FMO DATABASE

FMODB ID: LZ3Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-326018.909258
FMO2-HF: Nuclear repulsion	298331.946554
FMO2-HF: Total energy	-27686.962704
FMO2-MP2: Total energy	-27758.454418

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.
-18.47	-34.601	55.8	-6.717	-32.952	0.001

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 : -0.102 / q_NPA : -0.036

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	0.867	0.915	3.808	-2.189	0.114	-0.034	-1.070	-1.199	0.001
4	D	14	LYS	1	0.838	0.908	6.216	-2.119	-2.119	0.000	0.000	0.000	0.000
5	D	15	GLN	0	0.012	-0.076	8.863	0.059	0.059	0.000	0.000	0.000	0.000
6	D	16	PHE	0	0.323	0.232	12.062	0.026	0.026	0.000	0.000	0.000	0.000
7	D	17	PHE	0	-0.386	-0.184	13.955	0.074	0.074	0.000	0.000	0.000	0.000
8	D	18	VAL	0	-0.025	-0.009	17.160	-0.060	-0.060	0.000	0.000	0.000	0.000
9	D	19	SER	0	-0.010	0.011	19.782	-0.003	-0.003	0.000	0.000	0.000	0.000
10	D	29	ILE	0	-0.056	-0.060	26.515	-0.004	-0.004	0.000	0.000	0.000	0.000
11	D	30	ILE	0	0.080	0.003	29.752	-0.002	-0.002	0.000	0.000	0.000	0.000
12	D	31	ALA	0	-0.062	0.012	29.053	0.000	0.000	0.000	0.000	0.000	0.000
13	D	32	PRO	0	0.005	-0.022	24.159	0.006	0.006	0.000	0.000	0.000	0.000
14	D	33	SER	0	0.040	0.015	26.618	-0.008	-0.008	0.000	0.000	0.000	0.000
15	D	34	GLY	0	0.016	-0.001	22.864	-0.022	-0.022	0.000	0.000	0.000	0.000
16	D	35	TYR	0	0.009	0.023	16.572	0.001	0.001	0.000	0.000	0.000	0.000
17	D	36	HIS	0	0.063	0.008	15.422	-0.020	-0.020	0.000	0.000	0.000	0.000
18	D	37	ALA	0	-0.012	-0.010	14.384	0.123	0.123	0.000	0.000	0.000	0.000
19	D	38	ASN	0	-0.029	-0.019	10.289	-0.009	-0.009	0.000	0.000	0.000	0.000
20	D	39	TYR	0	0.020	0.008	8.206	-0.251	-0.251	0.000	0.000	0.000	0.000
21	D	40	CYS	0	-0.062	0.022	2.905	-2.779	-2.189	3.562	-0.867	-3.285	0.005
22	D	41	GLU	-1	-0.789	-0.893	3.797	-2.582	-1.390	0.698	-0.384	-1.506	-0.004
23	D	42	GLY	0	0.005	-0.012	2.139	2.376	-0.861	14.245	-6.757	-4.251	-0.014
24	D	43	GLU	-1	-0.885	-0.948	2.386	-13.658	-18.847	1.254	6.456	-2.522	-0.012
25	D	44	CYS	0	-0.084	-0.013	2.027	4.973	-3.336	26.471	-5.131	-13.030	0.008
26	D	45	PRO	0	-0.026	-0.008	4.979	0.261	0.330	-0.001	-0.006	-0.062	0.000
29	D	83	PRO	0	-0.004	-0.041	3.774	0.090	3.290	-0.042	-1.425	-1.733	0.009
30	D	84	THR	0	-0.022	-0.011	6.883	-0.909	-0.909	0.000	0.000	0.000	0.000
31	D	85	LYS	1	0.762	0.879	8.855	-2.592	-2.592	0.000	0.000	0.000	0.000
32	D	86	LEU	0	0.024	0.035	10.783	0.152	0.152	0.000	0.000	0.000	0.000
33	D	87	ARG	1	0.934	0.943	13.435	-1.278	-1.278	0.000	0.000	0.000	0.000
34	D	88	PRO	0	0.041	0.014	16.591	-0.065	-0.065	0.000	0.000	0.000	0.000
35	D	89	MET	0	-0.046	-0.043	20.132	0.040	0.040	0.000	0.000	0.000	0.000
36	D	90	SER	0	-0.033	-0.043	22.295	-0.029	-0.029	0.000	0.000	0.000	0.000
37	D	91	MET	0	-0.024	-0.014	24.540	0.005	0.005	0.000	0.000	0.000	0.000
38	D	92	LEU	0	-0.060	-0.018	27.637	-0.007	-0.007	0.000	0.000	0.000	0.000
39	D	93	TYR	0	0.026	0.066	29.295	0.012	0.012	0.000	0.000	0.000	0.000
40	D	94	TYR	-1	-0.851	-0.941	32.447	0.166	0.166	0.000	0.000	0.000	0.000
41	D	95	ASP	-1	-0.926	-0.968	34.193	0.201	0.201	0.000	0.000	0.000	0.000
42	D	96	ASP	-1	-0.839	-0.924	36.028	0.120	0.120	0.000	0.000	0.000	0.000
43	D	97	GLY	0	0.003	0.001	38.811	-0.002	-0.002	0.000	0.000	0.000	0.000
44	D	98	GLN	0	-0.129	-0.023	38.959	-0.007	-0.007	0.000	0.000	0.000	0.000
45	D	99	ASN	0	-0.038	-0.066	38.588	0.002	0.002	0.000	0.000	0.000	0.000
46	D	100	ILE	0	-0.042	0.001	35.211	0.007	0.007	0.000	0.000	0.000	0.000
47	D	101	ILE	0	0.002	0.001	32.318	0.002	0.002	0.000	0.000	0.000	0.000
48	D	102	LYS	1	0.840	0.934	29.457	-0.373	-0.373	0.000	0.000	0.000	0.000
49	D	103	LYS	1	0.992	0.989	26.323	-0.463	-0.463	0.000	0.000	0.000	0.000
50	D	104	ASP	-1	-0.824	-0.883	26.224	0.472	0.472	0.000	0.000	0.000	0.000
51	D	105	ILE	0	-0.061	-0.051	22.069	0.008	0.008	0.000	0.000	0.000	0.000
52	D	106	GLN	0	0.013	0.017	19.776	0.136	0.136	0.000	0.000	0.000	0.000
53	D	107	ASN	0	-0.018	-0.007	14.340	0.149	0.149	0.000	0.000	0.000	0.000
54	D	108	MET	0	0.016	0.033	17.455	-0.082	-0.082	0.000	0.000	0.000	0.000
55	D	109	ILE	0	-0.070	-0.031	13.795	-0.042	-0.042	0.000	0.000	0.000	0.000
56	D	110	VAL	0	0.062	0.025	8.046	0.066	0.066	0.000	0.000	0.000	0.000
57	D	111	GLU	-1	-0.860	-0.930	10.674	1.654	1.654	0.000	0.000	0.000	0.000
58	D	112	GLU	-1	-0.815	-0.907	6.963	3.463	3.463	0.000	0.000	0.000	0.000
59	D	114	GLY	0	0.091	0.023	2.657	-1.890	-4.070	8.582	-2.963	-3.439	-0.010
60	D	116	SER	0	-0.073	-0.081	2.464	-1.669	-6.239	1.065	5.430	-1.925	0.018

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