FMO DATABASE

FMODB ID: 4JJ4N

Calculation Name: 2NPS-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NPS

Chain ID: C

ChEMBL ID:

UniProt ID: G3V7P1

Base Structure: X-ray

Registration Date: 2023-09-21

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	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-366599.81044
FMO2-HF: Nuclear repulsion	333788.716398
FMO2-HF: Total energy	-32811.094043
FMO2-MP2: Total energy	-32905.642448

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:112:GLY)

Summations of interaction energy for fragment #1(C:112:GLY)

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.
1.471	3.492	0.012	-0.896	-1.138	0.001

Interaction energy analysis for fragmet #1(C:112:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / 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

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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	114	MET	0	0.033	0.022	3.039	-1.188	0.572	0.013	-0.831	-0.942	0.001
4	C	115	ARG	1	0.979	0.982	4.253	1.738	1.999	-0.001	-0.065	-0.196	0.000
5	C	116	ALA	0	-0.010	-0.005	5.993	0.364	0.364	0.000	0.000	0.000	0.000
6	C	117	HIS	0	0.064	0.038	7.823	0.252	0.252	0.000	0.000	0.000	0.000
7	C	118	LEU	0	-0.023	-0.018	8.861	0.083	0.083	0.000	0.000	0.000	0.000
8	C	119	LEU	0	-0.026	0.003	9.827	0.054	0.054	0.000	0.000	0.000	0.000
9	C	120	ASP	-1	-0.766	-0.873	12.088	-0.029	-0.029	0.000	0.000	0.000	0.000
10	C	121	ASN	0	-0.020	-0.028	13.639	0.064	0.064	0.000	0.000	0.000	0.000
11	C	122	THR	0	0.011	0.007	15.058	0.011	0.011	0.000	0.000	0.000	0.000
12	C	123	GLU	-1	-0.786	-0.852	16.484	-0.068	-0.068	0.000	0.000	0.000	0.000
13	C	124	ARG	1	0.829	0.896	15.866	0.130	0.130	0.000	0.000	0.000	0.000
14	C	125	LEU	0	-0.018	-0.006	19.476	0.017	0.017	0.000	0.000	0.000	0.000
15	C	126	GLU	-1	-0.827	-0.878	20.050	-0.127	-0.127	0.000	0.000	0.000	0.000
16	C	127	ARG	1	0.791	0.855	20.027	0.085	0.085	0.000	0.000	0.000	0.000
17	C	128	SER	0	-0.014	-0.004	24.112	0.012	0.012	0.000	0.000	0.000	0.000
18	C	129	SER	0	0.009	0.001	25.621	0.006	0.006	0.000	0.000	0.000	0.000
19	C	130	ARG	1	0.851	0.893	24.193	0.107	0.107	0.000	0.000	0.000	0.000
20	C	131	ARG	1	0.919	0.964	27.395	0.039	0.039	0.000	0.000	0.000	0.000
21	C	132	LEU	0	-0.017	-0.001	29.456	0.005	0.005	0.000	0.000	0.000	0.000
22	C	133	GLU	-1	-0.927	-0.955	31.118	-0.062	-0.062	0.000	0.000	0.000	0.000
23	C	134	ALA	0	0.029	0.010	32.904	0.004	0.004	0.000	0.000	0.000	0.000
24	C	135	GLY	0	-0.016	-0.007	34.327	0.004	0.004	0.000	0.000	0.000	0.000
25	C	136	TYR	0	-0.012	-0.008	36.104	0.002	0.002	0.000	0.000	0.000	0.000
26	C	137	GLN	0	-0.051	-0.033	37.482	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	138	ILE	0	0.021	0.003	37.196	0.002	0.002	0.000	0.000	0.000	0.000
28	C	139	ALA	0	-0.031	0.007	40.384	0.002	0.002	0.000	0.000	0.000	0.000
29	C	140	VAL	0	0.075	0.034	42.223	0.002	0.002	0.000	0.000	0.000	0.000
30	C	141	GLU	-1	-0.920	-0.955	41.991	-0.025	-0.025	0.000	0.000	0.000	0.000
31	C	142	THR	0	-0.030	-0.029	44.095	0.003	0.003	0.000	0.000	0.000	0.000
32	C	143	GLU	-1	-0.950	-0.982	44.835	-0.025	-0.025	0.000	0.000	0.000	0.000
33	C	144	GLN	0	-0.057	-0.022	47.331	0.001	0.001	0.000	0.000	0.000	0.000
34	C	145	ILE	0	0.005	0.007	48.166	0.001	0.001	0.000	0.000	0.000	0.000
