FMO DATABASE

FMODB ID: LN469

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-544226.190013
FMO2-HF: Nuclear repulsion	509892.966063
FMO2-HF: Total energy	-34333.22395
FMO2-MP2: Total energy	-34429.801479

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.
-4.831	-3.106	3.392	-1.767	-3.349	-0.004

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 : 0.002 / q_NPA : -0.015

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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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	-0.011	0.002	2.729	-6.475	-4.860	3.393	-1.752	-3.256	-0.004
4	A	36	GLY	0	0.018	0.019	4.627	1.638	1.748	-0.001	-0.015	-0.093	0.000
5	A	37	ILE	0	-0.005	-0.013	8.132	-0.417	-0.417	0.000	0.000	0.000	0.000
6	A	38	PRO	0	-0.006	-0.005	10.520	0.295	0.295	0.000	0.000	0.000	0.000
7	A	39	ILE	0	0.012	0.011	13.642	0.019	0.019	0.000	0.000	0.000	0.000
8	A	40	GLN	0	0.020	0.013	17.110	0.109	0.109	0.000	0.000	0.000	0.000
9	A	41	PRO	0	0.035	0.033	20.532	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	42	THR	0	0.005	-0.013	24.154	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	43	TYR	0	-0.005	-0.013	25.466	0.001	0.001	0.000	0.000	0.000	0.000
12	A	44	GLU	-1	-0.750	-0.858	27.472	-0.308	-0.308	0.000	0.000	0.000	0.000
13	A	45	LYS	1	0.813	0.907	23.971	0.452	0.452	0.000	0.000	0.000	0.000
14	A	46	CYS	0	-0.020	-0.015	27.150	0.033	0.033	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.007	0.016	27.274	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	48	ILE	0	0.012	0.003	28.947	0.019	0.019	0.000	0.000	0.000	0.000
17	A	49	LEU	0	0.014	0.018	31.072	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	50	SER	0	-0.001	-0.008	33.856	0.007	0.007	0.000	0.000	0.000	0.000
19	A	51	ASN	0	0.000	-0.003	34.657	0.005	0.005	0.000	0.000	0.000	0.000
20	A	52	ILE	0	0.043	0.030	35.683	0.004	0.004	0.000	0.000	0.000	0.000
21	A	53	LEU	0	0.012	0.013	30.546	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	54	ASN	0	-0.037	-0.026	32.564	0.014	0.014	0.000	0.000	0.000	0.000
23	A	55	VAL	0	0.061	0.027	31.177	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	56	SER	0	-0.036	-0.023	31.539	0.015	0.015	0.000	0.000	0.000	0.000
25	A	57	PHE	0	0.011	0.007	31.304	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	58	GLY	0	0.003	-0.008	31.641	0.013	0.013	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.910	0.952	32.102	0.282	0.282	0.000	0.000	0.000	0.000
28	A	60	ALA	0	0.024	0.015	34.588	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	61	LYS	1	0.783	0.896	30.863	0.288	0.288	0.000	0.000	0.000	0.000
30	A	62	ASP	-1	-0.859	-0.931	37.243	-0.148	-0.148	0.000	0.000	0.000	0.000
31	A	63	TYR	0	-0.029	-0.009	35.663	0.011	0.011	0.000	0.000	0.000	0.000
32	A	64	ALA	0	0.000	-0.002	34.391	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	65	ILE	0	-0.021	0.002	34.631	0.010	0.010	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.021	0.011	32.961	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	67	THR	0	-0.024	-0.013	32.889	0.022	0.022	0.000	0.000	0.000	0.000
36	A	68	VAL	0	-0.024	-0.010	32.048	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	69	THR	0	-0.001	-0.001	31.189	0.017	0.017	0.000	0.000	0.000	0.000
38	A	70	ASN	0	0.014	0.000	31.247	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	71	LYS	1	0.834	0.896	22.792	0.228	0.228	0.000	0.000	0.000	0.000
40	A	72	ALA	0	-0.028	-0.003	29.636	0.009	0.009	0.000	0.000	0.000	0.000
41	A	73	THR	0	0.006	0.002	31.736	0.010	0.010	0.000	0.000	0.000	0.000
