FMO DATABASE

FMODB ID: JQGR9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-543498.954646
FMO2-HF: Nuclear repulsion	509166.377275
FMO2-HF: Total energy	-34332.577371
FMO2-MP2: Total energy	-34429.099228

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.
-6.786	-5.285	3.341	-1.798	-3.044	-0.01

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 : -0.013 / q_NPA : -0.021

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	-0.003	0.001	2.353	-8.637	-7.247	3.342	-1.780	-2.953	-0.010
4	A	36	GLY	0	0.017	0.021	4.504	1.842	1.953	-0.001	-0.018	-0.091	0.000
5	A	37	ILE	0	-0.001	-0.014	7.943	-0.347	-0.347	0.000	0.000	0.000	0.000
6	A	38	PRO	0	-0.018	-0.010	10.300	0.329	0.329	0.000	0.000	0.000	0.000
7	A	39	ILE	0	0.028	0.026	13.362	0.036	0.036	0.000	0.000	0.000	0.000
8	A	40	GLN	0	-0.026	-0.021	16.759	0.098	0.098	0.000	0.000	0.000	0.000
9	A	41	PRO	0	0.024	0.028	20.041	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	42	THR	0	-0.014	-0.022	23.653	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	43	TYR	0	-0.032	-0.027	25.191	0.012	0.012	0.000	0.000	0.000	0.000
12	A	44	GLU	-1	-0.800	-0.888	27.243	-0.378	-0.378	0.000	0.000	0.000	0.000
13	A	45	LYS	1	0.908	0.959	23.329	0.547	0.547	0.000	0.000	0.000	0.000
14	A	46	CYS	0	0.000	0.001	26.807	0.034	0.034	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.009	0.012	27.063	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	48	ILE	0	-0.001	-0.002	28.920	0.019	0.019	0.000	0.000	0.000	0.000
17	A	49	LEU	0	0.016	0.015	31.098	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	50	SER	0	-0.004	-0.009	33.830	0.006	0.006	0.000	0.000	0.000	0.000
19	A	51	ASN	0	0.001	-0.007	34.384	0.000	0.000	0.000	0.000	0.000	0.000
20	A	52	ILE	0	0.034	0.036	35.597	0.005	0.005	0.000	0.000	0.000	0.000
21	A	53	LEU	0	-0.002	-0.004	30.443	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	54	ASN	0	-0.028	-0.019	32.523	0.021	0.021	0.000	0.000	0.000	0.000
23	A	55	VAL	0	0.044	0.016	30.797	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	56	SER	0	-0.048	-0.027	31.239	0.021	0.021	0.000	0.000	0.000	0.000
25	A	57	PHE	0	0.011	0.003	31.108	-0.029	-0.029	0.000	0.000	0.000	0.000
26	A	58	GLY	0	0.006	-0.003	31.628	0.014	0.014	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.930	0.958	31.733	0.331	0.331	0.000	0.000	0.000	0.000
28	A	60	ALA	0	-0.007	-0.002	34.560	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	61	LYS	1	0.874	0.943	30.281	0.364	0.364	0.000	0.000	0.000	0.000
30	A	62	ASP	-1	-0.868	-0.944	36.687	-0.185	-0.185	0.000	0.000	0.000	0.000
31	A	63	TYR	0	-0.045	-0.023	35.263	0.012	0.012	0.000	0.000	0.000	0.000
32	A	64	ALA	0	-0.009	0.008	33.886	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	65	ILE	0	-0.011	0.015	34.304	0.015	0.015	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.004	0.001	32.694	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	67	THR	0	-0.004	-0.009	32.755	0.024	0.024	0.000	0.000	0.000	0.000
36	A	68	VAL	0	-0.030	-0.011	31.885	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	69	THR	0	0.015	0.005	31.047	0.020	0.020	0.000	0.000	0.000	0.000
38	A	70	ASN	0	0.055	0.039	31.067	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	71	LYS	1	0.930	0.956	22.537	0.285	0.285	0.000	0.000	0.000	0.000
40	A	72	ALA	0	-0.042	-0.012	29.584	0.007	0.007	0.000	0.000	0.000	0.000
41	A	73	THR	0	0.025	0.000	31.431	0.007	0.007	0.000	0.000	0.000	0.000
