FMO DATABASE

FMODB ID: G6991

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	OptH
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	-255102.313228
FMO2-HF: Nuclear repulsion	229473.51209
FMO2-HF: Total energy	-25628.801138
FMO2-MP2: Total energy	-25700.867551

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.
2.947	5.649	0.036	-0.93	-1.809	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 : -0.970 / q_NPA : -0.987

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	-0.059	0.003	3.386	-1.942	0.568	0.037	-0.915	-1.633	0.002
4	D	173	LEU	0	0.035	-0.012	4.548	-4.593	-4.401	-0.001	-0.015	-0.176	0.000
5	D	174	GLU	-1	-0.882	-0.921	6.795	20.774	20.774	0.000	0.000	0.000	0.000
6	D	175	LEU	0	-0.018	-0.027	6.566	-2.407	-2.407	0.000	0.000	0.000	0.000
7	D	176	VAL	0	-0.031	-0.005	8.952	-2.257	-2.257	0.000	0.000	0.000	0.000
8	D	177	SER	0	0.023	-0.004	10.747	-2.516	-2.516	0.000	0.000	0.000	0.000
9	D	178	GLY	0	0.058	0.028	12.127	-1.508	-1.508	0.000	0.000	0.000	0.000
10	D	179	SER	0	-0.052	-0.027	13.259	-1.839	-1.839	0.000	0.000	0.000	0.000
11	D	180	ILE	0	0.020	0.015	14.804	-1.213	-1.213	0.000	0.000	0.000	0.000
12	D	181	GLY	0	0.041	0.028	16.469	-1.086	-1.086	0.000	0.000	0.000	0.000
13	D	182	VAL	0	0.024	0.007	18.247	-0.997	-0.997	0.000	0.000	0.000	0.000
14	D	183	LEU	0	0.009	0.033	18.535	-0.886	-0.886	0.000	0.000	0.000	0.000
15	D	184	LYS	1	0.918	0.959	20.741	-13.272	-13.272	0.000	0.000	0.000	0.000
16	D	185	ASN	0	-0.036	-0.019	22.456	-0.653	-0.653	0.000	0.000	0.000	0.000
17	D	186	MET	0	-0.046	-0.055	22.933	-0.501	-0.501	0.000	0.000	0.000	0.000
18	D	187	SER	0	-0.002	0.003	24.972	-0.525	-0.525	0.000	0.000	0.000	0.000
19	D	188	GLN	0	0.025	0.001	26.341	0.047	0.047	0.000	0.000	0.000	0.000
20	D	189	ARG	1	0.921	0.963	26.557	-11.094	-11.094	0.000	0.000	0.000	0.000
21	D	190	ILE	0	-0.004	0.022	28.052	-0.243	-0.243	0.000	0.000	0.000	0.000
22	D	191	GLY	0	0.017	0.007	31.278	-0.263	-0.263	0.000	0.000	0.000	0.000
23	D	192	GLY	0	-0.014	-0.009	32.982	-0.250	-0.250	0.000	0.000	0.000	0.000
24	D	193	GLU	-1	-0.834	-0.919	34.466	7.992	7.992	0.000	0.000	0.000	0.000
25	D	194	LEU	0	-0.049	-0.036	34.141	-0.193	-0.193	0.000	0.000	0.000	0.000
26	D	195	GLU	-1	-0.957	-0.971	37.252	7.458	7.458	0.000	0.000	0.000	0.000
27	D	196	GLU	-1	-0.933	-0.971	38.897	7.679	7.679	0.000	0.000	0.000	0.000
28	D	197	GLN	0	-0.106	-0.061	38.703	-0.287	-0.287	0.000	0.000	0.000	0.000
29	D	198	ALA	0	0.003	0.011	41.522	-0.198	-0.198	0.000	0.000	0.000	0.000
30	D	199	VAL	0	0.023	0.015	43.342	-0.181	-0.181	0.000	0.000	0.000	0.000
