FMO DATABASE

FMODB ID: G5RK1

Calculation Name: 2D2A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D2A

Chain ID: A

ChEMBL ID:

UniProt ID: P77667

Base Structure: X-ray

Registration Date: 2023-09-23

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-834928.695726
FMO2-HF: Nuclear repulsion	791071.589655
FMO2-HF: Total energy	-43857.106071
FMO2-MP2: Total energy	-43983.572243

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:9:ASN)

Summations of interaction energy for fragment #1(A:9:ASN)

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.
-3.253	-0.056000000000001	0.24	-1.302	-2.134	0.003

Interaction energy analysis for fragmet #1(A:9:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.006

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	11	GLN	0	0.033	-0.006	3.914	-1.784	-0.066	-0.012	-0.839	-0.867	0.002
4	A	12	ASP	-1	-0.900	-0.940	5.544	1.918	1.976	-0.001	-0.002	-0.054	0.000
5	A	13	PHE	0	-0.026	-0.028	3.099	-1.451	-0.239	0.255	-0.443	-1.024	0.001
6	A	14	ALA	0	-0.075	-0.020	7.906	-0.312	-0.312	0.000	0.000	0.000	0.000
7	A	15	TRP	0	0.008	-0.004	4.352	-0.100	-0.019	-0.001	-0.005	-0.075	0.000
8	A	16	GLN	0	-0.060	-0.033	10.849	0.158	0.158	0.000	0.000	0.000	0.000
9	A	17	GLY	0	0.001	-0.002	13.156	0.056	0.056	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.061	-0.018	13.739	-0.091	-0.091	0.000	0.000	0.000	0.000
11	A	19	THR	0	-0.022	-0.043	16.888	0.053	0.053	0.000	0.000	0.000	0.000
12	A	20	LEU	0	-0.015	-0.010	20.692	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	21	THR	0	0.037	-0.002	23.952	0.032	0.032	0.000	0.000	0.000	0.000
14	A	22	PRO	0	0.039	-0.001	26.994	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	23	ALA	0	0.013	0.022	30.324	0.007	0.007	0.000	0.000	0.000	0.000
16	A	24	ALA	0	0.018	0.010	26.135	0.001	0.001	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.018	0.010	27.770	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	26	ILE	0	-0.004	-0.011	28.815	0.009	0.009	0.000	0.000	0.000	0.000
19	A	27	HIS	1	0.845	0.925	30.381	0.256	0.256	0.000	0.000	0.000	0.000
20	A	28	ILE	0	0.023	0.006	25.429	0.002	0.002	0.000	0.000	0.000	0.000
21	A	29	ARG	1	0.898	0.942	29.790	0.161	0.161	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.825	-0.886	32.702	-0.185	-0.185	0.000	0.000	0.000	0.000
23	A	31	LEU	0	-0.055	-0.030	29.972	0.009	0.009	0.000	0.000	0.000	0.000
24	A	32	VAL	0	0.058	0.016	30.293	0.006	0.006	0.000	0.000	0.000	0.000
25	A	33	ALA	0	-0.041	-0.014	33.132	0.010	0.010	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.844	0.933	35.627	0.212	0.212	0.000	0.000	0.000	0.000
27	A	35	GLN	0	-0.027	-0.005	32.348	0.003	0.003	0.000	0.000	0.000	0.000
28	A	36	PRO	0	0.037	0.017	34.314	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	37	GLY	0	0.028	0.007	33.313	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	38	MET	0	-0.083	0.013	28.438	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	39	VAL	0	-0.014	-0.020	26.038	0.020	0.020	0.000	0.000	0.000	0.000
32	A	40	GLY	0	-0.008	-0.012	25.735	0.011	0.011	0.000	0.000	0.000	0.000
33	A	41	VAL	0	-0.025	-0.008	23.095	0.003	0.003	0.000	0.000	0.000	0.000
