FMO DATABASE

FMODB ID: 4927N

Calculation Name: 2NPS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NPS

Chain ID: B

ChEMBL ID:

UniProt ID: G3V7P1

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	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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-284656.125763
FMO2-HF: Nuclear repulsion	256971.477553
FMO2-HF: Total energy	-27684.64821
FMO2-MP2: Total energy	-27763.751147

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(B:181:GLY)

Summations of interaction energy for fragment #1(B:181: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.
-0.293	2.065	0.014	-0.979	-1.392	0.002

Interaction energy analysis for fragmet #1(B:181:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.005

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	B	183	MET	0	0.015	0.021	3.448	-0.717	0.984	0.012	-0.814	-0.899	0.002
4	B	184	ARG	1	0.954	0.974	3.472	1.388	1.866	0.003	-0.146	-0.334	0.000
5	B	185	GLU	-1	-0.924	-0.962	5.091	-1.450	-1.271	-0.001	-0.019	-0.159	0.000
6	B	186	THR	0	0.004	-0.012	7.125	0.433	0.433	0.000	0.000	0.000	0.000
7	B	187	ALA	0	0.011	0.006	7.954	0.097	0.097	0.000	0.000	0.000	0.000
8	B	188	ILE	0	-0.036	-0.015	8.808	0.061	0.061	0.000	0.000	0.000	0.000
9	B	189	GLN	0	0.026	0.019	11.218	0.075	0.075	0.000	0.000	0.000	0.000
10	B	190	GLN	0	-0.023	-0.021	11.464	0.062	0.062	0.000	0.000	0.000	0.000
11	B	191	LEU	0	0.027	0.023	13.477	0.024	0.024	0.000	0.000	0.000	0.000
12	B	192	GLU	-1	-0.958	-0.980	15.280	-0.247	-0.247	0.000	0.000	0.000	0.000
13	B	193	ALA	0	-0.008	-0.006	17.052	0.028	0.028	0.000	0.000	0.000	0.000
14	B	194	ASP	-1	-0.884	-0.942	17.517	-0.053	-0.053	0.000	0.000	0.000	0.000
15	B	195	ILE	0	-0.064	-0.039	18.241	0.013	0.013	0.000	0.000	0.000	0.000
16	B	196	LEU	0	-0.038	-0.027	21.230	0.013	0.013	0.000	0.000	0.000	0.000
17	B	197	ASP	-1	-0.908	-0.944	22.681	-0.035	-0.035	0.000	0.000	0.000	0.000
18	B	198	VAL	0	0.002	-0.006	23.531	0.008	0.008	0.000	0.000	0.000	0.000
19	B	199	ASN	0	-0.039	-0.012	25.392	0.008	0.008	0.000	0.000	0.000	0.000
20	B	200	GLN	0	-0.037	-0.028	27.199	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	201	ILE	0	0.046	0.021	26.885	0.005	0.005	0.000	0.000	0.000	0.000
22	B	202	PHE	0	-0.045	-0.030	28.900	0.004	0.004	0.000	0.000	0.000	0.000
23	B	203	LYS	1	0.850	0.935	29.966	0.074	0.074	0.000	0.000	0.000	0.000
24	B	204	ASP	-1	-0.814	-0.895	32.585	-0.034	-0.034	0.000	0.000	0.000	0.000
25	B	205	LEU	0	-0.037	-0.018	34.195	0.004	0.004	0.000	0.000	0.000	0.000
26	B	206	ALA	0	-0.007	-0.010	35.794	0.002	0.002	0.000	0.000	0.000	0.000
27	B	207	MET	0	-0.018	0.001	37.362	0.001	0.001	0.000	0.000	0.000	0.000
28	B	208	MET	0	0.004	-0.004	36.312	0.003	0.003	0.000	0.000	0.000	0.000
29	B	209	ILE	0	-0.039	-0.014	38.778	0.002	0.002	0.000	0.000	0.000	0.000
30	B	210	HIS	0	-0.073	-0.046	41.754	0.000	0.000	0.000	0.000	0.000	0.000
