FMO DATABASE

FMODB ID: 7JRGK

Calculation Name: 2CLY-B-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CLY

Chain ID: B

ChEMBL ID:

UniProt ID: P13619

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-736012.314361
FMO2-HF: Nuclear repulsion	688230.862359
FMO2-HF: Total energy	-47781.452002
FMO2-MP2: Total energy	-47922.851925

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(B:3:ACE )

Summations of interaction energy for fragment #1(B:3:ACE )

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.
-1.45	-0.688	-0.004	-0.342	-0.416	0

Interaction energy analysis for fragmet #1(B:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.017

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].
3	B	5	LEU	0	0.053	0.045	3.888	0.726	1.488	-0.004	-0.342	-0.416
4	B	6	ALA	0	0.007	0.018	7.046	0.084	0.084	0.000	0.000	0.000
5	B	7	LEU	0	0.021	-0.019	10.334	0.020	0.020	0.000	0.000	0.000
6	B	8	LYS	1	0.967	0.996	13.277	0.163	0.163	0.000	0.000	0.000
7	B	9	THR	0	0.030	0.013	16.829	0.001	0.001	0.000	0.000	0.000
8	B	10	ILE	0	0.001	-0.007	18.676	0.024	0.024	0.000	0.000	0.000
9	B	11	ASP	-1	-0.878	-0.942	21.717	-0.124	-0.124	0.000	0.000	0.000
10	B	12	TRP	0	0.045	0.001	20.728	0.023	0.023	0.000	0.000	0.000
11	B	13	VAL	0	-0.034	-0.004	26.463	0.006	0.006	0.000	0.000	0.000
12	B	14	ALA	0	0.080	0.048	28.175	0.008	0.008	0.000	0.000	0.000
13	B	15	PHE	0	-0.043	-0.022	25.786	0.005	0.005	0.000	0.000	0.000
14	B	16	GLY	0	-0.042	-0.034	28.353	0.006	0.006	0.000	0.000	0.000
15	B	17	GLU	-1	-0.940	-0.965	31.259	-0.069	-0.069	0.000	0.000	0.000
16	B	18	ILE	0	-0.015	-0.003	28.115	0.005	0.005	0.000	0.000	0.000
17	B	19	ILE	0	-0.074	-0.019	29.217	0.004	0.004	0.000	0.000	0.000
18	B	20	PRO	0	0.041	0.016	33.234	0.003	0.003	0.000	0.000	0.000
19	B	21	ARG	1	1.048	1.008	35.757	0.043	0.043	0.000	0.000	0.000
20	B	22	ASN	0	-0.043	-0.014	37.473	-0.002	-0.002	0.000	0.000	0.000
21	B	23	GLN	0	0.008	-0.009	33.188	-0.001	-0.001	0.000	0.000	0.000
22	B	24	LYS	1	0.964	0.991	32.575	0.055	0.055	0.000	0.000	0.000
23	B	25	ALA	0	-0.011	0.004	32.169	-0.004	-0.004	0.000	0.000	0.000
24	B	26	VAL	0	0.068	0.028	28.472	-0.004	-0.004	0.000	0.000	0.000
25	B	27	ALA	0	0.049	0.037	28.087	-0.006	-0.006	0.000	0.000	0.000
26	B	28	ASN	0	-0.030	-0.032	27.435	-0.003	-0.003	0.000	0.000	0.000
27	B	29	SER	0	0.010	0.012	26.850	-0.011	-0.011	0.000	0.000	0.000
28	B	30	LEU	0	0.042	0.012	23.200	-0.008	-0.008	0.000	0.000	0.000
29	B	31	LYS	1	0.901	0.962	22.780	0.105	0.105	0.000	0.000	0.000
30	B	32	SER	0	0.036	0.024	23.020	-0.011	-0.011	0.000	0.000	0.000
31	B	33	TRP	0	0.003	0.019	19.119	-0.012	-0.012	0.000	0.000	0.000
32	B	34	ASN	0	0.042	0.021	18.189	-0.023	-0.023	0.000	0.000	0.000
33	B	35	GLU	-1	-0.843	-0.901	18.422	-0.171	-0.171	0.000	0.000	0.000
34	B	36	THR	0	-0.013	-0.003	19.564	-0.011	-0.011	0.000	0.000	0.000
35	B	37	LEU	0	-0.060	-0.035	15.164	-0.014	-0.014	0.000	0.000	0.000
