FMO DATABASE

FMODB ID: 94V42

Calculation Name: 1NYU-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYU

Chain ID: D

ChEMBL ID:

UniProt ID: P38444

Base Structure: X-ray

Registration Date: 2023-09-19

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	60
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-324471.536872
FMO2-HF: Nuclear repulsion	296783.13003
FMO2-HF: Total energy	-27688.406841
FMO2-MP2: Total energy	-27759.691067

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:11:CYS)

Summations of interaction energy for fragment #1(D:11:CYS)

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.
-47.082	-28.644	27.642	-16.126	-29.954	-0.015

Interaction energy analysis for fragmet #1(D:11:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.100 / q_NPA : -0.054

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	D	13	LYS	1	0.870	0.914	3.875	-1.996	0.025	-0.014	-0.862	-1.145	0.001
4	D	14	LYS	1	0.831	0.907	6.246	-2.804	-2.804	0.000	0.000	0.000	0.000
5	D	15	GLN	0	-0.042	-0.053	8.846	0.030	0.030	0.000	0.000	0.000	0.000
6	D	16	PHE	0	0.037	0.016	12.052	0.018	0.018	0.000	0.000	0.000	0.000
7	D	17	PHE	0	-0.045	0.002	14.635	0.067	0.067	0.000	0.000	0.000	0.000
8	D	18	VAL	0	-0.006	0.006	17.300	-0.073	-0.073	0.000	0.000	0.000	0.000
9	D	19	SER	0	-0.013	-0.023	20.008	-0.007	-0.007	0.000	0.000	0.000	0.000
10	D	29	ILE	0	-0.003	-0.024	26.513	-0.001	-0.001	0.000	0.000	0.000	0.000
11	D	30	ILE	0	-0.013	0.015	29.745	-0.001	-0.001	0.000	0.000	0.000	0.000
12	D	31	ALA	0	-0.019	0.003	29.548	-0.001	-0.001	0.000	0.000	0.000	0.000
13	D	32	PRO	0	-0.010	-0.017	24.620	0.004	0.004	0.000	0.000	0.000	0.000
14	D	33	SER	0	0.056	0.013	26.591	0.005	0.005	0.000	0.000	0.000	0.000
15	D	34	GLY	0	0.007	0.018	23.112	-0.026	-0.026	0.000	0.000	0.000	0.000
16	D	35	TYR	0	-0.007	0.001	16.716	-0.019	-0.019	0.000	0.000	0.000	0.000
17	D	36	HIS	0	0.073	0.021	15.712	-0.001	-0.001	0.000	0.000	0.000	0.000
18	D	37	ALA	0	0.002	0.010	14.647	0.147	0.147	0.000	0.000	0.000	0.000
19	D	38	ASN	0	-0.059	-0.039	10.234	-0.149	-0.149	0.000	0.000	0.000	0.000
20	D	39	TYR	0	0.002	0.005	7.847	-0.088	-0.088	0.000	0.000	0.000	0.000
21	D	40	CYS	0	-0.015	0.018	2.892	-2.444	-2.050	3.907	-0.976	-3.325	0.006
22	D	41	GLU	-1	-0.770	-0.876	3.619	-1.703	-1.077	1.167	-0.128	-1.665	-0.003
23	D	42	GLY	0	0.009	0.000	2.229	0.741	1.976	5.764	-3.137	-3.862	-0.016
24	D	43	GLU	-1	-0.875	-0.946	2.161	-19.009	-17.574	2.234	-0.686	-2.983	-0.003
25	D	44	CYS	0	-0.048	-0.005	2.164	-9.714	-1.506	12.716	-8.508	-12.416	-0.031
26	D	45	PRO	0	-0.040	-0.012	4.869	0.759	0.841	-0.001	-0.011	-0.070	0.000
29	D	83	PRO	0	0.004	-0.029	3.876	-1.334	1.536	-0.016	-1.383	-1.471	0.007
30	D	84	THR	0	-0.058	-0.009	7.093	-0.158	-0.158	0.000	0.000	0.000	0.000
31	D	85	LYS	1	0.797	0.888	8.805	-2.613	-2.613	0.000	0.000	0.000	0.000
32	D	86	LEU	0	0.025	0.024	10.919	0.226	0.226	0.000	0.000	0.000	0.000
33	D	87	ARG	1	0.916	0.955	13.747	-1.366	-1.366	0.000	0.000	0.000	0.000
34	D	88	PRO	0	0.006	0.008	16.833	-0.027	-0.027	0.000	0.000	0.000	0.000
35	D	89	MET	0	-0.039	-0.023	20.334	0.045	0.045	0.000	0.000	0.000	0.000
36	D	90	SER	0	-0.015	-0.028	22.566	-0.033	-0.033	0.000	0.000	0.000	0.000
37	D	91	MET	0	-0.054	-0.016	24.343	0.014	0.014	0.000	0.000	0.000	0.000
38	D	92	LEU	0	-0.001	-0.001	27.654	-0.011	-0.011	0.000	0.000	0.000	0.000
39	D	93	TYR	0	0.012	-0.003	29.476	0.018	0.018	0.000	0.000	0.000	0.000
40	D	94	TYR	-1	-0.899	-0.961	32.447	0.217	0.217	0.000	0.000	0.000	0.000
41	D	95	ASP	-1	-0.905	-0.953	34.109	0.267	0.267	0.000	0.000	0.000	0.000
42	D	96	ASP	-1	-0.866	-0.940	36.245	0.177	0.177	0.000	0.000	0.000	0.000
43	D	97	GLY	0	-0.034	-0.012	38.888	-0.012	-0.012	0.000	0.000	0.000	0.000
44	D	98	GLN	0	-0.094	-0.044	38.859	-0.015	-0.015	0.000	0.000	0.000	0.000
45	D	99	ASN	0	-0.037	-0.027	38.643	0.003	0.003	0.000	0.000	0.000	0.000
46	D	100	ILE	0	-0.028	-0.007	35.667	0.004	0.004	0.000	0.000	0.000	0.000
47	D	101	ILE	0	0.019	0.022	32.820	-0.001	-0.001	0.000	0.000	0.000	0.000
48	D	102	LYS	1	0.790	0.902	29.399	-0.451	-0.451	0.000	0.000	0.000	0.000
49	D	103	LYS	1	0.957	0.971	26.330	-0.540	-0.540	0.000	0.000	0.000	0.000
50	D	104	ASP	-1	-0.785	-0.860	26.178	0.533	0.533	0.000	0.000	0.000	0.000
51	D	105	ILE	0	-0.037	-0.024	22.351	-0.007	-0.007	0.000	0.000	0.000	0.000
52	D	106	GLN	0	0.067	0.011	19.299	0.137	0.137	0.000	0.000	0.000	0.000
53	D	107	ASN	0	-0.003	-0.015	14.022	0.110	0.110	0.000	0.000	0.000	0.000
54	D	108	MET	0	0.029	0.028	17.164	-0.047	-0.047	0.000	0.000	0.000	0.000
55	D	109	ILE	0	-0.067	-0.018	14.209	-0.040	-0.040	0.000	0.000	0.000	0.000
56	D	110	VAL	0	0.048	0.027	8.023	0.045	0.045	0.000	0.000	0.000	0.000
57	D	111	GLU	-1	-0.874	-0.932	11.290	1.513	1.513	0.000	0.000	0.000	0.000
58	D	112	GLU	-1	-0.810	-0.903	7.423	3.016	3.016	0.000	0.000	0.000	0.000
59	D	114	GLY	0	0.025	0.006	3.699	-3.907	-3.062	0.342	-0.374	-0.813	-0.003
60	D	116	SER	0	-0.093	-0.110	2.308	-6.580	-5.858	1.543	-0.061	-2.204	0.027

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:11:CYS)