FMO DATABASE

FMODB ID: MN2QZ

Calculation Name: 2DST-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DST

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SI36

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-986774.748304
FMO2-HF: Nuclear repulsion	941316.326404
FMO2-HF: Total energy	-45458.4219
FMO2-MP2: Total energy	-45592.893107

3D Structure Molmil

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:2:ARG)

Summations of interaction energy for fragment #1(A:2:ARG)

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.
-203.934	-193.585	23.892	-15.01	-19.232	-0.132

Interaction energy analysis for fragmet #1(A:2:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.898 / q_NPA : 0.946

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	4	ALA	0	0.079	0.038	3.800	-1.534	0.714	-0.027	-1.105	-1.116	0.006
4	A	5	GLY	0	-0.045	-0.022	6.046	2.367	2.367	0.000	0.000	0.000	0.000
5	A	6	TYR	0	-0.022	-0.017	9.131	-0.401	-0.401	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.011	0.011	12.298	0.623	0.623	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.058	-0.035	15.086	0.359	0.359	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.013	-0.014	17.755	0.356	0.356	0.000	0.000	0.000	0.000
9	A	10	TYR	0	-0.002	-0.009	20.010	0.107	0.107	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.014	0.009	23.225	0.116	0.116	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.007	0.013	19.270	0.078	0.078	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.008	0.015	16.409	0.125	0.125	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.015	0.012	12.051	-0.427	-0.427	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.025	0.005	8.951	-0.328	-0.328	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.035	-0.018	7.498	-0.546	-0.546	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.759	-0.856	2.265	-47.811	-47.119	0.885	-0.460	-1.117	-0.002
17	A	18	ARG	1	0.819	0.918	3.630	27.962	28.527	0.007	-0.174	-0.398	-0.001
18	A	19	VAL	0	0.009	-0.011	2.209	-4.778	-3.852	7.681	-3.909	-4.699	-0.024
19	A	20	GLY	0	0.072	0.065	3.785	0.651	0.844	0.010	-0.088	-0.115	0.000
20	A	21	LYS	1	0.924	0.941	7.280	20.700	20.700	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.067	0.047	10.633	0.009	0.009	0.000	0.000	0.000	0.000
22	A	23	PRO	0	0.011	-0.005	13.324	-0.387	-0.387	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.003	0.014	12.346	-1.552	-1.552	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.022	-0.011	10.941	0.977	0.977	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.001	0.007	10.295	-2.553	-2.553	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.026	0.002	5.567	0.817	0.817	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.012	-0.016	8.958	-1.076	-1.076	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.057	0.023	8.802	1.191	1.191	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.779	-0.873	10.787	-22.690	-22.690	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.829	-0.906	8.179	-31.469	-31.469	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.018	0.014	3.985	-1.674	-1.569	-0.001	-0.013	-0.091	0.000
32	A	33	SER	0	-0.066	-0.054	3.735	-11.829	-11.437	0.003	-0.144	-0.251	-0.001
33	A	34	ARG	1	0.808	0.903	5.220	26.273	26.323	-0.001	0.000	-0.049	0.000
34	A	35	TRP	0	-0.016	-0.007	2.858	5.206	6.123	0.059	-0.368	-0.608	-0.001
35	A	36	PRO	0	0.010	0.002	1.916	-49.347	-49.708	11.308	-5.928	-5.019	-0.085
36	A	37	GLU	-1	-0.707	-0.815	3.419	-47.205	-46.511	0.034	-0.267	-0.461	-0.002
37	A	38	ALA	0	-0.011	-0.004	2.543	-24.161	-21.830	1.294	-1.692	-1.933	-0.023
38	A	39	LEU	0	-0.050	-0.031	2.768	4.984	6.305	0.344	-0.376	-1.289	0.002
39	A	40	PRO	0	-0.003	0.010	5.073	2.307	2.336	-0.001	0.000	-0.028	0.000
40	A	41	GLU	-1	-0.910	-0.963	8.765	-23.359	-23.359	0.000	0.000	0.000	0.000
41	A	42	GLY	0	-0.008	-0.011	10.766	1.017	1.017	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.014	-0.002	10.153	1.469	1.469	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.110	-0.039	8.681	-1.859	-1.859	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.080	0.019	5.769	0.586	0.586	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.017	-0.023	6.678	-1.165	-1.165	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.026	-0.007	2.546	-0.631	-0.384	2.297	-0.486	-2.058	-0.001
47	A	48	LEU	0	0.028	0.010	6.633	-0.027	-0.027	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.707	-0.799	8.235	-33.546	-33.546	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.009	0.004	10.580	1.897	1.897	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.046	0.007	13.947	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.034	0.007	17.165	0.416	0.416	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.045	-0.038	13.589	0.813	0.813	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.027	0.018	11.410	-0.720	-0.720	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.697	0.779	5.893	36.930	36.930	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.026	-0.014	13.038	0.763	0.763	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.930	-0.948	15.146	-13.728	-13.728	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.033	-0.003	18.811	0.090	0.090	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.019	0.003	20.661	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.872	0.918	17.882	15.361	15.361	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.033	-0.005	21.566	0.389	0.389	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.010	0.009	22.230	-0.440	-0.440	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.037	0.003	21.012	-0.415	-0.415	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.823	-0.931	21.708	-12.476	-12.476	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.900	-0.949	23.823	-11.984	-11.984	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.001	-0.009	17.729	-0.403	-0.403	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.003	-0.005	19.014	-0.763	-0.763	0.000	0.000	0.000	0.000
