FMO DATABASE

FMODB ID: YY442

Calculation Name: 3IX0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IX0

Chain ID: A

ChEMBL ID:

UniProt ID: P08118

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554235.477548
FMO2-HF: Nuclear repulsion	516383.348267
FMO2-HF: Total energy	-37852.129281
FMO2-MP2: Total energy	-37953.58091

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:SER)

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

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.
-19.19	-32.243	33.793	-13.584	-7.156	0.033

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.034

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	TYR	0	-0.058	-0.029	3.830	0.961	2.927	-0.022	-1.020	-0.924	-0.001
4	A	4	PHE	0	0.012	0.007	6.331	-0.320	-0.320	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.024	-0.007	10.189	0.049	0.049	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.068	0.027	13.681	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.066	-0.027	17.322	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.914	-0.957	19.386	0.027	0.027	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.090	-0.031	22.111	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.948	0.965	23.567	0.024	0.024	0.000	0.000	0.000	0.000
11	A	18	CYS	0	-0.027	0.026	13.427	0.026	0.026	0.000	0.000	0.000	0.000
12	A	19	MET	0	-0.035	-0.035	20.397	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.685	-0.820	16.718	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.016	-0.006	14.114	0.005	0.005	0.000	0.000	0.000	0.000
15	A	22	LYS	1	0.792	0.893	17.244	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.015	0.017	20.533	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.079	-0.041	19.933	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.935	0.962	21.151	0.003	0.003	0.000	0.000	0.000	0.000
19	A	26	HIS	1	0.842	0.907	18.470	0.051	0.051	0.000	0.000	0.000	0.000
20	A	27	PRO	0	-0.017	-0.009	21.429	0.006	0.006	0.000	0.000	0.000	0.000
21	A	28	ILE	0	0.038	0.030	20.073	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	29	ASN	0	-0.022	-0.017	18.237	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	30	SER	0	-0.054	-0.016	18.163	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	31	GLU	-1	-0.811	-0.888	12.229	-0.239	-0.239	0.000	0.000	0.000	0.000
25	A	32	TRP	0	-0.050	-0.046	13.962	0.036	0.036	0.000	0.000	0.000	0.000
26	A	33	GLN	0	0.039	0.033	11.823	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	34	THR	0	-0.022	-0.016	11.780	0.033	0.033	0.000	0.000	0.000	0.000
28	A	35	ASP	-1	-0.843	-0.915	13.996	0.067	0.067	0.000	0.000	0.000	0.000
29	A	36	ASN	0	-0.117	-0.095	11.000	0.033	0.033	0.000	0.000	0.000	0.000
30	A	37	CYS	0	-0.062	-0.004	10.362	0.065	0.065	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.753	-0.847	7.700	0.168	0.168	0.000	0.000	0.000	0.000
32	A	39	THR	0	-0.057	-0.047	7.020	0.027	0.027	0.000	0.000	0.000	0.000
33	A	40	CYS	0	0.014	0.015	8.463	-0.144	-0.144	0.000	0.000	0.000	0.000
34	A	41	THR	0	-0.007	-0.014	11.119	0.015	0.015	0.000	0.000	0.000	0.000
35	A	43	TYR	0	0.044	0.018	12.199	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	44	GLU	-1	-0.910	-0.973	17.741	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	45	THR	0	0.021	0.007	17.679	0.006	0.006	0.000	0.000	0.000	0.000
38	A	46	GLU	-1	-0.943	-0.969	13.163	0.023	0.023	0.000	0.000	0.000	0.000
