FMO DATABASE

FMODB ID: R5M48

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

Total energy (hartree)

FMO2-HF: Electronic energy	-564241.347758
FMO2-HF: Nuclear repulsion	519117.037469
FMO2-HF: Total energy	-45124.310289
FMO2-MP2: Total energy	-45254.2616

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.
-5.047	-1.831	1.807	-1.974	-3.049	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 : 0.015 / q_NPA : -0.009

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	-0.067	-0.038	2.604	-4.039	-1.224	1.809	-1.858	-2.766	0.015
4	A	82	ALA	0	0.016	0.016	4.173	0.013	0.315	-0.001	-0.102	-0.200	0.000
5	A	83	ASP	-1	-0.862	-0.935	5.519	-2.375	-2.276	-0.001	-0.014	-0.083	0.000
6	A	84	LYS	1	0.872	0.927	5.239	1.329	1.329	0.000	0.000	0.000	0.000
7	A	85	LEU	0	-0.012	0.007	8.765	0.180	0.180	0.000	0.000	0.000	0.000
8	A	86	ASN	0	-0.017	-0.031	8.656	0.209	0.209	0.000	0.000	0.000	0.000
9	A	87	GLU	-1	-0.922	-0.952	11.376	-0.436	-0.436	0.000	0.000	0.000	0.000
10	A	88	GLN	0	0.017	0.010	13.144	0.076	0.076	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.899	0.941	13.777	-0.037	-0.037	0.000	0.000	0.000	0.000
12	A	90	ILE	0	0.006	0.002	15.661	0.032	0.032	0.000	0.000	0.000	0.000
13	A	91	ALA	0	0.087	0.055	17.307	0.024	0.024	0.000	0.000	0.000	0.000
14	A	92	GLN	0	-0.054	-0.029	18.838	0.019	0.019	0.000	0.000	0.000	0.000
15	A	93	LEU	0	-0.038	-0.023	20.257	0.015	0.015	0.000	0.000	0.000	0.000
16	A	94	GLU	-1	-0.921	-0.963	21.493	-0.144	-0.144	0.000	0.000	0.000	0.000
17	A	95	GLU	-1	-0.836	-0.913	23.239	-0.072	-0.072	0.000	0.000	0.000	0.000
18	A	96	VAL	0	-0.046	-0.027	24.719	0.010	0.010	0.000	0.000	0.000	0.000
19	A	97	LYS	1	0.890	0.952	25.239	0.048	0.048	0.000	0.000	0.000	0.000
20	A	98	GLN	0	0.030	0.013	27.592	0.009	0.009	0.000	0.000	0.000	0.000
21	A	99	ALA	0	-0.005	0.004	29.153	0.004	0.004	0.000	0.000	0.000	0.000
22	A	100	SER	0	0.018	0.007	30.445	0.005	0.005	0.000	0.000	0.000	0.000
23	A	101	ILE	0	-0.042	-0.019	31.942	0.003	0.003	0.000	0.000	0.000	0.000
24	A	102	LYS	1	0.925	0.959	32.330	0.057	0.057	0.000	0.000	0.000	0.000
25	A	103	GLN	0	-0.009	-0.013	33.256	0.001	0.001	0.000	0.000	0.000	0.000
26	A	104	ILE	0	-0.009	0.004	36.457	0.003	0.003	0.000	0.000	0.000	0.000
27	A	105	GLN	0	-0.027	-0.026	36.438	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	106	ASP	-1	-0.900	-0.943	39.447	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	107	ALA	0	0.025	0.014	40.890	0.002	0.002	0.000	0.000	0.000	0.000
30	A	108	ILE	0	0.030	0.012	41.262	0.001	0.001	0.000	0.000	0.000	0.000
31	A	109	ASP	-1	-0.818	-0.903	43.951	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	110	MET	0	-0.002	0.012	44.480	0.002	0.002	0.000	0.000	0.000	0.000
