FMO DATABASE

FMODB ID: 8533Y

Calculation Name: 2NPS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NPS

Chain ID: D

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	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	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-254751.805076
FMO2-HF: Nuclear repulsion	229122.459148
FMO2-HF: Total energy	-25629.345927
FMO2-MP2: Total energy	-25701.32921

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(D:170:ASP)

Summations of interaction energy for fragment #1(D:170:ASP)

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.
3.752	6.149	0.012	-0.866	-1.543	0.002

Interaction energy analysis for fragmet #1(D:170:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.974 / q_NPA : -0.992

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	D	172	GLN	0	-0.060	0.000	3.562	-1.132	1.088	0.013	-0.853	-1.380	0.002
4	D	173	LEU	0	0.028	-0.011	4.755	-4.474	-4.297	-0.001	-0.013	-0.163	0.000
5	D	174	GLU	-1	-0.859	-0.914	7.058	20.258	20.258	0.000	0.000	0.000	0.000
6	D	175	LEU	0	-0.023	-0.028	6.844	-2.333	-2.333	0.000	0.000	0.000	0.000
7	D	176	VAL	0	-0.044	-0.014	8.959	-2.240	-2.240	0.000	0.000	0.000	0.000
8	D	177	SER	0	0.020	0.006	10.973	-2.446	-2.446	0.000	0.000	0.000	0.000
9	D	178	GLY	0	0.047	0.028	12.374	-1.455	-1.455	0.000	0.000	0.000	0.000
10	D	179	SER	0	-0.051	-0.028	13.472	-1.797	-1.797	0.000	0.000	0.000	0.000
11	D	180	ILE	0	0.020	0.004	15.001	-1.181	-1.181	0.000	0.000	0.000	0.000
12	D	181	GLY	0	0.052	0.036	16.696	-1.044	-1.044	0.000	0.000	0.000	0.000
13	D	182	VAL	0	0.017	0.000	18.401	-0.976	-0.976	0.000	0.000	0.000	0.000
14	D	183	LEU	0	0.022	0.042	18.676	-0.869	-0.869	0.000	0.000	0.000	0.000
15	D	184	LYS	1	0.919	0.969	20.948	-12.926	-12.926	0.000	0.000	0.000	0.000
16	D	185	ASN	0	-0.034	-0.015	22.677	-0.674	-0.674	0.000	0.000	0.000	0.000
17	D	186	MET	0	-0.035	-0.047	23.306	-0.453	-0.453	0.000	0.000	0.000	0.000
18	D	187	SER	0	-0.006	-0.017	24.790	-0.463	-0.463	0.000	0.000	0.000	0.000
19	D	188	GLN	0	0.016	0.006	26.810	-0.003	-0.003	0.000	0.000	0.000	0.000
20	D	189	ARG	1	0.913	0.955	26.417	-11.101	-11.101	0.000	0.000	0.000	0.000
21	D	190	ILE	0	0.004	0.018	28.452	-0.252	-0.252	0.000	0.000	0.000	0.000
22	D	191	GLY	0	0.019	0.011	31.472	-0.258	-0.258	0.000	0.000	0.000	0.000
23	D	192	GLY	0	-0.012	-0.008	33.190	-0.246	-0.246	0.000	0.000	0.000	0.000
24	D	193	GLU	-1	-0.839	-0.908	34.667	7.946	7.946	0.000	0.000	0.000	0.000
25	D	194	LEU	0	-0.044	-0.034	34.349	-0.195	-0.195	0.000	0.000	0.000	0.000
26	D	195	GLU	-1	-0.962	-0.972	37.446	7.427	7.427	0.000	0.000	0.000	0.000
27	D	196	GLU	-1	-0.936	-0.976	39.100	7.576	7.576	0.000	0.000	0.000	0.000