34	A	42	ARG	1	0.813	0.880	16.442	0.711	0.711	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.005	-0.003	16.813	0.006	0.006	0.000	0.000	0.000	0.000
36	A	44	GLY	0	0.021	0.000	15.408	-0.066	-0.066	0.000	0.000	0.000	0.000
37	A	45	VAL	0	-0.040	-0.023	12.112	0.054	0.054	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.902	0.969	15.499	0.684	0.684	0.000	0.000	0.000	0.000
39	A	47	GLN	0	0.073	0.028	13.231	0.129	0.129	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.051	-0.036	16.687	0.137	0.137	0.000	0.000	0.000	0.000
41	A	49	GLY	0	0.040	0.026	18.927	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	50	CYS	0	-0.030	-0.021	19.457	0.053	0.053	0.000	0.000	0.000	0.000
43	A	51	ALA	0	-0.009	0.002	14.257	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	52	GLY	0	0.010	0.018	14.387	-0.135	-0.135	0.000	0.000	0.000	0.000
45	A	53	PHE	0	-0.004	-0.016	11.351	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	54	GLY	0	0.039	0.031	15.664	0.071	0.071	0.000	0.000	0.000	0.000
47	A	55	TYR	0	0.027	-0.009	15.732	-0.073	-0.073	0.000	0.000	0.000	0.000
48	A	56	VAL	0	-0.054	-0.033	18.598	0.071	0.071	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.006	0.005	19.820	-0.042	-0.042	0.000	0.000	0.000	0.000
50	A	58	ASP	-1	-0.857	-0.911	22.475	-0.406	-0.406	0.000	0.000	0.000	0.000
51	A	59	SER	0	-0.025	-0.025	24.367	0.006	0.006	0.000	0.000	0.000	0.000
52	A	60	VAL	0	0.000	0.008	22.705	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	61	SER	0	-0.027	-0.036	25.765	0.025	0.025	0.000	0.000	0.000	0.000
54	A	62	GLU	-1	-0.896	-0.934	24.151	-0.296	-0.296	0.000	0.000	0.000	0.000
55	A	63	PRO	0	-0.025	0.001	21.002	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	64	ASP	-1	-0.823	-0.905	17.874	-0.498	-0.498	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.753	0.833	17.783	0.413	0.413	0.000	0.000	0.000	0.000
58	A	66	ASP	-1	-0.824	-0.928	13.036	-0.966	-0.966	0.000	0.000	0.000	0.000
59	A	67	ASP	-1	-0.800	-0.874	13.923	-0.710	-0.710	0.000	0.000	0.000	0.000
60	A	68	LEU	0	-0.022	0.000	11.704	0.119	0.119	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.035	-0.024	15.794	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	70	PHE	0	0.019	0.022	14.014	0.043	0.043	0.000	0.000	0.000	0.000
63	A	71	GLU	-1	-0.799	-0.902	20.032	-0.183	-0.183	0.000	0.000	0.000	0.000
64	A	72	HIS	0	0.000	0.001	23.837	0.018	0.018	0.000	0.000	0.000	0.000
65	A	73	ASP	-1	-0.873	-0.932	26.392	-0.160	-0.160	0.000	0.000	0.000	0.000
66	A	74	GLY	0	-0.031	-0.012	28.866	0.005	0.005	0.000	0.000	0.000	0.000
67	A	75	ALA	0	-0.064	-0.016	27.507	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.823	0.896	24.085	0.176	0.176	0.000	0.000	0.000	0.000
69	A	77	LEU	0	0.023	0.010	19.147	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	78	PHE	0	0.015	0.001	19.010	0.012	0.012	0.000	0.000	0.000	0.000
71	A	79	VAL	0	0.002	-0.009	13.197	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	80	PRO	0	0.039	0.040	12.802	0.036	0.036	0.000	0.000	0.000	0.000
73	A	81	LEU	0	0.027	0.017	9.336	-0.210	-0.210	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.035	-0.024	6.920	-0.289	-0.289	0.000	0.000	0.000	0.000
