FMO DATABASE

FMODB ID: 98212

Calculation Name: 2DST-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-987879.805962
FMO2-HF: Nuclear repulsion	942421.869979
FMO2-HF: Total energy	-45457.935983
FMO2-MP2: Total energy	-45592.475294

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: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.
-200.932	-189.13	20.151	-13.173	-18.782	-0.119

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 : 0.883 / q_NPA : 0.928

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	0.068	0.030	3.800	-1.362	0.119	-0.024	-0.607	-0.850	0.002
4	A	5	GLY	0	-0.043	-0.021	6.114	2.498	2.498	0.000	0.000	0.000	0.000
5	A	6	TYR	0	-0.015	-0.013	9.195	-0.534	-0.534	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.012	0.014	12.359	0.611	0.611	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.067	-0.047	15.140	0.369	0.369	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.018	-0.015	17.678	0.362	0.362	0.000	0.000	0.000	0.000
9	A	10	TYR	0	0.003	-0.005	20.057	0.126	0.126	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.002	0.002	23.270	0.111	0.111	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.002	0.014	19.288	0.085	0.085	0.000	0.000	0.000	0.000
12	A	13	ASN	0	0.034	0.031	16.372	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.015	0.018	12.160	-0.433	-0.433	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.031	0.007	8.987	-0.336	-0.336	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.049	-0.023	7.576	-0.655	-0.655	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.787	-0.886	2.375	-49.048	-48.249	0.609	-0.390	-1.019	-0.001
17	A	18	ARG	1	0.886	0.970	3.690	28.146	28.693	0.006	-0.165	-0.388	0.000
18	A	19	VAL	0	0.005	-0.009	2.196	-2.890	-2.016	6.996	-3.576	-4.295	-0.023
19	A	20	GLY	0	0.059	0.051	3.784	0.302	0.472	0.009	-0.068	-0.111	0.000
20	A	21	LYS	1	0.861	0.909	7.290	21.870	21.870	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.060	0.043	10.645	-0.108	-0.108	0.000	0.000	0.000	0.000
22	A	23	PRO	0	0.008	-0.003	13.322	-0.296	-0.296	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.009	0.005	12.411	-1.655	-1.655	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.002	0.005	10.521	0.944	0.944	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.009	-0.003	10.169	-2.623	-2.623	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.025	0.005	5.271	0.747	0.747	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.016	-0.011	8.887	-0.992	-0.992	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.051	0.018	9.002	1.146	1.146	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.794	-0.894	10.903	-22.762	-22.762	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.833	-0.911	8.655	-30.516	-30.516	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.009	0.009	4.181	-1.510	-1.427	-0.001	-0.007	-0.075	0.000
32	A	33	SER	0	-0.071	-0.052	4.017	-10.609	-10.379	0.000	-0.058	-0.172	0.000
33	A	34	ARG	1	0.826	0.909	5.598	26.237	26.237	0.000	0.000	0.000	0.000
34	A	35	TRP	0	-0.024	-0.012	2.798	4.517	5.337	0.073	-0.312	-0.582	-0.001
35	A	36	PRO	0	0.008	-0.005	1.939	-44.486	-42.121	6.378	-4.623	-4.119	-0.070
36	A	37	GLU	-1	-0.701	-0.805	3.563	-46.126	-45.510	0.011	-0.235	-0.392	-0.002
37	A	38	ALA	0	-0.008	-0.003	2.317	-27.204	-25.200	2.378	-2.025	-2.357	-0.028
38	A	39	LEU	0	-0.059	-0.037	2.714	5.182	6.404	2.025	-0.685	-2.562	0.004
39	A	40	PRO	0	-0.003	0.006	4.646	2.246	2.288	-0.001	-0.005	-0.036	0.000
40	A	41	GLU	-1	-0.901	-0.957	8.295	-23.918	-23.918	0.000	0.000	0.000	0.000
41	A	42	GLY	0	-0.003	-0.006	10.340	1.071	1.071	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.023	0.003	10.179	1.644	1.644	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.125	-0.044	8.677	-1.986	-1.986	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.078	0.021	6.062	0.660	0.660	0.000	0.000	0.000	0.000
45	A	46	TYR	0	-0.005	-0.025	6.718	-1.143	-1.143	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.020	-0.010	2.497	-0.572	-0.023	1.692	-0.417	-1.824	0.000
47	A	48	LEU	0	0.028	0.008	6.689	0.018	0.018	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.704	-0.796	8.522	-32.987	-32.987	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.021	-0.005	10.797	1.885	1.885	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.044	0.004	14.144	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.030	0.005	17.385	0.419	0.419	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.071	-0.051	13.937	0.750	0.750	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.026	0.021	11.704	-0.688	-0.688	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.749	0.828	6.151	35.724	35.724	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.021	-0.010	13.251	0.743	0.743	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.912	-0.946	15.294	-13.733	-13.733	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.010	-0.008	18.963	0.100	0.100	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.025	0.000	20.907	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.908	0.940	18.584	15.064	15.064	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.015	0.005	21.777	0.347	0.347	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.021	0.023	22.406	-0.434	-0.434	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.030	0.004	21.118	-0.432	-0.432	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.803	-0.921	21.772	-12.627	-12.627	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.917	-0.967	24.058	-11.960	-11.960	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.002	-0.009	18.101	-0.409	-0.409	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.002	-0.006	19.117	-0.763	-0.763	0.000	0.000	0.000	0.000