31	B	211	ASP	-1	-0.839	-0.912	43.068	-0.024	-0.024	0.000	0.000	0.000	0.000
32	B	212	GLN	0	-0.108	-0.062	42.584	0.003	0.003	0.000	0.000	0.000	0.000
33	B	213	GLY	0	0.018	0.009	46.736	0.001	0.001	0.000	0.000	0.000	0.000
34	B	214	ASP	-1	-0.855	-0.923	48.580	-0.019	-0.019	0.000	0.000	0.000	0.000
35	B	215	LEU	0	-0.060	-0.024	48.495	0.002	0.002	0.000	0.000	0.000	0.000
36	B	216	ILE	0	-0.006	-0.005	48.144	0.001	0.001	0.000	0.000	0.000	0.000
37	B	217	ASP	-1	-0.911	-0.941	52.312	-0.017	-0.017	0.000	0.000	0.000	0.000
38	B	218	SER	0	-0.019	-0.022	54.653	0.001	0.001	0.000	0.000	0.000	0.000
39	B	219	ILE	0	-0.053	-0.025	53.170	0.001	0.001	0.000	0.000	0.000	0.000
40	B	220	GLU	-1	-0.941	-0.965	56.207	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	221	ALA	0	0.041	0.020	58.019	0.001	0.001	0.000	0.000	0.000	0.000
42	B	222	ASN	0	-0.089	-0.058	59.912	0.001	0.001	0.000	0.000	0.000	0.000
43	B	223	VAL	0	-0.007	0.006	59.511	0.001	0.001	0.000	0.000	0.000	0.000
44	B	224	GLU	-1	-0.873	-0.930	62.115	-0.012	-0.012	0.000	0.000	0.000	0.000
45	B	225	SER	0	-0.041	-0.021	64.027	0.001	0.001	0.000	0.000	0.000	0.000
46	B	226	SER	0	-0.037	-0.033	64.779	0.001	0.001	0.000	0.000	0.000	0.000
47	B	227	GLH	0	-0.055	-0.053	66.074	0.000	0.000	0.000	0.000	0.000	0.000
48	B	228	VAL	0	0.077	0.034	67.958	0.000	0.000	0.000	0.000	0.000	0.000
49	B	229	HIS	0	-0.077	-0.049	69.282	0.001	0.001	0.000	0.000	0.000	0.000
50	B	230	VAL	0	-0.001	0.001	70.139	0.000	0.000	0.000	0.000	0.000	0.000
51	B	231	GLU	-1	-0.868	-0.887	71.749	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	232	ARG	1	0.917	0.967	72.425	0.009	0.009	0.000	0.000	0.000	0.000
53	B	233	ALA	0	-0.009	-0.011	75.535	0.000	0.000	0.000	0.000	0.000	0.000
54	B	234	SER	0	-0.035	-0.034	76.300	0.000	0.000	0.000	0.000	0.000	0.000
55	B	235	ASP	-1	-0.743	-0.863	78.150	-0.007	-0.007	0.000	0.000	0.000	0.000
56	B	236	GLN	0	-0.043	-0.027	80.128	0.000	0.000	0.000	0.000	0.000	0.000
57	B	237	LEU	0	0.006	0.008	79.298	0.000	0.000	0.000	0.000	0.000	0.000
58	B	238	GLN	0	-0.037	-0.014	81.720	0.000	0.000	0.000	0.000	0.000	0.000
59	B	239	ARG	1	0.797	0.892	82.393	0.007	0.007	0.000	0.000	0.000	0.000
60	B	240	ALA	0	0.002	0.008	85.679	0.000	0.000	0.000	0.000	0.000	0.000
61	B	241	ALA	0	0.041	0.019	86.704	0.000	0.000	0.000	0.000	0.000	0.000
62	B	242	TYR	0	-0.026	-0.014	88.461	0.000	0.000	0.000	0.000	0.000	0.000
63	B	243	TYR	0	0.007	-0.021	88.751	0.000	0.000	0.000	0.000	0.000	0.000
64	B	244	GLN	0	-0.004	0.004	90.085	0.000	0.000	0.000	0.000	0.000	0.000
65	B	245	LYS	1	0.947	0.966	91.803	0.005	0.005	0.000	0.000	0.000	0.000
66	B	246	LYS	1	0.928	0.981	94.478	0.005	0.005	0.000	0.000	0.000	0.000
67	B	247	SER	0	-0.024	0.006	96.008	0.000	0.000	0.000	0.000	0.000	0.000
68	B	248	ARG	1	0.902	0.952	97.825	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:181:GLY)