75	A	83	ALA	0	-0.025	-0.013	8.578	-0.473	-0.473	0.000	0.000	0.000	0.000
76	A	84	MET	0	0.009	0.020	8.313	-0.145	-0.145	0.000	0.000	0.000	0.000
77	A	85	PRO	0	-0.011	-0.002	4.016	0.043	0.171	-0.001	-0.013	-0.114	0.000
78	A	86	PHE	0	-0.053	-0.015	6.163	0.088	0.088	0.000	0.000	0.000	0.000
79	A	87	ILE	0	-0.033	-0.014	9.156	0.403	0.403	0.000	0.000	0.000	0.000
80	A	88	ASP	-1	-0.730	-0.843	9.614	-0.471	-0.471	0.000	0.000	0.000	0.000
81	A	89	GLY	0	0.043	0.023	11.466	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	90	THR	0	-0.089	-0.056	14.634	0.059	0.059	0.000	0.000	0.000	0.000
83	A	91	GLU	-1	-0.866	-0.886	16.745	-0.289	-0.289	0.000	0.000	0.000	0.000
84	A	92	VAL	0	-0.031	-0.026	19.793	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	93	ASP	-1	-0.794	-0.884	22.177	-0.255	-0.255	0.000	0.000	0.000	0.000
86	A	94	PHE	0	-0.079	-0.058	25.841	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	95	VAL	0	0.033	0.039	28.976	0.022	0.022	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.851	0.896	32.103	0.183	0.183	0.000	0.000	0.000	0.000
89	A	97	GLU	-1	-0.923	-0.953	35.482	-0.168	-0.168	0.000	0.000	0.000	0.000
90	A	98	GLY	0	0.006	-0.005	38.397	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	99	LEU	0	-0.031	-0.017	39.970	0.000	0.000	0.000	0.000	0.000	0.000
92	A	100	ASN	0	0.007	0.012	33.668	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	101	GLN	0	-0.050	-0.051	33.786	0.010	0.010	0.000	0.000	0.000	0.000
94	A	102	ILE	0	-0.013	0.003	28.229	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	103	PHE	0	0.013	0.004	25.158	0.016	0.016	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.838	0.900	24.630	0.398	0.398	0.000	0.000	0.000	0.000
97	A	105	PHE	0	0.033	-0.002	19.441	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	106	HIS	0	0.009	0.014	20.753	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	107	ASN	0	0.046	0.018	13.257	0.063	0.063	0.000	0.000	0.000	0.000
100	A	108	PRO	0	0.020	0.012	15.688	0.014	0.014	0.000	0.000	0.000	0.000
101	A	109	LYS	1	0.813	0.886	9.721	1.212	1.212	0.000	0.000	0.000	0.000
102	A	110	ALA	0	-0.012	0.012	15.234	-0.045	-0.045	0.000	0.000	0.000	0.000
103	A	111	GLN	0	-0.041	-0.033	16.933	0.021	0.021	0.000	0.000	0.000	0.000
104	A	112	ASN	0	-0.070	-0.047	18.819	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	113	GLU	-1	-0.787	-0.857	22.169	-0.493	-0.493	0.000	0.000	0.000	0.000
106	A	114	CYS	0	-0.130	-0.092	23.594	0.027	0.027	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.019	0.009	25.429	0.027	0.027	0.000	0.000	0.000	0.000
108	A	116	CYM	-1	-0.800	-0.865	26.546	-0.394	-0.394	0.000	0.000	0.000	0.000
109	A	117	GLY	0	-0.021	-0.005	29.158	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	118	GLU	-1	-1.007	-1.003	30.896	-0.293	-0.293	0.000	0.000	0.000	0.000
111	A	119	SER	0	-0.070	-0.055	29.626	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	120	PHE	0	-0.010	-0.002	31.724	0.008	0.008	0.000	0.000	0.000	0.000
113	A	121	GLY	0	0.017	0.025	32.209	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	122	VAL	0	0.014	0.017	33.054	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASN)