FMO DATABASE

FMODB ID: JQ699

Calculation Name: 2PIM-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2PIM

Chain ID: A

ChEMBL ID:
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UniProt ID: Q46RV7

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	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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1021252.01407
FMO2-HF: Nuclear repulsion	971779.023043
FMO2-HF: Total energy	-49472.991027
FMO2-MP2: Total energy	-49612.57994

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:ASN)

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

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.
-80.593	-82.842	47.534	-22.31	-22.973	-0.081

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.002

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	PHE	0	0.069	0.035	2.457	-5.042	-1.957	4.106	-2.867	-4.324	0.030
4	A	8	SER	0	-0.028	-0.037	1.827	-18.104	-20.128	10.840	-4.026	-4.790	0.039
5	A	9	ARG	1	0.793	0.867	2.352	-2.740	-0.549	0.414	-1.282	-1.323	0.009
6	A	10	MET	0	-0.014	0.007	5.834	-1.266	-1.266	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.028	-0.021	6.202	-1.286	-1.286	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.853	0.931	4.992	-2.799	-2.799	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.003	0.009	10.590	-0.385	-0.385	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.958	-0.966	8.621	0.605	0.605	0.000	0.000	0.000	0.000
11	A	15	ALA	0	-0.040	-0.035	7.925	-0.308	-0.308	0.000	0.000	0.000	0.000
12	A	16	PRO	0	0.001	0.014	10.043	0.270	0.270	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.068	0.028	10.562	0.259	0.259	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.009	0.007	10.289	-0.283	-0.283	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.049	0.016	13.384	0.005	0.005	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.010	0.020	15.199	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.081	0.043	13.632	-0.028	-0.028	0.000	0.000	0.000	0.000
18	A	22	GLY	0	-0.002	0.000	15.698	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.060	-0.043	17.815	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.036	-0.012	17.540	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.039	0.017	19.983	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	26	GLY	0	-0.014	-0.016	15.904	0.000	0.000	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.055	-0.027	14.644	0.126	0.126	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.028	0.007	9.479	-0.127	-0.127	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.792	0.882	12.768	-0.862	-0.862	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.002	0.002	13.336	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	31	VAL	0	0.006	-0.014	7.530	0.074	0.074	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.832	-0.897	10.930	0.418	0.418	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.028	0.003	5.874	-0.221	-0.221	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.954	-0.948	9.614	-0.366	-0.366	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.004	-0.007	13.031	-0.153	-0.153	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.031	-0.005	11.063	-0.103	-0.103	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.032	-0.029	11.922	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.009	0.003	8.643	0.233	0.233	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.779	-0.842	12.172	0.312	0.312	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.015	0.009	13.655	0.277	0.277	0.000	0.000	0.000	0.000
37	A	41	ASP	-1	-0.776	-0.846	15.503	0.484	0.484	0.000	0.000	0.000	0.000
38	A	42	TYR	0	-0.033	-0.041	14.074	0.075	0.075	0.000	0.000	0.000	0.000
39	A	43	VAL	0	-0.011	-0.016	20.093	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	44	ALA	0	-0.011	0.010	23.422	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	45	THR	0	0.031	0.010	25.648	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.837	-0.937	28.146	0.184	0.184	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.045	-0.016	29.450	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.052	-0.021	23.659	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.024	0.005	29.057	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	50	ASN	0	0.011	0.006	32.237	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.006	-0.027	34.736	0.005	0.005	0.000	0.000	0.000	0.000
48	A	52	VAL	0	-0.045	-0.010	37.524	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.023	0.017	36.092	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	GLN	0	-0.013	-0.004	33.198	0.006	0.006	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.020	-0.013	26.524	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	56	GLN	0	0.011	0.010	28.473	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	57	GLY	0	0.048	0.013	27.328	0.012	0.012	0.000	0.000	0.000	0.000
54	A	58	GLY	0	0.024	0.010	25.108	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.017	-0.003	23.381	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.009	-0.002	22.287	0.031	0.031	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.015	-0.008	21.309	0.013	0.013	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.010	0.003	19.117	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.020	-0.004	17.442	0.028	0.028	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.040	-0.010	16.685	0.047	0.047	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.856	-0.919	15.392	-0.170	-0.170	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.837	-0.890	13.110	0.764	0.764	0.000	0.000	0.000	0.000
