FMO DATABASE

FMODB ID: 85KLY

Calculation Name: 3SDL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SDL

Chain ID: B

ChEMBL ID:

UniProt ID: P05161

Base Structure: X-ray

Registration Date: 2023-06-26

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-683261.28949
FMO2-HF: Nuclear repulsion	643497.563321
FMO2-HF: Total energy	-39763.726169
FMO2-MP2: Total energy	-39877.838246

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:7:THR)

Summations of interaction energy for fragment #1(B:7:THR)

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.
-0.311	1.821	0.047	-0.859	-1.318	0

Interaction energy analysis for fragmet #1(B:7:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.023

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].
3	B	9	GLN	0	-0.020	-0.012	3.223	-0.686	1.406	0.048	-0.858	-1.281
4	B	10	ILE	0	0.009	0.000	5.195	0.441	0.481	-0.001	-0.001	-0.037
5	B	11	GLU	-1	-0.948	-0.959	8.575	-0.407	-0.407	0.000	0.000	0.000
6	B	12	VAL	0	-0.011	-0.017	11.002	0.084	0.084	0.000	0.000	0.000
7	B	13	GLY	0	0.058	0.037	13.753	0.053	0.053	0.000	0.000	0.000
8	B	14	PRO	0	0.017	-0.016	17.065	0.004	0.004	0.000	0.000	0.000
9	B	15	GLY	0	0.000	0.005	19.595	0.009	0.009	0.000	0.000	0.000
10	B	16	ALA	0	0.048	0.028	14.925	0.025	0.025	0.000	0.000	0.000
11	B	17	THR	0	0.012	0.019	17.078	0.016	0.016	0.000	0.000	0.000
12	B	18	ASN	0	0.069	0.035	18.456	0.026	0.026	0.000	0.000	0.000
13	B	19	ALA	0	0.016	0.015	17.986	0.016	0.016	0.000	0.000	0.000
14	B	20	THR	0	0.008	-0.011	14.365	0.022	0.022	0.000	0.000	0.000
15	B	21	ILE	0	-0.049	-0.020	16.884	0.027	0.027	0.000	0.000	0.000
16	B	22	ASN	0	0.047	0.018	19.958	0.014	0.014	0.000	0.000	0.000
17	B	23	PHE	0	0.083	0.041	14.175	0.010	0.010	0.000	0.000	0.000
18	B	24	GLU	-1	-0.782	-0.877	15.944	0.077	0.077	0.000	0.000	0.000
19	B	25	ALA	0	0.004	0.004	18.508	0.010	0.010	0.000	0.000	0.000
20	B	26	GLY	0	0.043	0.021	21.399	0.003	0.003	0.000	0.000	0.000
21	B	27	ILE	0	-0.017	0.000	16.278	0.009	0.009	0.000	0.000	0.000
22	B	28	LEU	0	-0.018	-0.017	19.702	0.008	0.008	0.000	0.000	0.000
23	B	29	GLU	-1	-0.774	-0.864	22.360	0.083	0.083	0.000	0.000	0.000
24	B	30	CYS	0	-0.047	-0.021	21.455	0.002	0.002	0.000	0.000	0.000
25	B	31	TYR	0	0.006	-0.003	17.396	0.002	0.002	0.000	0.000	0.000
26	B	32	GLU	-1	-0.788	-0.894	23.374	0.065	0.065	0.000	0.000	0.000
27	B	33	ARG	1	0.880	0.928	26.939	-0.096	-0.096	0.000	0.000	0.000
28	B	34	PHE	0	0.034	0.013	24.117	-0.003	-0.003	0.000	0.000	0.000
29	B	35	SER	0	0.023	-0.003	26.852	0.000	0.000	0.000	0.000	0.000
30	B	36	TRP	0	-0.044	-0.014	28.327	-0.005	-0.005	0.000	0.000	0.000
31	B	37	GLN	0	-0.055	-0.029	29.522	-0.008	-0.008	0.000	0.000	0.000
32	B	38	ARG	1	0.866	0.936	31.152	-0.081	-0.081	0.000	0.000	0.000
33	B	39	ALA	0	0.053	0.038	27.425	0.001	0.001	0.000	0.000	0.000
34	B	40	LEU	0	-0.068	-0.003	22.764	0.015	0.015	0.000	0.000	0.000
35	B	41	ASP	-1	-0.698	-0.827	22.768	0.184	0.184	0.000	0.000	0.000
36	B	42	TYR	0	0.058	0.015	25.446	0.000	0.000	0.000	0.000	0.000
37	B	43	PRO	0	0.027	0.001	22.176	-0.006	-0.006	0.000	0.000	0.000
38	B	44	GLY	0	0.023	0.003	21.500	0.003	0.003	0.000	0.000	0.000
39	B	45	GLN	0	-0.013	-0.013	22.545	-0.011	-0.011	0.000	0.000	0.000
40	B	46	ASP	-1	-0.772	-0.864	23.370	0.071	0.071	0.000	0.000	0.000
41	B	47	ARG	1	0.776	0.878	17.289	-0.236	-0.236	0.000	0.000	0.000
42	B	48	LEU	0	0.001	0.019	20.399	-0.005	-0.005	0.000	0.000	0.000
43	B	49	HIS	0	0.052	0.016	22.763	-0.014	-0.014	0.000	0.000	0.000
44	B	50	ARG	1	0.802	0.871	19.961	-0.088	-0.088	0.000	0.000	0.000
