FMO DATABASE

FMODB ID: 6NVNZ

Calculation Name: 1NYS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYS

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:

Apendix: None

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455421.235579
FMO2-HF: Nuclear repulsion	422067.245116
FMO2-HF: Total energy	-33353.990463
FMO2-MP2: Total energy	-33442.5026

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:10:ILE)

Summations of interaction energy for fragment #1(D:10:ILE)

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.
-9.631	-1.982	2.629	-4.406	-5.872	-0.019

Interaction energy analysis for fragmet #1(D:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.007

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	12	CYS	0	-0.035	-0.012	3.149	-3.449	-1.062	0.109	-1.144	-1.353	-0.003
4	D	13	LYS	1	0.884	0.963	5.274	1.079	1.152	-0.001	-0.006	-0.065	0.000
5	D	14	LYS	1	0.869	0.920	8.910	0.018	0.018	0.000	0.000	0.000	0.000
6	D	15	GLN	0	0.004	-0.030	10.717	0.066	0.066	0.000	0.000	0.000	0.000
7	D	16	PHE	0	0.027	0.017	14.204	0.033	0.033	0.000	0.000	0.000	0.000
8	D	17	PHE	0	0.010	0.022	16.906	-0.007	-0.007	0.000	0.000	0.000	0.000
9	D	18	VAL	0	-0.002	0.014	20.456	0.017	0.017	0.000	0.000	0.000	0.000
10	D	19	SER	0	0.021	-0.003	23.489	-0.007	-0.007	0.000	0.000	0.000	0.000
11	D	20	PHE	0	0.075	0.022	27.303	0.005	0.005	0.000	0.000	0.000	0.000
12	D	21	LYS	1	0.854	0.932	30.356	0.028	0.028	0.000	0.000	0.000	0.000
13	D	22	ASP	-1	-0.873	-0.940	27.581	-0.018	-0.018	0.000	0.000	0.000	0.000
14	D	23	ILE	0	-0.006	0.014	25.513	0.007	0.007	0.000	0.000	0.000	0.000
15	D	24	GLY	0	-0.019	-0.016	29.721	0.005	0.005	0.000	0.000	0.000	0.000
16	D	25	TRP	0	-0.004	-0.009	31.171	-0.001	-0.001	0.000	0.000	0.000	0.000
17	D	26	ASN	0	-0.039	-0.016	34.117	-0.002	-0.002	0.000	0.000	0.000	0.000
18	D	27	ASP	-1	-0.862	-0.929	35.235	-0.014	-0.014	0.000	0.000	0.000	0.000
19	D	28	TRP	0	-0.049	-0.009	35.665	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	29	ILE	0	-0.059	-0.052	31.903	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	30	ILE	0	-0.017	-0.008	35.096	0.000	0.000	0.000	0.000	0.000	0.000
22	D	31	ALA	0	-0.031	-0.001	33.509	-0.003	-0.003	0.000	0.000	0.000	0.000
23	D	32	PRO	0	-0.012	-0.022	28.368	0.002	0.002	0.000	0.000	0.000	0.000
24	D	33	SER	0	0.047	0.014	29.903	0.004	0.004	0.000	0.000	0.000	0.000
25	D	34	GLY	0	0.031	0.007	26.868	0.008	0.008	0.000	0.000	0.000	0.000
26	D	35	TYR	0	-0.011	-0.008	21.419	-0.002	-0.002	0.000	0.000	0.000	0.000
27	D	36	HIS	0	0.035	0.006	19.014	0.010	0.010	0.000	0.000	0.000	0.000
28	D	37	ALA	0	0.025	0.008	19.201	-0.011	-0.011	0.000	0.000	0.000	0.000
29	D	38	ASN	0	-0.127	-0.080	13.841	-0.034	-0.034	0.000	0.000	0.000	0.000
30	D	39	TYR	0	0.029	0.018	13.278	0.058	0.058	0.000	0.000	0.000	0.000
31	D	40	CYS	0	-0.050	-0.005	7.595	-0.004	-0.004	0.000	0.000	0.000	0.000
32	D	41	GLU	-1	-0.783	-0.862	7.979	0.278	0.278	0.000	0.000	0.000	0.000
33	D	42	GLY	0	0.037	-0.010	4.469	-1.190	-1.103	0.000	-0.048	-0.039	0.000
