FMO DATABASE

FMODB ID: 3JR4L

Calculation Name: 3SD2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SD2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A1T7

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:

Apendix: None

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-544081.353933
FMO2-HF: Nuclear repulsion	509748.352177
FMO2-HF: Total energy	-34333.001755
FMO2-MP2: Total energy	-34429.540436

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:33:ASN)

Summations of interaction energy for fragment #1(A:33:ASN)

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.
-5.363	-3.74	2.999	-1.614	-3.008	-0.003

Interaction energy analysis for fragmet #1(A:33:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.019

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	35	MET	0	-0.010	-0.003	2.782	-7.061	-5.542	3.000	-1.602	-2.917	-0.003
4	A	36	GLY	0	0.015	0.020	4.701	1.618	1.722	-0.001	-0.012	-0.091	0.000
5	A	37	ILE	0	0.000	-0.012	8.086	-0.445	-0.445	0.000	0.000	0.000	0.000
6	A	38	PRO	0	-0.015	-0.009	10.325	0.326	0.326	0.000	0.000	0.000	0.000
7	A	39	ILE	0	0.023	0.019	13.416	0.020	0.020	0.000	0.000	0.000	0.000
8	A	40	GLN	0	0.010	0.002	16.837	0.120	0.120	0.000	0.000	0.000	0.000
9	A	41	PRO	0	0.037	0.036	20.078	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	42	THR	0	0.002	-0.022	23.693	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	43	TYR	0	-0.025	-0.025	25.162	0.008	0.008	0.000	0.000	0.000	0.000
12	A	44	GLU	-1	-0.753	-0.855	27.238	-0.316	-0.316	0.000	0.000	0.000	0.000
13	A	45	LYS	1	0.845	0.927	23.320	0.496	0.496	0.000	0.000	0.000	0.000
14	A	46	CYS	0	-0.015	-0.014	26.795	0.035	0.035	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.008	0.015	26.974	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	48	ILE	0	0.003	-0.001	28.691	0.020	0.020	0.000	0.000	0.000	0.000
17	A	49	LEU	0	0.014	0.014	30.900	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	50	SER	0	0.000	-0.007	33.634	0.007	0.007	0.000	0.000	0.000	0.000
19	A	51	ASN	0	-0.012	-0.008	34.391	0.003	0.003	0.000	0.000	0.000	0.000
20	A	52	ILE	0	0.040	0.037	35.443	0.006	0.006	0.000	0.000	0.000	0.000
21	A	53	LEU	0	0.001	0.000	30.176	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	54	ASN	0	-0.021	-0.015	32.344	0.017	0.017	0.000	0.000	0.000	0.000
23	A	55	VAL	0	0.057	0.027	30.870	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	56	SER	0	-0.029	-0.014	31.221	0.016	0.016	0.000	0.000	0.000	0.000
25	A	57	PHE	0	-0.007	-0.006	31.091	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	58	GLY	0	-0.003	-0.009	31.604	0.012	0.012	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.917	0.950	31.583	0.297	0.297	0.000	0.000	0.000	0.000
28	A	60	ALA	0	-0.003	-0.001	34.542	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	61	LYS	1	0.826	0.915	30.322	0.313	0.313	0.000	0.000	0.000	0.000
30	A	62	ASP	-1	-0.869	-0.942	36.754	-0.155	-0.155	0.000	0.000	0.000	0.000
31	A	63	TYR	0	-0.043	-0.016	35.276	0.012	0.012	0.000	0.000	0.000	0.000
32	A	64	ALA	0	-0.005	0.010	34.008	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	65	ILE	0	-0.019	0.005	34.490	0.012	0.012	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.012	0.010	32.635	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	67	THR	0	0.000	-0.001	32.662	0.021	0.021	0.000	0.000	0.000	0.000
36	A	68	VAL	0	-0.023	-0.009	31.803	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	69	THR	0	-0.002	-0.004	31.052	0.017	0.017	0.000	0.000	0.000	0.000
38	A	70	ASN	0	0.039	0.025	31.022	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	71	LYS	1	0.912	0.940	22.471	0.218	0.218	0.000	0.000	0.000	0.000
