FMO DATABASE

FMODB ID: K35G3

Calculation Name: 1Y96-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y96

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WXD5

Base Structure: X-ray

Registration Date: 2023-06-20

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-598652.824034
FMO2-HF: Nuclear repulsion	562896.285751
FMO2-HF: Total energy	-35756.538282
FMO2-MP2: Total energy	-35857.469785

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-10.118	-3.635	5.376	-3.354	-8.504	-0.015

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.001

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	A	3	GLU	-1	-0.911	-0.973	3.110	-3.680	-1.251	0.091	-1.176	-1.344	-0.004
4	A	4	TRP	0	0.019	0.006	5.843	-0.140	-0.140	0.000	0.000	0.000	0.000
5	A	5	MET	0	-0.004	-0.019	2.198	-2.023	-0.709	3.016	-1.044	-3.285	-0.006
6	A	6	LYS	1	0.831	0.916	2.526	-4.375	-1.758	2.240	-1.219	-3.639	-0.005
7	A	7	LYS	1	0.865	0.958	3.460	1.240	1.363	0.029	0.085	-0.236	0.000
8	A	8	GLY	0	0.024	0.022	6.878	-0.066	-0.066	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.023	-0.017	8.949	0.072	0.072	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.001	-0.003	11.301	0.046	0.046	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.812	-0.886	10.129	-0.637	-0.637	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.010	-0.010	5.934	0.146	0.146	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.020	-0.016	12.535	0.040	0.040	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.885	-0.936	15.924	-0.198	-0.198	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.059	-0.040	12.810	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.027	-0.006	17.023	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.045	-0.043	19.440	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.829	0.927	20.005	0.206	0.206	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.851	-0.907	21.440	-0.132	-0.132	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.000	-0.006	17.020	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.804	0.866	19.136	0.227	0.227	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.007	-0.011	13.644	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.010	0.008	14.983	0.036	0.036	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.017	-0.007	12.975	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.003	-0.016	11.465	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.979	-0.985	13.798	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.912	0.952	16.845	0.196	0.196	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.016	0.014	17.196	0.031	0.031	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.852	-0.914	17.690	-0.241	-0.241	0.000	0.000	0.000	0.000
30	A	30	TYR	0	0.003	-0.003	16.820	0.023	0.023	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.862	0.911	20.010	0.112	0.112	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.018	0.024	21.487	0.018	0.018	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.011	-0.006	21.556	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.003	0.013	16.533	0.009	0.009	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.003	0.012	19.598	0.007	0.007	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.012	-0.013	16.293	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.006	0.001	10.376	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.805	-0.861	12.320	0.064	0.064	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.024	-0.009	9.390	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.059	-0.016	8.098	-0.050	-0.050	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.065	-0.080	7.801	0.214	0.214	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.017	0.003	6.492	0.116	0.116	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.030	0.012	8.625	-0.079	-0.079	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.008	0.020	11.502	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.009	-0.006	14.089	0.030	0.030	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.018	-0.011	17.606	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.016	0.008	20.343	0.017	0.017	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.031	-0.033	23.832	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.001	-0.012	26.489	0.008	0.008	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.007	0.002	28.035	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.925	-0.974	31.498	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.880	-0.906	34.542	-0.047	-0.047	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.048	-0.019	35.460	0.003	0.003	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.095	-0.054	33.234	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.015	-0.026	28.093	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.008	0.004	26.378	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.008	-0.009	22.219	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.002	0.004	19.214	0.013	0.013	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.004	0.011	17.298	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.021	-0.005	12.911	0.012	0.012	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.026	0.000	10.982	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.072	0.039	8.214	-0.086	-0.086	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.033	-0.041	5.847	-0.164	-0.164	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.071	-0.026	6.893	-0.176	-0.176	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.003	0.016	8.582	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.082	-0.033	8.437	-0.180	-0.180	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.001	-0.008	10.320	-0.095	-0.095	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.016	0.009	11.739	0.047	0.047	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.845	-0.890	14.240	-0.241	-0.241	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.012	-0.009	17.606	0.008	0.008	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.063	-0.010	20.185	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.005	-0.016	23.626	0.016	0.016	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.776	-0.871	23.071	-0.180	-0.180	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.038	0.027	25.613	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.860	-0.940	27.751	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.075	-0.053	30.299	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.961	0.973	32.341	0.059	0.059	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.033	-0.017	27.887	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.905	0.952	24.758	0.119	0.119	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.818	-0.899	28.666	-0.065	-0.065	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.882	0.938	30.786	0.069	0.069	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.012	-0.008	24.670	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.041	-0.010	26.705	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.026	-0.008	28.023	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.049	-0.002	25.721	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.010	0.000	24.668	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)