45	B	51	LEU	0	-0.026	0.010	17.702	-0.016	-0.016	0.000	0.000	0.000
46	B	52	LYS	1	0.878	0.923	20.391	-0.072	-0.072	0.000	0.000	0.000
47	B	53	ARG	1	0.884	0.937	23.487	-0.063	-0.063	0.000	0.000	0.000
48	B	54	LYS	1	0.883	0.934	15.234	-0.097	-0.097	0.000	0.000	0.000
49	B	55	LEU	0	-0.041	0.009	20.702	-0.019	-0.019	0.000	0.000	0.000
50	B	56	GLU	-1	-0.762	-0.870	22.107	-0.006	-0.006	0.000	0.000	0.000
51	B	57	SER	0	-0.063	-0.033	22.885	-0.012	-0.012	0.000	0.000	0.000
52	B	58	ARG	1	0.872	0.909	16.427	-0.003	-0.003	0.000	0.000	0.000
53	B	59	ILE	0	0.010	0.022	23.094	-0.009	-0.009	0.000	0.000	0.000
54	B	60	LYS	1	0.882	0.918	25.724	0.001	0.001	0.000	0.000	0.000
55	B	61	THR	0	-0.061	-0.041	24.250	-0.005	-0.005	0.000	0.000	0.000
56	B	62	HIS	0	0.018	0.004	23.641	0.000	0.000	0.000	0.000	0.000
57	B	63	ASN	0	0.024	0.009	25.661	-0.004	-0.004	0.000	0.000	0.000
58	B	64	LYS	1	0.907	0.964	28.592	0.058	0.058	0.000	0.000	0.000
59	B	65	SER	0	-0.072	-0.040	26.795	-0.005	-0.005	0.000	0.000	0.000
60	B	66	GLU	-1	-0.781	-0.873	27.398	-0.055	-0.055	0.000	0.000	0.000
61	B	67	PRO	0	0.019	0.001	30.369	0.004	0.004	0.000	0.000	0.000
62	B	68	GLU	-1	-0.812	-0.907	33.208	-0.020	-0.020	0.000	0.000	0.000
63	B	69	ASN	0	-0.024	-0.013	34.774	0.004	0.004	0.000	0.000	0.000
64	B	70	LYS	1	0.793	0.879	28.216	0.049	0.049	0.000	0.000	0.000
65	B	71	ARG	1	0.805	0.926	29.649	0.022	0.022	0.000	0.000	0.000
66	B	72	MET	0	0.014	0.019	28.400	0.006	0.006	0.000	0.000	0.000
67	B	73	SER	0	-0.042	-0.048	29.172	-0.002	-0.002	0.000	0.000	0.000
68	B	74	LEU	0	0.024	-0.007	25.508	0.003	0.003	0.000	0.000	0.000
69	B	75	GLU	-1	-0.791	-0.902	27.767	0.053	0.053	0.000	0.000	0.000
70	B	76	GLU	-1	-0.800	-0.857	30.144	0.016	0.016	0.000	0.000	0.000
71	B	77	ARG	1	0.829	0.886	24.616	0.014	0.014	0.000	0.000	0.000
72	B	78	LYS	1	0.761	0.864	25.207	-0.060	-0.060	0.000	0.000	0.000
73	B	79	ALA	0	-0.010	0.005	26.078	0.009	0.009	0.000	0.000	0.000
74	B	80	ILE	0	-0.033	-0.015	24.156	0.003	0.003	0.000	0.000	0.000
75	B	81	GLY	0	0.063	0.023	22.286	0.005	0.005	0.000	0.000	0.000
76	B	82	VAL	0	-0.027	-0.038	22.347	0.015	0.015	0.000	0.000	0.000
77	B	83	LYS	1	0.912	0.980	24.651	-0.039	-0.039	0.000	0.000	0.000
78	B	84	MET	0	-0.016	-0.006	20.156	0.004	0.004	0.000	0.000	0.000
79	B	85	MET	0	-0.010	-0.009	18.223	0.022	0.022	0.000	0.000	0.000
80	B	86	LYS	1	0.864	0.942	21.226	-0.068	-0.068	0.000	0.000	0.000
81	B	87	VAL	0	0.043	0.026	21.714	0.010	0.010	0.000	0.000	0.000
82	B	88	LEU	0	-0.032	-0.008	16.541	0.007	0.007	0.000	0.000	0.000
83	B	89	LEU	0	-0.073	-0.045	19.383	0.025	0.025	0.000	0.000	0.000
84	B	90	PHE	0	-0.032	-0.006	20.939	0.011	0.011	0.000	0.000	0.000
85	B	91	MET	0	-0.083	-0.032	17.749	0.006	0.006	0.000	0.000	0.000
86	B	92	ASP	-1	-0.756	-0.850	21.452	0.100	0.100	0.000	0.000	0.000
87	B	93	PRO	0	-0.069	-0.047	24.170	-0.002	-0.002	0.000	0.000	0.000
88	B	94	SER	0	-0.041	-0.048	26.323	-0.012	-0.012	0.000	0.000	0.000
89	B	95	ALA	0	0.015	0.026	29.840	0.004	0.004	0.000	0.000	0.000
90	B	96	GLY	0	0.052	0.028	27.705	-0.001	-0.001	0.000	0.000	0.000
91	B	97	ILE	0	-0.057	-0.039	26.824	0.004	0.004	0.000	0.000	0.000
92	B	98	GLU	-1	-0.921	-0.979	28.579	0.058	0.058	0.000	0.000	0.000
93	B	99	GLY	0	-0.036	-0.009	32.350	-0.003	-0.003	0.000	0.000	0.000
94	B	100	PHE	0	-0.090	-0.056	33.560	0.001	0.001	0.000	0.000	0.000
95	B	101	GLU	-1	-0.760	-0.872	29.836	0.109	0.109	0.000	0.000	0.000
96	B	102	PRO	0	-0.074	-0.027	30.768	0.004	0.004	0.000	0.000	0.000
97	B	103	TYR	0	-0.069	-0.037	27.917	0.001	0.001	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:7:THR)