28	D	197	GLN	0	-0.110	-0.073	38.821	-0.276	-0.276	0.000	0.000	0.000	0.000
29	D	198	ALA	0	0.002	0.008	41.707	-0.194	-0.194	0.000	0.000	0.000	0.000
30	D	199	VAL	0	0.001	0.007	43.522	-0.181	-0.181	0.000	0.000	0.000	0.000
31	D	200	MET	0	0.011	0.008	43.513	-0.169	-0.169	0.000	0.000	0.000	0.000
32	D	201	LEU	0	-0.050	-0.036	43.802	-0.154	-0.154	0.000	0.000	0.000	0.000
33	D	202	GLU	-1	-0.895	-0.927	47.525	6.052	6.052	0.000	0.000	0.000	0.000
34	D	203	ASP	-1	-0.893	-0.943	49.497	6.103	6.103	0.000	0.000	0.000	0.000
35	D	204	PHE	0	-0.041	-0.027	49.885	-0.159	-0.159	0.000	0.000	0.000	0.000
36	D	205	SER	0	-0.008	-0.005	51.494	-0.120	-0.120	0.000	0.000	0.000	0.000
37	D	206	HIS	0	-0.012	-0.018	53.271	-0.242	-0.242	0.000	0.000	0.000	0.000
38	D	207	GLU	-1	-0.956	-0.974	54.018	5.682	5.682	0.000	0.000	0.000	0.000
39	D	208	LEU	0	-0.056	-0.019	53.744	-0.167	-0.167	0.000	0.000	0.000	0.000
40	D	209	GLU	-1	-0.882	-0.942	56.693	5.369	5.369	0.000	0.000	0.000	0.000
41	D	210	SER	0	-0.024	0.007	59.540	-0.158	-0.158	0.000	0.000	0.000	0.000
42	D	211	THR	0	-0.070	-0.060	59.626	-0.139	-0.139	0.000	0.000	0.000	0.000
43	D	212	GLN	0	0.043	0.026	61.055	-0.108	-0.108	0.000	0.000	0.000	0.000
44	D	213	SER	0	0.006	0.006	63.314	-0.119	-0.119	0.000	0.000	0.000	0.000
45	D	214	ARG	1	0.861	0.921	62.178	-5.124	-5.124	0.000	0.000	0.000	0.000
46	D	215	LEU	0	0.030	0.011	64.372	-0.103	-0.103	0.000	0.000	0.000	0.000
47	D	216	ASP	-1	-0.851	-0.922	67.503	4.622	4.622	0.000	0.000	0.000	0.000
48	D	217	ASN	0	-0.073	-0.049	69.461	-0.128	-0.128	0.000	0.000	0.000	0.000
49	D	218	VAL	0	-0.038	-0.018	69.954	-0.096	-0.096	0.000	0.000	0.000	0.000
50	D	219	MET	0	0.025	0.011	68.521	-0.082	-0.082	0.000	0.000	0.000	0.000
51	D	220	LYS	1	0.919	0.972	71.052	-4.527	-4.527	0.000	0.000	0.000	0.000
52	D	221	LYS	1	0.916	0.951	74.586	-4.258	-4.258	0.000	0.000	0.000	0.000
53	D	222	LEU	0	0.008	0.017	74.445	-0.069	-0.069	0.000	0.000	0.000	0.000
54	D	223	ALA	0	0.071	0.035	77.093	-0.062	-0.062	0.000	0.000	0.000	0.000
55	D	224	LYS	1	0.963	0.988	78.947	-3.930	-3.930	0.000	0.000	0.000	0.000
56	D	225	VAL	0	-0.022	-0.015	80.687	-0.066	-0.066	0.000	0.000	0.000	0.000
57	D	226	SER	0	-0.021	-0.021	80.786	-0.037	-0.037	0.000	0.000	0.000	0.000
58	D	227	HIS	0	-0.039	-0.011	82.100	-0.045	-0.045	0.000	0.000	0.000	0.000
59	D	228	MET	0	-0.091	-0.059	84.696	-0.058	-0.058	0.000	0.000	0.000	0.000
60	D	229	THR	0	-0.035	-0.014	85.759	-0.041	-0.041	0.000	0.000	0.000	0.000
61	D	230	SER	0	0.008	0.008	86.609	-0.051	-0.051	0.000	0.000	0.000	0.000
62	D	231	ASP	-1	-0.888	-0.946	88.041	3.631	3.631	0.000	0.000	0.000	0.000
63	D	232	ARG	1	0.870	0.958	90.117	-3.533	-3.533	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:170:ASP)