FMO DATABASE

FMODB ID: 76ZNK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-733490.285464
FMO2-HF: Nuclear repulsion	684997.898106
FMO2-HF: Total energy	-48492.387359
FMO2-MP2: Total energy	-48621.446512

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.
0.08	2.556	-0.008	-1.07	-1.398	0.006

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 : 0.023 / q_NPA : 0.006

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	0.125	0.044	3.769	-0.221	2.107	-0.007	-1.058	-1.263	0.006
4	R	3	VAL	0	0.003	-0.022	5.308	-0.222	-0.074	-0.001	-0.012	-0.135	0.000
5	R	4	LEU	0	-0.049	-0.001	7.772	0.037	0.037	0.000	0.000	0.000	0.000
6	R	5	CYS	0	-0.057	-0.018	7.387	-0.165	-0.165	0.000	0.000	0.000	0.000
7	R	6	ASN	0	0.008	0.010	10.720	0.068	0.068	0.000	0.000	0.000	0.000
8	R	7	ASN	0	0.045	0.009	12.811	-0.003	-0.003	0.000	0.000	0.000	0.000
9	R	8	PRO	0	-0.056	-0.020	14.476	0.009	0.009	0.000	0.000	0.000	0.000
10	R	9	HIS	0	-0.044	-0.017	16.738	0.018	0.018	0.000	0.000	0.000	0.000
11	R	10	THR	0	-0.033	-0.013	18.900	0.014	0.014	0.000	0.000	0.000	0.000
12	R	11	ALA	0	-0.063	-0.028	21.387	0.010	0.010	0.000	0.000	0.000	0.000
13	R	12	ASP	-1	-0.870	-0.944	25.187	-0.120	-0.120	0.000	0.000	0.000	0.000
14	R	13	CYS	0	-0.030	0.010	19.685	0.012	0.012	0.000	0.000	0.000	0.000
15	R	14	ASN	0	0.059	0.036	24.084	0.007	0.007	0.000	0.000	0.000	0.000
16	R	15	ASN	0	-0.131	-0.071	25.950	0.003	0.003	0.000	0.000	0.000	0.000
17	R	16	ASP	-1	-0.822	-0.924	21.787	-0.167	-0.167	0.000	0.000	0.000	0.000
18	R	17	ALA	0	-0.039	-0.014	24.806	0.007	0.007	0.000	0.000	0.000	0.000
19	R	18	GLN	0	-0.014	-0.016	24.114	-0.015	-0.015	0.000	0.000	0.000	0.000
20	R	19	VAL	0	-0.063	-0.032	23.748	0.012	0.012	0.000	0.000	0.000	0.000
21	R	20	ASP	-1	-0.813	-0.930	23.300	-0.143	-0.143	0.000	0.000	0.000	0.000
22	R	21	ARG	1	0.773	0.916	16.961	0.203	0.203	0.000	0.000	0.000	0.000
23	R	22	TYR	0	-0.057	-0.043	17.392	0.009	0.009	0.000	0.000	0.000	0.000
24	R	23	PHE	0	0.024	0.016	14.517	-0.019	-0.019	0.000	0.000	0.000	0.000
25	R	24	ARG	1	0.873	0.923	9.211	0.558	0.558	0.000	0.000	0.000	0.000
26	R	25	GLU	-1	-0.831	-0.912	13.458	-0.420	-0.420	0.000	0.000	0.000	0.000
27	R	26	GLY	0	-0.035	-0.016	15.673	0.036	0.036	0.000	0.000	0.000	0.000
28	R	27	THR	0	-0.043	-0.034	14.588	-0.029	-0.029	0.000	0.000	0.000	0.000
29	R	28	THR	0	-0.010	-0.026	15.471	0.019	0.019	0.000	0.000	0.000	0.000
30	R	29	CYS	0	0.010	0.061	12.858	-0.088	-0.088	0.000	0.000	0.000	0.000
31	R	30	LEU	0	-0.021	-0.006	16.522	0.037	0.037	0.000	0.000	0.000	0.000
32	R	31	MET	0	-0.053	-0.004	19.159	-0.016	-0.016	0.000	0.000	0.000	0.000
33	R	32	SER	0	-0.081	-0.025	20.097	0.002	0.002	0.000	0.000	0.000	0.000
34	R	33	PRO	0	0.060	0.029	21.752	-0.005	-0.005	0.000	0.000	0.000	0.000
35	R	34	ALA	0	-0.031	-0.021	19.369	-0.014	-0.014	0.000	0.000	0.000	0.000
36	R	36	THR	0	-0.029	-0.018	19.402	-0.012	-0.012	0.000	0.000	0.000	0.000
