FMO DATABASE

FMODB ID: ZYL9N

Calculation Name: 2CLY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CLY

Chain ID: A

ChEMBL ID:

UniProt ID: P13619

Base Structure: X-ray

Registration Date: 2023-03-13

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	OptHSide
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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-565044.82771
FMO2-HF: Nuclear repulsion	519921.468551
FMO2-HF: Total energy	-45123.359159
FMO2-MP2: Total energy	-45253.523551

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:79:GLY)

Summations of interaction energy for fragment #1(A:79:GLY)

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.
-5.191	-3.717	3.735	-1.948	-3.262	0.016

Interaction energy analysis for fragmet #1(A:79:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.001

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	81	PHE	0	-0.091	-0.064	2.411	-3.870	-2.851	3.736	-1.865	-2.891	0.016
4	A	82	ALA	0	0.013	0.028	4.074	-0.256	0.026	0.000	-0.070	-0.212	0.000
5	A	83	ASP	-1	-0.850	-0.913	5.205	-1.727	-1.554	-0.001	-0.013	-0.159	0.000
6	A	84	LYS	1	0.944	0.985	6.162	0.876	0.876	0.000	0.000	0.000	0.000
7	A	85	LEU	0	0.020	0.019	8.654	0.125	0.125	0.000	0.000	0.000	0.000
8	A	86	ASN	0	-0.012	-0.026	7.996	0.172	0.172	0.000	0.000	0.000	0.000
9	A	87	GLU	-1	-0.929	-0.963	10.851	-0.401	-0.401	0.000	0.000	0.000	0.000
10	A	88	GLN	0	0.003	-0.006	12.584	0.060	0.060	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.881	0.923	13.424	-0.137	-0.137	0.000	0.000	0.000	0.000
12	A	90	ILE	0	-0.020	-0.007	14.981	0.024	0.024	0.000	0.000	0.000	0.000
13	A	91	ALA	0	0.097	0.062	16.718	0.023	0.023	0.000	0.000	0.000	0.000
14	A	92	GLN	0	-0.048	-0.024	18.339	0.011	0.011	0.000	0.000	0.000	0.000
15	A	93	LEU	0	-0.015	-0.013	19.797	0.006	0.006	0.000	0.000	0.000	0.000
16	A	94	GLU	-1	-0.903	-0.946	20.838	-0.123	-0.123	0.000	0.000	0.000	0.000
17	A	95	GLU	-1	-0.827	-0.924	22.697	-0.057	-0.057	0.000	0.000	0.000	0.000
18	A	96	VAL	0	-0.111	-0.045	23.793	0.009	0.009	0.000	0.000	0.000	0.000
19	A	97	LYS	1	0.884	0.931	24.598	0.012	0.012	0.000	0.000	0.000	0.000
20	A	98	GLN	0	-0.026	0.003	26.802	0.007	0.007	0.000	0.000	0.000	0.000
21	A	99	ALA	0	0.029	0.012	28.550	0.003	0.003	0.000	0.000	0.000	0.000
22	A	100	SER	0	-0.006	0.001	29.815	0.003	0.003	0.000	0.000	0.000	0.000
23	A	101	ILE	0	-0.050	-0.024	31.014	0.002	0.002	0.000	0.000	0.000	0.000
24	A	102	LYS	1	1.005	1.006	32.859	0.037	0.037	0.000	0.000	0.000	0.000
25	A	103	GLN	0	-0.011	-0.021	32.607	0.001	0.001	0.000	0.000	0.000	0.000
26	A	104	ILE	0	0.006	0.017	35.723	0.002	0.002	0.000	0.000	0.000	0.000
27	A	105	GLN	0	-0.024	-0.030	35.694	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	106	ASP	-1	-0.908	-0.956	38.860	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	107	ALA	0	-0.022	-0.010	40.144	0.001	0.001	0.000	0.000	0.000	0.000
