FMO DATABASE

FMODB ID: 2N5RR

Calculation Name: 1TOC-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TOC

Chain ID: R

ChEMBL ID:

UniProt ID: P56409

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	OptHSide
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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-733040.788283
FMO2-HF: Nuclear repulsion	684547.11296
FMO2-HF: Total energy	-48493.675324
FMO2-MP2: Total energy	-48622.499894

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(R:1:SER)

Summations of interaction energy for fragment #1(R:1:SER)

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.
-1.264	1.25	-0.011	-1.11	-1.393	0.007

Interaction energy analysis for fragmet #1(R:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.008

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	R	2	ASN	0	0.030	0.005	3.769	1.399	3.766	-0.010	-1.100	-1.257	0.007
4	R	3	VAL	0	0.034	-0.009	5.496	-0.239	-0.092	-0.001	-0.010	-0.136	0.000
5	R	4	LEU	0	-0.013	0.018	7.791	-0.067	-0.067	0.000	0.000	0.000	0.000
6	R	5	CYS	0	-0.087	-0.044	7.219	-0.455	-0.455	0.000	0.000	0.000	0.000
7	R	6	ASN	0	-0.038	-0.012	10.507	-0.080	-0.080	0.000	0.000	0.000	0.000
8	R	7	ASN	0	0.070	0.027	12.748	0.115	0.115	0.000	0.000	0.000	0.000
9	R	8	PRO	0	-0.043	-0.021	14.498	-0.001	-0.001	0.000	0.000	0.000	0.000
10	R	9	HIS	0	-0.048	-0.019	16.608	0.007	0.007	0.000	0.000	0.000	0.000
11	R	10	THR	0	-0.059	-0.041	19.169	0.017	0.017	0.000	0.000	0.000	0.000
12	R	11	ALA	0	-0.061	-0.031	21.399	-0.007	-0.007	0.000	0.000	0.000	0.000
13	R	12	ASP	-1	-0.834	-0.919	25.183	-0.023	-0.023	0.000	0.000	0.000	0.000
14	R	13	CYS	0	-0.053	-0.004	19.906	0.018	0.018	0.000	0.000	0.000	0.000
15	R	14	ASN	0	0.047	0.027	25.019	-0.003	-0.003	0.000	0.000	0.000	0.000
16	R	15	ASN	0	-0.108	-0.057	26.520	0.000	0.000	0.000	0.000	0.000	0.000
17	R	16	ASP	-1	-0.797	-0.882	22.018	0.026	0.026	0.000	0.000	0.000	0.000
18	R	17	ALA	0	-0.018	-0.008	25.122	-0.004	-0.004	0.000	0.000	0.000	0.000
19	R	18	GLN	0	-0.020	-0.027	24.351	-0.012	-0.012	0.000	0.000	0.000	0.000
20	R	19	VAL	0	-0.078	-0.029	23.726	-0.006	-0.006	0.000	0.000	0.000	0.000
21	R	20	ASP	-1	-0.822	-0.936	23.490	-0.150	-0.150	0.000	0.000	0.000	0.000
22	R	21	ARG	1	0.791	0.908	16.805	0.108	0.108	0.000	0.000	0.000	0.000
23	R	22	TYR	0	-0.034	-0.018	17.292	-0.014	-0.014	0.000	0.000	0.000	0.000
24	R	23	PHE	0	0.034	0.025	14.472	-0.015	-0.015	0.000	0.000	0.000	0.000
25	R	24	ARG	1	0.892	0.927	9.578	1.313	1.313	0.000	0.000	0.000	0.000
26	R	25	GLU	-1	-0.871	-0.933	13.764	-0.612	-0.612	0.000	0.000	0.000	0.000
27	R	26	GLY	0	0.001	0.003	16.024	0.023	0.023	0.000	0.000	0.000	0.000
28	R	27	THR	0	-0.047	-0.036	14.839	-0.119	-0.119	0.000	0.000	0.000	0.000
29	R	28	THR	0	0.002	-0.005	15.919	-0.013	-0.013	0.000	0.000	0.000	0.000
30	R	29	CYS	0	0.000	0.037	12.684	-0.175	-0.175	0.000	0.000	0.000	0.000
31	R	30	LEU	0	-0.028	-0.008	16.735	0.048	0.048	0.000	0.000	0.000	0.000
32	R	31	MET	0	-0.065	-0.023	19.207	-0.011	-0.011	0.000	0.000	0.000	0.000
