60.136	-0.093	-0.093	0.000	0.000	0.000	0.000
56	B	179	CYS	0	-0.016	-0.021	61.331	-0.037	-0.037	0.000	0.000	0.000	0.000
57	B	180	ASN	0	-0.019	-0.004	61.714	0.023	0.023	0.000	0.000	0.000	0.000
58	B	181	CYS	0	-0.108	-0.048	56.909	-0.079	-0.079	0.000	0.000	0.000	0.000
59	B	182	PHE	0	-0.065	-0.028	55.721	-0.126	-0.126	0.000	0.000	0.000	0.000
60	B	183	ASN	0	-0.017	-0.008	59.735	0.133	0.133	0.000	0.000	0.000	0.000
61	B	184	GLY	0	0.005	0.011	61.648	-0.026	-0.026	0.000	0.000	0.000	0.000
62	B	185	ASP	-1	-0.902	-0.950	61.054	-5.127	-5.127	0.000	0.000	0.000	0.000
63	B	186	THR	0	-0.065	-0.032	64.009	0.087	0.087	0.000	0.000	0.000	0.000
64	B	187	LEU	0	0.036	0.027	60.502	-0.089	-0.089	0.000	0.000	0.000	0.000
65	B	188	LEU	0	-0.020	-0.021	61.799	0.088	0.088	0.000	0.000	0.000	0.000
66	B	189	ALA	0	0.016	0.018	60.973	-0.102	-0.102	0.000	0.000	0.000	0.000
67	B	190	ILE	0	-0.019	-0.014	59.261	0.084	0.084	0.000	0.000	0.000	0.000
68	B	191	GLN	0	0.009	0.007	59.636	-0.032	-0.032	0.000	0.000	0.000	0.000
69	B	192	ALA	0	0.010	-0.004	58.438	0.088	0.088	0.000	0.000	0.000	0.000
70	B	193	PRO	0	0.053	0.042	58.817	-0.054	-0.054	0.000	0.000	0.000	0.000
71	B	194	SER	0	0.049	0.055	54.067	-0.055	-0.055	0.000	0.000	0.000	0.000
72	B	195	GLY	0	-0.017	-0.006	52.388	0.028	0.028	0.000	0.000	0.000	0.000
73	B	196	THR	0	-0.046	-0.068	53.474	0.020	0.020	0.000	0.000	0.000	0.000
74	B	197	GLN	0	0.013	0.013	49.217	0.002	0.002	0.000	0.000	0.000	0.000
75	B	198	LEU	0	0.017	0.001	51.928	0.128	0.128	0.000	0.000	0.000	0.000
76	B	199	GLU	-1	-0.911	-0.936	51.036	-6.208	-6.208	0.000	0.000	0.000	0.000
77	B	200	VAL	0	0.008	-0.001	50.926	0.141	0.141	0.000	0.000	0.000	0.000
78	B	201	PRO	0	-0.036	0.007	50.445	-0.135	-0.135	0.000	0.000	0.000	0.000
79	B	202	ILE	0	0.042	0.013	47.820	0.015	0.015	0.000	0.000	0.000	0.000
80	B	203	PRO	0	-0.005	0.002	50.655	0.115	0.115	0.000	0.000	0.000	0.000
81	B	204	GLU	-1	-0.961	-0.981	51.868	-6.008	-6.008	0.000	0.000	0.000	0.000
82	B	205	MET	0	-0.059	-0.035	54.324	0.057	0.057	0.000	0.000	0.000	0.000
83	B	206	GLY	0	0.013	0.017	57.685	-0.047	-0.047	0.000	0.000	0.000	0.000
84	B	207	GLN	0	-0.032	-0.010	60.512	-0.027	-0.027	0.000	0.000	0.000	0.000
85	B	208	ASN	0	0.029	0.001	63.665	-0.065	-0.065	0.000	0.000	0.000	0.000
86	B	209	GLY	0	0.021	0.006	65.231	0.029	0.029	0.000	0.000	0.000	0.000
87	B	210	GLN	0	-0.019	-0.013	62.024	0.035	0.035	0.000	0.000	0.000	0.000
88	B	211	LYS	1	0.960	0.980	54.151	5.667	5.667	0.000	0.000	0.000	0.000
89	B	212	LYS	1	0.944	0.987	55.518	5.762	5.762	0.000	0.000	0.000	0.000
90	B	213	TYR	0	0.044	0.014	54.821	-0.149	-0.149	0.000	0.000	0.000	0.000
91	B	214	GLN	0	-0.001	-0.013	56.530	0.062	0.062	0.000	0.000	0.000	0.000
92	B	215	ILE	0	0.061	0.022	55.574	-0.110	-0.110	0.000	0.000	0.000	0.000
93	B	216	ASN	0	-0.033	-0.012	55.529	0.061	0.061	0.000	0.000	0.000	0.000
94	B	217	LEU	0	0.032	0.018	55.751	-0.113	-0.113	0.000	0.000	0.000	0.000
95	B	218	LYS	1	0.828	0.896	53.026	6.039	6.039	0.000	0.000	0.000	0.000
96	B	219	SER	0	-0.001	-0.006	57.040	-0.121	-0.121	0.000	0.000	0.000	0.000
97	B	220	HIS	0	0.008	0.007	55.474	0.135	0.135	0.000	0.000	0.000	0.000
98	B	221	SER	0	-0.004	-0.006	58.471	0.045	0.045	0.000	0.000	0.000	0.000
99	B	222	GLY	0	0.007	0.004	61.039	0.059	0.059	0.000	0.000	0.000	0.000
100	B	223	PRO	0	-0.024	0.006	63.482	-0.049	-0.049	0.000	0.000	0.000	0.000
101	B	224	ILE	0	0.002	-0.006	61.376	-0.051	-0.051	0.000	0.000	0.000	0.000
102	B	225	HIS	0	-0.001	0.002	64.020	0.086	0.086	0.000	0.000	0.000	0.000
103	B	226	VAL	0	0.003	-0.008	63.851	-0.087	-0.087	0.000	0.000	0.000	0.000
104	B	227	LEU	0	-0.029	-0.003	65.221	0.094	0.094	0.000	0.000	0.000	0.000
105	B	228	LEU	0	-0.017	-0.017	65.672	-0.072	-0.072	0.000	0.000	0.000	0.000
106	B	229	ILE	0	-0.026	-0.011	63.943	0.069	0.069	0.000	0.000	0.000	0.000
107	B	230	ASN	0	0.019	0.018	67.133	-0.024	-0.024	0.000	0.000	0.000	0.000

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