FMO DATABASE

FMODB ID: 898VY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1019388.498156
FMO2-HF: Nuclear repulsion	969916.229914
FMO2-HF: Total energy	-49472.268242
FMO2-MP2: Total energy	-49611.853583

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.
-49.382	-36.322	21.486	-15.184	-19.359	-0.04

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 : 0.042 / q_NPA : 0.023

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	0.061	0.031	2.344	-6.803	-1.164	2.800	-3.836	-4.602	0.043
4	A	8	SER	0	0.029	0.009	1.893	-6.230	-5.842	6.354	-2.955	-3.788	-0.004
5	A	9	ARG	1	0.863	0.934	2.643	5.193	6.474	0.543	-0.473	-1.351	0.001
6	A	10	MET	0	-0.020	0.009	5.508	0.057	0.057	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.021	-0.010	6.487	-0.285	-0.285	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.875	0.951	4.567	-1.380	-1.282	-0.001	-0.002	-0.095	0.000
9	A	13	GLY	0	0.017	0.011	9.740	-0.277	-0.277	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.935	-0.962	8.130	-0.178	-0.178	0.000	0.000	0.000	0.000
11	A	15	ALA	0	-0.077	-0.048	7.884	-0.540	-0.540	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.008	0.007	9.837	0.370	0.370	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.065	0.025	11.301	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.008	0.008	11.505	-0.196	-0.196	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.056	0.014	14.595	0.098	0.098	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.012	0.006	16.600	0.045	0.045	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.074	0.034	14.647	0.025	0.025	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.015	0.014	16.704	0.045	0.045	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.075	-0.034	19.165	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.022	-0.010	18.458	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.034	0.022	20.586	0.028	0.028	0.000	0.000	0.000	0.000
22	A	26	GLY	0	-0.019	-0.014	16.389	0.040	0.040	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.034	-0.014	15.028	0.034	0.034	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.029	0.016	9.581	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.791	0.875	12.826	-1.127	-1.127	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.011	0.005	12.899	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	31	VAL	0	0.013	-0.007	6.761	0.189	0.189	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.841	-0.910	10.112	1.684	1.684	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.031	0.008	4.876	-0.671	-0.550	-0.001	0.000	-0.120	0.000
30	A	34	GLU	-1	-0.954	-0.960	8.993	0.550	0.550	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.016	-0.003	12.386	-0.262	-0.262	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.061	-0.024	11.070	-0.211	-0.211	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.021	-0.022	11.607	-0.262	-0.262	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.002	0.000	8.234	0.544	0.544	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.850	-0.916	11.856	0.696	0.696	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.017	0.006	13.464	0.308	0.308	0.000	0.000	0.000	0.000
37	A	41	ASP	-1	-0.793	-0.864	15.273	0.752	0.752	0.000	0.000	0.000	0.000
38	A	42	TYR	0	-0.036	-0.096	14.685	0.056	0.056	0.000	0.000	0.000	0.000
39	A	43	VAL	0	-0.006	-0.012	20.431	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	44	ALA	0	-0.011	0.008	23.856	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	45	THR	0	0.025	0.000	26.519	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.821	-0.935	28.986	0.185	0.185	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.061	-0.027	29.851	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.054	-0.021	24.553	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.030	0.005	30.016	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	ASN	0	0.002	0.006	33.194	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.028	-0.015	35.681	0.004	0.004	0.000	0.000	0.000	0.000
48	A	52	VAL	0	-0.059	-0.015	37.946	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.030	0.019	36.692	0.006	0.006	0.000	0.000	0.000	0.000
50	A	54	GLN	0	-0.013	-0.005	33.739	0.014	0.014	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.009	0.002	27.325	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.009	-0.005	29.291	0.004	0.004	0.000	0.000	0.000	0.000
53	A	57	GLY	0	0.050	0.008	28.489	0.019	0.019	0.000	0.000	0.000	0.000
54	A	58	GLY	0	0.013	0.003	26.630	0.017	0.017	0.000	0.000	0.000	0.000
55	A	59	MET	0	0.012	0.009	24.496	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.002	-0.004	23.580	0.040	0.040	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.011	-0.007	22.340	0.047	0.047	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.024	0.017	20.544	0.010	0.010	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.029	-0.003	18.767	0.042	0.042	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.050	-0.021	17.635	0.107	0.107	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.892	-0.954	16.796	0.166	0.166	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.834	-0.848	13.966	1.019	1.019	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.017	0.013	12.760	0.193	0.193	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.062	-0.052	12.156	0.237	0.237	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.080	0.039	11.177	0.054	0.054	0.000	0.000	0.000	0.000