42	A	74	GLY	0	0.000	0.006	33.366	0.007	0.007	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.932	-0.970	34.312	-0.088	-0.088	0.000	0.000	0.000	0.000
44	A	76	ILE	0	-0.012	-0.010	35.111	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.021	0.021	35.529	0.003	0.003	0.000	0.000	0.000	0.000
46	A	78	HIS	0	0.000	0.003	36.529	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	79	SER	0	-0.005	-0.017	36.530	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	80	LYS	1	0.880	0.947	37.870	0.146	0.146	0.000	0.000	0.000	0.000
49	A	81	THR	0	0.031	0.027	38.108	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	82	TYR	0	-0.043	-0.032	37.884	0.011	0.011	0.000	0.000	0.000	0.000
51	A	83	HIS	0	0.061	0.003	39.543	0.000	0.000	0.000	0.000	0.000	0.000
52	A	84	ASN	0	-0.043	-0.011	40.785	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	85	THR	0	-0.024	-0.012	38.866	0.005	0.005	0.000	0.000	0.000	0.000
54	A	86	SER	0	0.029	0.006	37.029	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	87	ILE	0	-0.015	-0.011	35.913	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	88	VAL	0	-0.013	0.001	36.172	0.013	0.013	0.000	0.000	0.000	0.000
57	A	89	MET	0	-0.029	-0.011	36.199	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	90	ILE	0	-0.004	-0.002	35.295	0.010	0.010	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.796	-0.879	37.104	-0.142	-0.142	0.000	0.000	0.000	0.000
60	A	92	MET	0	0.015	0.011	33.741	0.004	0.004	0.000	0.000	0.000	0.000
61	A	93	SER	0	-0.094	-0.079	37.696	0.007	0.007	0.000	0.000	0.000	0.000
62	A	94	SER	0	0.002	-0.004	39.912	0.003	0.003	0.000	0.000	0.000	0.000
63	A	95	CYS	0	-0.064	-0.007	37.370	0.008	0.008	0.000	0.000	0.000	0.000
64	A	96	GLU	-1	-0.822	-0.901	36.782	-0.073	-0.073	0.000	0.000	0.000	0.000
65	A	97	LYS	1	0.815	0.920	34.906	0.107	0.107	0.000	0.000	0.000	0.000
66	A	98	GLY	0	0.038	0.019	31.179	0.012	0.012	0.000	0.000	0.000	0.000
67	A	99	GLU	-1	-0.829	-0.909	24.790	-0.233	-0.233	0.000	0.000	0.000	0.000
68	A	100	TYR	0	-0.005	-0.018	28.396	0.018	0.018	0.000	0.000	0.000	0.000
69	A	101	THR	0	-0.022	-0.012	25.655	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	102	ILE	0	-0.027	-0.020	27.276	0.017	0.017	0.000	0.000	0.000	0.000
71	A	103	HIS	0	0.037	0.020	26.129	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	104	ILE	0	-0.024	-0.025	28.647	0.016	0.016	0.000	0.000	0.000	0.000
73	A	105	ILE	0	0.013	0.004	29.229	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	106	LEU	0	0.000	0.003	29.357	0.011	0.011	0.000	0.000	0.000	0.000
75	A	107	ASN	0	-0.040	-0.032	30.081	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	108	ASP	-1	-0.859	-0.913	31.136	-0.207	-0.207	0.000	0.000	0.000	0.000
77	A	109	CYS	0	-0.066	-0.030	26.445	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	110	LEU	0	0.012	0.004	26.382	0.013	0.013	0.000	0.000	0.000	0.000
79	A	111	LEU	0	-0.039	-0.022	24.546	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	112	GLU	-1	-0.907	-0.955	21.931	-0.270	-0.270	0.000	0.000	0.000	0.000
81	A	113	GLY	0	0.014	0.003	22.878	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	114	THR	0	-0.037	-0.022	22.508	0.046	0.046	0.000	0.000	0.000	0.000
83	A	115	PHE	0	-0.023	-0.002	24.438	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	116	THR	0	0.017	-0.004	26.523	0.014	0.014	0.000	0.000	0.000	0.000
85	A	117	VAL	0	-0.034	0.010	28.784	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	118	GLN	0	0.018	0.000	29.901	0.027	0.027	0.000	0.000	0.000	0.000

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