FMO DATABASE

FMODB ID: LNM49

Calculation Name: 2PP6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PP6

Chain ID: A

ChEMBL ID:

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-580125.401174
FMO2-HF: Nuclear repulsion	544856.437877
FMO2-HF: Total energy	-35268.963297
FMO2-MP2: Total energy	-35369.430254

3D Structure Molmil

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.
-1.219	1.003	0.015	-0.852	-1.386	0.001

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 : 0.040 / q_NPA : 0.008

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	0	ALA	0	0.084	0.046	3.731	-2.527	-1.004	0.006	-0.689	-0.841	0.001
4	A	1	MET	0	-0.008	0.005	3.453	-0.198	0.384	0.010	-0.151	-0.441	0.000
5	A	2	ALA	0	0.003	0.003	4.925	0.329	0.446	-0.001	-0.012	-0.104	0.000
6	A	3	ASP	-1	-0.814	-0.903	6.999	1.060	1.060	0.000	0.000	0.000	0.000
7	A	4	LEU	0	-0.023	-0.003	8.187	0.013	0.013	0.000	0.000	0.000	0.000
8	A	5	PHE	0	0.021	-0.017	8.042	0.021	0.021	0.000	0.000	0.000	0.000
9	A	6	ASP	-1	-0.830	-0.894	10.704	0.164	0.164	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.027	0.014	12.474	0.016	0.016	0.000	0.000	0.000	0.000
11	A	8	MET	0	-0.076	-0.025	13.021	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.963	0.982	12.809	0.160	0.160	0.000	0.000	0.000	0.000
13	A	10	ARG	1	0.910	0.928	14.764	-0.130	-0.130	0.000	0.000	0.000	0.000
14	A	11	ARG	1	0.904	0.953	15.011	-0.065	-0.065	0.000	0.000	0.000	0.000
15	A	12	MET	0	-0.028	-0.014	18.118	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	13	ASP	-1	-0.800	-0.905	20.903	0.011	0.011	0.000	0.000	0.000	0.000
17	A	14	ALA	0	-0.004	0.001	22.723	0.001	0.001	0.000	0.000	0.000	0.000
18	A	15	LEU	0	0.009	0.005	24.002	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	16	ILE	0	-0.029	-0.015	23.896	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	17	ALA	0	-0.025	-0.019	27.032	0.000	0.000	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.919	-0.961	28.532	0.028	0.028	0.000	0.000	0.000	0.000
22	A	19	ARG	1	0.891	0.952	28.746	0.001	0.001	0.000	0.000	0.000	0.000
23	A	20	PHE	0	-0.043	-0.022	29.592	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	GLY	0	0.004	0.010	32.471	0.000	0.000	0.000	0.000	0.000	0.000
25	A	22	MET	0	-0.055	-0.026	33.317	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.847	0.923	36.182	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	24	VAL	0	-0.003	-0.004	37.174	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	25	ASN	0	-0.057	-0.033	38.531	0.002	0.002	0.000	0.000	0.000	0.000
29	A	26	ILE	0	0.020	-0.003	35.391	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	27	ASN	0	-0.057	-0.046	39.441	0.002	0.002	0.000	0.000	0.000	0.000
31	A	28	GLY	0	0.047	0.040	41.759	0.001	0.001	0.000	0.000	0.000	0.000
32	A	29	THR	0	-0.039	-0.008	36.284	0.001	0.001	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.778	-0.879	38.342	0.026	0.026	0.000	0.000	0.000	0.000
34	A	31	CYS	0	-0.090	-0.035	33.540	0.003	0.003	0.000	0.000	0.000	0.000
35	A	32	ILE	0	0.066	0.034	31.675	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	33	VAL	0	-0.015	-0.010	32.129	0.002	0.002	0.000	0.000	0.000	0.000
37	A	34	VAL	0	0.037	0.023	29.782	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.770	-0.856	32.739	0.005	0.005	0.000	0.000	0.000	0.000
39	A	36	SER	0	0.007	-0.038	32.168	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.804	-0.884	32.875	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	38	PHE	0	-0.038	-0.013	32.037	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	39	LEU	0	-0.048	-0.016	27.408	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	40	ALA	0	-0.066	-0.024	28.715	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	49	GLY	0	0.019	0.002	42.518	0.000	0.000	0.000	0.000	0.000	0.000
