FMO DATABASE

FMODB ID: JQL49

Calculation Name: 2P58-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: C

ChEMBL ID:

UniProt ID: O68690

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-871831.034835
FMO2-HF: Nuclear repulsion	827167.314204
FMO2-HF: Total energy	-44663.720631
FMO2-MP2: Total energy	-44793.825285

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(C:3:TYR)

Summations of interaction energy for fragment #1(C:3:TYR)

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.
-23.003	-13.423	2.924	-4.443	-8.062	-0.019

Interaction energy analysis for fragmet #1(C:3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.004

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

Sort

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	C	5	LEU	0	0.071	0.022	2.856	-3.110	-0.459	0.374	-1.335	-1.690	-0.003
4	C	6	ASN	0	0.070	0.019	4.830	-0.004	0.145	-0.001	-0.004	-0.144	0.000
5	C	7	VAL	0	0.011	0.021	2.568	-0.631	0.257	0.289	-0.222	-0.956	-0.001
6	C	8	LEU	0	0.017	0.013	2.229	-3.415	-0.908	2.020	-1.158	-3.369	0.003
7	C	9	LEU	0	0.003	-0.001	3.761	-0.339	-0.044	0.018	-0.067	-0.246	0.000
8	C	10	ALA	0	0.043	0.022	7.234	0.097	0.097	0.000	0.000	0.000	0.000
9	C	11	GLU	-1	-0.931	-0.974	2.915	-15.914	-12.824	0.224	-1.657	-1.657	-0.018
10	C	12	ILE	0	-0.001	-0.003	6.829	0.297	0.297	0.000	0.000	0.000	0.000
11	C	13	ALA	0	0.034	0.021	9.096	0.149	0.149	0.000	0.000	0.000	0.000
12	C	14	LEU	0	-0.005	0.002	8.979	0.152	0.152	0.000	0.000	0.000	0.000
13	C	15	ILE	0	-0.002	0.012	7.132	0.171	0.171	0.000	0.000	0.000	0.000
14	C	16	GLY	0	0.029	0.012	11.348	0.145	0.145	0.000	0.000	0.000	0.000
15	C	17	THR	0	-0.090	-0.043	14.423	0.074	0.074	0.000	0.000	0.000	0.000
16	C	18	GLY	0	-0.005	-0.002	14.713	0.059	0.059	0.000	0.000	0.000	0.000
17	C	19	ASN	0	-0.112	-0.062	13.731	0.104	0.104	0.000	0.000	0.000	0.000
18	C	20	HIS	0	-0.029	-0.019	17.184	0.038	0.038	0.000	0.000	0.000	0.000
19	C	21	TYR	0	-0.006	0.024	16.621	0.047	0.047	0.000	0.000	0.000	0.000
20	C	22	HIS	0	0.045	0.008	17.926	-0.057	-0.057	0.000	0.000	0.000	0.000
21	C	23	GLU	-1	-0.881	-0.930	19.683	-0.314	-0.314	0.000	0.000	0.000	0.000
22	C	24	GLU	-1	-0.868	-0.942	16.318	-0.335	-0.335	0.000	0.000	0.000	0.000
23	C	25	ALA	0	-0.012	-0.013	14.912	-0.039	-0.039	0.000	0.000	0.000	0.000
24	C	26	ASN	0	-0.041	-0.019	15.695	-0.064	-0.064	0.000	0.000	0.000	0.000
25	C	27	CYS	0	0.024	0.027	17.138	0.008	0.008	0.000	0.000	0.000	0.000
26	C	28	ILE	0	-0.065	-0.024	10.856	-0.008	-0.008	0.000	0.000	0.000	0.000
27	C	29	ALA	0	-0.010	-0.018	13.788	-0.031	-0.031	0.000	0.000	0.000	0.000
28	C	30	GLU	-1	-0.861	-0.937	15.473	-0.296	-0.296	0.000	0.000	0.000	0.000
29	C	31	TRP	0	-0.039	-0.020	10.733	0.080	0.080	0.000	0.000	0.000	0.000
30	C	32	LEU	0	-0.043	-0.045	9.786	0.001	0.001	0.000	0.000	0.000	0.000
31	C	33	HIS	0	-0.068	-0.048	13.788	0.045	0.045	0.000	0.000	0.000	0.000
32	C	34	LEU	0	-0.009	0.013	17.132	0.036	0.036	0.000	0.000	0.000	0.000