37	R	37	SER	0	-0.013	-0.007	16.574	0.008	0.008	0.000	0.000	0.000	0.000
38	R	38	GLU	-1	-0.828	-0.915	14.983	-0.277	-0.277	0.000	0.000	0.000	0.000
39	R	39	GLY	0	0.061	0.039	13.711	0.022	0.022	0.000	0.000	0.000	0.000
40	R	40	TYR	0	-0.032	-0.045	9.242	0.034	0.034	0.000	0.000	0.000	0.000
41	R	41	ALA	0	0.040	0.008	15.863	0.006	0.006	0.000	0.000	0.000	0.000
42	R	42	SER	0	0.007	-0.009	18.089	0.013	0.013	0.000	0.000	0.000	0.000
43	R	43	GLN	0	-0.045	-0.034	17.570	-0.031	-0.031	0.000	0.000	0.000	0.000
44	R	44	HIS	0	0.001	0.013	16.454	-0.031	-0.031	0.000	0.000	0.000	0.000
45	R	45	GLU	-1	-0.849	-0.939	15.102	-0.145	-0.145	0.000	0.000	0.000	0.000
46	R	47	GLN	0	0.062	0.001	11.590	-0.071	-0.071	0.000	0.000	0.000	0.000
47	R	48	GLN	0	-0.050	-0.031	11.970	0.029	0.029	0.000	0.000	0.000	0.000
48	R	49	ALA	0	-0.021	-0.005	8.691	0.038	0.038	0.000	0.000	0.000	0.000
49	R	51	PHE	0	-0.070	0.000	7.904	-0.181	-0.181	0.000	0.000	0.000	0.000
50	R	52	VAL	0	0.004	-0.012	5.964	-0.070	-0.070	0.000	0.000	0.000	0.000
51	R	53	GLY	0	0.008	0.007	8.102	0.125	0.125	0.000	0.000	0.000	0.000
52	R	54	GLY	0	-0.002	0.017	11.423	0.041	0.041	0.000	0.000	0.000	0.000
53	R	55	GLU	-1	-1.004	-1.011	12.822	0.013	0.013	0.000	0.000	0.000	0.000
54	R	56	ASP	-1	-0.861	-0.933	16.371	0.196	0.196	0.000	0.000	0.000	0.000
55	R	57	HIS	0	-0.055	-0.016	18.333	0.001	0.001	0.000	0.000	0.000	0.000
56	R	58	SER	0	-0.018	-0.004	17.402	0.023	0.023	0.000	0.000	0.000	0.000
57	R	59	SER	0	-0.052	-0.037	19.672	-0.009	-0.009	0.000	0.000	0.000	0.000
58	R	60	GLU	-1	-0.932	-0.973	18.950	0.248	0.248	0.000	0.000	0.000	0.000
59	R	61	MET	0	-0.067	-0.020	23.373	-0.007	-0.007	0.000	0.000	0.000	0.000
60	R	62	HIS	0	0.074	0.054	27.068	-0.006	-0.006	0.000	0.000	0.000	0.000
61	R	63	SER	0	-0.011	-0.040	28.421	-0.007	-0.007	0.000	0.000	0.000	0.000
62	R	64	SER	0	-0.016	-0.003	30.561	-0.008	-0.008	0.000	0.000	0.000	0.000
63	R	65	CYS	0	-0.063	-0.033	25.460	-0.009	-0.009	0.000	0.000	0.000	0.000
64	R	66	LEU	0	-0.057	-0.022	32.520	-0.007	-0.007	0.000	0.000	0.000	0.000
65	R	67	GLY	0	-0.021	0.002	35.355	-0.005	-0.005	0.000	0.000	0.000	0.000
66	R	68	ASP	-1	-0.931	-0.965	37.803	0.061	0.061	0.000	0.000	0.000	0.000
67	R	69	PRO	0	-0.003	-0.008	39.707	0.003	0.003	0.000	0.000	0.000	0.000
68	R	70	PRO	0	-0.029	0.008	39.405	-0.002	-0.002	0.000	0.000	0.000	0.000
69	R	71	THR	0	0.005	-0.006	42.278	-0.003	-0.003	0.000	0.000	0.000	0.000
70	R	72	SER	0	-0.008	-0.008	46.051	0.001	0.001	0.000	0.000	0.000	0.000
71	R	73	CYS	0	-0.062	0.020	43.853	-0.001	-0.001	0.000	0.000	0.000	0.000
72	R	74	ALA	0	-0.006	-0.020	49.400	0.000	0.000	0.000	0.000	0.000	0.000
73	R	75	GLU	-1	-0.986	-0.989	48.568	0.053	0.053	0.000	0.000	0.000	0.000
74	R	76	GLY	0	0.048	-0.026	46.270	0.003	0.003	0.000	0.000	0.000	0.000
75	R	77	THR	0	-0.045	-0.039	41.959	-0.002	-0.002	0.000	0.000	0.000	0.000
76	R	78	ASP	-1	-0.937	-0.964	39.381	0.063	0.063	0.000	0.000	0.000	0.000