30	A	108	ILE	0	-0.006	-0.008	40.477	0.000	0.000	0.000	0.000	0.000	0.000
31	A	109	ASP	-1	-0.806	-0.894	43.200	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	110	MET	0	-0.009	0.012	44.028	0.001	0.001	0.000	0.000	0.000	0.000
33	A	111	GLU	-1	-0.948	-0.974	45.969	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.824	0.908	44.454	0.015	0.015	0.000	0.000	0.000	0.000
35	A	113	SER	0	-0.028	-0.028	48.568	0.000	0.000	0.000	0.000	0.000	0.000
36	A	114	GLN	0	-0.012	-0.015	49.034	0.001	0.001	0.000	0.000	0.000	0.000
37	A	115	GLN	0	-0.008	-0.008	50.200	0.000	0.000	0.000	0.000	0.000	0.000
38	A	116	ALA	0	-0.036	-0.009	53.924	0.000	0.000	0.000	0.000	0.000	0.000
39	A	117	LEU	0	-0.031	-0.036	54.595	0.000	0.000	0.000	0.000	0.000	0.000
40	A	118	VAL	0	-0.018	0.008	56.339	0.001	0.001	0.000	0.000	0.000	0.000
41	A	119	GLN	0	0.083	0.036	58.633	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	120	LYN	0	0.005	-0.008	54.878	0.000	0.000	0.000	0.000	0.000	0.000
43	A	121	ARG	1	0.963	0.996	59.945	0.006	0.006	0.000	0.000	0.000	0.000
44	A	122	HIS	1	0.829	0.914	62.286	0.004	0.004	0.000	0.000	0.000	0.000
45	A	123	TYR	0	0.028	0.010	62.642	0.000	0.000	0.000	0.000	0.000	0.000
46	A	124	LEU	0	0.006	0.035	65.235	0.000	0.000	0.000	0.000	0.000	0.000
47	A	125	PHE	0	0.037	-0.001	65.702	0.000	0.000	0.000	0.000	0.000	0.000
48	A	126	ASP	-1	-0.790	-0.860	68.889	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	127	VAL	0	0.005	0.008	69.128	0.000	0.000	0.000	0.000	0.000	0.000
50	A	128	GLN	0	-0.031	-0.013	71.399	0.000	0.000	0.000	0.000	0.000	0.000
51	A	129	ARG	1	0.890	0.912	69.978	0.003	0.003	0.000	0.000	0.000	0.000
52	A	130	ASN	0	-0.002	-0.003	73.353	0.000	0.000	0.000	0.000	0.000	0.000
53	A	131	ASN	0	-0.004	-0.007	74.284	0.000	0.000	0.000	0.000	0.000	0.000
54	A	132	ILE	0	-0.016	-0.006	77.589	0.000	0.000	0.000	0.000	0.000	0.000
55	A	133	ALA	0	0.025	0.012	79.543	0.000	0.000	0.000	0.000	0.000	0.000
56	A	134	MET	0	0.030	0.014	77.954	0.000	0.000	0.000	0.000	0.000	0.000
57	A	135	ALA	0	0.014	0.015	81.873	0.000	0.000	0.000	0.000	0.000	0.000
58	A	136	LEU	0	-0.012	0.007	83.717	0.000	0.000	0.000	0.000	0.000	0.000
59	A	137	GLU	-1	-0.781	-0.873	84.939	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	138	VAL	0	-0.009	-0.005	84.963	0.000	0.000	0.000	0.000	0.000	0.000
61	A	139	THR	0	0.000	0.001	87.563	0.000	0.000	0.000	0.000	0.000	0.000
62	A	140	TYR	0	-0.032	-0.023	89.638	0.000	0.000	0.000	0.000	0.000	0.000
63	A	141	ARG	1	0.879	0.910	86.435	0.004	0.004	0.000	0.000	0.000	0.000
64	A	142	GLU	-1	-0.914	-0.966	90.207	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	143	ARG	1	0.875	0.949	92.302	0.003	0.003	0.000	0.000	0.000	0.000
66	A	144	LEU	0	0.024	0.010	94.638	0.000	0.000	0.000	0.000	0.000	0.000
67	A	145	HIS	0	-0.006	-0.008	94.136	0.000	0.000	0.000	0.000	0.000	0.000