34	D	43	GLU	-1	-0.900	-0.925	2.906	-0.017	1.933	0.940	-1.024	-1.866	0.008
35	D	44	CYS	0	-0.101	-0.059	2.529	-4.593	-1.589	1.581	-2.166	-2.419	-0.024
36	D	45	PRO	0	0.037	0.021	4.125	-0.279	-0.131	0.000	-0.018	-0.130	0.000
37	D	46	SER	0	0.012	0.020	7.184	-0.189	-0.189	0.000	0.000	0.000	0.000
38	D	77	LEU	0	-0.019	-0.018	13.783	-0.008	-0.008	0.000	0.000	0.000	0.000
39	D	78	LYS	1	0.939	0.974	9.838	-0.950	-0.950	0.000	0.000	0.000	0.000
40	D	79	SER	0	0.002	-0.010	7.825	-0.135	-0.135	0.000	0.000	0.000	0.000
41	D	80	CYS	0	-0.021	-0.024	8.996	0.255	0.255	0.000	0.000	0.000	0.000
42	D	82	VAL	0	0.016	0.014	7.676	-0.001	-0.001	0.000	0.000	0.000	0.000
43	D	83	PRO	0	0.039	-0.015	10.194	-0.127	-0.127	0.000	0.000	0.000	0.000
44	D	84	THR	0	-0.036	-0.017	10.845	0.054	0.054	0.000	0.000	0.000	0.000
45	D	85	LYS	1	0.847	0.946	12.914	0.400	0.400	0.000	0.000	0.000	0.000
46	D	86	LEU	0	-0.014	-0.003	15.114	-0.013	-0.013	0.000	0.000	0.000	0.000
47	D	87	ARG	1	0.872	0.931	18.067	0.199	0.199	0.000	0.000	0.000	0.000
48	D	88	PRO	0	-0.003	0.007	20.935	0.007	0.007	0.000	0.000	0.000	0.000
49	D	89	MET	0	-0.015	-0.012	24.457	-0.014	-0.014	0.000	0.000	0.000	0.000
50	D	90	SER	0	-0.072	-0.057	26.348	0.007	0.007	0.000	0.000	0.000	0.000
51	D	91	MET	0	-0.022	-0.010	29.332	-0.001	-0.001	0.000	0.000	0.000	0.000
52	D	92	LEU	0	-0.001	0.011	32.261	0.002	0.002	0.000	0.000	0.000	0.000
53	D	93	TYR	0	0.023	0.015	33.836	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	94	TYR	0	0.009	0.001	36.941	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	95	ASP	-1	-0.943	-0.959	38.761	-0.014	-0.014	0.000	0.000	0.000	0.000
56	D	96	ASP	-1	-0.849	-0.947	40.377	0.000	0.000	0.000	0.000	0.000	0.000
57	D	97	GLY	0	-0.041	-0.005	42.994	0.000	0.000	0.000	0.000	0.000	0.000
58	D	98	GLN	0	-0.069	-0.050	45.392	0.000	0.000	0.000	0.000	0.000	0.000
59	D	99	ASN	0	-0.003	0.015	43.791	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	100	ILE	0	0.015	0.018	40.461	-0.001	-0.001	0.000	0.000	0.000	0.000
61	D	101	ILE	0	-0.020	-0.004	37.203	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	102	LYS	1	0.933	0.952	33.401	0.057	0.057	0.000	0.000	0.000	0.000
63	D	103	LYS	1	0.912	0.966	32.524	0.030	0.030	0.000	0.000	0.000	0.000
64	D	104	ASP	-1	-0.840	-0.899	29.373	-0.073	-0.073	0.000	0.000	0.000	0.000
65	D	105	ILE	0	-0.020	0.001	27.261	0.004	0.004	0.000	0.000	0.000	0.000
66	D	106	GLN	0	0.039	-0.010	24.691	-0.022	-0.022	0.000	0.000	0.000	0.000
67	D	107	ASN	0	-0.051	-0.039	21.307	0.017	0.017	0.000	0.000	0.000	0.000
68	D	108	MET	0	0.069	0.047	21.649	0.010	0.010	0.000	0.000	0.000	0.000
69	D	109	ILE	0	-0.018	0.015	18.431	-0.002	-0.002	0.000	0.000	0.000	0.000
70	D	110	VAL	0	0.019	0.008	13.294	-0.004	-0.004	0.000	0.000	0.000	0.000
71	D	111	GLU	-1	-0.891	-0.936	14.933	-0.318	-0.318	0.000	0.000	0.000	0.000
72	D	112	GLU	-1	-0.852	-0.971	10.632	-0.565	-0.565	0.000	0.000	0.000	0.000
73	D	114	GLY	0	0.073	0.036	6.555	-0.206	-0.206	0.000	0.000	0.000	0.000
74	D	116	SER	0	0.032	0.033	7.142	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:ILE)