45	A	50	LYS	1	0.767	0.874	38.707	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	51	ASN	0	-0.025	-0.010	34.215	0.000	0.000	0.000	0.000	0.000	0.000
47	A	52	VAL	0	0.044	0.021	34.228	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	53	VAL	0	-0.015	-0.010	28.548	0.001	0.001	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.013	-0.002	30.476	0.000	0.000	0.000	0.000	0.000	0.000
50	A	55	PHE	0	0.011	-0.010	24.797	0.001	0.001	0.000	0.000	0.000	0.000
51	A	56	SER	0	-0.021	0.011	27.348	0.003	0.003	0.000	0.000	0.000	0.000
52	A	57	GLY	0	0.027	0.006	27.161	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	58	ASN	0	-0.045	-0.029	28.082	0.004	0.004	0.000	0.000	0.000	0.000
54	A	59	VAL	0	0.025	0.011	30.990	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	60	ILE	0	-0.019	-0.013	30.119	0.002	0.002	0.000	0.000	0.000	0.000
56	A	61	PRO	0	0.003	0.013	31.691	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	62	ARG	1	0.909	0.939	34.162	-0.038	-0.038	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.924	0.954	36.902	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	64	GLY	0	0.022	0.013	39.295	0.001	0.001	0.000	0.000	0.000	0.000
60	A	65	ASP	-1	-0.812	-0.885	38.148	0.028	0.028	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.897	0.940	41.482	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	67	VAL	0	-0.036	-0.033	39.373	0.002	0.002	0.000	0.000	0.000	0.000
63	A	68	VAL	0	0.023	0.022	42.263	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	69	LEU	0	0.004	-0.010	39.454	0.001	0.001	0.000	0.000	0.000	0.000
65	A	70	ARG	1	0.860	0.880	39.812	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	71	GLY	0	0.005	0.016	44.662	0.000	0.000	0.000	0.000	0.000	0.000
67	A	72	SER	0	-0.006	0.000	46.683	0.000	0.000	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.844	-0.895	46.155	0.017	0.017	0.000	0.000	0.000	0.000
69	A	74	PHE	0	-0.011	0.002	43.181	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	75	THR	0	0.016	-0.020	43.611	0.002	0.002	0.000	0.000	0.000	0.000
71	A	76	VAL	0	-0.044	-0.016	37.251	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	77	THR	0	-0.004	-0.019	40.407	0.001	0.001	0.000	0.000	0.000	0.000
73	A	78	ARG	1	0.801	0.891	36.686	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.005	0.001	31.599	0.000	0.000	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.906	0.961	30.950	0.000	0.000	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.895	0.928	25.202	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	82	PHE	0	0.052	0.031	25.723	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	83	ASN	0	0.038	0.015	21.002	0.003	0.003	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.039	0.022	22.018	0.007	0.007	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.807	0.923	21.998	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.001	-0.010	26.071	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	87	GLN	0	0.067	0.040	29.594	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	88	LEU	0	0.014	0.014	31.554	0.000	0.000	0.000	0.000	0.000	0.000
84	A	89	THR	0	-0.051	-0.034	35.184	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	90	LEU	0	0.003	0.015	38.328	0.002	0.002	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.740	-0.855	41.386	0.004	0.004	0.000	0.000	0.000	0.000
87	A	92	GLU	-1	-0.822	-0.897	45.080	0.009	0.009	0.000	0.000	0.000	0.000
88	A	93	ASN	0	-0.083	-0.034	46.895	-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)