36	B	38	THR	0	-0.027	-0.040	15.114	-0.046	-0.046	0.000	0.000	0.000
37	B	39	SER	0	-0.035	-0.043	15.550	-0.019	-0.019	0.000	0.000	0.000
38	B	40	ARG	1	0.902	0.962	14.890	0.142	0.142	0.000	0.000	0.000
39	B	41	LEU	0	0.016	-0.008	9.492	0.012	0.012	0.000	0.000	0.000
40	B	42	ALA	0	-0.019	0.017	12.218	-0.048	-0.048	0.000	0.000	0.000
41	B	43	THR	0	-0.119	-0.054	14.657	0.032	0.032	0.000	0.000	0.000
42	B	44	LEU	0	-0.037	-0.037	12.326	0.044	0.044	0.000	0.000	0.000
43	B	45	PRO	0	-0.005	0.010	11.129	-0.071	-0.071	0.000	0.000	0.000
44	B	46	GLU	-1	-0.930	-0.960	5.815	-1.296	-1.296	0.000	0.000	0.000
45	B	47	LYS	1	0.897	0.949	6.323	-0.433	-0.433	0.000	0.000	0.000
46	B	48	PRO	0	0.021	0.012	9.778	-0.062	-0.062	0.000	0.000	0.000
47	B	49	PRO	0	0.006	-0.007	13.320	0.022	0.022	0.000	0.000	0.000
48	B	50	ALA	0	-0.003	0.010	15.782	0.022	0.022	0.000	0.000	0.000
49	B	51	ILE	0	0.030	0.001	16.609	-0.018	-0.018	0.000	0.000	0.000
50	B	52	ASP	-1	-0.867	-0.926	20.069	0.057	0.057	0.000	0.000	0.000
51	B	53	TRP	0	0.058	0.021	19.015	-0.013	-0.013	0.000	0.000	0.000
52	B	54	ALA	0	-0.013	0.003	24.095	-0.005	-0.005	0.000	0.000	0.000
53	B	55	TYR	0	0.055	0.039	26.564	-0.005	-0.005	0.000	0.000	0.000
54	B	56	TYR	0	0.028	0.010	24.322	-0.003	-0.003	0.000	0.000	0.000
55	B	57	LYS	1	0.913	0.954	28.046	-0.069	-0.069	0.000	0.000	0.000
56	B	58	ALA	0	-0.066	-0.035	29.885	-0.003	-0.003	0.000	0.000	0.000
57	B	59	ASN	0	-0.103	-0.030	31.639	-0.007	-0.007	0.000	0.000	0.000
58	B	60	VAL	0	0.029	0.013	31.792	0.001	0.001	0.000	0.000	0.000
59	B	61	ALA	0	-0.013	-0.016	33.963	-0.003	-0.003	0.000	0.000	0.000
60	B	62	LYS	1	0.923	0.967	34.633	-0.041	-0.041	0.000	0.000	0.000
61	B	63	ALA	0	0.059	0.007	34.141	0.002	0.002	0.000	0.000	0.000
62	B	64	GLY	0	0.060	0.056	31.663	0.001	0.001	0.000	0.000	0.000
63	B	65	LEU	0	-0.032	-0.011	29.430	0.005	0.005	0.000	0.000	0.000
64	B	66	VAL	0	0.067	0.028	26.363	0.007	0.007	0.000	0.000	0.000
65	B	67	ASP	-1	-0.897	-0.940	25.879	0.085	0.085	0.000	0.000	0.000
66	B	68	ASP	-1	-0.896	-0.942	25.681	0.101	0.101	0.000	0.000	0.000
67	B	69	PHE	0	-0.028	-0.030	24.080	0.009	0.009	0.000	0.000	0.000
68	B	70	GLU	-1	-0.884	-0.957	20.832	0.135	0.135	0.000	0.000	0.000
69	B	71	LYS	1	0.887	0.925	20.586	-0.088	-0.088	0.000	0.000	0.000
70	B	72	LYS	1	0.849	0.908	20.548	-0.082	-0.082	0.000	0.000	0.000
71	B	73	PHE	0	-0.037	-0.001	15.398	0.013	0.013	0.000	0.000	0.000
72	B	74	ASN	0	0.014	-0.001	16.071	0.044	0.044	0.000	0.000	0.000
73	B	75	ALA	0	-0.091	-0.048	15.748	-0.007	-0.007	0.000	0.000	0.000
74	B	76	LEU	0	0.061	0.061	16.628	-0.018	-0.018	0.000	0.000	0.000
75	B	77	LYS	1	0.868	0.917	12.221	-0.483	-0.483	0.000	0.000	0.000
76	B	78	VAL	0	0.035	0.017	11.752	-0.037	-0.037	0.000	0.000	0.000
77	B	79	PRO	0	-0.019	0.006	11.730	0.070	0.070	0.000	0.000	0.000
78	B	80	ILE	0	0.018	-0.004	7.711	-0.004	-0.004	0.000	0.000	0.000
79	B	81	PRO	0	-0.036	-0.020	10.590	-0.011	-0.011	0.000	0.000	0.000