33	A	111	GLU	-1	-0.941	-0.964	46.319	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.798	0.895	45.320	0.026	0.026	0.000	0.000	0.000	0.000
35	A	113	SER	0	-0.026	-0.023	49.111	0.001	0.001	0.000	0.000	0.000	0.000
36	A	114	GLN	0	-0.039	-0.022	49.360	0.002	0.002	0.000	0.000	0.000	0.000
37	A	115	GLN	0	-0.017	-0.019	50.675	0.001	0.001	0.000	0.000	0.000	0.000
38	A	116	ALA	0	-0.002	-0.002	54.291	0.001	0.001	0.000	0.000	0.000	0.000
39	A	117	LEU	0	-0.036	-0.029	54.618	0.001	0.001	0.000	0.000	0.000	0.000
40	A	118	VAL	0	-0.007	0.005	57.210	0.001	0.001	0.000	0.000	0.000	0.000
41	A	119	GLN	0	-0.013	-0.010	58.894	0.000	0.000	0.000	0.000	0.000	0.000
42	A	120	LYN	0	0.035	0.013	55.772	0.000	0.000	0.000	0.000	0.000	0.000
43	A	121	ARG	1	0.951	0.970	59.918	0.012	0.012	0.000	0.000	0.000	0.000
44	A	122	HIS	1	0.846	0.921	63.085	0.009	0.009	0.000	0.000	0.000	0.000
45	A	123	TYR	0	0.052	0.025	63.505	0.000	0.000	0.000	0.000	0.000	0.000
46	A	124	LEU	0	-0.001	0.018	65.779	0.000	0.000	0.000	0.000	0.000	0.000
47	A	125	PHE	0	0.026	0.001	66.181	0.000	0.000	0.000	0.000	0.000	0.000
48	A	126	ASP	-1	-0.795	-0.866	69.668	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	127	VAL	0	-0.003	0.005	69.866	0.000	0.000	0.000	0.000	0.000	0.000
50	A	128	GLN	0	-0.013	-0.006	72.043	0.000	0.000	0.000	0.000	0.000	0.000
51	A	129	ARG	1	0.885	0.920	70.591	0.007	0.007	0.000	0.000	0.000	0.000
52	A	130	ASN	0	0.019	0.007	73.789	0.001	0.001	0.000	0.000	0.000	0.000
53	A	131	ASN	0	0.000	0.001	74.903	0.000	0.000	0.000	0.000	0.000	0.000
54	A	132	ILE	0	-0.011	0.001	78.336	0.000	0.000	0.000	0.000	0.000	0.000
55	A	133	ALA	0	0.014	0.005	80.196	0.000	0.000	0.000	0.000	0.000	0.000
56	A	134	MET	0	0.015	0.006	78.668	0.000	0.000	0.000	0.000	0.000	0.000
57	A	135	ALA	0	0.026	0.015	82.395	0.000	0.000	0.000	0.000	0.000	0.000
58	A	136	LEU	0	-0.015	0.003	84.242	0.000	0.000	0.000	0.000	0.000	0.000
59	A	137	GLU	-1	-0.790	-0.894	85.529	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	138	VAL	0	-0.038	-0.010	85.501	0.000	0.000	0.000	0.000	0.000	0.000
61	A	139	THR	0	0.011	-0.007	87.971	0.000	0.000	0.000	0.000	0.000	0.000
62	A	140	TYR	0	-0.051	-0.023	90.245	0.000	0.000	0.000	0.000	0.000	0.000
63	A	141	ARG	1	0.889	0.920	87.406	0.007	0.007	0.000	0.000	0.000	0.000
64	A	142	GLU	-1	-0.909	-0.957	90.828	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	143	ARG	1	0.895	0.952	92.662	0.006	0.006	0.000	0.000	0.000	0.000
66	A	144	LEU	0	0.010	0.010	94.936	0.000	0.000	0.000	0.000	0.000	0.000
67	A	145	HIS	0	0.017	-0.001	94.831	0.000	0.000	0.000	0.000	0.000	0.000
68	A	146	ARG	1	0.778	0.872	98.023	0.006	0.006	0.000	0.000	0.000	0.000
69	A	147	VAL	0	0.010	0.001	99.777	0.000	0.000	0.000	0.000	0.000	0.000
70	A	148	TYR	0	0.023	0.017	100.790	0.000	0.000	0.000	0.000	0.000	0.000
71	A	149	ARG	1	0.956	0.986	97.333	0.006	0.006	0.000	0.000	0.000	0.000
72	A	150	GLU	-1	-0.794	-0.887	102.009	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	151	VAL	0	0.008	0.013	105.533	0.000	0.000	0.000	0.000	0.000	0.000
74	A	152	LYS	1	0.850	0.913	106.005	0.006	0.006	0.000	0.000	0.000	0.000
75	A	153	ASN	0	0.014	0.006	106.871	0.000	0.000	0.000	0.000	0.000	0.000
76	A	154	ARG	1	0.880	0.934	108.039	0.005	0.005	0.000	0.000	0.000	0.000
77	A	155	LEU	0	0.016	0.008	111.378	0.000	0.000	0.000	0.000	0.000	0.000
78	A	156	ASP	-1	-0.775	-0.875	108.831	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	157	TYR	0	-0.010	0.016	112.402	0.000	0.000	0.000	0.000	0.000	0.000
80	A	158	HIS	0	0.024	0.016	114.199	0.000	0.000	0.000	0.000	0.000	0.000
81	A	159	ILE	0	0.038	0.018	114.127	0.000	0.000	0.000	0.000	0.000	0.000
82	A	160	SER	0	-0.030	-0.025	114.084	0.000	0.000	0.000	0.000	0.000	0.000
83	A	161	VAL	0	0.004	0.005	116.676	0.000	0.000	0.000	0.000	0.000	0.000
84	A	162	GLN	0	0.020	-0.002	119.651	0.000	0.000	0.000	0.000	0.000	0.000
85	A	163	ASN	0	-0.036	-0.019	118.181	0.000	0.000	0.000	0.000	0.000	0.000
86	A	164	MET	0	0.018	0.027	119.800	0.000	0.000	0.000	0.000	0.000	0.000
87	A	165	MET	0	-0.020	-0.018	121.642	0.000	0.000	0.000	0.000	0.000	0.000
88	A	166	ARG	1	0.891	0.944	121.732	0.005	0.005	0.000	0.000	0.000	0.000
89	A	167	GLN	0	-0.020	-0.012	121.365	0.000	0.000	0.000	0.000	0.000	0.000
90	A	168	LYS	1	0.869	0.922	125.097	0.005	0.005	0.000	0.000	0.000	0.000
91	A	169	GLU	-1	-0.875	-0.941	126.947	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	170	GLN	0	-0.034	-0.026	126.548	0.000	0.000	0.000	0.000	0.000	0.000
93	A	171	GLU	-1	-0.837	-0.905	125.295	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	172	HIS	0	-0.033	-0.005	129.758	0.000	0.000	0.000	0.000	0.000	0.000
95	A	173	MET	0	0.014	0.005	132.808	0.000	0.000	0.000	0.000	0.000	0.000
96	A	174	ILE	0	0.006	-0.003	130.160	0.000	0.000	0.000	0.000	0.000	0.000
97	A	175	ASN	0	0.001	0.006	133.361	0.000	0.000	0.000	0.000	0.000	0.000
98	A	176	TRP	0	-0.005	-0.011	135.248	0.000	0.000	0.000	0.000	0.000	0.000
99	A	177	VAL	0	-0.006	-0.017	137.398	0.000	0.000	0.000	0.000	0.000	0.000
100	A	178	GLU	-1	-0.860	-0.916	134.950	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	179	LYS	1	0.880	0.930	136.785	0.004	0.004	0.000	0.000	0.000	0.000
102	A	180	ARG	1	0.885	0.954	141.021	0.004	0.004	0.000	0.000	0.000	0.000
103	A	181	VAL	0	-0.017	-0.010	141.665	0.000	0.000	0.000	0.000	0.000	0.000
104	A	182	VAL	0	-0.002	0.009	140.602	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	GLN	0	-0.092	-0.029	143.800	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)