FMO DATABASE

FMODB ID: MNQ8Z

Calculation Name: 1B9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B9W

Chain ID: A

ChEMBL ID:

UniProt ID: Q25659

Base Structure: X-ray

Registration Date: 2023-09-24

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

Total energy (hartree)

FMO2-HF: Electronic energy	-611806.172093
FMO2-HF: Nuclear repulsion	572755.411844
FMO2-HF: Total energy	-39050.76025
FMO2-MP2: Total energy	-39153.541525

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.
-9.606	0.569	5.303	-4.208	-11.269	-0.023

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 : -0.010 / q_NPA : -0.009

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	A	3	SER	0	0.009	-0.022	2.768	-3.836	-1.277	0.421	-1.375	-1.605	-0.008
4	A	4	GLU	-1	-0.907	-0.960	5.429	-1.106	-1.106	0.000	0.000	0.000	0.000
5	A	5	HIS	0	-0.056	-0.018	2.771	-0.448	0.511	0.274	-0.208	-1.025	-0.001
6	A	6	ARG	1	0.924	0.973	2.454	1.862	3.801	0.903	-0.693	-2.150	-0.001
7	A	7	CYS	0	-0.115	-0.055	3.504	1.209	1.433	0.021	0.110	-0.354	0.000
8	A	8	ILE	0	-0.059	-0.029	6.243	-0.119	-0.119	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.898	-0.942	9.728	-0.430	-0.430	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.078	-0.038	9.503	0.153	0.153	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.080	-0.049	10.572	-0.155	-0.155	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.001	-0.006	7.320	0.083	0.083	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.011	0.021	10.660	0.012	0.012	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.932	-0.981	11.774	-0.292	-0.292	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.047	-0.020	12.683	0.037	0.037	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.020	0.007	10.115	0.110	0.110	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.016	0.008	5.306	-0.159	-0.159	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.006	0.005	2.817	-5.047	-3.187	2.536	-1.442	-2.954	-0.011
19	A	20	ARG	1	0.907	0.947	4.509	0.456	0.553	-0.001	-0.016	-0.080	0.000
20	A	21	TYR	0	-0.048	-0.034	6.909	0.416	0.416	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.014	-0.011	9.331	-0.153	-0.153	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.901	-0.924	11.684	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.052	-0.024	12.424	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.055	-0.031	12.485	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.677	-0.843	8.284	-0.917	-0.917	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.816	-0.887	8.119	0.314	0.314	0.000	0.000	0.000	0.000
27	A	28	TRP	0	-0.002	-0.026	7.630	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.885	0.934	8.777	-0.441	-0.441	0.000	0.000	0.000	0.000
29	A	30	CYS	0	-0.029	0.004	9.962	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.007	0.008	8.630	0.094	0.094	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.077	0.021	12.042	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.013	0.019	14.939	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	34	PHE	0	-0.029	-0.005	15.384	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.822	0.886	17.128	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.920	-0.963	15.603	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-1.010	-1.010	17.935	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.012	0.010	20.649	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.013	0.010	16.882	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.941	0.977	16.912	0.070	0.070	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.035	-0.022	16.880	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.025	0.011	19.759	0.018	0.018	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.025	-0.016	20.433	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	PRO	0	0.017	-0.002	21.574	0.018	0.018	0.000	0.000	0.000	0.000
44	A	46	ASN	0	0.002	0.005	22.996	0.021	0.021	0.000	0.000	0.000	0.000
45	A	47	MET	0	-0.028	0.014	18.990	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	48	THR	0	0.052	0.008	23.332	0.013	0.013	0.000	0.000	0.000	0.000
47	A	49	CYS	0	0.060	0.022	18.390	0.023	0.023	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.891	0.949	22.889	-0.095	-0.095	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.859	-0.904	22.973	0.070	0.070	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.957	0.965	19.197	-0.066	-0.066	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.016	0.009	17.047	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.009	-0.004	18.507	0.031	0.031	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.018	0.017	16.154	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	56	CYS	0	-0.063	-0.016	13.984	0.008	0.008	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.047	0.024	11.240	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.022	-0.025	13.102	-0.043	-0.043	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.921	-0.956	12.177	0.598	0.598	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.042	-0.022	14.158	0.011	0.011	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.912	-0.943	16.108	0.241	0.241	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.871	0.922	20.052	-0.314	-0.314	0.000	0.000	0.000	0.000
61	A	64	MET	0	0.027	0.017	21.638	0.014	0.014	0.000	0.000	0.000	0.000
62	A	65	ASN	0	-0.011	0.020	21.299	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.914	-0.984	24.397	0.124	0.124	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.892	0.942	24.962	-0.157	-0.157	0.000	0.000	0.000	0.000
65	A	68	ASN	0	-0.057	-0.030	25.977	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.932	-0.956	20.036	0.212	0.212	0.000	0.000	0.000	0.000
67	A	70	ILE	0	-0.015	-0.014	17.598	0.004	0.004	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.018	-0.004	17.629	0.019	0.019	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.930	0.950	15.299	-0.410	-0.410	0.000	0.000	0.000	0.000
70	A	74	CYS	0	-0.031	0.014	8.189	0.019	0.019	0.000	0.000	0.000	0.000
71	A	75	THR	0	0.015	-0.002	14.040	0.003	0.003	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.964	0.990	14.500	-0.390	-0.390	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.897	-0.950	14.999	0.378	0.378	0.000	0.000	0.000	0.000
74	A	78	GLY	0	-0.046	-0.014	13.685	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.069	-0.038	10.838	0.059	0.059	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.923	-0.990	8.047	1.440	1.440	0.000	0.000	0.000	0.000
77	A	81	PRO	0	-0.014	-0.005	8.059	0.110	0.110	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.039	0.011	2.750	-1.210	0.252	0.571	-0.290	-1.742	-0.001
79	A	83	PHE	0	-0.025	-0.036	2.603	-1.476	-0.401	0.578	-0.294	-1.359	-0.001
80	A	84	GLU	-1	-0.916	-0.959	7.427	0.234	0.234	0.000	0.000	0.000	0.000
81	A	85	GLY	0	0.016	-0.002	9.374	-0.101	-0.101	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.012	0.019	9.085	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	87	PHE	0	0.027	0.012	6.066	0.102	0.102	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.018	0.003	5.386	0.024	0.024	0.000	0.000	0.000	0.000
85	A	90	HIS	0	-0.039	-0.005	7.351	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	91	HIS	0	0.022	0.023	5.485	-0.229	-0.229	0.000	0.000	0.000	0.000

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