FMO DATABASE

FMODB ID: 6675Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-565537.849719
FMO2-HF: Nuclear repulsion	520416.050948
FMO2-HF: Total energy	-45121.798771
FMO2-MP2: Total energy	-45252.169429

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.
-5.354	-6.117	7.182	-2.472	-3.947	0.015

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 : 0.013 / q_NPA : -0.002

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	81	PHE	0	-0.086	-0.057	2.254	-3.547	-4.770	7.183	-2.388	-3.573	0.015
4	A	82	ALA	0	-0.001	0.020	4.077	-0.369	-0.084	0.000	-0.072	-0.213	0.000
5	A	83	ASP	-1	-0.853	-0.917	5.198	-1.651	-1.476	-0.001	-0.012	-0.161	0.000
6	A	84	LYS	1	0.960	0.996	6.329	0.561	0.561	0.000	0.000	0.000	0.000
7	A	85	LEU	0	0.006	0.012	8.651	0.107	0.107	0.000	0.000	0.000	0.000
8	A	86	ASN	0	-0.023	-0.033	8.306	0.118	0.118	0.000	0.000	0.000	0.000
9	A	87	GLU	-1	-0.913	-0.955	10.852	-0.384	-0.384	0.000	0.000	0.000	0.000
10	A	88	GLN	0	0.019	0.005	12.584	0.027	0.027	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.876	0.915	13.500	-0.154	-0.154	0.000	0.000	0.000	0.000
12	A	90	ILE	0	-0.022	-0.005	14.985	0.023	0.023	0.000	0.000	0.000	0.000
13	A	91	ALA	0	0.092	0.060	16.721	0.020	0.020	0.000	0.000	0.000	0.000
14	A	92	GLN	0	-0.044	-0.014	18.138	0.006	0.006	0.000	0.000	0.000	0.000
15	A	93	LEU	0	-0.025	-0.032	19.797	0.005	0.005	0.000	0.000	0.000	0.000
16	A	94	GLU	-1	-0.903	-0.937	21.029	-0.111	-0.111	0.000	0.000	0.000	0.000
17	A	95	GLU	-1	-0.829	-0.924	22.439	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	96	VAL	0	-0.134	-0.063	24.036	0.008	0.008	0.000	0.000	0.000	0.000
19	A	97	LYS	1	0.863	0.925	24.464	0.003	0.003	0.000	0.000	0.000	0.000
20	A	98	GLN	0	0.071	0.042	26.802	0.002	0.002	0.000	0.000	0.000	0.000
21	A	99	ALA	0	-0.017	-0.008	28.546	0.002	0.002	0.000	0.000	0.000	0.000
22	A	100	SER	0	-0.037	-0.009	29.819	0.001	0.001	0.000	0.000	0.000	0.000
23	A	101	ILE	0	0.008	0.008	30.974	0.002	0.002	0.000	0.000	0.000	0.000
24	A	102	LYS	1	0.982	0.990	32.860	0.028	0.028	0.000	0.000	0.000	0.000
25	A	103	GLN	0	-0.007	-0.019	32.495	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	104	ILE	0	0.000	0.019	35.724	0.001	0.001	0.000	0.000	0.000	0.000
27	A	105	GLN	0	-0.032	-0.039	35.849	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	106	ASP	-1	-0.877	-0.945	38.856	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	107	ALA	0	-0.040	-0.013	40.150	0.001	0.001	0.000	0.000	0.000	0.000
30	A	108	ILE	0	-0.013	-0.014	40.773	0.000	0.000	0.000	0.000	0.000	0.000
31	A	109	ASP	-1	-0.877	-0.937	43.203	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	110	MET	0	-0.043	-0.006	44.273	0.001	0.001	0.000	0.000	0.000	0.000
33	A	111	GLU	-1	-0.942	-0.973	46.165	0.002	0.002	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.919	0.959	45.126	0.012	0.012	0.000	0.000	0.000	0.000
35	A	113	SER	0	-0.009	-0.011	48.654	0.000	0.000	0.000	0.000	0.000	0.000
36	A	114	GLN	0	-0.015	-0.014	49.686	0.000	0.000	0.000	0.000	0.000	0.000
37	A	115	GLN	0	-0.019	-0.015	50.293	0.000	0.000	0.000	0.000	0.000	0.000
38	A	116	ALA	0	-0.008	-0.021	53.926	0.000	0.000	0.000	0.000	0.000	0.000
39	A	117	LEU	0	-0.028	-0.019	54.627	0.000	0.000	0.000	0.000	0.000	0.000
40	A	118	VAL	0	-0.014	0.017	55.737	0.000	0.000	0.000	0.000	0.000	0.000
41	A	119	GLN	0	0.093	0.041	58.635	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	120	LYN	0	-0.026	-0.014	54.423	0.000	0.000	0.000	0.000	0.000	0.000
43	A	121	ARG	1	0.961	0.989	60.204	0.004	0.004	0.000	0.000	0.000	0.000
44	A	122	HIS	1	0.799	0.905	62.288	0.003	0.003	0.000	0.000	0.000	0.000
45	A	123	TYR	0	0.045	0.013	62.780	0.000	0.000	0.000	0.000	0.000	0.000
46	A	124	LEU	0	0.011	0.035	65.488	0.000	0.000	0.000	0.000	0.000	0.000
47	A	125	PHE	0	0.034	-0.007	65.642	0.000	0.000	0.000	0.000	0.000	0.000
48	A	126	ASP	-1	-0.812	-0.881	68.577	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	127	VAL	0	0.008	0.013	69.180	0.000	0.000	0.000	0.000	0.000	0.000
50	A	128	GLN	0	-0.051	-0.022	71.241	0.000	0.000	0.000	0.000	0.000	0.000
51	A	129	ARG	1	0.924	0.939	70.380	0.002	0.002	0.000	0.000	0.000	0.000
52	A	130	ASN	0	0.002	0.002	73.960	0.000	0.000	0.000	0.000	0.000	0.000
53	A	131	ASN	0	0.002	-0.004	74.751	0.000	0.000	0.000	0.000	0.000	0.000
54	A	132	ILE	0	-0.023	-0.008	77.590	0.000	0.000	0.000	0.000	0.000	0.000
55	A	133	ALA	0	0.020	0.009	79.542	0.000	0.000	0.000	0.000	0.000	0.000
56	A	134	MET	0	0.039	0.013	77.386	0.000	0.000	0.000	0.000	0.000	0.000
57	A	135	ALA	0	0.004	0.013	81.872	0.000	0.000	0.000	0.000	0.000	0.000
58	A	136	LEU	0	-0.013	0.005	83.718	0.000	0.000	0.000	0.000	0.000	0.000
59	A	137	GLU	-1	-0.842	-0.910	84.962	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	138	VAL	0	-0.007	0.000	85.110	0.000	0.000	0.000	0.000	0.000	0.000
61	A	139	THR	0	0.003	0.000	87.539	0.000	0.000	0.000	0.000	0.000	0.000
62	A	140	TYR	0	-0.025	-0.019	89.636	0.000	0.000	0.000	0.000	0.000	0.000
63	A	141	ARG	1	0.922	0.941	86.375	0.004	0.004	0.000	0.000	0.000	0.000
64	A	142	GLU	-1	-0.901	-0.963	89.987	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	143	ARG	1	0.869	0.944	92.715	0.002	0.002	0.000	0.000	0.000	0.000
66	A	144	LEU	0	0.027	0.013	95.224	0.000	0.000	0.000	0.000	0.000	0.000
67	A	145	HIS	0	0.008	-0.003	93.774	0.000	0.000	0.000	0.000	0.000	0.000
68	A	146	ARG	1	0.891	0.935	97.395	0.003	0.003	0.000	0.000	0.000	0.000
69	A	147	VAL	0	0.007	0.001	99.202	0.000	0.000	0.000	0.000	0.000	0.000
70	A	148	TYR	0	0.027	0.019	100.675	0.000	0.000	0.000	0.000	0.000	0.000
71	A	149	ARG	1	0.946	0.991	96.944	0.004	0.004	0.000	0.000	0.000	0.000
72	A	150	GLU	-1	-0.936	-0.970	102.488	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	151	VAL	0	0.060	0.021	105.061	0.000	0.000	0.000	0.000	0.000	0.000
74	A	152	LYS	1	0.914	0.972	105.081	0.004	0.004	0.000	0.000	0.000	0.000
75	A	153	ASN	0	-0.013	0.001	106.258	0.000	0.000	0.000	0.000	0.000	0.000
76	A	154	ARG	1	0.904	0.954	108.134	0.003	0.003	0.000	0.000	0.000	0.000
77	A	155	LEU	0	0.011	-0.008	110.555	0.000	0.000	0.000	0.000	0.000	0.000
78	A	156	ASP	-1	-0.828	-0.934	108.958	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	157	TYR	0	-0.042	0.000	112.149	0.000	0.000	0.000	0.000	0.000	0.000
80	A	158	HIS	0	0.021	0.006	113.932	0.000	0.000	0.000	0.000	0.000	0.000
81	A	159	ILE	0	0.008	0.018	114.148	0.000	0.000	0.000	0.000	0.000	0.000
82	A	160	SER	0	-0.025	-0.004	113.616	0.000	0.000	0.000	0.000	0.000	0.000
83	A	161	VAL	0	0.026	0.009	116.245	0.000	0.000	0.000	0.000	0.000	0.000
84	A	162	GLN	0	0.008	-0.006	119.162	0.000	0.000	0.000	0.000	0.000	0.000
85	A	163	ASN	0	-0.052	-0.044	116.977	0.000	0.000	0.000	0.000	0.000	0.000
86	A	164	MET	0	0.009	0.038	119.597	0.000	0.000	0.000	0.000	0.000	0.000
87	A	165	MET	0	-0.005	-0.028	121.356	0.000	0.000	0.000	0.000	0.000	0.000
88	A	166	ARG	1	0.937	0.982	121.747	0.003	0.003	0.000	0.000	0.000	0.000
89	A	167	GLN	0	0.017	0.024	120.719	0.000	0.000	0.000	0.000	0.000	0.000
90	A	168	LYS	1	1.029	1.016	124.799	0.003	0.003	0.000	0.000	0.000	0.000
91	A	169	GLU	-1	-0.943	-0.971	126.712	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	170	GLN	0	-0.054	-0.043	126.730	0.000	0.000	0.000	0.000	0.000	0.000
93	A	171	GLU	-1	-0.947	-0.985	124.841	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	172	HIS	0	-0.033	-0.017	129.191	0.000	0.000	0.000	0.000	0.000	0.000
95	A	173	MET	0	-0.001	-0.008	132.225	0.000	0.000	0.000	0.000	0.000	0.000
96	A	174	ILE	0	0.013	0.003	130.492	0.000	0.000	0.000	0.000	0.000	0.000
97	A	175	ASN	0	0.014	0.014	132.799	0.000	0.000	0.000	0.000	0.000	0.000
98	A	176	TRP	0	-0.037	-0.024	135.092	0.000	0.000	0.000	0.000	0.000	0.000
99	A	177	VAL	0	-0.021	-0.015	137.013	0.000	0.000	0.000	0.000	0.000	0.000
100	A	178	GLU	-1	-0.882	-0.924	134.627	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	179	LYS	1	0.925	0.960	137.928	0.003	0.003	0.000	0.000	0.000	0.000
102	A	180	ARG	1	0.924	0.975	140.590	0.003	0.003	0.000	0.000	0.000	0.000
103	A	181	VAL	0	-0.020	-0.017	141.457	0.000	0.000	0.000	0.000	0.000	0.000
104	A	182	VAL	0	-0.085	-0.039	140.152	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	GLN	0	-0.040	-0.007	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)