FMO DATABASE

FMODB ID: 82Y5Y

Calculation Name: 3P9A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P9A

Chain ID: A

ChEMBL ID:

UniProt ID: P04893

Base Structure: X-ray

Registration Date: 2023-06-20

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1137465.60699
FMO2-HF: Nuclear repulsion	1081154.755482
FMO2-HF: Total energy	-56310.851508
FMO2-MP2: Total energy	-56473.496092

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:1:MET)

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

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.
-1.969	1.151	-0.025	-1.6	-1.496	-0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.022

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	3	ALA	0	0.027	0.026	3.819	-2.823	0.297	-0.025	-1.600	-1.496	-0.002
4	A	4	PRO	0	-0.022	-0.021	5.439	-0.053	-0.053	0.000	0.000	0.000	0.000
5	A	5	LYN	0	0.030	0.024	5.512	0.410	0.410	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.035	-0.010	7.766	-0.199	-0.199	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.048	-0.026	9.905	-0.196	-0.196	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.863	0.920	12.962	-0.559	-0.559	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.045	0.008	16.604	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	10	TRP	0	-0.063	-0.027	18.097	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.844	-0.922	18.482	0.424	0.424	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.070	-0.009	16.783	0.000	0.000	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.846	0.912	18.079	-0.281	-0.281	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.033	0.003	18.142	0.021	0.021	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.073	-0.077	17.678	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.013	-0.011	19.392	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.029	-0.001	22.218	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.887	0.927	23.734	-0.154	-0.154	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.085	-0.032	26.835	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.051	0.056	25.860	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.819	0.882	28.802	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.012	-0.010	25.142	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.786	-0.884	30.836	0.056	0.056	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.075	-0.067	30.749	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.055	0.034	30.386	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.812	-0.880	27.396	0.036	0.036	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.008	0.005	26.059	0.007	0.007	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.034	0.019	25.351	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.057	0.014	23.690	0.012	0.012	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.022	0.015	21.951	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.019	0.017	20.712	0.019	0.019	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.095	-0.055	20.990	0.020	0.020	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.006	-0.017	18.958	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.721	-0.825	16.577	0.260	0.260	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.010	0.005	16.202	0.037	0.037	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.015	-0.036	17.146	0.020	0.020	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.853	-0.926	12.982	0.184	0.184	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.015	-0.004	12.397	0.041	0.041	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.052	-0.044	13.013	0.061	0.061	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.967	-0.972	11.822	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.022	-0.003	8.683	-0.063	-0.063	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.066	-0.028	8.760	0.385	0.385	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.059	0.054	9.412	-0.049	-0.049	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.034	-0.021	12.366	0.119	0.119	0.000	0.000	0.000	0.000
45	A	45	TRP	0	0.045	0.010	7.265	0.024	0.024	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.819	-0.882	14.033	0.134	0.134	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.017	0.001	14.017	0.046	0.046	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.839	0.914	16.157	-0.203	-0.203	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.030	0.013	17.047	0.037	0.037	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.001	-0.003	15.579	-0.048	-0.048	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.028	-0.019	19.845	0.016	0.016	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.004	-0.005	20.882	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.003	-0.001	22.797	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.009	0.011	25.838	0.004	0.004	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.940	-0.950	21.620	0.126	0.126	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.036	-0.039	21.041	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.009	0.008	15.303	0.026	0.026	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.024	-0.024	16.100	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.871	-0.945	9.756	0.897	0.897	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.053	-0.016	9.779	-0.117	-0.117	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.012	0.001	11.154	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.018	0.012	10.169	0.043	0.043	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.846	0.906	12.248	-0.196	-0.196	0.000	0.000	0.000	0.000
64	A	64	MET	0	0.038	0.032	15.027	0.035	0.035	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.868	0.931	14.100	-0.380	-0.380	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.007	0.010	17.517	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.007	0.021	17.829	0.022	0.022	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.023	-0.011	21.505	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.062	0.031	24.606	0.010	0.010	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.004	-0.004	27.096	0.005	0.005	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.022	0.013	23.093	0.010	0.010	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.019	0.014	22.775	0.018	0.018	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.047	-0.028	23.835	0.003	0.003	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.010	-0.013	24.067	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.010	0.032	16.583	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.031	-0.034	21.918	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.792	-0.891	23.748	0.173	0.173	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.033	-0.006	26.237	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.019	-0.012	29.446	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.054	0.003	30.706	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.858	-0.911	33.355	0.088	0.088	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.031	-0.006	32.772	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.013	-0.019	27.592	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.922	0.949	32.887	-0.083	-0.083	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.010	-0.018	36.294	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.036	0.011	30.151	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.808	0.900	34.074	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.031	-0.005	38.092	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.802	0.899	36.041	-0.047	-0.047	0.000	0.000	0.000	0.000
90	A	90	GLH	0	-0.053	-0.081	37.784	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.813	-0.906	36.135	0.032	0.032	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.055	0.027	32.270	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.013	0.015	33.037	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.834	-0.867	33.311	0.015	0.015	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.033	-0.006	27.966	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.026	-0.009	29.100	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.000	-0.007	30.185	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.927	0.972	26.618	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.011	0.004	25.639	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.828	-0.927	25.883	0.066	0.066	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.043	-0.019	28.059	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.013	0.009	21.862	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.030	-0.016	23.326	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.035	-0.012	24.444	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.840	-0.928	24.907	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.018	0.024	17.546	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.811	0.886	21.919	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.015	0.014	23.866	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.014	-0.027	22.196	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.043	0.004	20.934	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.060	-0.035	21.726	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.020	-0.002	25.053	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.047	-0.016	21.625	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.942	-0.962	22.634	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.065	-0.029	17.438	0.005	0.005	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.066	-0.031	19.949	0.031	0.031	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.003	-0.009	22.643	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.148	0.069	26.029	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.025	0.019	28.658	0.006	0.006	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.013	-0.016	27.067	0.001	0.001	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.041	0.017	24.552	0.004	0.004	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.011	0.016	28.458	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.867	0.919	31.892	-0.059	-0.059	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.873	-0.915	28.479	0.078	0.078	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.019	-0.003	27.786	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.026	-0.001	31.690	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.054	-0.028	31.433	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.918	0.951	35.572	-0.023	-0.023	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.883	-0.933	38.550	0.012	0.012	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.084	-0.043	40.870	0.001	0.001	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.002	-0.004	43.975	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.026	-0.017	46.997	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.009	-0.007	50.512	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.947	-0.965	53.200	0.003	0.003	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.876	-0.920	56.693	0.011	0.011	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.006	-0.007	58.987	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.079	-0.055	61.528	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.075	-0.047	64.082	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.966	-0.962	66.891	0.009	0.009	0.000	0.000	0.000	0.000

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