FMO DATABASE

FMODB ID: ZVZYN

Calculation Name: 2FNJ-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FNJ

Chain ID: C

ChEMBL ID:

UniProt ID: P62869

Base Structure: X-ray

Registration Date: 2023-09-23

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-603021.959282
FMO2-HF: Nuclear repulsion	567279.242578
FMO2-HF: Total energy	-35742.716704
FMO2-MP2: Total energy	-35843.992892

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(C:17:MET)

Summations of interaction energy for fragment #1(C:17:MET)

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.
-6.465	-0.539	0.247	-2.675	-3.501	-0.003

Interaction energy analysis for fragmet #1(C:17:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.007

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	C	19	VAL	0	0.008	0.015	3.881	0.431	2.418	-0.019	-1.074	-0.895	0.001
4	C	20	LYS	1	0.764	0.880	6.972	-0.434	-0.434	0.000	0.000	0.000	0.000
5	C	21	LEU	0	-0.016	-0.012	10.779	0.001	0.001	0.000	0.000	0.000	0.000
6	C	22	ILE	0	-0.007	-0.001	13.464	0.000	0.000	0.000	0.000	0.000	0.000
7	C	23	SER	0	-0.013	-0.047	16.912	-0.007	-0.007	0.000	0.000	0.000	0.000
8	C	24	SER	0	-0.016	-0.001	19.975	0.007	0.007	0.000	0.000	0.000	0.000
9	C	25	ASP	-1	-0.761	-0.828	22.874	0.071	0.071	0.000	0.000	0.000	0.000
10	C	26	GLY	0	-0.002	0.000	21.163	0.001	0.001	0.000	0.000	0.000	0.000
11	C	27	HIS	0	-0.062	-0.029	18.261	0.012	0.012	0.000	0.000	0.000	0.000
12	C	28	GLU	-1	-0.828	-0.914	14.365	0.186	0.186	0.000	0.000	0.000	0.000
13	C	29	PHE	0	0.015	-0.004	13.047	0.009	0.009	0.000	0.000	0.000	0.000
14	C	30	ILE	0	-0.003	0.006	7.093	-0.028	-0.028	0.000	0.000	0.000	0.000
15	C	31	VAL	0	-0.005	-0.004	7.619	0.034	0.034	0.000	0.000	0.000	0.000
16	C	32	LYS	1	0.971	0.981	3.370	-4.505	-3.543	0.087	-0.288	-0.762	0.002
17	C	33	ARG	1	0.922	0.963	2.930	0.696	2.097	0.090	-0.585	-0.906	0.000
18	C	34	GLU	-1	-0.838	-0.940	3.181	-3.997	-2.421	0.089	-0.728	-0.938	-0.006
19	C	35	HIS	0	-0.054	-0.029	6.289	0.504	0.504	0.000	0.000	0.000	0.000
20	C	36	ALA	0	0.064	0.038	8.183	0.053	0.053	0.000	0.000	0.000	0.000
21	C	37	LEU	0	-0.071	-0.029	7.404	0.075	0.075	0.000	0.000	0.000	0.000
22	C	38	THR	0	-0.066	-0.043	10.474	0.044	0.044	0.000	0.000	0.000	0.000
23	C	39	SER	0	-0.063	-0.032	13.260	0.022	0.022	0.000	0.000	0.000	0.000
24	C	40	GLY	0	0.049	0.025	14.048	-0.030	-0.030	0.000	0.000	0.000	0.000
25	C	41	THR	0	-0.019	-0.032	15.884	-0.012	-0.012	0.000	0.000	0.000	0.000
26	C	42	ILE	0	0.020	0.001	10.736	0.006	0.006	0.000	0.000	0.000	0.000
27	C	43	LYS	1	0.940	0.970	11.157	0.234	0.234	0.000	0.000	0.000	0.000
28	C	44	ALA	0	-0.007	0.014	12.241	-0.016	-0.016	0.000	0.000	0.000	0.000
29	C	45	MET	0	-0.016	-0.016	13.683	0.009	0.009	0.000	0.000	0.000	0.000
30	C	46	LEU	0	-0.078	-0.032	7.240	0.029	0.029	0.000	0.000	0.000	0.000
31	C	47	SER	0	-0.072	-0.038	9.679	-0.051	-0.051	0.000	0.000	0.000	0.000
32	C	48	GLY	0	0.011	0.023	12.373	0.020	0.020	0.000	0.000	0.000	0.000
33	C	49	PRO	0	-0.058	-0.035	15.566	-0.023	-0.023	0.000	0.000	0.000	0.000
34	C	58	ASN	0	0.031	0.010	6.939	0.118	0.118	0.000	0.000	0.000	0.000
35	C	59	GLU	-1	-0.873	-0.949	8.818	0.303	0.303	0.000	0.000	0.000	0.000
36	C	60	VAL	0	-0.008	-0.005	11.292	-0.030	-0.030	0.000	0.000	0.000	0.000
37	C	61	ASN	0	-0.011	-0.006	13.935	-0.004	-0.004	0.000	0.000	0.000	0.000
38	C	62	PHE	0	0.018	0.000	14.643	-0.011	-0.011	0.000	0.000	0.000	0.000
39	C	63	ARG	1	0.948	0.967	20.021	-0.061	-0.061	0.000	0.000	0.000	0.000
40	C	64	GLU	-1	-0.872	-0.933	23.575	0.038	0.038	0.000	0.000	0.000	0.000