42	A	74	GLY	0	0.000	0.007	33.072	0.007	0.007	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.960	-0.975	33.999	-0.111	-0.111	0.000	0.000	0.000	0.000
44	A	76	ILE	0	-0.029	-0.013	35.230	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.037	0.014	35.468	0.006	0.006	0.000	0.000	0.000	0.000
46	A	78	HIS	0	-0.007	0.004	36.374	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	79	SER	0	-0.003	-0.016	36.516	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	80	LYS	1	0.931	0.989	37.825	0.169	0.169	0.000	0.000	0.000	0.000
49	A	81	THR	0	0.037	0.016	37.947	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	82	TYR	0	-0.089	-0.067	37.289	0.014	0.014	0.000	0.000	0.000	0.000
51	A	83	HIS	0	0.066	0.025	39.231	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	84	ASN	0	-0.008	0.001	40.530	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	85	THR	0	-0.015	-0.006	38.568	0.008	0.008	0.000	0.000	0.000	0.000
54	A	86	SER	0	-0.005	-0.006	37.041	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	87	ILE	0	0.009	0.003	35.895	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	88	VAL	0	-0.009	0.006	35.777	0.014	0.014	0.000	0.000	0.000	0.000
57	A	89	MET	0	-0.022	-0.009	36.042	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	90	ILE	0	-0.015	-0.011	35.149	0.010	0.010	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.812	-0.878	37.173	-0.154	-0.154	0.000	0.000	0.000	0.000
60	A	92	MET	0	-0.006	-0.006	33.525	0.005	0.005	0.000	0.000	0.000	0.000
61	A	93	SER	0	-0.105	-0.079	37.539	0.008	0.008	0.000	0.000	0.000	0.000
62	A	94	SER	0	-0.048	-0.023	39.669	0.006	0.006	0.000	0.000	0.000	0.000
63	A	95	CYS	0	-0.038	-0.006	36.994	0.007	0.007	0.000	0.000	0.000	0.000
64	A	96	GLU	-1	-0.891	-0.934	36.720	-0.094	-0.094	0.000	0.000	0.000	0.000
65	A	97	LYS	1	0.866	0.923	34.680	0.114	0.114	0.000	0.000	0.000	0.000
66	A	98	GLY	0	0.020	0.014	31.087	0.011	0.011	0.000	0.000	0.000	0.000
67	A	99	GLU	-1	-0.842	-0.865	25.019	-0.257	-0.257	0.000	0.000	0.000	0.000
68	A	100	TYR	0	-0.004	-0.026	28.346	0.017	0.017	0.000	0.000	0.000	0.000
69	A	101	THR	0	0.003	-0.004	25.846	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	102	ILE	0	-0.054	-0.029	27.103	0.024	0.024	0.000	0.000	0.000	0.000
71	A	103	HIS	0	0.049	0.024	26.770	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	104	ILE	0	-0.024	-0.026	28.011	0.022	0.022	0.000	0.000	0.000	0.000
73	A	105	ILE	0	-0.014	-0.002	28.875	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	106	LEU	0	-0.032	-0.024	28.446	0.019	0.019	0.000	0.000	0.000	0.000
75	A	107	ASN	0	0.018	0.032	30.176	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	108	ASP	-1	-0.889	-0.959	29.840	-0.276	-0.276	0.000	0.000	0.000	0.000
77	A	109	CYS	0	-0.081	-0.045	25.577	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	110	LEU	0	0.022	0.017	26.311	0.025	0.025	0.000	0.000	0.000	0.000
79	A	111	LEU	0	-0.034	-0.022	24.020	-0.040	-0.040	0.000	0.000	0.000	0.000
80	A	112	GLU	-1	-0.901	-0.952	20.977	-0.423	-0.423	0.000	0.000	0.000	0.000
81	A	113	GLY	0	-0.016	-0.010	22.744	-0.060	-0.060	0.000	0.000	0.000	0.000
82	A	114	THR	0	-0.043	-0.030	22.508	0.048	0.048	0.000	0.000	0.000	0.000
83	A	115	PHE	0	-0.036	-0.012	24.098	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	116	THR	0	0.016	-0.047	26.510	0.012	0.012	0.000	0.000	0.000	0.000
85	A	117	VAL	0	-0.034	0.001	28.587	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	118	GLN	0	0.050	0.034	30.209	0.018	0.018	0.000	0.000	0.000	0.000

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