FMO DATABASE

FMODB ID: 8552Y

Calculation Name: 4DOT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DOT

Chain ID: A

ChEMBL ID:

UniProt ID: P53816

Base Structure: X-ray

Registration Date: 2023-06-21

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816887.286886
FMO2-HF: Nuclear repulsion	776198.171147
FMO2-HF: Total energy	-40689.115739
FMO2-MP2: Total energy	-40809.848769

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:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
-1.151	0.904	0.005	-1.014	-1.046	0.001

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.027

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	A	8	PRO	0	-0.042	-0.019	3.591	-1.738	0.317	0.005	-1.014	-1.046	0.001
4	A	9	LYS	1	0.955	0.987	5.826	0.532	0.532	0.000	0.000	0.000	0.000
5	A	10	PRO	0	0.026	-0.001	8.325	0.070	0.070	0.000	0.000	0.000	0.000
6	A	11	GLY	0	0.002	-0.012	11.921	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	12	ASP	-1	-0.835	-0.903	7.807	-0.298	-0.298	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.024	-0.007	11.244	0.028	0.028	0.000	0.000	0.000	0.000
9	A	14	ILE	0	-0.027	-0.013	8.498	0.030	0.030	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.798	-0.871	10.785	0.130	0.130	0.000	0.000	0.000	0.000
11	A	16	ILE	0	0.011	-0.010	11.342	0.096	0.096	0.000	0.000	0.000	0.000
12	A	17	PHE	0	-0.061	-0.038	10.647	-0.069	-0.069	0.000	0.000	0.000	0.000
13	A	18	ARG	1	0.940	0.991	15.106	-0.146	-0.146	0.000	0.000	0.000	0.000
14	A	19	PRO	0	0.018	0.005	18.087	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	20	PHE	0	-0.077	-0.046	20.796	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	21	TYR	0	-0.048	-0.017	20.949	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.917	0.972	16.509	-0.103	-0.103	0.000	0.000	0.000	0.000
18	A	23	HIS	0	-0.025	-0.047	16.878	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	24	TRP	0	-0.009	-0.001	14.092	0.036	0.036	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.000	-0.003	14.256	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.010	0.010	14.178	0.006	0.006	0.000	0.000	0.000	0.000
22	A	27	TYR	0	-0.034	-0.050	9.158	0.041	0.041	0.000	0.000	0.000	0.000
23	A	28	VAL	0	-0.027	-0.036	12.422	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	29	GLY	0	0.023	0.017	11.803	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	30	ASP	-1	-0.925	-0.961	12.283	-0.110	-0.110	0.000	0.000	0.000	0.000
26	A	31	GLY	0	0.009	0.007	10.572	0.031	0.031	0.000	0.000	0.000	0.000
27	A	32	TYR	0	-0.034	-0.010	11.596	0.067	0.067	0.000	0.000	0.000	0.000
28	A	33	VAL	0	-0.015	-0.010	12.511	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	34	VAL	0	0.010	0.007	14.973	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	35	HIS	0	-0.073	-0.044	17.902	0.019	0.019	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.031	0.036	19.958	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	37	ALA	0	0.036	0.002	22.306	0.012	0.012	0.000	0.000	0.000	0.000
33	A	38	PRO	0	0.023	0.007	24.114	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	39	PRO	0	0.007	0.013	26.977	0.003	0.003	0.000	0.000	0.000	0.000
35	A	58	ALA	0	0.013	0.005	27.325	0.002	0.002	0.000	0.000	0.000	0.000
36	A	59	ILE	0	-0.036	-0.029	27.159	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	60	VAL	0	0.018	0.016	23.165	0.007	0.007	0.000	0.000	0.000	0.000
38	A	61	LYS	1	0.903	0.962	22.211	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	62	LYS	1	0.882	0.927	18.090	0.042	0.042	0.000	0.000	0.000	0.000
40	A	63	GLU	-1	-0.887	-0.927	17.961	0.063	0.063	0.000	0.000	0.000	0.000
41	A	64	LEU	0	0.037	0.028	14.001	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	65	LEU	0	0.009	-0.005	8.151	0.016	0.016	0.000	0.000	0.000	0.000
43	A	66	TYR	0	-0.072	-0.026	11.292	0.062	0.062	0.000	0.000	0.000	0.000
44	A	67	ASP	-1	-0.830	-0.932	12.518	0.098	0.098	0.000	0.000	0.000	0.000
45	A	68	VAL	0	-0.079	-0.031	14.656	0.009	0.009	0.000	0.000	0.000	0.000
46	A	69	ALA	0	-0.040	-0.030	11.266	0.003	0.003	0.000	0.000	0.000	0.000
47	A	70	GLY	0	0.070	0.046	13.319	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	71	SER	0	-0.069	-0.042	13.264	0.031	0.031	0.000	0.000	0.000	0.000