40	A	72	ALA	0	-0.039	-0.012	29.577	0.011	0.011	0.000	0.000	0.000	0.000
41	A	73	THR	0	0.019	0.002	31.450	0.009	0.009	0.000	0.000	0.000	0.000
42	A	74	GLY	0	-0.002	0.007	33.082	0.007	0.007	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.960	-0.976	34.013	-0.083	-0.083	0.000	0.000	0.000	0.000
44	A	76	ILE	0	-0.022	-0.010	35.131	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.024	0.008	35.378	0.005	0.005	0.000	0.000	0.000	0.000
46	A	78	HIS	0	-0.006	-0.002	36.307	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	79	SER	0	-0.005	-0.016	36.438	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	80	LYS	1	0.884	0.962	37.729	0.147	0.147	0.000	0.000	0.000	0.000
49	A	81	THR	0	0.034	0.021	37.952	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	82	TYR	0	-0.061	-0.052	37.573	0.012	0.012	0.000	0.000	0.000	0.000
51	A	83	HIS	0	0.062	0.011	39.343	0.000	0.000	0.000	0.000	0.000	0.000
52	A	84	ASN	0	-0.013	0.006	40.578	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	85	THR	0	-0.017	-0.008	38.857	0.006	0.006	0.000	0.000	0.000	0.000
54	A	86	SER	0	0.014	0.005	37.023	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	87	ILE	0	0.000	-0.005	35.869	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	88	VAL	0	-0.006	0.007	35.833	0.014	0.014	0.000	0.000	0.000	0.000
57	A	89	MET	0	-0.020	-0.008	35.991	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	90	ILE	0	-0.013	-0.009	35.078	0.010	0.010	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.812	-0.881	37.021	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	92	MET	0	-0.005	-0.005	33.504	0.006	0.006	0.000	0.000	0.000	0.000
61	A	93	SER	0	-0.096	-0.073	37.433	0.008	0.008	0.000	0.000	0.000	0.000
62	A	94	SER	0	-0.008	-0.008	39.542	0.005	0.005	0.000	0.000	0.000	0.000
63	A	95	CYS	0	-0.088	-0.028	37.003	0.008	0.008	0.000	0.000	0.000	0.000
64	A	96	GLU	-1	-0.854	-0.917	36.552	-0.070	-0.070	0.000	0.000	0.000	0.000
65	A	97	LYS	1	0.870	0.940	34.640	0.103	0.103	0.000	0.000	0.000	0.000
66	A	98	GLY	0	0.029	0.017	31.038	0.012	0.012	0.000	0.000	0.000	0.000
67	A	99	GLU	-1	-0.864	-0.917	24.691	-0.223	-0.223	0.000	0.000	0.000	0.000
68	A	100	TYR	0	-0.003	-0.027	28.273	0.017	0.017	0.000	0.000	0.000	0.000
69	A	101	THR	0	-0.010	-0.005	25.460	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	102	ILE	0	-0.045	-0.027	26.975	0.019	0.019	0.000	0.000	0.000	0.000
71	A	103	HIS	0	0.041	0.019	26.051	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	104	ILE	0	-0.024	-0.022	28.253	0.015	0.015	0.000	0.000	0.000	0.000
73	A	105	ILE	0	-0.019	-0.008	29.014	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	106	LEU	0	-0.008	-0.016	28.773	0.011	0.011	0.000	0.000	0.000	0.000
75	A	107	ASN	0	0.012	0.007	30.121	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	108	ASP	-1	-0.879	-0.933	30.182	-0.210	-0.210	0.000	0.000	0.000	0.000
77	A	109	CYS	0	-0.101	-0.053	25.867	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	110	LEU	0	0.033	0.023	26.321	0.017	0.017	0.000	0.000	0.000	0.000
79	A	111	LEU	0	-0.032	-0.021	24.230	-0.033	-0.033	0.000	0.000	0.000	0.000
80	A	112	GLU	-1	-0.889	-0.952	21.307	-0.290	-0.290	0.000	0.000	0.000	0.000
81	A	113	GLY	0	-0.017	-0.005	22.634	-0.056	-0.056	0.000	0.000	0.000	0.000
82	A	114	THR	0	-0.027	-0.013	22.373	0.051	0.051	0.000	0.000	0.000	0.000
83	A	115	PHE	0	-0.027	-0.007	23.979	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	116	THR	0	0.034	-0.003	26.386	0.014	0.014	0.000	0.000	0.000	0.000
85	A	117	VAL	0	-0.040	0.002	28.483	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	118	GLN	0	0.037	0.012	30.120	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:ASN)