31	D	200	MET	0	0.001	0.003	43.245	-0.168	-0.168	0.000	0.000	0.000	0.000
32	D	201	LEU	0	-0.056	-0.038	43.531	-0.153	-0.153	0.000	0.000	0.000	0.000
33	D	202	GLU	-1	-0.938	-0.962	47.354	6.110	6.110	0.000	0.000	0.000	0.000
34	D	203	ASP	-1	-0.892	-0.937	49.322	6.138	6.138	0.000	0.000	0.000	0.000
35	D	204	PHE	0	-0.042	-0.027	49.340	-0.163	-0.163	0.000	0.000	0.000	0.000
36	D	205	SER	0	0.000	-0.008	51.327	-0.131	-0.131	0.000	0.000	0.000	0.000
37	D	206	HIS	0	0.012	0.009	53.101	-0.233	-0.233	0.000	0.000	0.000	0.000
38	D	207	GLU	-1	-0.966	-0.979	53.310	5.748	5.748	0.000	0.000	0.000	0.000
39	D	208	LEU	0	-0.057	-0.026	53.941	-0.160	-0.160	0.000	0.000	0.000	0.000
40	D	209	GLU	-1	-0.892	-0.947	56.969	5.380	5.380	0.000	0.000	0.000	0.000
41	D	210	SER	0	-0.038	0.001	59.369	-0.152	-0.152	0.000	0.000	0.000	0.000
42	D	211	THR	0	-0.058	-0.055	59.524	-0.138	-0.138	0.000	0.000	0.000	0.000
43	D	212	GLN	0	0.055	0.022	61.076	-0.161	-0.161	0.000	0.000	0.000	0.000
44	D	213	SER	0	0.020	0.028	63.160	-0.116	-0.116	0.000	0.000	0.000	0.000
45	D	214	ARG	1	0.849	0.919	62.061	-5.136	-5.136	0.000	0.000	0.000	0.000
46	D	215	LEU	0	0.019	0.006	64.509	-0.103	-0.103	0.000	0.000	0.000	0.000
47	D	216	ASP	-1	-0.848	-0.916	66.977	4.684	4.684	0.000	0.000	0.000	0.000
48	D	217	ASN	0	-0.066	-0.047	69.309	-0.126	-0.126	0.000	0.000	0.000	0.000
49	D	218	VAL	0	-0.060	-0.030	69.981	-0.100	-0.100	0.000	0.000	0.000	0.000
50	D	219	MET	0	0.015	0.002	67.966	-0.092	-0.092	0.000	0.000	0.000	0.000
51	D	220	LYS	1	0.965	0.994	72.786	-4.452	-4.452	0.000	0.000	0.000	0.000
52	D	221	LYS	1	0.928	0.955	74.637	-4.267	-4.267	0.000	0.000	0.000	0.000
53	D	222	LEU	0	0.006	0.015	74.051	-0.072	-0.072	0.000	0.000	0.000	0.000
54	D	223	ALA	0	0.055	0.028	76.952	-0.063	-0.063	0.000	0.000	0.000	0.000
55	D	224	LYS	1	0.962	0.982	78.807	-3.965	-3.965	0.000	0.000	0.000	0.000
56	D	225	VAL	0	-0.035	-0.018	80.097	-0.066	-0.066	0.000	0.000	0.000	0.000
57	D	226	SER	0	-0.033	-0.034	80.762	-0.038	-0.038	0.000	0.000	0.000	0.000
58	D	227	HIS	0	-0.005	0.015	82.469	-0.044	-0.044	0.000	0.000	0.000	0.000
59	D	228	MET	0	-0.068	-0.051	84.701	-0.060	-0.060	0.000	0.000	0.000	0.000
60	D	229	THR	0	-0.029	-0.009	85.664	-0.040	-0.040	0.000	0.000	0.000	0.000
61	D	230	SER	0	-0.002	0.002	86.524	-0.052	-0.052	0.000	0.000	0.000	0.000
62	D	231	ASP	-1	-0.936	-0.966	87.883	3.645	3.645	0.000	0.000	0.000	0.000
63	D	232	ARG	1	0.891	0.970	89.984	-3.553	-3.553	0.000	0.000	0.000	0.000

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