FMO DATABASE

FMODB ID: 6Y45Z

Calculation Name: 3B33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B33

Chain ID: A

ChEMBL ID:

UniProt ID: Q87TF0

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	OptAll
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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-824842.121811
FMO2-HF: Nuclear repulsion	782786.57298
FMO2-HF: Total energy	-42055.548831
FMO2-MP2: Total energy	-42177.655497

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-0.364	1.639	0.032	-0.986	-1.048	0.002

Interaction energy analysis for fragmet #1(A:3:THR)

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 : -0.009

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	5	LEU	0	0.070	0.034	3.871	1.843	3.196	-0.018	-0.670	-0.664	0.000
4	A	6	PRO	0	0.061	0.012	7.134	0.412	0.412	0.000	0.000	0.000	0.000
5	A	7	SER	0	0.026	0.024	3.609	-0.892	-0.242	0.050	-0.316	-0.384	0.002
6	A	8	ALA	0	-0.005	0.008	5.635	0.002	0.002	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.031	0.016	6.875	-0.513	-0.513	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.026	0.003	8.807	-0.172	-0.172	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.029	-0.022	5.880	-0.799	-0.799	0.000	0.000	0.000	0.000
10	A	12	ASN	0	-0.076	-0.044	9.226	-0.422	-0.422	0.000	0.000	0.000	0.000
11	A	13	MET	0	-0.041	0.014	12.293	-0.243	-0.243	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.010	-0.008	14.878	0.011	0.011	0.000	0.000	0.000	0.000
13	A	15	THR	0	0.005	0.008	17.573	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.003	0.021	16.944	0.103	0.103	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.005	-0.022	14.958	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.017	-0.020	16.542	0.078	0.078	0.000	0.000	0.000	0.000
17	A	19	ILE	0	-0.016	-0.002	15.389	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.004	0.006	18.250	0.008	0.008	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.747	-0.872	21.665	0.222	0.222	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.857	-0.926	23.408	0.161	0.161	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.027	-0.001	26.433	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.065	-0.035	25.519	0.003	0.003	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.002	0.008	23.400	0.013	0.013	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.004	-0.015	18.650	0.011	0.011	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.760	0.832	18.007	-0.262	-0.262	0.000	0.000	0.000	0.000
26	A	28	TYR	0	-0.048	-0.021	9.852	0.140	0.140	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.020	0.012	13.952	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	30	ASN	0	0.020	0.013	12.182	0.037	0.037	0.000	0.000	0.000	0.000
29	A	31	PRO	0	0.078	0.037	10.971	-0.164	-0.164	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.002	0.010	13.978	-0.138	-0.138	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.013	0.005	16.521	-0.109	-0.109	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.847	-0.924	13.560	0.998	0.998	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.036	-0.021	17.441	-0.083	-0.083	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.074	-0.028	19.971	-0.063	-0.063	0.000	0.000	0.000	0.000
35	A	37	PHE	0	0.030	-0.009	20.783	-0.047	-0.047	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.055	-0.019	22.332	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.000	0.001	21.213	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	40	SER	0	0.030	0.017	16.716	0.022	0.022	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.064	0.024	13.822	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.882	0.938	15.760	-0.474	-0.474	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.848	0.922	17.226	-0.405	-0.405	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.021	0.021	17.563	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.011	-0.004	15.115	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.858	-0.899	18.568	0.289	0.289	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.103	-0.045	21.459	-0.058	-0.058	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.030	0.017	23.653	0.011	0.011	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.039	0.001	24.537	0.008	0.008	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.025	-0.020	26.428	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	51	GLN	0	-0.021	0.000	27.431	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.018	0.006	22.507	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.024	-0.013	25.924	0.009	0.009	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.044	-0.025	29.350	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	55	HIS	0	-0.028	-0.020	32.900	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.009	0.001	32.052	0.016	0.016	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.023	0.003	33.945	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.021	0.005	30.566	0.013	0.013	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.808	-0.895	33.563	0.139	0.139	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.008	-0.018	32.929	0.010	0.010	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.000	0.001	33.462	0.001	0.001	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.004	-0.002	28.297	0.003	0.003	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.027	-0.016	28.054	0.012	0.012	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.041	-0.020	29.833	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.007	-0.002	31.320	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.016	0.034	26.568	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.009	-0.013	26.817	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.046	-0.014	28.813	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.039	-0.031	31.463	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.016	-0.007	28.163	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	71	GLN	0	-0.058	-0.029	27.795	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.006	-0.015	24.779	0.003	0.003	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.049	-0.013	27.379	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	74	THR	0	0.030	0.001	27.943	0.025	0.025	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.816	-0.901	29.597	0.173	0.173	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.033	0.001	30.287	0.016	0.016	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.961	-0.981	32.254	0.175	0.175	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.012	0.025	29.605	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	79	THR	0	-0.027	-0.029	32.133	0.003	0.003	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.009	-0.011	25.990	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.019	-0.018	30.832	0.007	0.007	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.025	0.008	26.346	0.004	0.004	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.851	-0.922	28.134	0.287	0.287	0.000	0.000	0.000	0.000
82	A	84	GLY	0	-0.010	0.008	30.879	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.890	0.934	31.571	-0.234	-0.234	0.000	0.000	0.000	0.000
84	A	86	PRO	0	0.013	0.020	31.945	0.011	0.011	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.045	-0.027	26.606	0.007	0.007	0.000	0.000	0.000	0.000
86	A	88	MET	0	0.002	0.021	30.513	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.054	-0.055	25.658	0.024	0.024	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.910	-0.935	27.458	0.230	0.230	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.048	-0.045	25.092	0.037	0.037	0.000	0.000	0.000	0.000
90	A	92	THR	0	0.010	-0.003	23.990	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.028	-0.014	23.910	0.034	0.034	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.059	0.039	22.042	-0.041	-0.041	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.012	0.013	22.946	0.019	0.019	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.025	-0.020	15.892	0.012	0.012	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.034	-0.004	20.535	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	98	TRP	0	0.023	0.002	11.716	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.003	-0.013	15.658	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.900	0.942	18.991	0.009	0.009	0.000	0.000	0.000	0.000
99	A	101	GLN	0	-0.010	0.003	21.354	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.026	-0.010	21.650	0.015	0.015	0.000	0.000	0.000	0.000
101	A	103	MET	0	0.036	0.028	17.421	0.008	0.008	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.031	0.007	22.248	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.010	0.000	16.923	0.042	0.042	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.003	0.000	19.699	-0.038	-0.038	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.926	-0.967	18.964	0.496	0.496	0.000	0.000	0.000	0.000
106	A	108	MET	0	-0.011	-0.002	21.004	-0.059	-0.059	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.901	0.937	21.607	-0.378	-0.378	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.959	0.993	24.399	-0.385	-0.385	0.000	0.000	0.000	0.000
109	A	111	ILE	0	-0.026	0.016	27.102	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)