33	R	32	SER	0	-0.056	-0.008	20.278	0.007	0.007	0.000	0.000	0.000	0.000
34	R	33	PRO	0	0.063	0.028	21.817	0.001	0.001	0.000	0.000	0.000	0.000
35	R	34	ALA	0	-0.035	-0.025	19.530	-0.008	-0.008	0.000	0.000	0.000	0.000
36	R	36	THR	0	-0.043	-0.060	19.610	-0.014	-0.014	0.000	0.000	0.000	0.000
37	R	37	SER	0	-0.073	-0.029	16.975	-0.001	-0.001	0.000	0.000	0.000	0.000
38	R	38	GLU	-1	-0.798	-0.880	15.221	-0.009	-0.009	0.000	0.000	0.000	0.000
39	R	39	GLY	0	0.055	0.034	13.896	-0.029	-0.029	0.000	0.000	0.000	0.000
40	R	40	TYR	0	-0.004	-0.022	9.206	0.047	0.047	0.000	0.000	0.000	0.000
41	R	41	ALA	0	0.033	0.009	15.765	0.004	0.004	0.000	0.000	0.000	0.000
42	R	42	SER	0	-0.013	-0.049	17.770	0.005	0.005	0.000	0.000	0.000	0.000
43	R	43	GLN	0	-0.019	-0.019	17.406	-0.068	-0.068	0.000	0.000	0.000	0.000
44	R	44	HIS	0	0.003	0.013	16.503	-0.070	-0.070	0.000	0.000	0.000	0.000
45	R	45	GLU	-1	-0.812	-0.888	14.802	-0.305	-0.305	0.000	0.000	0.000	0.000
46	R	47	GLN	0	0.050	0.018	11.593	-0.149	-0.149	0.000	0.000	0.000	0.000
47	R	48	GLN	0	-0.077	-0.032	12.159	-0.061	-0.061	0.000	0.000	0.000	0.000
48	R	49	ALA	0	-0.011	0.002	8.479	-0.085	-0.085	0.000	0.000	0.000	0.000
49	R	51	PHE	0	-0.049	-0.016	8.312	-0.254	-0.254	0.000	0.000	0.000	0.000
50	R	52	VAL	0	-0.006	-0.019	6.089	-0.216	-0.216	0.000	0.000	0.000	0.000
51	R	53	GLY	0	0.016	0.011	8.201	0.161	0.161	0.000	0.000	0.000	0.000
52	R	54	GLY	0	-0.005	0.015	11.413	0.107	0.107	0.000	0.000	0.000	0.000
53	R	55	GLU	-1	-1.005	-1.010	12.765	-0.500	-0.500	0.000	0.000	0.000	0.000
54	R	56	ASP	-1	-0.867	-0.938	16.372	-0.274	-0.274	0.000	0.000	0.000	0.000
55	R	57	HIS	0	-0.044	-0.011	18.339	0.019	0.019	0.000	0.000	0.000	0.000
56	R	58	SER	0	-0.013	-0.001	17.111	0.016	0.016	0.000	0.000	0.000	0.000
57	R	59	SER	0	-0.063	-0.046	19.483	0.004	0.004	0.000	0.000	0.000	0.000
58	R	60	GLU	-1	-0.929	-0.966	18.922	-0.211	-0.211	0.000	0.000	0.000	0.000
59	R	61	MET	0	-0.078	-0.028	23.054	0.015	0.015	0.000	0.000	0.000	0.000
60	R	62	HIS	0	0.081	0.069	26.658	0.007	0.007	0.000	0.000	0.000	0.000
61	R	63	SER	0	-0.022	-0.035	28.056	0.001	0.001	0.000	0.000	0.000	0.000
62	R	64	SER	0	-0.001	-0.011	29.925	-0.001	-0.001	0.000	0.000	0.000	0.000
63	R	65	CYS	0	-0.058	-0.033	25.032	0.009	0.009	0.000	0.000	0.000	0.000
64	R	66	LEU	0	-0.061	-0.024	32.141	0.001	0.001	0.000	0.000	0.000	0.000
65	R	67	GLY	0	-0.017	0.003	35.014	0.004	0.004	0.000	0.000	0.000	0.000
66	R	68	ASP	-1	-0.927	-0.967	37.415	-0.051	-0.051	0.000	0.000	0.000	0.000
67	R	69	PRO	0	-0.003	-0.008	39.289	0.001	0.001	0.000	0.000	0.000	0.000
68	R	70	PRO	0	-0.016	0.013	38.942	0.004	0.004	0.000	0.000	0.000	0.000
69	R	71	THR	0	-0.006	0.000	41.820	0.000	0.000	0.000	0.000	0.000	0.000
70	R	72	SER	0	0.000	-0.004	45.593	0.000	0.000	0.000	0.000	0.000	0.000
71	R	73	CYS	0	-0.067	-0.009	43.353	0.004	0.004	0.000	0.000	0.000	0.000
72	R	74	ALA	0	-0.006	-0.020	48.894	0.000	0.000	0.000	0.000	0.000	0.000
73	R	75	GLU	-1	-0.985	-0.985	48.231	-0.021	-0.021	0.000	0.000	0.000	0.000
