FMO DATABASE

FMODB ID: QVV3Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-367154.025813
FMO2-HF: Nuclear repulsion	334344.199191
FMO2-HF: Total energy	-32809.826622
FMO2-MP2: Total energy	-32904.526088

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.
3.35	5.414	0.026	-0.957	-1.132	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 : 0.060 / q_NPA : 0.017

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	C	114	MET	0	-0.005	0.009	3.059	0.562	2.449	0.027	-0.936	-0.978	0.001
4	C	115	ARG	1	1.003	0.979	4.733	1.893	2.070	-0.001	-0.021	-0.154	0.000
5	C	116	ALA	0	-0.011	-0.004	6.140	0.359	0.359	0.000	0.000	0.000	0.000
6	C	117	HIS	0	0.076	0.036	7.762	0.300	0.300	0.000	0.000	0.000	0.000
7	C	118	LEU	0	-0.040	-0.018	8.681	0.113	0.113	0.000	0.000	0.000	0.000
8	C	119	LEU	0	-0.004	0.006	9.782	0.061	0.061	0.000	0.000	0.000	0.000
9	C	120	ASP	-1	-0.784	-0.888	12.043	-0.124	-0.124	0.000	0.000	0.000	0.000
10	C	121	ASN	0	-0.021	-0.037	13.596	0.097	0.097	0.000	0.000	0.000	0.000
11	C	122	THR	0	0.007	-0.001	14.910	0.037	0.037	0.000	0.000	0.000	0.000
12	C	123	GLU	-1	-0.904	-0.936	16.556	-0.195	-0.195	0.000	0.000	0.000	0.000
13	C	124	ARG	1	0.785	0.884	16.005	0.192	0.192	0.000	0.000	0.000	0.000
14	C	125	LEU	0	-0.023	-0.013	18.920	0.028	0.028	0.000	0.000	0.000	0.000
15	C	126	GLU	-1	-0.885	-0.937	20.190	-0.216	-0.216	0.000	0.000	0.000	0.000
16	C	127	ARG	1	0.924	0.961	22.418	0.123	0.123	0.000	0.000	0.000	0.000
17	C	128	SER	0	-0.060	-0.035	24.250	0.019	0.019	0.000	0.000	0.000	0.000
18	C	129	SER	0	0.035	0.018	25.798	0.014	0.014	0.000	0.000	0.000	0.000
19	C	130	ARG	1	0.995	0.996	26.015	0.131	0.131	0.000	0.000	0.000	0.000
20	C	131	ARG	1	0.900	0.951	26.283	0.078	0.078	0.000	0.000	0.000	0.000
21	C	132	LEU	0	-0.009	0.005	29.576	0.007	0.007	0.000	0.000	0.000	0.000
22	C	133	GLU	-1	-0.917	-0.947	31.606	-0.089	-0.089	0.000	0.000	0.000	0.000
23	C	134	ALA	0	0.002	0.003	33.068	0.005	0.005	0.000	0.000	0.000	0.000
24	C	135	GLY	0	-0.025	-0.019	34.343	0.004	0.004	0.000	0.000	0.000	0.000
25	C	136	TYR	0	-0.007	0.009	36.198	0.003	0.003	0.000	0.000	0.000	0.000
26	C	137	GLN	0	0.028	0.012	37.614	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	138	ILE	0	0.020	0.007	37.477	0.003	0.003	0.000	0.000	0.000	0.000
28	C	139	ALA	0	-0.023	0.007	40.535	0.003	0.003	0.000	0.000	0.000	0.000
29	C	140	VAL	0	0.090	0.032	42.166	0.002	0.002	0.000	0.000	0.000	0.000
30	C	141	GLU	-1	-0.959	-0.975	42.549	-0.039	-0.039	0.000	0.000	0.000	0.000
31	C	142	THR	0	-0.079	-0.057	44.304	0.003	0.003	0.000	0.000	0.000	0.000
32	C	143	GLU	-1	-0.948	-0.977	45.250	-0.036	-0.036	0.000	0.000	0.000	0.000
33	C	144	GLN	0	-0.025	-0.011	48.640	0.000	0.000	0.000	0.000	0.000	0.000
34	C	145	ILE	0	-0.032	-0.010	48.229	0.002	0.002	0.000	0.000	0.000	0.000
35	C	146	GLY	0	-0.014	-0.015	50.776	0.002	0.002	0.000	0.000	0.000	0.000
36	C	147	GLN	0	0.012	0.003	52.539	0.002	0.002	0.000	0.000	0.000	0.000
37	C	148	GLU	-1	-0.889	-0.948	54.299	-0.020	-0.020	0.000	0.000	0.000	0.000
38	C	149	MET	0	0.000	0.008	52.518	0.002	0.002	0.000	0.000	0.000	0.000