63	A	67	VAL	0	-0.004	0.002	11.700	0.074	0.074	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.023	-0.039	11.620	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.040	0.012	10.051	-0.234	-0.234	0.000	0.000	0.000	0.000
66	A	70	MET	0	-0.034	-0.001	7.526	-0.072	-0.072	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.028	0.001	6.193	0.086	0.086	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.013	-0.005	6.578	-0.509	-0.509	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.020	-0.020	3.654	-1.859	-1.444	0.001	-0.186	-0.230	-0.001
70	A	74	ALA	0	-0.022	-0.006	1.956	-14.788	-14.713	6.019	-3.091	-3.003	-0.039
71	A	75	THR	0	-0.109	-0.068	3.324	0.625	1.139	0.101	-0.088	-0.527	0.000
72	A	76	LEU	0	-0.037	0.010	2.960	0.998	1.982	0.087	-0.349	-0.721	-0.001
73	A	77	GLU	-1	-0.866	-0.932	1.775	-22.949	-25.760	11.401	-4.861	-3.729	-0.057
74	A	78	ASP	-1	-0.778	-0.869	1.805	-14.636	-19.427	14.560	-5.508	-4.261	-0.061
75	A	79	GLY	0	-0.021	-0.014	3.948	0.862	0.975	0.005	-0.052	-0.065	0.000
76	A	80	ALA	0	-0.017	0.023	6.498	0.640	0.640	0.000	0.000	0.000	0.000
77	A	81	SER	0	0.014	-0.003	7.099	-0.267	-0.267	0.000	0.000	0.000	0.000
78	A	82	CYS	0	0.010	0.029	7.638	0.113	0.113	0.000	0.000	0.000	0.000
79	A	83	SER	0	0.013	0.007	9.232	0.303	0.303	0.000	0.000	0.000	0.000
80	A	84	THR	0	-0.023	-0.031	13.044	-0.087	-0.087	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.025	-0.003	15.065	0.059	0.059	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.069	-0.043	18.196	0.077	0.077	0.000	0.000	0.000	0.000
83	A	87	LEU	0	0.063	0.031	17.367	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	88	ASN	0	-0.017	0.006	20.159	0.042	0.042	0.000	0.000	0.000	0.000
85	A	89	LEU	0	0.025	0.017	21.006	0.012	0.012	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.021	-0.010	24.195	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	91	PHE	0	0.004	-0.004	25.249	0.017	0.017	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.035	-0.010	27.176	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.871	0.918	30.108	-0.098	-0.098	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.001	0.020	30.463	0.006	0.006	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.041	0.024	28.066	0.007	0.007	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.008	-0.020	30.053	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	97	ALA	0	0.058	0.030	29.456	0.016	0.016	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.001	0.004	28.426	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.015	-0.007	22.766	0.014	0.014	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.020	-0.008	22.907	-0.047	-0.047	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.762	0.840	19.187	-0.514	-0.514	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.028	0.011	18.109	-0.072	-0.072	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.824	0.875	16.080	-0.280	-0.280	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.038	0.023	12.702	-0.081	-0.081	0.000	0.000	0.000	0.000
101	A	105	ARG	1	0.820	0.870	14.337	0.111	0.111	0.000	0.000	0.000	0.000
102	A	106	LEU	0	0.005	-0.009	9.224	-0.072	-0.072	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.791	-0.853	13.890	-0.158	-0.158	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.906	0.949	15.850	0.619	0.619	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.909	0.947	9.791	0.815	0.815	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.003	-0.016	13.026	0.166	0.166	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.918	0.963	12.849	0.718	0.718	0.000	0.000	0.000	0.000
108	A	112	ASN	0	0.050	0.017	12.860	-0.053	-0.053	0.000	0.000	0.000	0.000
109	A	113	VAL	0	-0.004	0.001	14.263	0.021	0.021	0.000	0.000	0.000	0.000
110	A	114	CYS	0	-0.034	0.016	9.946	0.020	0.020	0.000	0.000	0.000	0.000
111	A	115	ASN	0	-0.037	-0.028	13.537	0.049	0.049	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.016	0.007	12.447	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	117	VAL	0	-0.003	0.012	15.310	0.025	0.025	0.000	0.000	0.000	0.000
114	A	118	GLY	0	0.037	0.013	16.401	0.028	0.028	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.931	-0.969	18.015	0.081	0.081	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.009	0.010	19.989	0.057	0.057	0.000	0.000	0.000	0.000
117	A	121	SER	0	-0.002	-0.010	21.960	-0.048	-0.048	0.000	0.000	0.000	0.000
118	A	122	GLN	0	0.032	0.015	24.554	0.014	0.014	0.000	0.000	0.000	0.000
119	A	123	ASP	-1	-0.866	-0.926	27.396	0.198	0.198	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.001	0.003	28.650	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.833	0.905	29.154	-0.174	-0.174	0.000	0.000	0.000	0.000
122	A	126	LEU	0	0.042	0.031	23.684	0.014	0.014	0.000	0.000	0.000	0.000
123	A	127	VAL	0	-0.025	-0.004	25.623	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	128	ALA	0	0.012	0.004	24.084	-0.020	-0.020	0.000	0.000	0.000	0.000
125	A	129	THR	0	0.010	0.004	22.265	0.022	0.022	0.000	0.000	0.000	0.000
126	A	130	ALA	0	0.026	0.011	19.066	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	131	THR	0	0.003	0.006	19.498	0.000	0.000	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.023	0.020	15.428	0.005	0.005	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.045	-0.028	16.402	-0.042	-0.042	0.000	0.000	0.000	0.000
130	A	134	CYS	0	0.009	0.013	11.882	0.079	0.079	0.000	0.000	0.000	0.000
131	A	135	MET	0	-0.011	0.003	13.349	-0.076	-0.076	0.000	0.000	0.000	0.000
132	A	136	VAL	0	-0.052	-0.041	9.155	0.091	0.091	0.000	0.000	0.000	0.000

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