66	A	70	MET	0	-0.017	0.006	8.716	0.169	0.169	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.050	-0.016	7.261	1.045	1.045	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.009	-0.014	7.217	0.372	0.372	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.019	-0.021	4.666	-1.282	-1.253	-0.001	-0.005	-0.023	0.000
70	A	74	ALA	0	-0.029	-0.012	2.975	-6.821	-4.561	0.273	-1.162	-1.370	0.001
71	A	75	THR	0	-0.119	-0.064	3.018	2.695	3.984	0.875	-0.827	-1.337	-0.004
72	A	76	LEU	0	-0.075	-0.007	2.953	-1.497	-0.488	0.047	-0.341	-0.715	-0.003
73	A	77	GLU	-1	-0.882	-0.955	2.170	-19.145	-21.492	8.445	-2.889	-3.209	-0.038
74	A	78	ASP	-1	-0.825	-0.938	2.377	-20.197	-16.980	2.153	-2.674	-2.695	-0.036
75	A	79	GLY	0	-0.063	-0.031	4.470	1.667	1.743	-0.001	-0.020	-0.054	0.000
76	A	80	ALA	0	-0.033	0.005	6.289	1.163	1.163	0.000	0.000	0.000	0.000
77	A	81	SER	0	-0.010	-0.025	6.887	-0.568	-0.568	0.000	0.000	0.000	0.000
78	A	82	CYS	0	0.025	0.019	8.453	0.334	0.334	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.036	-0.001	9.878	0.233	0.233	0.000	0.000	0.000	0.000
80	A	84	THR	0	0.047	0.005	13.655	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.043	-0.008	15.868	0.002	0.002	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.040	-0.031	19.166	0.052	0.052	0.000	0.000	0.000	0.000
83	A	87	LEU	0	0.038	0.015	18.534	0.007	0.007	0.000	0.000	0.000	0.000
84	A	88	ASN	0	-0.052	-0.010	21.162	0.008	0.008	0.000	0.000	0.000	0.000
85	A	89	LEU	0	0.019	0.009	22.195	0.039	0.039	0.000	0.000	0.000	0.000
86	A	90	SER	0	0.002	0.010	25.301	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.014	-0.012	26.826	0.030	0.030	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.039	-0.018	27.942	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.869	0.921	30.745	-0.278	-0.278	0.000	0.000	0.000	0.000
90	A	94	PRO	0	-0.008	0.013	30.999	0.011	0.011	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.026	0.016	28.755	0.014	0.014	0.000	0.000	0.000	0.000
92	A	96	GLN	0	0.030	-0.003	30.702	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	97	ALA	0	0.042	0.030	29.831	0.025	0.025	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.005	0.006	28.595	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.013	-0.013	22.690	0.010	0.010	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.036	-0.010	22.886	-0.039	-0.039	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.754	0.869	18.759	-0.900	-0.900	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.020	0.003	18.007	-0.084	-0.084	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.897	0.940	16.373	-0.645	-0.645	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.040	0.026	13.168	-0.149	-0.149	0.000	0.000	0.000	0.000
101	A	105	ARG	1	0.926	0.959	14.638	-0.351	-0.351	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.021	-0.017	9.701	-0.162	-0.162	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.891	-0.945	14.301	0.287	0.287	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.931	0.958	15.955	0.153	0.153	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.925	0.967	9.042	-0.800	-0.800	0.000	0.000	0.000	0.000
106	A	110	GLY	0	-0.042	-0.031	13.152	0.000	0.000	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.948	0.968	12.866	0.571	0.571	0.000	0.000	0.000	0.000
108	A	112	ASN	0	0.032	0.006	13.003	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	113	VAL	0	0.016	0.019	14.336	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	114	CYS	0	-0.017	0.019	11.173	0.008	0.008	0.000	0.000	0.000	0.000
111	A	115	ASN	0	-0.019	-0.011	13.746	-0.027	-0.027	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.012	0.014	12.958	0.070	0.070	0.000	0.000	0.000	0.000
113	A	117	VAL	0	0.009	0.009	15.657	-0.075	-0.075	0.000	0.000	0.000	0.000
114	A	118	GLY	0	0.032	0.005	17.171	0.135	0.135	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.985	-0.991	18.692	0.424	0.424	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.045	0.026	20.277	0.085	0.085	0.000	0.000	0.000	0.000
117	A	121	SER	0	-0.045	-0.025	22.529	-0.064	-0.064	0.000	0.000	0.000	0.000
118	A	122	GLN	0	0.053	0.017	24.482	0.013	0.013	0.000	0.000	0.000	0.000
119	A	123	ASP	-1	-0.891	-0.936	27.285	0.326	0.326	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.045	-0.020	27.985	-0.019	-0.019	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.907	0.953	28.976	-0.276	-0.276	0.000	0.000	0.000	0.000
122	A	126	LEU	0	0.049	0.026	24.572	0.011	0.011	0.000	0.000	0.000	0.000
123	A	127	VAL	0	0.008	-0.009	26.209	-0.032	-0.032	0.000	0.000	0.000	0.000
124	A	128	ALA	0	0.014	0.008	25.133	-0.041	-0.041	0.000	0.000	0.000	0.000
125	A	129	THR	0	-0.007	-0.001	23.282	0.042	0.042	0.000	0.000	0.000	0.000
126	A	130	ALA	0	0.043	0.014	20.094	-0.040	-0.040	0.000	0.000	0.000	0.000
127	A	131	THR	0	-0.012	0.014	20.006	0.043	0.043	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.036	0.022	16.014	-0.042	-0.042	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.035	-0.017	17.181	0.010	0.010	0.000	0.000	0.000	0.000
130	A	134	CYS	0	0.018	0.018	12.606	0.034	0.034	0.000	0.000	0.000	0.000
131	A	135	MET	0	-0.004	-0.009	14.286	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	136	VAL	0	0.004	0.005	9.267	0.014	0.014	0.000	0.000	0.000	0.000

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