FMO DATABASE

FMODB ID: YZLK2

Calculation Name: 2P9M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P9M

Chain ID: A

ChEMBL ID:

UniProt ID: Q58332

Base Structure: X-ray

Registration Date: 2023-09-20

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1136721.407679
FMO2-HF: Nuclear repulsion	1084732.546549
FMO2-HF: Total energy	-51988.861129
FMO2-MP2: Total energy	-52140.932261

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-9.213	-1.793	4.581	-2.532	-9.469	-0.004

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.014

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	7	ASN	0	-0.052	-0.040	3.362	-2.433	-0.745	0.005	-0.670	-1.023	0.002
4	A	8	ILE	0	-0.001	0.021	2.333	-1.504	-0.071	0.886	-0.518	-1.800	-0.001
5	A	9	LYS	1	0.919	0.949	4.720	-0.097	-0.084	-0.001	-0.007	-0.005	0.000
6	A	10	VAL	0	0.030	0.010	7.839	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.836	0.892	9.227	0.196	0.196	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.870	-0.928	8.248	-0.549	-0.549	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.098	-0.058	6.093	0.000	0.000	0.000	0.000	0.000	0.000
10	A	14	MET	0	-0.015	0.024	9.479	0.029	0.029	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.008	0.003	12.111	0.033	0.033	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.842	0.900	13.400	0.400	0.400	0.000	0.000	0.000	0.000
13	A	17	ASN	0	0.012	0.020	18.257	0.013	0.013	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.019	-0.008	18.754	0.005	0.005	0.000	0.000	0.000	0.000
15	A	19	ILE	0	0.012	0.001	21.917	0.013	0.013	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.006	-0.006	23.981	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	21	ALA	0	-0.004	0.008	26.179	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.846	0.909	29.006	0.081	0.081	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.999	0.970	31.767	0.064	0.064	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.015	0.000	33.345	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.828	-0.889	32.389	-0.093	-0.093	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.112	0.069	35.284	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.045	-0.036	32.090	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.028	0.006	33.360	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.844	-0.920	34.779	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.037	-0.017	30.527	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.008	-0.009	29.399	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.871	-0.943	30.863	-0.089	-0.089	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.845	0.932	29.861	0.101	0.101	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.040	-0.026	26.397	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.001	0.004	27.541	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.877	0.950	29.534	0.094	0.094	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.029	-0.029	27.294	0.003	0.003	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.910	0.967	24.582	0.157	0.157	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.014	0.015	22.803	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.033	0.011	19.218	0.007	0.007	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.020	-0.017	19.814	0.003	0.003	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.008	-0.006	22.281	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.001	0.007	20.649	0.009	0.009	0.000	0.000	0.000	0.000
40	A	44	VAL	0	0.002	-0.004	23.399	0.006	0.006	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.005	-0.001	25.382	0.000	0.000	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.805	-0.904	27.906	-0.067	-0.067	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.859	-0.942	30.572	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.842	-0.898	30.437	-0.055	-0.055	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.030	-0.016	24.558	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.876	0.938	25.629	0.046	0.046	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.004	-0.009	21.245	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.038	-0.032	24.598	0.007	0.007	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.043	0.016	25.277	0.007	0.007	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.039	-0.015	20.019	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.024	0.033	24.236	0.008	0.008	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.031	-0.011	21.744	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.025	0.000	24.427	0.009	0.009	0.000	0.000	0.000	0.000
54	A	58	THR	0	0.017	0.006	22.834	0.012	0.012	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.818	-0.886	24.585	-0.132	-0.132	0.000	0.000	0.000	0.000
