FMO DATABASE

FMODB ID: NNVGQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1020199.931602
FMO2-HF: Nuclear repulsion	970727.19319
FMO2-HF: Total energy	-49472.738413
FMO2-MP2: Total energy	-49612.275373

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.
-71.636	-60.898	28.806	-17.522	-22.023	-0.042

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 : 0.011 / q_NPA : 0.006

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	0.066	0.031	2.342	-4.040	-0.231	4.245	-3.173	-4.882	0.034
4	A	8	SER	0	0.044	0.011	1.921	-14.894	-16.147	9.870	-3.454	-5.163	0.035
5	A	9	ARG	1	0.793	0.860	2.214	1.202	2.915	1.773	-1.463	-2.023	0.007
6	A	10	MET	0	-0.022	0.010	5.673	-0.874	-0.874	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.032	-0.015	5.936	-0.959	-0.959	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.846	0.938	4.506	-3.500	-3.396	-0.001	-0.005	-0.097	0.000
9	A	13	GLY	0	0.010	0.007	10.155	-0.410	-0.410	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.951	-0.969	8.128	0.430	0.430	0.000	0.000	0.000	0.000
11	A	15	ALA	0	-0.065	-0.040	7.903	-0.465	-0.465	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.004	0.009	9.894	0.334	0.334	0.000	0.000	0.000	0.000
13	A	17	VAL	0	0.056	0.023	11.124	0.129	0.129	0.000	0.000	0.000	0.000
14	A	18	PRO	0	0.019	0.011	10.791	-0.249	-0.249	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.051	0.014	13.915	0.055	0.055	0.000	0.000	0.000	0.000
16	A	20	VAL	0	0.011	0.006	15.840	0.024	0.024	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.069	0.035	14.050	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.018	0.015	16.082	0.025	0.025	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.076	-0.038	18.433	-0.042	-0.042	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.020	-0.008	17.949	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.037	0.023	20.001	0.002	0.002	0.000	0.000	0.000	0.000
22	A	26	GLY	0	-0.020	-0.014	15.872	0.019	0.019	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.040	-0.019	14.460	0.102	0.102	0.000	0.000	0.000	0.000
24	A	28	ILE	0	0.021	0.011	9.271	-0.125	-0.125	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.806	0.891	12.470	-1.021	-1.021	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.005	0.001	12.911	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	31	VAL	0	0.009	-0.008	6.967	0.128	0.128	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.814	-0.889	10.378	0.867	0.867	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.027	0.006	5.497	-0.362	-0.362	0.000	0.000	0.000	0.000
30	A	34	GLU	-1	-0.948	-0.957	9.557	-0.089	-0.089	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.021	-0.016	12.883	-0.168	-0.168	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.056	-0.021	10.998	-0.146	-0.146	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.019	-0.022	11.852	-0.095	-0.095	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.011	-0.005	8.393	0.333	0.333	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.778	-0.837	12.118	0.456	0.456	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.016	0.005	13.333	0.331	0.331	0.000	0.000	0.000	0.000
37	A	41	ASP	-1	-0.779	-0.850	15.082	0.613	0.613	0.000	0.000	0.000	0.000
38	A	42	TYR	0	-0.015	-0.052	14.369	0.060	0.060	0.000	0.000	0.000	0.000
39	A	43	VAL	0	-0.015	-0.013	20.055	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	44	ALA	0	-0.010	0.007	23.405	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	45	THR	0	0.025	0.002	25.986	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.836	-0.943	28.470	0.192	0.192	0.000	0.000	0.000	0.000
43	A	47	ALA	0	-0.053	-0.022	29.342	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.054	-0.022	24.028	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.030	0.004	29.550	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	50	ASN	0	-0.003	-0.003	32.742	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.030	-0.012	35.080	0.005	0.005	0.000	0.000	0.000	0.000
48	A	52	VAL	0	-0.048	-0.012	37.649	0.000	0.000	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.028	0.021	36.330	0.004	0.004	0.000	0.000	0.000	0.000
50	A	54	GLN	0	-0.013	-0.002	33.354	0.009	0.009	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.009	-0.002	26.982	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	56	GLN	0	-0.015	-0.004	28.470	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	57	GLY	0	0.058	0.013	27.814	0.015	0.015	0.000	0.000	0.000	0.000
54	A	58	GLY	0	0.024	0.006	25.796	0.007	0.007	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.002	0.003	24.031	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.000	-0.004	22.946	0.036	0.036	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.015	-0.010	21.661	0.026	0.026	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.015	0.014	19.685	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	63	MET	0	-0.019	0.002	18.010	0.035	0.035	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.049	-0.019	17.052	0.067	0.067	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.882	-0.943	16.151	-0.067	-0.067	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.845	-0.886	13.606	0.862	0.862	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.013	0.009	12.044	0.108	0.108	0.000	0.000	0.000	0.000
64	A	68	THR	0	-0.048	-0.048	11.581	0.059	0.059	0.000	0.000	0.000	0.000