67	A	68	HIS	0	0.042	0.013	20.477	-0.339	-0.339	0.000	0.000	0.000	0.000
68	A	69	PHE	0	-0.009	0.007	17.959	-0.103	-0.103	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.003	0.010	15.146	-0.537	-0.537	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.016	0.009	17.355	-0.352	-0.352	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.002	-0.011	20.164	0.166	0.166	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.009	-0.019	10.982	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.029	0.005	16.456	-0.223	-0.223	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.010	0.010	17.411	0.178	0.178	0.000	0.000	0.000	0.000
75	A	76	MET	0	-0.030	-0.003	17.979	0.448	0.448	0.000	0.000	0.000	0.000
76	A	77	MET	0	-0.063	-0.033	11.988	0.333	0.333	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.065	-0.032	15.932	-0.141	-0.141	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.030	-0.021	13.205	-0.329	-0.329	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.005	0.007	16.978	-0.171	-0.171	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.004	-0.009	20.441	0.059	0.059	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.042	-0.005	15.069	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.027	0.004	15.248	0.249	0.249	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.017	-0.003	13.646	-1.364	-1.364	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.021	-0.004	9.534	1.066	1.066	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.049	-0.019	11.652	-0.923	-0.923	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.810	0.872	6.743	34.284	34.284	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.009	-0.005	12.061	-0.275	-0.275	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.023	-0.010	13.982	1.021	1.021	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.025	0.012	13.814	0.943	0.943	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.012	-0.010	14.792	0.779	0.779	0.000	0.000	0.000	0.000
91	A	92	ALA	0	-0.024	-0.010	17.027	0.864	0.864	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.016	-0.010	16.505	0.707	0.707	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.009	0.009	19.032	0.383	0.383	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.008	-0.004	20.018	0.216	0.216	0.000	0.000	0.000	0.000
95	A	96	HIS	0	0.024	0.010	22.853	0.409	0.409	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.007	-0.002	17.072	0.136	0.136	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.820	-0.916	21.524	-13.891	-13.891	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.088	-0.035	23.584	0.399	0.399	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.056	-0.021	22.711	0.425	0.425	0.000	0.000	0.000	0.000
100	A	101	GLY	0	-0.047	-0.019	24.924	0.038	0.038	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.064	-0.027	18.122	-0.236	-0.236	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.908	0.961	19.908	13.270	13.270	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.009	0.019	17.233	-1.113	-1.113	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.049	-0.031	15.216	0.885	0.885	0.000	0.000	0.000	0.000
105	A	106	PRO	0	-0.002	0.004	14.687	-1.436	-1.436	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.022	-0.003	10.743	0.294	0.294	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.875	-0.937	11.533	-23.275	-23.275	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.000	-0.003	12.952	-0.746	-0.746	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.022	0.007	12.335	-0.104	-0.104	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.866	-0.934	8.074	-33.693	-33.693	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.007	-0.030	6.327	2.619	2.619	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.006	-0.009	8.398	2.469	2.469	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.911	-0.934	10.173	-17.541	-17.541	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.010	0.007	11.699	1.778	1.778	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.015	-0.018	10.431	1.640	1.640	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.015	-0.005	14.009	1.746	1.746	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.033	0.010	15.935	1.653	1.653	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.895	0.953	17.035	16.028	16.028	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.063	-0.034	16.252	0.743	0.743	0.000	0.000	0.000	0.000
120	A	121	SER	0	-0.048	-0.016	19.330	0.773	0.773	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.058	-0.021	19.920	0.957	0.957	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.009	0.007	23.126	-0.035	-0.035	0.000	0.000	0.000	0.000

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