39	C	150	LEU	0	-0.024	-0.004	56.118	0.001	0.001	0.000	0.000	0.000	0.000
40	C	151	GLU	-1	-0.936	-0.949	58.821	-0.020	-0.020	0.000	0.000	0.000	0.000
41	C	152	ASN	0	-0.044	-0.024	59.955	0.002	0.002	0.000	0.000	0.000	0.000
42	C	153	LEU	0	0.048	0.001	59.420	0.001	0.001	0.000	0.000	0.000	0.000
43	C	154	SER	0	-0.081	-0.034	62.873	0.001	0.001	0.000	0.000	0.000	0.000
44	C	155	HIS	0	0.057	0.032	64.724	0.001	0.001	0.000	0.000	0.000	0.000
45	C	156	ASP	-1	-0.875	-0.944	64.457	-0.014	-0.014	0.000	0.000	0.000	0.000
46	C	157	ARG	1	0.904	0.946	66.931	0.014	0.014	0.000	0.000	0.000	0.000
47	C	158	GLU	-1	-0.939	-0.965	68.751	-0.014	-0.014	0.000	0.000	0.000	0.000
48	C	159	ARG	1	0.883	0.936	67.794	0.014	0.014	0.000	0.000	0.000	0.000
49	C	160	ILE	0	0.001	0.007	68.921	0.001	0.001	0.000	0.000	0.000	0.000
50	C	161	GLN	0	0.036	0.008	72.617	0.001	0.001	0.000	0.000	0.000	0.000
51	C	162	ARG	1	1.001	0.999	72.867	0.013	0.013	0.000	0.000	0.000	0.000
52	C	163	ALA	0	-0.019	0.004	75.956	0.000	0.000	0.000	0.000	0.000	0.000
53	C	164	ARG	1	0.883	0.937	75.011	0.010	0.010	0.000	0.000	0.000	0.000
54	C	165	GLU	-1	-0.988	-0.991	78.756	-0.010	-0.010	0.000	0.000	0.000	0.000
55	C	166	ARG	1	0.925	0.956	80.523	0.009	0.009	0.000	0.000	0.000	0.000
56	C	167	LEU	0	0.018	0.008	81.020	0.000	0.000	0.000	0.000	0.000	0.000
57	C	168	ARG	1	0.985	0.996	79.194	0.009	0.009	0.000	0.000	0.000	0.000
58	C	169	GLU	-1	-0.877	-0.928	84.806	-0.009	-0.009	0.000	0.000	0.000	0.000
59	C	170	THR	0	-0.057	-0.034	85.347	0.000	0.000	0.000	0.000	0.000	0.000
60	C	171	ASP	-1	-0.866	-0.934	86.613	-0.007	-0.007	0.000	0.000	0.000	0.000
61	C	172	ALA	0	-0.042	-0.014	89.084	0.000	0.000	0.000	0.000	0.000	0.000
62	C	173	ASN	0	-0.029	-0.031	90.297	0.000	0.000	0.000	0.000	0.000	0.000
63	C	174	LEU	0	0.028	0.022	89.435	0.000	0.000	0.000	0.000	0.000	0.000
64	C	175	GLY	0	0.004	0.006	93.181	0.000	0.000	0.000	0.000	0.000	0.000
65	C	176	LYS	1	0.943	0.968	95.135	0.007	0.007	0.000	0.000	0.000	0.000
66	C	177	SER	0	0.000	-0.006	95.665	0.000	0.000	0.000	0.000	0.000	0.000
67	C	178	SER	0	0.021	0.028	97.003	0.000	0.000	0.000	0.000	0.000	0.000
68	C	179	ARG	1	0.968	0.982	98.791	0.006	0.006	0.000	0.000	0.000	0.000
69	C	180	ILE	0	-0.031	-0.027	100.405	0.000	0.000	0.000	0.000	0.000	0.000
70	C	181	LEU	0	0.058	0.020	99.493	0.000	0.000	0.000	0.000	0.000	0.000
71	C	182	THR	0	-0.015	0.013	102.443	0.000	0.000	0.000	0.000	0.000	0.000
72	C	183	GLY	0	-0.044	-0.034	104.814	0.000	0.000	0.000	0.000	0.000	0.000
73	C	184	MET	0	-0.041	-0.032	105.563	0.000	0.000	0.000	0.000	0.000	0.000
74	C	185	LEU	0	0.047	0.010	104.509	0.000	0.000	0.000	0.000	0.000	0.000
75	C	186	ARG	1	0.911	0.968	107.929	0.004	0.004	0.000	0.000	0.000	0.000
76	C	187	ARG	1	0.938	0.956	109.069	0.005	0.005	0.000	0.000	0.000	0.000
77	C	188	ILE	0	0.029	0.046	108.661	0.000	0.000	0.000	0.000	0.000	0.000
78	C	189	ILE	0	-0.079	-0.023	112.128	0.000	0.000	0.000	0.000	0.000	0.000
79	C	190	GLN	0	-0.003	0.000	115.450	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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