FMO DATABASE

FMODB ID: K3Y53

Calculation Name: 2D27-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D27

Chain ID: A

ChEMBL ID:

UniProt ID: P31742

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1311649.718225
FMO2-HF: Nuclear repulsion	1252966.011316
FMO2-HF: Total energy	-58683.70691
FMO2-MP2: Total energy	-58854.68941

3D Structure Molmil

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.
-5.391	-1.213	1.339	-2.474	-3.043	-0.017

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 : 0.011 / q_NPA : 0.005

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	GLN	0	0.004	-0.003	2.481	-6.065	-2.047	1.340	-2.455	-2.903	-0.017
4	A	4	ARG	1	0.884	0.927	4.597	1.787	1.947	-0.001	-0.019	-0.140	0.000
5	A	5	SER	0	0.108	0.053	8.351	-0.012	-0.012	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.007	-0.014	11.147	0.058	0.058	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.902	-0.947	13.159	-0.492	-0.492	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.027	-0.002	11.976	0.075	0.075	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.911	0.951	8.981	1.137	1.137	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.001	0.016	13.573	0.100	0.100	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.024	0.011	16.837	0.067	0.067	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.828	-0.903	13.630	-0.631	-0.631	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.003	0.015	16.350	0.062	0.062	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.024	-0.022	17.925	0.059	0.059	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.001	0.000	18.299	0.042	0.042	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.859	-0.902	16.262	-0.224	-0.224	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.801	0.886	16.969	0.202	0.202	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.921	0.964	23.586	0.152	0.152	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.865	0.923	24.643	0.142	0.142	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.023	0.003	22.056	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.865	0.922	24.843	0.198	0.198	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.840	-0.925	21.900	-0.311	-0.311	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.016	-0.007	24.088	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.828	-0.912	25.825	-0.212	-0.212	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.015	0.008	19.867	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.001	0.009	23.753	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.912	0.958	25.452	0.221	0.221	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.011	-0.008	24.581	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	ARG	1	1.007	1.002	17.823	0.520	0.520	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.013	0.009	24.559	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.024	-0.024	27.815	0.009	0.009	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.042	-0.026	21.965	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.021	0.039	26.031	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.860	-0.930	27.237	-0.222	-0.222	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.088	-0.047	28.195	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.068	0.043	29.799	0.012	0.012	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.070	-0.037	27.687	0.014	0.014	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.060	0.040	24.862	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.011	-0.017	22.648	0.025	0.025	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.084	0.033	25.667	0.025	0.025	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.036	0.031	27.898	0.024	0.024	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.036	-0.017	29.023	0.024	0.024	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.009	-0.015	28.135	0.018	0.018	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.037	0.030	31.602	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.860	0.916	31.661	0.251	0.251	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.086	-0.048	32.725	0.013	0.013	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.004	0.017	36.342	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.091	-0.048	33.316	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.004	-0.001	31.289	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.025	-0.031	34.733	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.769	-0.892	35.283	-0.194	-0.194	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.839	0.894	35.360	0.157	0.157	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.826	-0.888	34.099	-0.189	-0.189	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.020	0.009	28.549	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.005	0.009	30.715	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.790	-0.892	31.659	-0.191	-0.191	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.003	0.000	27.508	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.078	-0.035	26.934	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.026	-0.017	26.930	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.928	-0.961	28.106	-0.261	-0.261	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.091	-0.047	22.743	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.038	-0.025	21.690	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.010	0.018	24.337	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.097	-0.046	25.933	0.010	0.010	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.023	-0.005	28.838	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.017	-0.001	32.457	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.063	-0.021	34.790	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.752	-0.841	37.622	-0.142	-0.142	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.076	0.017	40.896	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.731	0.826	42.734	0.132	0.132	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.072	-0.025	40.016	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.002	0.012	39.887	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.020	0.014	44.281	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.835	-0.911	46.272	-0.114	-0.114	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.029	-0.016	47.996	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.001	0.016	43.681	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.037	-0.025	42.485	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.950	-0.969	44.274	-0.112	-0.112	0.000	0.000	0.000	0.000