39	A	47	ILE	0	-0.011	-0.018	13.591	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	48	SER	0	0.002	0.003	8.764	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	51	THR	0	-0.012	0.004	2.927	-0.576	0.471	0.358	-0.512	-0.894	0.003
42	A	52	LEU	0	0.056	0.022	4.104	-0.572	-0.407	-0.001	-0.045	-0.119	0.000
43	A	53	VAL	0	-0.055	-0.024	6.788	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	54	SER	0	0.013	0.010	7.072	0.542	0.542	0.000	0.000	0.000	0.000
45	A	55	THR	0	-0.026	-0.021	7.982	-0.358	-0.358	0.000	0.000	0.000	0.000
46	A	56	PRO	0	-0.037	0.012	9.855	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	57	VAL	0	0.008	-0.021	10.625	0.010	0.010	0.000	0.000	0.000	0.000
48	A	58	GLY	0	0.035	0.035	13.677	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	59	TYR	0	-0.023	-0.028	15.690	0.008	0.008	0.000	0.000	0.000	0.000
50	A	60	ASP	-1	-0.755	-0.856	19.474	0.048	0.048	0.000	0.000	0.000	0.000
51	A	61	LYS	1	0.901	0.940	16.627	-0.086	-0.086	0.000	0.000	0.000	0.000
52	A	62	ASP	-1	-0.884	-0.919	22.533	0.043	0.043	0.000	0.000	0.000	0.000
53	A	63	ASN	0	-0.029	-0.039	26.355	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	64	CYS	0	-0.120	-0.040	22.343	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	65	GLN	0	0.026	0.008	21.186	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	66	ARG	1	0.898	0.961	12.336	-0.308	-0.308	0.000	0.000	0.000	0.000
57	A	67	ILE	0	-0.017	-0.012	18.280	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	68	PHE	0	0.010	0.007	12.113	0.004	0.004	0.000	0.000	0.000	0.000
59	A	69	LYS	1	0.954	0.976	15.843	-0.139	-0.139	0.000	0.000	0.000	0.000
60	A	70	LYS	1	0.934	0.961	15.189	-0.123	-0.123	0.000	0.000	0.000	0.000
61	A	71	GLU	-1	-0.922	-0.967	15.785	0.065	0.065	0.000	0.000	0.000	0.000
62	A	72	ASP	-1	-0.838	-0.913	16.676	0.072	0.072	0.000	0.000	0.000	0.000
63	A	74	LYS	1	0.874	0.943	11.195	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	75	TYR	0	0.006	-0.014	11.085	-0.084	-0.084	0.000	0.000	0.000	0.000
65	A	76	ILE	0	-0.035	-0.006	14.827	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	77	VAL	0	0.022	-0.007	16.944	0.020	0.020	0.000	0.000	0.000	0.000
67	A	78	VAL	0	-0.023	0.002	19.619	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	79	GLU	-1	-0.758	-0.885	23.415	0.045	0.045	0.000	0.000	0.000	0.000
69	A	80	LYS	1	0.774	0.873	24.644	-0.062	-0.062	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.809	0.895	27.712	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	82	ASP	-1	-0.794	-0.894	29.527	0.039	0.039	0.000	0.000	0.000	0.000
72	A	83	PRO	0	0.020	0.007	25.742	0.001	0.001	0.000	0.000	0.000	0.000
73	A	84	LYS	1	0.905	0.959	25.949	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	85	LYS	1	0.842	0.918	27.653	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	86	THR	0	0.026	0.013	22.507	0.004	0.004	0.000	0.000	0.000	0.000
76	A	88	SER	0	0.017	0.012	21.219	0.006	0.006	0.000	0.000	0.000	0.000
77	A	89	VAL	0	-0.060	-0.038	15.140	0.005	0.005	0.000	0.000	0.000	0.000
78	A	90	SER	0	0.006	0.005	17.583	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	91	GLU	-1	-0.932	-0.961	12.220	0.028	0.028	0.000	0.000	0.000	0.000
80	A	92	TRP	0	0.026	-0.011	10.091	0.036	0.036	0.000	0.000	0.000	0.000
81	A	93	ILE	0	0.026	0.022	5.314	-0.137	-0.137	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.017	-0.036	1.685	-18.096	-34.327	33.458	-12.007	-5.219	0.031

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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