56	A	60	ILE	0	-0.030	-0.016	27.518	0.010	0.010	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.058	0.014	29.289	0.008	0.008	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.021	-0.011	29.566	0.008	0.008	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.038	-0.037	31.104	0.012	0.012	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.012	0.020	33.616	0.005	0.005	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.020	-0.008	34.367	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.826	0.924	33.157	0.083	0.083	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.888	-0.937	38.104	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.871	0.941	36.341	0.066	0.066	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.051	-0.026	32.719	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.039	0.010	38.906	0.001	0.001	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.001	-0.010	39.992	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.894	-0.933	41.171	-0.051	-0.051	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.080	-0.024	37.756	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.042	0.000	36.519	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.013	-0.024	29.880	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.023	-0.034	32.329	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.907	-0.915	33.901	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.046	-0.029	31.323	0.001	0.001	0.000	0.000	0.000	0.000
75	A	79	MET	0	-0.035	0.018	28.169	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.012	-0.014	25.720	0.010	0.010	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.912	0.938	27.393	0.067	0.067	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.922	-0.938	25.299	-0.063	-0.063	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.044	-0.006	21.507	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	84	ILE	0	0.030	0.016	16.761	0.001	0.001	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.028	0.019	17.369	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.050	-0.021	10.442	0.018	0.018	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.050	0.037	14.257	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.814	-0.922	12.832	-0.217	-0.217	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.858	-0.935	11.997	-0.215	-0.215	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.009	0.030	10.155	0.041	0.041	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.046	-0.056	4.916	-0.101	-0.101	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.039	0.003	2.735	-1.273	-0.043	0.483	-0.274	-1.438	0.000
89	A	93	LEU	0	-0.015	-0.001	3.404	-0.688	0.129	0.020	-0.182	-0.656	0.000
90	A	94	GLU	-1	-0.818	-0.883	4.699	0.040	0.126	-0.001	-0.013	-0.072	0.000
91	A	95	ALA	0	0.013	-0.002	7.237	0.065	0.065	0.000	0.000	0.000	0.000
92	A	96	ILE	0	0.008	0.001	3.323	-0.309	0.051	0.028	-0.070	-0.318	0.000
93	A	97	LYS	1	0.919	0.956	7.437	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.866	0.945	9.915	0.196	0.196	0.000	0.000	0.000	0.000
95	A	99	MET	0	0.024	0.002	10.691	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	100	ASP	-1	-0.912	-0.940	11.398	-0.160	-0.160	0.000	0.000	0.000	0.000
97	A	101	ILE	0	-0.040	-0.017	13.255	0.049	0.049	0.000	0.000	0.000	0.000
98	A	102	SER	0	0.015	-0.028	16.542	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.025	-0.016	19.397	0.010	0.010	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.696	0.852	15.280	0.153	0.153	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.794	0.877	20.481	0.078	0.078	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.787	-0.877	21.792	-0.089	-0.089	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.818	-0.880	17.481	-0.142	-0.142	0.000	0.000	0.000	0.000
104	A	108	ILE	0	0.018	0.006	13.634	0.000	0.000	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.024	0.024	15.631	0.013	0.013	0.000	0.000	0.000	0.000
106	A	110	ASN	0	-0.010	-0.019	14.809	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	111	GLN	0	-0.027	-0.039	14.422	-0.045	-0.045	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.024	0.006	12.071	0.034	0.034	0.000	0.000	0.000	0.000
109	A	113	PRO	0	0.011	0.006	15.102	-0.029	-0.029	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.025	-0.016	13.331	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	115	VAL	0	0.009	0.013	16.147	0.022	0.022	0.000	0.000	0.000	0.000
112	A	116	ASP	-1	-0.745	-0.875	17.357	-0.108	-0.108	0.000	0.000	0.000	0.000
113	A	117	LYS	1	0.904	0.937	19.345	0.056	0.056	0.000	0.000	0.000	0.000
114	A	118	ASN	0	-0.080	-0.031	20.946	0.021	0.021	0.000	0.000	0.000	0.000
115	A	119	ASN	0	-0.029	-0.029	21.387	0.011	0.011	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.824	0.917	22.745	0.068	0.068	0.000	0.000	0.000	0.000
117	A	121	LEU	0	0.009	0.001	19.866	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.043	-0.028	16.984	0.007	0.007	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.031	0.016	16.649	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.028	0.002	15.477	0.015	0.015	0.000	0.000	0.000	0.000
121	A	125	ILE	0	-0.034	-0.013	7.584	-0.039	-0.039	0.000	0.000	0.000	0.000
122	A	126	SER	0	-0.015	-0.047	11.563	0.041	0.041	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.734	-0.876	10.239	-0.513	-0.513	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.008	0.011	10.038	-0.103	-0.103	0.000	0.000	0.000	0.000
125	A	129	ASP	-1	-0.785	-0.849	9.354	-0.588	-0.588	0.000	0.000	0.000	0.000
126	A	130	ILE	0	0.024	0.017	4.860	-0.182	-0.182	0.000	0.000	0.000	0.000
127	A	131	ILE	0	0.016	0.018	5.445	-0.318	-0.318	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.841	0.905	7.281	0.539	0.539	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.068	-0.049	3.154	-0.293	0.071	0.072	-0.082	-0.354	0.000
130	A	134	ILE	0	-0.013	-0.025	2.507	-1.495	-0.445	0.823	-0.310	-1.564	-0.002
131	A	135	SER	0	-0.012	0.008	3.874	0.197	0.271	0.002	-0.010	-0.067	0.000
132	A	136	LYS	1	0.902	0.956	6.326	0.848	0.848	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.056	-0.007	2.373	-0.708	-0.403	2.264	-0.396	-2.172	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)