41	C	65	ILE	0	-0.040	-0.016	19.745	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	66	PRO	0	0.062	0.048	21.830	0.006	0.006	0.000	0.000	0.000	0.000
43	C	67	SER	0	-0.005	-0.042	20.189	-0.002	-0.002	0.000	0.000	0.000	0.000
44	C	68	HIS	0	-0.037	-0.021	20.295	0.007	0.007	0.000	0.000	0.000	0.000
45	C	69	VAL	0	0.031	0.020	22.097	0.001	0.001	0.000	0.000	0.000	0.000
46	C	70	LEU	0	-0.003	0.000	15.737	-0.001	-0.001	0.000	0.000	0.000	0.000
47	C	71	SER	0	-0.005	-0.009	16.498	-0.001	-0.001	0.000	0.000	0.000	0.000
48	C	72	LYS	1	0.891	0.939	16.934	-0.064	-0.064	0.000	0.000	0.000	0.000
49	C	73	VAL	0	0.048	0.023	16.017	0.003	0.003	0.000	0.000	0.000	0.000
50	C	74	CYS	0	-0.050	-0.017	12.815	-0.009	-0.009	0.000	0.000	0.000	0.000
51	C	75	MET	0	-0.047	-0.019	13.557	0.028	0.028	0.000	0.000	0.000	0.000
52	C	76	TYR	0	0.031	0.019	16.015	0.016	0.016	0.000	0.000	0.000	0.000
53	C	77	PHE	0	0.041	0.002	11.999	-0.003	-0.003	0.000	0.000	0.000	0.000
54	C	78	THR	0	-0.048	-0.025	11.416	0.043	0.043	0.000	0.000	0.000	0.000
55	C	79	TYR	0	-0.047	-0.033	12.869	0.029	0.029	0.000	0.000	0.000	0.000
56	C	80	LYS	1	0.945	0.974	15.455	-0.006	-0.006	0.000	0.000	0.000	0.000
57	C	81	VAL	0	0.009	0.020	9.786	-0.019	-0.019	0.000	0.000	0.000	0.000
58	C	82	ARG	1	0.874	0.934	13.226	-0.156	-0.156	0.000	0.000	0.000	0.000
59	C	83	TYR	0	0.017	-0.010	14.370	-0.014	-0.014	0.000	0.000	0.000	0.000
60	C	84	THR	0	-0.017	-0.009	16.113	-0.026	-0.026	0.000	0.000	0.000	0.000
61	C	85	ASN	0	-0.094	-0.041	13.025	-0.055	-0.055	0.000	0.000	0.000	0.000
62	C	86	SER	0	0.007	-0.009	15.624	0.024	0.024	0.000	0.000	0.000	0.000
63	C	87	SER	0	-0.007	-0.003	18.566	-0.017	-0.017	0.000	0.000	0.000	0.000
64	C	88	THR	0	-0.051	-0.008	20.841	0.002	0.002	0.000	0.000	0.000	0.000
65	C	89	GLU	-1	-0.907	-0.949	23.113	0.032	0.032	0.000	0.000	0.000	0.000
66	C	90	ILE	0	-0.025	-0.013	21.609	0.011	0.011	0.000	0.000	0.000	0.000
67	C	91	PRO	0	-0.009	0.015	21.763	-0.006	-0.006	0.000	0.000	0.000	0.000
68	C	92	GLU	-1	-0.872	-0.941	23.917	0.042	0.042	0.000	0.000	0.000	0.000
69	C	93	PHE	0	-0.027	-0.011	18.915	0.010	0.010	0.000	0.000	0.000	0.000
70	C	94	PRO	0	0.026	0.024	23.168	-0.005	-0.005	0.000	0.000	0.000	0.000
71	C	95	ILE	0	-0.031	-0.027	24.610	0.005	0.005	0.000	0.000	0.000	0.000
72	C	96	ALA	0	0.019	0.026	26.820	-0.003	-0.003	0.000	0.000	0.000	0.000
73	C	97	PRO	0	0.039	-0.003	29.492	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	98	GLU	-1	-0.905	-0.954	31.211	0.035	0.035	0.000	0.000	0.000	0.000
75	C	99	ILE	0	-0.009	0.007	24.380	0.000	0.000	0.000	0.000	0.000	0.000
76	C	100	ALA	0	-0.013	-0.002	27.726	-0.001	-0.001	0.000	0.000	0.000	0.000
77	C	101	LEU	0	0.019	0.013	28.628	-0.002	-0.002	0.000	0.000	0.000	0.000
78	C	102	GLU	-1	-0.790	-0.896	26.950	0.039	0.039	0.000	0.000	0.000	0.000
79	C	103	LEU	0	0.000	-0.013	21.668	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	104	LEU	0	-0.010	0.012	24.285	-0.003	-0.003	0.000	0.000	0.000	0.000
81	C	105	MET	0	-0.021	-0.017	25.877	-0.004	-0.004	0.000	0.000	0.000	0.000
82	C	106	ALA	0	0.009	0.005	21.480	-0.003	-0.003	0.000	0.000	0.000	0.000
83	C	107	ALA	0	0.008	-0.012	21.200	-0.005	-0.005	0.000	0.000	0.000	0.000
84	C	108	ASN	0	-0.017	-0.015	21.872	-0.009	-0.009	0.000	0.000	0.000	0.000
85	C	109	PHE	0	-0.028	-0.004	19.853	-0.005	-0.005	0.000	0.000	0.000	0.000
86	C	110	LEU	0	-0.021	-0.001	16.666	-0.004	-0.004	0.000	0.000	0.000	0.000
87	C	111	ASP	-1	-0.861	-0.889	17.848	-0.059	-0.059	0.000	0.000	0.000	0.000
88	C	112	CYS	0	-0.013	0.008	17.357	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:17:MET)