68	A	146	ARG	1	0.766	0.854	97.393	0.003	0.003	0.000	0.000	0.000	0.000
69	A	147	VAL	0	0.005	-0.001	99.202	0.000	0.000	0.000	0.000	0.000	0.000
70	A	148	TYR	0	0.030	0.020	100.431	0.000	0.000	0.000	0.000	0.000	0.000
71	A	149	ARG	1	0.970	0.991	96.893	0.004	0.004	0.000	0.000	0.000	0.000
72	A	150	GLU	-1	-0.815	-0.880	101.995	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	151	VAL	0	0.040	0.017	105.060	0.000	0.000	0.000	0.000	0.000	0.000
74	A	152	LYS	1	0.837	0.911	105.495	0.004	0.004	0.000	0.000	0.000	0.000
75	A	153	ASN	0	-0.001	0.010	106.254	0.000	0.000	0.000	0.000	0.000	0.000
76	A	154	ARG	1	0.905	0.948	108.134	0.003	0.003	0.000	0.000	0.000	0.000
77	A	155	LEU	0	0.008	-0.008	110.506	0.000	0.000	0.000	0.000	0.000	0.000
78	A	156	ASP	-1	-0.782	-0.892	108.657	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	157	TYR	0	-0.015	0.019	112.148	0.000	0.000	0.000	0.000	0.000	0.000
80	A	158	HIS	0	0.033	0.016	113.932	0.000	0.000	0.000	0.000	0.000	0.000
81	A	159	ILE	0	0.015	0.017	113.808	0.000	0.000	0.000	0.000	0.000	0.000
82	A	160	SER	0	-0.032	-0.016	113.688	0.000	0.000	0.000	0.000	0.000	0.000
83	A	161	VAL	0	0.019	0.003	116.245	0.000	0.000	0.000	0.000	0.000	0.000
84	A	162	GLN	0	0.014	0.001	119.162	0.000	0.000	0.000	0.000	0.000	0.000
85	A	163	ASN	0	-0.031	-0.024	116.925	0.000	0.000	0.000	0.000	0.000	0.000
86	A	164	MET	0	0.019	0.028	119.540	0.000	0.000	0.000	0.000	0.000	0.000
87	A	165	MET	0	-0.010	-0.011	121.356	0.000	0.000	0.000	0.000	0.000	0.000
88	A	166	ARG	1	0.892	0.951	121.052	0.003	0.003	0.000	0.000	0.000	0.000
89	A	167	GLN	0	-0.021	-0.006	120.902	0.000	0.000	0.000	0.000	0.000	0.000
90	A	168	LYS	1	1.004	1.015	124.799	0.003	0.003	0.000	0.000	0.000	0.000
91	A	169	GLU	-1	-0.916	-0.970	126.712	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	170	GLN	0	-0.045	-0.042	126.028	0.000	0.000	0.000	0.000	0.000	0.000
93	A	171	GLU	-1	-0.903	-0.954	124.820	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	172	HIS	0	-0.045	-0.025	129.191	0.000	0.000	0.000	0.000	0.000	0.000
95	A	173	MET	0	0.011	0.006	132.225	0.000	0.000	0.000	0.000	0.000	0.000
96	A	174	ILE	0	0.013	0.004	130.137	0.000	0.000	0.000	0.000	0.000	0.000
97	A	175	ASN	0	-0.009	-0.002	133.267	0.000	0.000	0.000	0.000	0.000	0.000
98	A	176	TRP	0	-0.012	-0.018	135.092	0.000	0.000	0.000	0.000	0.000	0.000
99	A	177	VAL	0	-0.023	-0.017	137.017	0.000	0.000	0.000	0.000	0.000	0.000
100	A	178	GLU	-1	-0.843	-0.899	134.701	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	179	LYS	1	0.889	0.940	136.486	0.003	0.003	0.000	0.000	0.000	0.000
102	A	180	ARG	1	0.922	0.977	140.590	0.003	0.003	0.000	0.000	0.000	0.000
103	A	181	VAL	0	-0.029	-0.023	141.371	0.000	0.000	0.000	0.000	0.000	0.000
104	A	182	VAL	0	-0.080	-0.039	140.094	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	GLN	0	-0.036	-0.001	143.391	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:79:GLY)