33	C	35	LYS	1	0.785	0.881	13.205	0.321	0.321	0.000	0.000	0.000	0.000
34	C	36	GLY	0	0.038	0.033	15.535	0.005	0.005	0.000	0.000	0.000	0.000
35	C	37	GLU	-1	-0.952	-0.960	11.656	-0.589	-0.589	0.000	0.000	0.000	0.000
36	C	38	GLU	-1	-0.823	-0.915	14.829	-0.437	-0.437	0.000	0.000	0.000	0.000
37	C	39	GLU	-1	-0.923	-0.954	15.562	-0.563	-0.563	0.000	0.000	0.000	0.000
38	C	40	ALA	0	0.010	0.001	11.624	-0.049	-0.049	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.007	0.010	13.599	-0.038	-0.038	0.000	0.000	0.000	0.000
40	C	42	GLN	0	0.004	0.008	16.118	0.016	0.016	0.000	0.000	0.000	0.000
41	C	43	LEU	0	-0.020	-0.008	12.121	0.020	0.020	0.000	0.000	0.000	0.000
42	C	44	ILE	0	0.010	0.006	11.956	0.001	0.001	0.000	0.000	0.000	0.000
43	C	45	ARG	1	0.984	0.999	15.565	0.390	0.390	0.000	0.000	0.000	0.000
44	C	46	LEU	0	-0.026	-0.021	18.712	0.044	0.044	0.000	0.000	0.000	0.000
45	C	47	SER	0	0.003	-0.009	15.524	0.046	0.046	0.000	0.000	0.000	0.000
46	C	48	SER	0	-0.018	-0.023	17.790	0.052	0.052	0.000	0.000	0.000	0.000
47	C	49	LEU	0	-0.051	-0.029	19.486	0.041	0.041	0.000	0.000	0.000	0.000
48	C	50	MET	0	-0.046	-0.024	20.686	0.027	0.027	0.000	0.000	0.000	0.000
49	C	51	ASN	0	-0.041	-0.018	16.996	0.050	0.050	0.000	0.000	0.000	0.000
50	C	52	ARG	1	0.872	0.955	21.090	0.349	0.349	0.000	0.000	0.000	0.000
51	C	53	GLY	0	-0.001	0.007	24.307	0.029	0.029	0.000	0.000	0.000	0.000
52	C	54	ASP	-1	-0.849	-0.900	25.834	-0.229	-0.229	0.000	0.000	0.000	0.000
53	C	55	TYR	0	0.066	-0.003	24.096	-0.003	-0.003	0.000	0.000	0.000	0.000
54	C	56	ALA	0	0.027	0.023	27.401	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	57	SER	0	-0.056	-0.050	27.669	0.009	0.009	0.000	0.000	0.000	0.000
56	C	58	ALA	0	0.002	0.007	23.895	-0.005	-0.005	0.000	0.000	0.000	0.000
57	C	59	LEU	0	0.017	0.006	25.495	-0.005	-0.005	0.000	0.000	0.000	0.000
58	C	60	GLN	0	-0.056	-0.031	27.736	0.017	0.017	0.000	0.000	0.000	0.000
59	C	61	GLN	0	0.001	-0.025	24.702	-0.012	-0.012	0.000	0.000	0.000	0.000
60	C	62	GLY	0	0.053	0.017	24.270	-0.006	-0.006	0.000	0.000	0.000	0.000
61	C	63	ASN	0	-0.029	-0.008	25.190	-0.002	-0.002	0.000	0.000	0.000	0.000
62	C	64	LYS	1	0.863	0.939	27.698	0.219	0.219	0.000	0.000	0.000	0.000
63	C	65	LEU	0	-0.022	-0.006	23.157	0.011	0.011	0.000	0.000	0.000	0.000
64	C	66	ALA	0	-0.011	0.000	24.480	-0.018	-0.018	0.000	0.000	0.000	0.000
65	C	67	TYR	0	0.086	0.037	19.686	0.002	0.002	0.000	0.000	0.000	0.000
66	C	68	PRO	0	0.005	-0.004	21.880	-0.016	-0.016	0.000	0.000	0.000	0.000
67	C	69	ASP	-1	-0.848	-0.919	17.079	-0.461	-0.461	0.000	0.000	0.000	0.000
68	C	70	LEU	0	-0.035	-0.023	16.090	-0.043	-0.043	0.000	0.000	0.000	0.000
69	C	71	GLU	-1	-0.889	-0.938	19.591	-0.261	-0.261	0.000	0.000	0.000	0.000
70	C	72	PRO	0	-0.019	-0.021	20.200	0.020	0.020	0.000	0.000	0.000	0.000
71	C	73	TRP	0	0.045	0.029	14.825	0.032	0.032	0.000	0.000	0.000	0.000
72	C	74	LEU	0	-0.006	0.006	21.328	0.026	0.026	0.000	0.000	0.000	0.000
73	C	75	ALA	0	0.015	0.011	24.714	0.025	0.025	0.000	0.000	0.000	0.000