67	A	68	HIS	0	0.052	0.018	20.459	-0.345	-0.345	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.003	0.008	17.837	-0.088	-0.088	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.008	0.006	15.195	-0.551	-0.551	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.019	0.009	17.306	-0.340	-0.340	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.000	-0.008	20.152	0.165	0.165	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.010	-0.022	10.929	-0.059	-0.059	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.025	0.007	16.439	-0.241	-0.241	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.011	0.006	17.393	0.179	0.179	0.000	0.000	0.000	0.000
75	A	76	MET	0	-0.019	0.005	18.105	0.450	0.450	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.062	-0.028	11.752	0.290	0.290	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.077	-0.039	15.943	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.024	-0.021	13.159	-0.293	-0.293	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.007	0.009	16.994	-0.134	-0.134	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.000	-0.009	20.457	0.048	0.048	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.038	-0.003	15.164	0.009	0.009	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.018	-0.002	15.634	0.287	0.287	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.015	-0.003	13.837	-1.323	-1.323	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.019	-0.003	9.808	1.012	1.012	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.049	-0.020	11.748	-0.938	-0.938	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.807	0.864	6.441	34.443	34.443	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.002	-0.010	12.021	-0.305	-0.305	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.031	-0.025	13.843	1.111	1.111	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.023	0.011	13.757	0.970	0.970	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.011	-0.007	14.722	0.836	0.836	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.028	-0.013	16.997	0.880	0.880	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.027	-0.013	16.194	0.716	0.716	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.023	0.012	19.033	0.387	0.387	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.004	-0.006	20.063	0.219	0.219	0.000	0.000	0.000	0.000
95	A	96	HIS	0	0.041	0.024	22.818	0.379	0.379	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.009	-0.001	17.145	0.127	0.127	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.781	-0.869	21.592	-13.608	-13.608	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.061	-0.023	23.699	0.388	0.388	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.045	-0.014	22.966	0.412	0.412	0.000	0.000	0.000	0.000
100	A	101	GLY	0	-0.059	-0.027	25.072	0.039	0.039	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.044	-0.016	18.299	-0.207	-0.207	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.818	0.904	20.239	13.229	13.229	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.009	0.007	17.381	-1.109	-1.109	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.052	-0.033	15.349	0.888	0.888	0.000	0.000	0.000	0.000
105	A	106	PRO	0	0.004	0.008	14.829	-1.391	-1.391	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.014	-0.007	10.829	0.312	0.312	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.851	-0.921	11.508	-23.349	-23.349	0.000	0.000	0.000	0.000
108	A	109	GLY	0	-0.011	-0.007	12.840	-0.754	-0.754	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.035	-0.004	12.602	-0.115	-0.115	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.856	-0.919	8.246	-32.944	-32.944	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.007	-0.024	6.664	2.643	2.643	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.004	-0.003	8.801	2.373	2.373	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.894	-0.924	10.523	-17.028	-17.028	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.012	0.015	12.085	1.732	1.732	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.013	-0.014	11.037	1.594	1.594	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.010	-0.013	14.421	1.630	1.630	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.018	0.000	16.332	1.571	1.571	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.887	0.949	17.404	15.776	15.776	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.062	-0.031	16.659	0.716	0.716	0.000	0.000	0.000	0.000
120	A	121	SER	0	-0.045	-0.019	19.687	0.731	0.731	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.043	-0.017	20.150	0.940	0.940	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.031	-0.004	23.489	0.165	0.165	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ARG)