35	C	146	GLY	0	-0.009	-0.003	50.737	0.001	0.001	0.000	0.000	0.000	0.000
36	C	147	GLN	0	-0.004	-0.008	52.458	0.001	0.001	0.000	0.000	0.000	0.000
37	C	148	GLU	-1	-0.848	-0.910	54.277	-0.011	-0.011	0.000	0.000	0.000	0.000
38	C	149	MET	0	0.027	0.003	52.449	0.001	0.001	0.000	0.000	0.000	0.000
39	C	150	LEU	0	-0.024	-0.008	55.795	0.001	0.001	0.000	0.000	0.000	0.000
40	C	151	GLU	-1	-0.952	-0.952	58.719	-0.013	-0.013	0.000	0.000	0.000	0.000
41	C	152	ASN	0	-0.081	-0.050	59.525	0.001	0.001	0.000	0.000	0.000	0.000
42	C	153	LEU	0	0.017	-0.002	59.367	0.001	0.001	0.000	0.000	0.000	0.000
43	C	154	SER	0	-0.078	-0.049	62.528	0.001	0.001	0.000	0.000	0.000	0.000
44	C	155	HIS	0	0.015	0.013	64.574	0.001	0.001	0.000	0.000	0.000	0.000
45	C	156	ASP	-1	-0.786	-0.888	65.280	-0.007	-0.007	0.000	0.000	0.000	0.000
46	C	157	ARG	1	0.919	0.965	66.739	0.009	0.009	0.000	0.000	0.000	0.000
47	C	158	GLU	-1	-0.878	-0.925	68.549	-0.008	-0.008	0.000	0.000	0.000	0.000
48	C	159	ARG	1	0.857	0.904	67.508	0.007	0.007	0.000	0.000	0.000	0.000
49	C	160	ILE	0	0.009	0.008	68.875	0.000	0.000	0.000	0.000	0.000	0.000
50	C	161	GLN	0	-0.022	-0.011	72.674	0.001	0.001	0.000	0.000	0.000	0.000
51	C	162	ARG	1	0.927	0.947	72.676	0.008	0.008	0.000	0.000	0.000	0.000
52	C	163	ALA	0	-0.007	0.011	75.681	0.000	0.000	0.000	0.000	0.000	0.000
53	C	164	ARG	1	0.933	0.948	75.014	0.006	0.006	0.000	0.000	0.000	0.000
54	C	165	GLU	-1	-0.992	-0.975	78.702	-0.006	-0.006	0.000	0.000	0.000	0.000
55	C	166	ARG	1	0.910	0.937	80.459	0.005	0.005	0.000	0.000	0.000	0.000
56	C	167	LEU	0	-0.012	-0.001	80.247	0.000	0.000	0.000	0.000	0.000	0.000
57	C	168	ARG	1	0.952	0.968	79.715	0.006	0.006	0.000	0.000	0.000	0.000
58	C	169	GLU	-1	-0.833	-0.896	84.781	-0.005	-0.005	0.000	0.000	0.000	0.000
59	C	170	THR	0	-0.050	-0.019	85.439	0.000	0.000	0.000	0.000	0.000	0.000
60	C	171	ASP	-1	-0.848	-0.931	85.864	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	172	ALA	0	-0.014	-0.002	88.973	0.000	0.000	0.000	0.000	0.000	0.000
62	C	173	ASN	0	-0.033	-0.037	90.440	0.000	0.000	0.000	0.000	0.000	0.000
63	C	174	LEU	0	0.041	0.044	89.302	0.000	0.000	0.000	0.000	0.000	0.000
64	C	175	GLY	0	0.030	0.017	93.134	0.000	0.000	0.000	0.000	0.000	0.000
65	C	176	LYS	1	0.884	0.935	94.972	0.004	0.004	0.000	0.000	0.000	0.000
66	C	177	SER	0	-0.006	-0.022	95.468	0.000	0.000	0.000	0.000	0.000	0.000
67	C	178	SER	0	0.049	0.027	96.980	0.000	0.000	0.000	0.000	0.000	0.000
68	C	179	ARG	1	0.911	0.974	98.839	0.003	0.003	0.000	0.000	0.000	0.000
69	C	180	ILE	0	0.002	-0.002	99.760	0.000	0.000	0.000	0.000	0.000	0.000
70	C	181	LEU	0	0.051	0.016	99.247	0.000	0.000	0.000	0.000	0.000	0.000
71	C	182	THR	0	-0.029	-0.019	102.358	0.000	0.000	0.000	0.000	0.000	0.000
72	C	183	GLY	0	-0.035	-0.020	104.797	0.000	0.000	0.000	0.000	0.000	0.000
73	C	184	MET	0	-0.033	-0.009	105.042	0.000	0.000	0.000	0.000	0.000	0.000
74	C	185	LEU	0	0.042	0.008	104.081	0.000	0.000	0.000	0.000	0.000	0.000
75	C	186	ARG	1	0.943	0.968	108.284	0.002	0.002	0.000	0.000	0.000	0.000
76	C	187	ARG	1	0.927	0.957	108.930	0.002	0.002	0.000	0.000	0.000	0.000
77	C	188	ILE	0	0.021	0.029	108.959	0.000	0.000	0.000	0.000	0.000	0.000
78	C	189	ILE	0	-0.048	-0.008	111.809	0.000	0.000	0.000	0.000	0.000	0.000
79	C	190	GLN	0	-0.056	-0.022	115.276	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:112:GLY)