FMO DATABASE

FMODB ID: 3J3RL

Calculation Name: 2PP6-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: 2PP6

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8ZQ92

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-580014.46368
FMO2-HF: Nuclear repulsion	544745.876693
FMO2-HF: Total energy	-35268.586987
FMO2-MP2: Total energy	-35369.058628

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-2.404	0.392	0.041	-1.078	-1.758	0.003

Interaction energy analysis for fragmet #1(A:-2:SER)

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

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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	0	ALA	0	0.087	0.058	3.461	-2.832	-0.944	0.012	-0.830	-1.069	0.003
4	A	1	MET	0	0.017	0.008	3.073	-1.228	-0.504	0.030	-0.206	-0.548	0.000
5	A	2	ALA	0	0.003	0.001	4.288	0.363	0.547	-0.001	-0.042	-0.141	0.000
6	A	3	ASP	-1	-0.839	-0.913	6.312	1.461	1.461	0.000	0.000	0.000	0.000
7	A	4	LEU	0	-0.067	-0.031	7.585	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	5	PHE	0	0.003	-0.025	8.322	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	6	ASP	-1	-0.802	-0.874	10.313	0.233	0.233	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.038	0.017	12.212	0.004	0.004	0.000	0.000	0.000	0.000
11	A	8	MET	0	-0.086	-0.042	12.777	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.977	0.988	12.513	0.086	0.086	0.000	0.000	0.000	0.000
13	A	10	ARG	1	0.888	0.927	14.489	-0.210	-0.210	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.923	0.966	14.573	-0.150	-0.150	0.000	0.000	0.000	0.000
15	A	12	MET	0	-0.034	-0.021	17.780	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.805	-0.897	20.643	0.035	0.035	0.000	0.000	0.000	0.000
17	A	14	ALA	0	-0.007	-0.006	22.428	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	15	LEU	0	0.014	0.018	23.800	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	16	ILE	0	-0.015	-0.009	23.947	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	17	ALA	0	-0.028	-0.016	26.782	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.922	-0.951	28.259	0.047	0.047	0.000	0.000	0.000	0.000
22	A	19	ARG	1	0.900	0.956	28.974	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	20	PHE	0	-0.040	-0.033	29.417	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	GLY	0	-0.013	0.001	31.915	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	MET	0	-0.059	-0.031	32.978	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.847	0.922	35.902	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	24	VAL	0	0.003	-0.014	37.208	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	25	ASN	0	-0.022	-0.011	38.286	0.002	0.002	0.000	0.000	0.000	0.000
29	A	26	ILE	0	0.006	-0.006	35.099	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	27	ASN	0	-0.068	-0.043	38.916	0.002	0.002	0.000	0.000	0.000	0.000
31	A	28	GLY	0	0.052	0.032	40.913	0.001	0.001	0.000	0.000	0.000	0.000
32	A	29	THR	0	-0.050	-0.015	35.885	0.002	0.002	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.801	-0.874	38.252	0.035	0.035	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.105	-0.055	33.302	0.004	0.004	0.000	0.000	0.000	0.000
35	A	32	ILE	0	0.065	0.027	31.119	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	33	VAL	0	-0.018	-0.002	31.864	0.002	0.002	0.000	0.000	0.000	0.000
37	A	34	VAL	0	0.044	0.027	29.611	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.789	-0.872	32.576	0.014	0.014	0.000	0.000	0.000	0.000
39	A	36	SER	0	0.002	-0.042	32.271	0.000	0.000	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.856	-0.910	32.930	0.005	0.005	0.000	0.000	0.000	0.000
41	A	38	PHE	0	-0.015	-0.015	31.797	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.052	-0.019	27.251	0.000	0.000	0.000	0.000	0.000	0.000
43	A	40	ALA	0	-0.054	-0.012	28.614	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	49	GLY	0	0.049	0.031	43.028	0.000	0.000	0.000	0.000	0.000	0.000
45	A	50	LYS	1	0.799	0.899	38.806	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	51	ASN	0	-0.006	-0.006	34.267	0.000	0.000	0.000	0.000	0.000	0.000
47	A	52	VAL	0	0.057	0.036	33.987	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	VAL	0	-0.004	0.003	27.969	0.001	0.001	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.030	-0.023	30.296	0.001	0.001	0.000	0.000	0.000	0.000
50	A	55	PHE	0	0.012	-0.010	24.813	0.003	0.003	0.000	0.000	0.000	0.000
51	A	56	SER	0	-0.018	0.020	27.051	0.005	0.005	0.000	0.000	0.000	0.000
52	A	57	GLY	0	0.031	0.011	26.713	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	58	ASN	0	-0.026	-0.016	27.615	0.004	0.004	0.000	0.000	0.000	0.000
54	A	59	VAL	0	0.032	0.020	30.731	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	60	ILE	0	-0.015	-0.016	29.953	0.002	0.002	0.000	0.000	0.000	0.000
56	A	61	PRO	0	-0.006	0.005	31.443	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.910	0.940	34.087	-0.044	-0.044	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.930	0.962	36.760	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	64	GLY	0	0.006	0.006	39.150	0.001	0.001	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.807	-0.893	38.019	0.034	0.034	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.929	0.973	41.423	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	67	VAL	0	-0.038	-0.044	38.998	0.002	0.002	0.000	0.000	0.000	0.000
63	A	68	VAL	0	0.019	0.014	41.889	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	69	LEU	0	-0.014	-0.021	39.392	0.002	0.002	0.000	0.000	0.000	0.000
65	A	70	ARG	1	0.869	0.896	39.831	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	71	GLY	0	0.017	0.022	44.391	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	72	SER	0	0.026	0.028	46.275	0.000	0.000	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.870	-0.922	45.712	0.022	0.022	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.009	-0.004	42.739	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	75	THR	0	0.017	-0.002	43.312	0.002	0.002	0.000	0.000	0.000	0.000
71	A	76	VAL	0	-0.031	-0.009	36.849	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	77	THR	0	0.024	0.008	40.041	0.000	0.000	0.000	0.000	0.000	0.000
73	A	78	ARG	1	0.865	0.924	35.987	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.010	0.004	31.381	0.001	0.001	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.926	0.972	30.477	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.949	0.964	24.882	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	82	PHE	0	0.042	0.029	25.613	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	83	ASN	0	0.017	0.006	20.819	0.003	0.003	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.012	0.000	21.575	0.008	0.008	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.808	0.916	21.838	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	86	PRO	0	-0.002	-0.008	25.730	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	87	GLN	0	0.085	0.059	29.280	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	88	LEU	0	-0.018	-0.019	31.253	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	89	THR	0	-0.047	-0.027	34.886	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	90	LEU	0	-0.026	-0.016	37.956	0.001	0.001	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.886	-0.955	40.917	0.009	0.009	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.867	-0.931	44.618	0.014	0.014	0.000	0.000	0.000	0.000
88	A	93	ASN	0	-0.039	-0.006	47.083	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)