65	A	69	ALA	0	0.073	0.036	10.514	-0.148	-0.148	0.000	0.000	0.000	0.000
66	A	70	MET	0	-0.021	0.008	7.916	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.049	-0.013	6.576	0.346	0.346	0.000	0.000	0.000	0.000
68	A	72	VAL	0	0.005	-0.015	6.645	-0.367	-0.367	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.014	-0.018	3.871	-1.438	-1.278	-0.001	-0.043	-0.116	0.000
70	A	74	ALA	0	-0.023	-0.011	2.392	-12.171	-8.950	1.082	-2.028	-2.275	-0.020
71	A	75	THR	0	-0.123	-0.074	2.949	-0.858	0.240	0.304	-0.582	-0.821	-0.005
72	A	76	LEU	0	-0.064	0.001	3.003	0.482	1.263	0.041	-0.281	-0.541	-0.001
73	A	77	GLU	-1	-0.863	-0.938	1.989	-19.648	-19.349	5.044	-2.692	-2.651	-0.039
74	A	78	ASP	-1	-0.760	-0.869	2.013	-19.285	-18.557	6.450	-3.777	-3.401	-0.053
75	A	79	GLY	0	-0.042	-0.018	4.440	1.097	1.175	-0.001	-0.024	-0.053	0.000
76	A	80	ALA	0	-0.036	0.005	6.325	0.915	0.915	0.000	0.000	0.000	0.000
77	A	81	SER	0	0.016	-0.014	6.928	-0.449	-0.449	0.000	0.000	0.000	0.000
78	A	82	CYS	0	0.001	0.010	7.952	0.221	0.221	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.013	0.005	9.619	0.303	0.303	0.000	0.000	0.000	0.000
80	A	84	THR	0	0.018	-0.005	13.365	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.056	-0.016	15.449	0.041	0.041	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.039	-0.034	18.823	0.071	0.071	0.000	0.000	0.000	0.000
83	A	87	LEU	0	0.042	0.020	17.739	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	88	ASN	0	-0.051	-0.010	20.597	0.030	0.030	0.000	0.000	0.000	0.000
85	A	89	LEU	0	0.018	0.013	21.321	0.021	0.021	0.000	0.000	0.000	0.000
86	A	90	SER	0	0.006	0.015	24.605	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.007	-0.016	25.695	0.022	0.022	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.037	-0.014	27.709	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.864	0.910	30.255	-0.160	-0.160	0.000	0.000	0.000	0.000
90	A	94	PRO	0	-0.002	0.015	30.573	0.008	0.008	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.025	0.017	28.487	0.010	0.010	0.000	0.000	0.000	0.000
92	A	96	GLN	0	0.017	-0.010	30.460	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	97	ALA	0	0.043	0.026	29.533	0.020	0.020	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.011	0.009	28.187	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	99	LEU	0	-0.020	-0.013	22.457	0.009	0.009	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.036	-0.012	22.704	-0.047	-0.047	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.748	0.831	18.697	-0.686	-0.686	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.022	0.007	17.900	-0.084	-0.084	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.834	0.886	16.457	-0.428	-0.428	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.030	0.017	12.821	-0.113	-0.113	0.000	0.000	0.000	0.000
101	A	105	ARG	1	0.891	0.913	14.399	0.006	0.006	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.025	-0.021	9.377	-0.108	-0.108	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.831	-0.883	14.004	0.005	0.005	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.918	0.945	15.822	0.509	0.509	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.915	0.961	9.296	0.458	0.458	0.000	0.000	0.000	0.000
106	A	110	GLY	0	-0.039	-0.025	13.304	0.046	0.046	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.950	0.971	13.215	0.744	0.744	0.000	0.000	0.000	0.000
108	A	112	ASN	0	0.034	0.002	13.185	-0.070	-0.070	0.000	0.000	0.000	0.000
109	A	113	VAL	0	0.009	0.013	14.513	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	114	CYS	0	-0.028	0.014	10.021	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	115	ASN	0	-0.019	-0.004	13.683	0.028	0.028	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.018	0.010	12.552	0.009	0.009	0.000	0.000	0.000	0.000
113	A	117	VAL	0	0.003	0.008	15.229	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	118	GLY	0	0.033	0.008	16.551	0.065	0.065	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.979	-0.989	18.060	0.204	0.204	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.034	0.019	20.028	0.068	0.068	0.000	0.000	0.000	0.000
117	A	121	SER	0	-0.024	-0.020	22.274	-0.056	-0.056	0.000	0.000	0.000	0.000
118	A	122	GLN	0	0.055	0.023	24.395	0.015	0.015	0.000	0.000	0.000	0.000
119	A	123	ASP	-1	-0.889	-0.937	27.188	0.261	0.261	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.047	-0.020	27.960	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	125	LYS	1	0.897	0.951	29.018	-0.206	-0.206	0.000	0.000	0.000	0.000
122	A	126	LEU	0	0.041	0.023	24.151	0.013	0.013	0.000	0.000	0.000	0.000
123	A	127	VAL	0	0.015	0.005	25.685	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	128	ALA	0	0.008	0.004	24.552	-0.029	-0.029	0.000	0.000	0.000	0.000
125	A	129	THR	0	-0.008	-0.005	22.636	0.030	0.030	0.000	0.000	0.000	0.000
126	A	130	ALA	0	0.036	0.015	19.333	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	131	THR	0	0.003	0.016	19.463	0.010	0.010	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.025	0.022	15.513	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.040	-0.019	16.797	-0.033	-0.033	0.000	0.000	0.000	0.000
130	A	134	CYS	0	0.019	0.016	12.335	0.058	0.058	0.000	0.000	0.000	0.000
131	A	135	MET	0	0.001	-0.007	14.212	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	136	VAL	0	0.005	0.010	9.449	0.054	0.054	0.000	0.000	0.000	0.000

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