49	A	72	ASP	-1	-0.902	-0.948	14.101	0.205	0.205	0.000	0.000	0.000	0.000
50	A	73	LYS	1	0.945	0.955	10.499	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	74	TYR	0	0.009	0.001	5.977	-0.087	-0.087	0.000	0.000	0.000	0.000
52	A	75	GLN	0	-0.058	-0.025	6.508	0.300	0.300	0.000	0.000	0.000	0.000
53	A	76	VAL	0	0.036	0.020	5.943	-0.103	-0.103	0.000	0.000	0.000	0.000
54	A	77	ASN	0	-0.080	-0.065	7.855	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	78	ASN	0	0.020	0.015	10.673	0.024	0.024	0.000	0.000	0.000	0.000
56	A	79	LYS	1	0.888	0.938	13.145	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	80	HIS	0	0.026	0.019	15.544	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	81	ASP	-1	-0.729	-0.837	14.670	-0.065	-0.065	0.000	0.000	0.000	0.000
59	A	82	ASP	-1	-0.932	-0.949	17.642	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	83	LYS	1	0.855	0.923	19.346	0.005	0.005	0.000	0.000	0.000	0.000
61	A	84	TYR	0	-0.016	-0.011	21.166	0.002	0.002	0.000	0.000	0.000	0.000
62	A	85	SER	0	-0.020	-0.011	20.327	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	86	PRO	0	-0.001	0.015	16.339	0.005	0.005	0.000	0.000	0.000	0.000
64	A	87	LEU	0	-0.017	-0.019	19.048	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	88	PRO	0	-0.024	-0.025	18.960	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	89	CYS	0	0.064	0.020	13.869	0.008	0.008	0.000	0.000	0.000	0.000
67	A	90	SER	0	-0.019	-0.009	17.437	0.002	0.002	0.000	0.000	0.000	0.000
68	A	91	LYS	1	0.965	0.979	19.977	0.040	0.040	0.000	0.000	0.000	0.000
69	A	92	ILE	0	0.002	0.032	16.482	0.004	0.004	0.000	0.000	0.000	0.000
70	A	93	ILE	0	0.005	0.012	14.918	0.007	0.007	0.000	0.000	0.000	0.000
71	A	94	GLN	0	0.024	0.016	18.820	0.006	0.006	0.000	0.000	0.000	0.000
72	A	95	ARG	1	0.940	0.988	22.527	0.014	0.014	0.000	0.000	0.000	0.000
73	A	96	ALA	0	-0.009	-0.023	19.423	0.006	0.006	0.000	0.000	0.000	0.000
74	A	97	GLU	-1	-0.826	-0.921	19.346	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	98	GLU	-1	-0.956	-0.982	22.473	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	99	LEU	0	-0.061	-0.018	23.932	0.003	0.003	0.000	0.000	0.000	0.000
77	A	100	VAL	0	-0.026	-0.002	22.318	0.005	0.005	0.000	0.000	0.000	0.000
78	A	101	GLY	0	-0.040	-0.022	25.208	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	102	GLN	0	-0.046	-0.026	28.191	0.002	0.002	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.935	-0.962	28.618	0.020	0.020	0.000	0.000	0.000	0.000
81	A	104	VAL	0	-0.027	0.000	27.718	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	105	LEU	0	-0.002	-0.018	30.415	0.002	0.002	0.000	0.000	0.000	0.000
83	A	106	TYR	0	-0.015	0.008	26.607	0.002	0.002	0.000	0.000	0.000	0.000
84	A	107	LYS	1	1.005	0.991	30.026	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	108	LEU	0	0.021	0.012	24.289	0.000	0.000	0.000	0.000	0.000	0.000
86	A	109	THR	0	-0.030	-0.016	25.684	0.000	0.000	0.000	0.000	0.000	0.000
87	A	110	SER	0	0.055	0.005	20.687	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	111	GLU	-1	-0.878	-0.935	21.466	0.055	0.055	0.000	0.000	0.000	0.000
89	A	112	ASN	0	-0.032	-0.013	23.812	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	113	CYS	0	-0.033	0.001	20.383	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	114	GLU	-1	-0.875	-0.946	18.322	0.064	0.064	0.000	0.000	0.000	0.000
92	A	115	HIS	0	-0.043	-0.026	20.211	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	116	PHE	0	0.045	0.022	21.101	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	117	VAL	0	0.005	0.005	16.722	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	118	ASN	0	0.027	-0.012	18.767	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	119	GLU	-1	-0.909	-0.949	20.370	0.002	0.002	0.000	0.000	0.000	0.000
97	A	120	LEU	0	-0.069	-0.023	19.722	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	121	ARG	1	0.799	0.883	13.488	0.064	0.064	0.000	0.000	0.000	0.000
99	A	122	TYR	0	-0.045	-0.057	16.648	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	123	GLY	0	-0.004	0.020	21.579	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	124	VAL	0	-0.023	-0.021	24.834	0.003	0.003	0.000	0.000	0.000	0.000
102	A	125	ALA	0	-0.034	-0.003	25.859	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)