77	R	79	ILE	0	-0.029	-0.024	37.531	0.004	0.004	0.000	0.000	0.000	0.000
78	R	80	THR	0	0.039	0.025	32.223	-0.004	-0.004	0.000	0.000	0.000	0.000
79	R	81	TYR	0	-0.052	-0.018	34.909	0.002	0.002	0.000	0.000	0.000	0.000
80	R	82	TYR	0	0.064	0.049	31.524	-0.002	-0.002	0.000	0.000	0.000	0.000
81	R	83	ASP	-1	-0.812	-0.918	34.018	0.056	0.056	0.000	0.000	0.000	0.000
82	R	84	SER	0	-0.045	-0.056	35.545	0.000	0.000	0.000	0.000	0.000	0.000
83	R	85	ASP	-1	-0.979	-0.961	36.590	0.047	0.047	0.000	0.000	0.000	0.000
84	R	86	SER	0	-0.072	-0.083	35.449	-0.001	-0.001	0.000	0.000	0.000	0.000
85	R	87	LYS	1	0.955	0.995	28.996	-0.076	-0.076	0.000	0.000	0.000	0.000
86	R	88	THR	0	0.003	-0.002	31.140	0.002	0.002	0.000	0.000	0.000	0.000
87	R	89	CYS	0	-0.015	0.016	26.068	0.006	0.006	0.000	0.000	0.000	0.000
88	R	90	LYS	1	0.874	0.954	32.983	-0.063	-0.063	0.000	0.000	0.000	0.000
89	R	91	VAL	0	0.049	0.017	35.934	0.004	0.004	0.000	0.000	0.000	0.000
90	R	92	LEU	0	-0.078	-0.015	38.245	-0.005	-0.005	0.000	0.000	0.000	0.000
91	R	93	ALA	0	0.070	0.026	41.749	0.002	0.002	0.000	0.000	0.000	0.000
92	R	94	ALA	0	-0.036	-0.012	44.024	-0.002	-0.002	0.000	0.000	0.000	0.000
93	R	95	SER	0	-0.063	-0.026	42.951	-0.002	-0.002	0.000	0.000	0.000	0.000
94	R	97	PRO	0	0.033	0.025	40.014	-0.002	-0.002	0.000	0.000	0.000	0.000
95	R	98	SER	0	0.008	0.000	41.705	-0.002	-0.002	0.000	0.000	0.000	0.000
96	R	99	GLY	0	-0.028	-0.023	39.957	-0.002	-0.002	0.000	0.000	0.000	0.000
97	R	100	GLU	-1	-0.926	-0.965	33.779	0.120	0.120	0.000	0.000	0.000	0.000
98	R	101	ASN	0	-0.053	-0.004	34.499	0.012	0.012	0.000	0.000	0.000	0.000
99	R	102	THR	0	-0.063	-0.057	34.901	-0.008	-0.008	0.000	0.000	0.000	0.000
100	R	103	PHE	0	0.029	0.010	30.501	0.005	0.005	0.000	0.000	0.000	0.000
101	R	104	GLU	-1	-0.945	-0.969	29.719	0.134	0.134	0.000	0.000	0.000	0.000
102	R	105	SER	0	-0.021	-0.036	29.085	-0.004	-0.004	0.000	0.000	0.000	0.000
103	R	106	GLU	-1	-0.914	-0.939	30.134	0.093	0.093	0.000	0.000	0.000	0.000
104	R	107	VAL	0	0.041	-0.002	23.930	0.005	0.005	0.000	0.000	0.000	0.000
105	R	108	GLU	-1	-0.928	-0.959	25.253	0.168	0.168	0.000	0.000	0.000	0.000
106	R	110	GLN	0	0.004	-0.016	25.994	0.012	0.012	0.000	0.000	0.000	0.000
107	R	111	VAL	0	-0.018	-0.009	21.533	0.001	0.001	0.000	0.000	0.000	0.000
108	R	112	ALA	0	-0.009	0.015	23.507	0.006	0.006	0.000	0.000	0.000	0.000
109	R	114	GLY	0	0.019	0.015	23.834	-0.011	-0.011	0.000	0.000	0.000	0.000
110	R	115	ALA	0	-0.081	-0.018	24.838	-0.011	-0.011	0.000	0.000	0.000	0.000
111	R	116	PRO	0	-0.047	-0.041	25.019	0.007	0.007	0.000	0.000	0.000	0.000
112	R	117	ILE	0	0.035	0.028	22.195	-0.003	-0.003	0.000	0.000	0.000	0.000
113	R	118	GLU	-1	-0.902	-0.953	25.430	0.073	0.073	0.000	0.000	0.000	0.000
114	R	119	GLY	0	-0.059	-0.024	26.724	0.008	0.008	0.000	0.000	0.000	0.000

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