74	C	76	LEU	0	-0.003	0.002	21.148	0.024	0.024	0.000	0.000	0.000	0.000
75	C	77	CYS	0	-0.031	-0.018	24.015	0.017	0.017	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.802	-0.909	26.420	-0.217	-0.217	0.000	0.000	0.000	0.000
77	C	79	TYR	0	-0.023	-0.008	26.704	0.020	0.020	0.000	0.000	0.000	0.000
78	C	80	ARG	1	0.886	0.946	25.493	0.293	0.293	0.000	0.000	0.000	0.000
79	C	81	LEU	0	-0.028	-0.010	28.866	0.011	0.011	0.000	0.000	0.000	0.000
80	C	82	GLY	0	0.010	0.028	31.741	0.015	0.015	0.000	0.000	0.000	0.000
81	C	83	LEU	0	-0.032	-0.014	32.177	0.014	0.014	0.000	0.000	0.000	0.000
82	C	84	GLY	0	0.020	-0.006	33.923	-0.006	-0.006	0.000	0.000	0.000	0.000
83	C	85	SER	0	-0.002	-0.005	35.502	-0.003	-0.003	0.000	0.000	0.000	0.000
84	C	86	ALA	0	0.020	0.015	33.193	0.002	0.002	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.060	0.038	28.821	-0.005	-0.005	0.000	0.000	0.000	0.000
86	C	88	GLU	-1	-0.862	-0.928	31.774	-0.165	-0.165	0.000	0.000	0.000	0.000
87	C	89	SER	0	-0.029	-0.017	34.011	0.001	0.001	0.000	0.000	0.000	0.000
88	C	90	ARG	1	0.755	0.855	26.815	0.263	0.263	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.028	0.010	28.094	-0.008	-0.008	0.000	0.000	0.000	0.000
90	C	92	ASN	0	-0.006	0.001	30.512	0.003	0.003	0.000	0.000	0.000	0.000
91	C	93	ARG	1	0.872	0.934	29.166	0.224	0.224	0.000	0.000	0.000	0.000
92	C	94	LEU	0	0.014	0.003	25.178	0.003	0.003	0.000	0.000	0.000	0.000
93	C	95	ALA	0	0.019	0.015	27.966	-0.003	-0.003	0.000	0.000	0.000	0.000
94	C	96	ARG	1	0.910	0.968	30.169	0.147	0.147	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.023	0.009	24.467	0.014	0.014	0.000	0.000	0.000	0.000
96	C	98	GLN	0	0.037	0.010	26.924	0.004	0.004	0.000	0.000	0.000	0.000
97	C	99	ASP	-1	-0.786	-0.869	20.348	-0.342	-0.342	0.000	0.000	0.000	0.000
98	C	100	PRO	0	0.044	0.012	21.118	-0.009	-0.009	0.000	0.000	0.000	0.000
99	C	101	ARG	1	0.885	0.922	15.094	0.488	0.488	0.000	0.000	0.000	0.000
100	C	102	ILE	0	0.013	0.015	20.375	-0.014	-0.014	0.000	0.000	0.000	0.000
101	C	103	GLN	0	-0.047	-0.051	22.817	0.011	0.011	0.000	0.000	0.000	0.000
102	C	104	THR	0	-0.037	-0.009	21.259	0.016	0.016	0.000	0.000	0.000	0.000
103	C	105	PHE	0	0.007	0.008	21.580	0.004	0.004	0.000	0.000	0.000	0.000
104	C	106	VAL	0	0.000	-0.005	23.271	0.012	0.012	0.000	0.000	0.000	0.000
105	C	107	ASN	0	-0.013	-0.013	26.746	0.017	0.017	0.000	0.000	0.000	0.000
106	C	108	GLY	0	0.047	0.029	24.919	0.013	0.013	0.000	0.000	0.000	0.000
107	C	109	MET	0	-0.008	-0.003	25.332	0.013	0.013	0.000	0.000	0.000	0.000
108	C	110	ARG	1	0.853	0.918	27.533	0.183	0.183	0.000	0.000	0.000	0.000
109	C	111	GLU	-1	-0.990	-0.995	28.619	-0.169	-0.169	0.000	0.000	0.000	0.000
110	C	112	GLN	0	-0.056	-0.019	27.066	-0.001	-0.001	0.000	0.000	0.000	0.000
111	C	113	LEU	0	-0.049	-0.038	29.459	0.008	0.008	0.000	0.000	0.000	0.000
112	C	114	LYS	1	0.915	0.989	32.598	0.160	0.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3:TYR)