80	B	82	GLU	-1	-0.918	-0.959	12.739	0.086	0.086	0.000	0.000	0.000
81	B	83	ASP	-1	-0.845	-0.921	13.631	-0.071	-0.071	0.000	0.000	0.000
82	B	84	LYS	1	0.917	0.952	15.379	-0.033	-0.033	0.000	0.000	0.000
83	B	85	TYR	0	-0.056	-0.042	16.119	0.000	0.000	0.000	0.000	0.000
84	B	86	THR	0	-0.031	0.009	16.967	-0.016	-0.016	0.000	0.000	0.000
85	B	87	ALA	0	0.025	-0.006	19.802	0.008	0.008	0.000	0.000	0.000
86	B	88	GLN	0	-0.084	-0.036	19.832	-0.007	-0.007	0.000	0.000	0.000
87	B	89	VAL	0	0.074	0.035	20.280	0.000	0.000	0.000	0.000	0.000
88	B	90	ASP	-1	-0.784	-0.876	23.078	-0.027	-0.027	0.000	0.000	0.000
89	B	91	ALA	0	-0.093	-0.062	26.404	0.001	0.001	0.000	0.000	0.000
90	B	92	GLU	-1	-0.987	-0.987	24.024	-0.085	-0.085	0.000	0.000	0.000
91	B	93	GLU	-1	-0.874	-0.926	27.020	-0.020	-0.020	0.000	0.000	0.000
92	B	94	LYS	1	0.860	0.930	28.899	0.027	0.027	0.000	0.000	0.000
93	B	95	GLU	-1	-0.937	-0.997	29.804	-0.054	-0.054	0.000	0.000	0.000
94	B	96	ASP	-1	-0.787	-0.900	29.183	-0.053	-0.053	0.000	0.000	0.000
95	B	97	VAL	0	-0.067	-0.042	32.539	0.003	0.003	0.000	0.000	0.000
96	B	98	LYS	1	0.816	0.913	34.827	0.028	0.028	0.000	0.000	0.000
97	B	99	SER	0	-0.011	0.003	32.923	0.002	0.002	0.000	0.000	0.000
98	B	100	CYS	0	0.039	0.002	33.009	0.003	0.003	0.000	0.000	0.000
99	B	101	ALA	0	0.059	0.047	35.040	0.002	0.002	0.000	0.000	0.000
100	B	102	GLU	-1	-0.904	-0.906	37.718	-0.024	-0.024	0.000	0.000	0.000
101	B	103	PHE	0	0.014	0.005	38.786	0.001	0.001	0.000	0.000	0.000
102	B	104	LEU	0	-0.039	-0.016	35.297	0.001	0.001	0.000	0.000	0.000
103	B	105	THR	0	-0.078	-0.077	39.965	0.001	0.001	0.000	0.000	0.000
104	B	106	GLN	0	-0.016	-0.015	42.565	0.000	0.000	0.000	0.000	0.000
105	B	107	SER	0	-0.045	-0.020	42.393	0.001	0.001	0.000	0.000	0.000
106	B	108	LYS	1	1.001	0.985	38.772	0.035	0.035	0.000	0.000	0.000
107	B	109	THR	0	0.009	0.019	44.861	0.001	0.001	0.000	0.000	0.000
108	B	110	ARG	1	0.986	0.982	45.341	0.030	0.030	0.000	0.000	0.000
109	B	111	ILE	0	-0.067	-0.003	45.337	0.000	0.000	0.000	0.000	0.000
110	B	112	GLN	0	0.022	0.007	47.784	0.002	0.002	0.000	0.000	0.000
111	B	113	GLU	-1	-0.926	-0.946	50.482	-0.021	-0.021	0.000	0.000	0.000
112	B	114	TYR	0	0.003	-0.009	49.685	0.000	0.000	0.000	0.000	0.000
113	B	115	GLU	-1	-0.898	-0.952	49.834	-0.027	-0.027	0.000	0.000	0.000
114	B	116	LYS	1	0.934	0.961	53.385	0.018	0.018	0.000	0.000	0.000
115	B	117	GLU	-1	-0.961	-1.000	56.036	-0.018	-0.018	0.000	0.000	0.000
116	B	118	LEU	0	-0.043	-0.031	53.807	0.000	0.000	0.000	0.000	0.000
117	B	119	GLU	-1	-0.985	-0.980	57.500	-0.018	-0.018	0.000	0.000	0.000
118	B	120	LYS	1	0.882	0.944	58.994	0.017	0.017	0.000	0.000	0.000
119	B	121	MET	0	-0.003	0.005	60.496	0.000	0.000	0.000	0.000	0.000
120	B	122	ARG	1	0.922	0.992	59.722	0.018	0.018	0.000	0.000	0.000
121	B	123	ASN	0	-0.081	-0.049	62.596	0.000	0.000	0.000	0.000	0.000
122	B	124	NME	0	0.002	0.004	65.891	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:ACE )