74	R	76	GLY	0	0.037	-0.012	45.755	0.000	0.000	0.000	0.000	0.000	0.000
75	R	77	THR	0	-0.048	-0.033	41.145	0.001	0.001	0.000	0.000	0.000	0.000
76	R	78	ASP	-1	-0.929	-0.968	38.995	-0.049	-0.049	0.000	0.000	0.000	0.000
77	R	79	ILE	0	-0.042	-0.027	37.583	0.001	0.001	0.000	0.000	0.000	0.000
78	R	80	THR	0	0.039	0.024	31.863	0.000	0.000	0.000	0.000	0.000	0.000
79	R	81	TYR	0	-0.067	-0.043	34.463	0.004	0.004	0.000	0.000	0.000	0.000
80	R	82	TYR	0	0.058	0.013	30.834	-0.009	-0.009	0.000	0.000	0.000	0.000
81	R	83	ASP	-1	-0.783	-0.886	33.626	-0.071	-0.071	0.000	0.000	0.000	0.000
82	R	84	SER	0	-0.033	-0.039	35.229	-0.005	-0.005	0.000	0.000	0.000	0.000
83	R	85	ASP	-1	-0.990	-0.969	36.288	-0.080	-0.080	0.000	0.000	0.000	0.000
84	R	86	SER	0	-0.044	-0.060	35.354	-0.002	-0.002	0.000	0.000	0.000	0.000
85	R	87	LYS	1	0.921	0.982	27.784	0.143	0.143	0.000	0.000	0.000	0.000
86	R	88	THR	0	0.019	0.009	30.865	-0.008	-0.008	0.000	0.000	0.000	0.000
87	R	89	CYS	0	-0.018	0.025	25.588	0.000	0.000	0.000	0.000	0.000	0.000
88	R	90	LYS	1	0.846	0.941	32.585	0.078	0.078	0.000	0.000	0.000	0.000
89	R	91	VAL	0	0.049	0.017	35.464	0.002	0.002	0.000	0.000	0.000	0.000
90	R	92	LEU	0	-0.059	-0.007	37.780	0.001	0.001	0.000	0.000	0.000	0.000
91	R	93	ALA	0	0.055	0.021	41.280	0.002	0.002	0.000	0.000	0.000	0.000
92	R	94	ALA	0	-0.049	-0.017	43.524	0.001	0.001	0.000	0.000	0.000	0.000
93	R	95	SER	0	-0.029	-0.009	42.429	0.000	0.000	0.000	0.000	0.000	0.000
94	R	97	PRO	0	0.023	0.014	39.344	-0.002	-0.002	0.000	0.000	0.000	0.000
95	R	98	SER	0	-0.014	-0.015	41.203	0.004	0.004	0.000	0.000	0.000	0.000
96	R	99	GLY	0	-0.032	-0.028	39.507	0.001	0.001	0.000	0.000	0.000	0.000
97	R	100	GLU	-1	-0.918	-0.957	33.386	-0.036	-0.036	0.000	0.000	0.000	0.000
98	R	101	ASN	0	-0.059	0.003	34.027	-0.006	-0.006	0.000	0.000	0.000	0.000
99	R	102	THR	0	-0.057	-0.059	34.431	0.001	0.001	0.000	0.000	0.000	0.000
100	R	103	PHE	0	0.023	0.010	29.170	0.001	0.001	0.000	0.000	0.000	0.000
101	R	104	GLU	-1	-0.964	-0.980	29.843	-0.038	-0.038	0.000	0.000	0.000	0.000
102	R	105	SER	0	-0.034	-0.037	28.411	-0.003	-0.003	0.000	0.000	0.000	0.000
103	R	106	GLU	-1	-0.870	-0.936	29.641	-0.097	-0.097	0.000	0.000	0.000	0.000
104	R	107	VAL	0	0.018	-0.001	23.375	-0.006	-0.006	0.000	0.000	0.000	0.000
105	R	108	GLU	-1	-0.878	-0.938	24.737	-0.075	-0.075	0.000	0.000	0.000	0.000
106	R	110	GLN	0	0.009	-0.021	25.663	-0.007	-0.007	0.000	0.000	0.000	0.000
107	R	111	VAL	0	-0.014	-0.010	20.852	-0.011	-0.011	0.000	0.000	0.000	0.000
108	R	112	ALA	0	0.004	0.025	23.114	-0.005	-0.005	0.000	0.000	0.000	0.000
109	R	114	GLY	0	0.018	0.011	23.516	-0.001	-0.001	0.000	0.000	0.000	0.000
110	R	115	ALA	0	-0.110	-0.035	24.526	-0.010	-0.010	0.000	0.000	0.000	0.000
111	R	116	PRO	0	-0.028	-0.026	24.735	-0.009	-0.009	0.000	0.000	0.000	0.000
112	R	117	ILE	0	0.041	0.031	21.635	0.011	0.011	0.000	0.000	0.000	0.000
113	R	118	GLU	-1	-0.950	-0.970	25.071	-0.143	-0.143	0.000	0.000	0.000	0.000
114	R	119	GLY	0	-0.047	-0.021	26.321	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(R:1:SER)