FMO DATABASE

FMODB ID: R5NQ8

Calculation Name: 3S63-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3S63

Chain ID: A

ChEMBL ID:

UniProt ID: H2L2M0

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-677394.407186
FMO2-HF: Nuclear repulsion	639226.801504
FMO2-HF: Total energy	-38167.605682
FMO2-MP2: Total energy	-38272.370725

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:1:LEU )

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

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.
59.592	72.675	9.423	-8.091	-14.416	-0.077

Interaction energy analysis for fragmet #1(A:1:LEU )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.794 / q_NPA : 0.889

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	3	PRO	0	0.084	0.026	3.017	-6.510	-4.420	0.153	-1.015	-1.229	-0.005
4	A	4	LYS	1	1.009	1.007	5.607	28.123	28.123	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.836	-0.930	2.309	-79.203	-74.236	4.709	-4.395	-5.281	-0.054
6	A	6	THR	0	-0.051	-0.032	2.433	-2.051	0.589	1.539	-1.560	-2.618	-0.015
7	A	81	CYS	0	-0.013	0.046	3.589	2.960	3.163	0.019	0.008	-0.230	-0.001
8	A	8	ASP	-1	-0.837	-0.940	6.495	-25.591	-25.591	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.039	-0.046	2.617	2.080	2.697	0.824	-0.192	-1.249	-0.001
10	A	75	CYS	0	-0.076	-0.031	6.143	2.901	2.901	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.032	0.001	7.964	3.957	3.957	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.018	-0.017	8.055	1.930	1.930	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.012	0.004	9.098	1.586	1.586	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.028	-0.002	10.990	1.580	1.580	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.978	0.999	13.576	18.607	18.607	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.037	-0.014	13.701	1.230	1.230	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.008	-0.009	14.629	0.847	0.847	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.007	-0.003	17.050	0.660	0.660	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.023	0.005	18.891	0.667	0.667	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.057	-0.017	19.419	0.729	0.729	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.079	-0.045	19.909	0.407	0.407	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.041	0.025	23.485	0.432	0.432	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.008	0.003	23.647	0.322	0.322	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.033	0.000	24.861	0.074	0.074	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.005	-0.009	22.030	-0.211	-0.211	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.004	0.012	24.634	0.217	0.217	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.082	0.013	25.476	0.124	0.124	0.000	0.000	0.000	0.000
28	A	28	ARG	1	1.008	1.018	21.142	11.921	11.921	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.927	0.971	20.855	11.578	11.578	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.989	0.998	22.199	10.778	10.778	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.054	0.024	18.232	-0.373	-0.373	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.003	-0.007	17.393	-0.719	-0.719	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.042	-0.025	17.238	-1.067	-1.067	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.007	0.006	17.787	-0.731	-0.731	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.051	0.033	13.855	-0.753	-0.753	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.932	0.952	12.856	13.567	13.567	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.022	-0.009	13.090	-0.660	-0.660	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.760	-0.864	11.238	-20.122	-20.122	0.000	0.000	0.000	0.000
39	A	49	CYS	0	-0.007	0.009	5.816	1.614	1.614	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.839	0.911	8.548	14.757	14.757	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.917	0.969	10.887	19.412	19.412	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.029	-0.009	5.552	-2.047	-2.047	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.028	0.014	6.522	-1.708	-1.708	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.027	-0.001	2.772	1.828	2.524	0.287	-0.181	-0.802	0.000
45	A	45	TYR	0	0.048	0.024	2.281	-6.501	-4.942	1.845	-0.975	-2.430	-0.001
46	A	46	ARG	1	0.987	1.011	3.331	23.496	23.362	0.020	0.293	-0.179	0.000
47	A	47	ARG	1	0.966	0.959	6.722	29.162	29.162	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.829	0.867	3.247	38.898	39.343	0.027	-0.074	-0.398	0.000
49	A	50	LEU	0	-0.037	-0.030	7.351	2.381	2.381	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.047	-0.025	9.502	1.872	1.872	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.058	0.039	7.864	1.349	1.349	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.030	0.014	9.695	1.841	1.841	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.862	0.937	13.328	17.298	17.298	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.048	-0.029	13.986	0.947	0.947	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.052	0.037	13.148	1.353	1.353	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.013	-0.004	16.328	0.587	0.587	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.912	-0.950	17.984	-12.948	-12.948	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.055	0.024	16.432	0.385	0.385	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.006	-0.020	13.788	0.087	0.087	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.023	-0.032	17.932	0.269	0.269	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.898	0.956	21.206	12.280	12.280	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.813	-0.909	19.390	-12.466	-12.466	0.000	0.000	0.000	0.000
63	A	64	MET	0	-0.107	-0.043	16.643	0.220	0.220	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.072	-0.051	21.470	0.384	0.384	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.853	-0.906	24.747	-10.285	-10.285	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.046	-0.013	25.203	0.328	0.328	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.054	-0.033	23.247	-0.147	-0.147	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.014	-0.017	16.044	-0.419	-0.419	0.000	0.000	0.000	0.000
69	A	70	LYS	1	1.018	1.018	19.198	12.201	12.201	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.006	-0.002	14.083	-0.326	-0.326	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.044	-0.012	12.776	-0.529	-0.529	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.895	-0.937	14.659	-14.146	-14.146	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.030	0.012	14.421	-0.086	-0.086	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.004	0.016	12.048	-1.264	-1.264	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.021	0.001	14.536	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	78	MET	0	-0.078	-0.035	11.214	0.217	0.217	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.879	0.941	12.406	18.030	18.030	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.799	-0.855	6.409	-34.960	-34.960	0.000	0.000	0.000	0.000
79	A	82	ASN	0	0.007	0.002	10.935	2.986	2.986	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.042	-0.004	13.462	-0.281	-0.281	0.000	0.000	0.000	0.000
81	A	84	HIS	0	-0.058	-0.018	12.024	1.240	1.240	0.000	0.000	0.000	0.000
82	A	85	ASP	-1	-0.881	-0.926	10.474	-26.791	-26.791	0.000	0.000	0.000	0.000
83	A	86	SER	0	0.031	0.001	12.709	1.196	1.196	0.000	0.000	0.000	0.000
84	A	87	PRO	0	-0.003	-0.008	13.055	-1.259	-1.259	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.043	-0.027	10.959	-1.045	-1.045	0.000	0.000	0.000	0.000
86	A	89	NME	0	0.018	0.034	15.178	0.915	0.915	0.000	0.000	0.000	0.000

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