79	A	79	MET	0	-0.061	-0.028	39.654	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.016	-0.016	37.285	0.007	0.007	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.021	-0.010	39.705	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.954	-0.970	36.130	-0.147	-0.147	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.078	0.043	35.850	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.035	-0.018	37.620	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.022	0.021	34.918	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.050	-0.037	32.265	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.010	0.004	35.934	0.009	0.009	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.102	0.038	37.432	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.938	0.957	37.425	0.167	0.167	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.002	0.001	29.201	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.041	0.018	33.980	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.826	0.894	35.622	0.145	0.145	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.106	-0.039	32.452	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	PHE	0	-0.007	-0.020	28.735	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	95	HIS	0	-0.046	-0.025	31.616	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.003	-0.001	30.482	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	97	CYS	0	-0.010	-0.013	33.877	0.012	0.012	0.000	0.000	0.000	0.000
98	A	98	PRO	0	0.025	0.019	34.878	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.011	-0.012	36.284	0.009	0.009	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.041	0.015	37.946	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.828	-0.915	36.626	-0.170	-0.170	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.808	0.887	35.302	0.185	0.185	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.918	-0.954	35.291	-0.175	-0.175	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.011	-0.023	34.622	0.005	0.005	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.815	0.907	27.118	0.251	0.251	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.074	0.042	32.284	0.009	0.009	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.796	-0.850	32.147	-0.208	-0.208	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.018	-0.011	29.132	0.007	0.007	0.000	0.000	0.000	0.000
109	A	109	TRP	0	0.013	0.004	32.198	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.014	-0.018	27.689	0.000	0.000	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.072	0.034	31.685	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.800	-0.844	27.109	-0.299	-0.299	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.014	0.005	26.061	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.049	-0.048	21.974	-0.022	-0.022	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.899	-0.952	21.604	-0.437	-0.437	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.912	-0.964	18.782	-0.605	-0.605	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.021	-0.008	21.354	0.031	0.031	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.023	0.001	22.885	0.024	0.024	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.024	0.016	23.609	0.027	0.027	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.849	-0.903	20.215	-0.475	-0.475	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.048	-0.016	23.720	0.020	0.020	0.000	0.000	0.000	0.000
122	A	122	VAL	0	0.016	-0.002	26.756	0.023	0.023	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.811	0.869	19.999	0.451	0.451	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.069	-0.023	25.277	0.015	0.015	0.000	0.000	0.000	0.000
125	A	125	ALA	0	-0.051	-0.021	27.460	0.016	0.016	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.009	-0.009	30.393	0.014	0.014	0.000	0.000	0.000	0.000
127	A	127	GLY	0	-0.021	0.001	29.345	0.011	0.011	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.011	0.012	30.393	0.005	0.005	0.000	0.000	0.000	0.000
129	A	129	PRO	0	-0.068	-0.034	27.731	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.042	0.009	26.723	0.013	0.013	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.051	-0.025	28.175	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.012	0.006	25.517	0.008	0.008	0.000	0.000	0.000	0.000
133	A	133	HIS	0	-0.032	-0.035	29.598	0.004	0.004	0.000	0.000	0.000	0.000
134	A	134	VAL	0	0.027	0.019	29.675	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.036	0.021	32.309	0.015	0.015	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.038	-0.013	34.505	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.838	0.885	30.998	0.251	0.251	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.031	-0.040	36.430	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.847	-0.935	39.673	-0.154	-0.154	0.000	0.000	0.000	0.000
140	A	140	ILE	0	-0.034	0.004	34.515	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.852	-0.919	38.078	-0.186	-0.186	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.949	-0.970	40.311	-0.130	-0.130	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.073	-0.038	40.408	0.006	0.006	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.014	0.012	37.324	0.005	0.005	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.859	-0.907	41.919	-0.133	-0.133	0.000	0.000	0.000	0.000
146	A	146	ARG	1	0.787	0.913	45.242	0.123	0.123	0.000	0.000	0.000	0.000
147	A	147	TRP	0	-0.083	-0.052	40.999	0.002	0.002	0.000	0.000	0.000	0.000
148	A	148	TYR	0	-0.082	-0.062	40.572	0.006	0.006	0.000	0.000	0.000	0.000

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