FMO DATABASE

FMODB ID: 39V9L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-326568.30747
FMO2-HF: Nuclear repulsion	298882.316223
FMO2-HF: Total energy	-27685.991247
FMO2-MP2: Total energy	-27757.592563

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.
-14.009	-33.353	55.84	-4.137	-32.363	0.003

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 : -0.086 / q_NPA : -0.032

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	13	LYS	1	0.855	0.917	3.808	-1.771	0.411	-0.031	-1.032	-1.120	0.001
4	D	14	LYS	1	0.823	0.903	6.336	-1.732	-1.732	0.000	0.000	0.000	0.000
5	D	15	GLN	0	-0.029	-0.062	8.865	0.051	0.051	0.000	0.000	0.000	0.000
6	D	16	PHE	0	0.182	0.118	11.997	0.058	0.058	0.000	0.000	0.000	0.000
7	D	17	PHE	0	-0.241	-0.106	13.985	0.043	0.043	0.000	0.000	0.000	0.000
8	D	18	VAL	0	-0.015	0.005	17.161	-0.067	-0.067	0.000	0.000	0.000	0.000
9	D	19	SER	0	0.024	0.025	19.821	0.016	0.016	0.000	0.000	0.000	0.000
10	D	29	ILE	0	0.009	-0.060	26.508	0.000	0.000	0.000	0.000	0.000	0.000
11	D	30	ILE	0	0.011	0.009	29.750	-0.003	-0.003	0.000	0.000	0.000	0.000
12	D	31	ALA	0	-0.053	0.009	29.007	-0.003	-0.003	0.000	0.000	0.000	0.000
13	D	32	PRO	0	0.001	-0.015	24.010	0.009	0.009	0.000	0.000	0.000	0.000
14	D	33	SER	0	0.022	0.002	26.729	-0.011	-0.011	0.000	0.000	0.000	0.000
15	D	34	GLY	0	0.026	0.009	22.876	-0.019	-0.019	0.000	0.000	0.000	0.000
16	D	35	TYR	0	-0.016	0.008	16.663	0.037	0.037	0.000	0.000	0.000	0.000
17	D	36	HIS	0	0.043	-0.001	15.456	-0.023	-0.023	0.000	0.000	0.000	0.000
18	D	37	ALA	0	0.023	0.004	14.410	0.121	0.121	0.000	0.000	0.000	0.000
19	D	38	ASN	0	0.020	-0.010	10.272	-0.045	-0.045	0.000	0.000	0.000	0.000
20	D	39	TYR	0	0.019	0.006	8.283	-0.207	-0.207	0.000	0.000	0.000	0.000
21	D	40	CYS	0	-0.055	0.021	3.131	-3.189	-2.095	2.921	-0.873	-3.142	0.005
22	D	41	GLU	-1	-0.788	-0.895	3.886	-2.789	-1.625	0.490	-0.384	-1.270	-0.003
23	D	42	GLY	0	0.006	-0.010	2.179	1.800	-1.346	13.922	-6.729	-4.047	-0.014
24	D	43	GLU	-1	-0.879	-0.944	2.500	-12.160	-17.514	1.032	6.612	-2.291	-0.010
25	D	44	CYS	0	-0.085	-0.020	2.035	6.935	-2.780	24.383	-2.145	-12.523	0.005
26	D	45	PRO	0	-0.005	0.007	4.980	-0.140	-0.075	-0.001	-0.007	-0.057	0.000
29	D	83	PRO	0	0.001	-0.043	3.774	0.041	3.299	-0.045	-1.443	-1.771	0.010
30	D	84	THR	0	-0.024	-0.008	6.880	-0.950	-0.950	0.000	0.000	0.000	0.000
31	D	85	LYS	1	0.754	0.892	8.849	-2.609	-2.609	0.000	0.000	0.000	0.000
32	D	86	LEU	0	0.012	0.014	10.816	0.109	0.109	0.000	0.000	0.000	0.000
33	D	87	ARG	1	0.924	0.937	13.475	-1.232	-1.232	0.000	0.000	0.000	0.000
34	D	88	PRO	0	0.021	-0.009	16.649	-0.070	-0.070	0.000	0.000	0.000	0.000
35	D	89	MET	0	-0.030	-0.020	20.196	0.030	0.030	0.000	0.000	0.000	0.000
36	D	90	SER	0	-0.025	-0.014	22.299	-0.027	-0.027	0.000	0.000	0.000	0.000
37	D	91	MET	0	0.002	0.001	24.583	0.006	0.006	0.000	0.000	0.000	0.000
38	D	92	LEU	0	-0.065	-0.015	27.597	-0.003	-0.003	0.000	0.000	0.000	0.000
39	D	93	TYR	0	0.035	0.061	29.037	-0.003	-0.003	0.000	0.000	0.000	0.000
40	D	94	TYR	-1	-0.877	-0.954	32.432	0.157	0.157	0.000	0.000	0.000	0.000
41	D	95	ASP	-1	-0.925	-0.970	34.189	0.196	0.196	0.000	0.000	0.000	0.000
42	D	96	ASP	-1	-0.839	-0.921	36.019	0.120	0.120	0.000	0.000	0.000	0.000
43	D	97	GLY	0	0.013	0.008	38.812	-0.002	-0.002	0.000	0.000	0.000	0.000
44	D	98	GLN	0	-0.107	-0.007	39.275	-0.008	-0.008	0.000	0.000	0.000	0.000
45	D	99	ASN	0	-0.038	-0.069	38.865	0.003	0.003	0.000	0.000	0.000	0.000
46	D	100	ILE	0	-0.065	-0.022	35.131	0.006	0.006	0.000	0.000	0.000	0.000
47	D	101	ILE	0	0.022	0.019	32.510	0.003	0.003	0.000	0.000	0.000	0.000
48	D	102	LYS	1	0.821	0.922	29.702	-0.351	-0.351	0.000	0.000	0.000	0.000
49	D	103	LYS	1	0.976	0.984	26.432	-0.459	-0.459	0.000	0.000	0.000	0.000
50	D	104	ASP	-1	-0.848	-0.925	26.376	0.456	0.456	0.000	0.000	0.000	0.000
51	D	105	ILE	0	-0.041	-0.043	22.052	0.013	0.013	0.000	0.000	0.000	0.000
52	D	106	GLN	0	-0.016	0.002	19.926	0.139	0.139	0.000	0.000	0.000	0.000
53	D	107	ASN	0	0.015	-0.001	14.314	0.212	0.212	0.000	0.000	0.000	0.000
54	D	108	MET	0	0.013	0.037	17.404	-0.073	-0.073	0.000	0.000	0.000	0.000
55	D	109	ILE	0	-0.067	-0.017	13.687	-0.045	-0.045	0.000	0.000	0.000	0.000
56	D	110	VAL	0	0.070	0.029	8.003	0.127	0.127	0.000	0.000	0.000	0.000
57	D	111	GLU	-1	-0.872	-0.930	10.751	1.595	1.595	0.000	0.000	0.000	0.000
58	D	112	GLU	-1	-0.824	-0.911	7.090	3.089	3.089	0.000	0.000	0.000	0.000
59	D	114	GLY	0	0.090	0.017	2.640	-1.136	-4.557	11.287	-3.949	-3.918	-0.009
60	D	116	SER	0	0.017	0.041	2.455	-0.254	-5.725	1.882	5.813	-2.224	0.018

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