FMO DATABASE

FMODB ID: M38ZZ

Calculation Name: 2CLY-B-Xray372

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: 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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-731189.984256
FMO2-HF: Nuclear repulsion	683579.461314
FMO2-HF: Total energy	-47610.522942
FMO2-MP2: Total energy	-47751.392598

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:4:LYS)

Summations of interaction energy for fragment #1(B:4:LYS)

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.
-35.991	-33.804	-0.025	-1.063	-1.099	0.003

Interaction energy analysis for fragmet #1(B:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.967 / q_NPA : 0.971

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	B	6	ALA	0	0.008	0.017	3.833	-1.367	0.727	-0.024	-1.062	-1.008	0.003
4	B	7	LEU	0	0.023	-0.018	6.362	1.003	1.003	0.000	0.000	0.000	0.000
5	B	8	LYS	1	0.967	0.996	9.386	17.151	17.151	0.000	0.000	0.000	0.000
6	B	9	THR	0	0.022	0.007	12.172	0.305	0.305	0.000	0.000	0.000	0.000
7	B	10	ILE	0	0.003	-0.005	14.003	0.764	0.764	0.000	0.000	0.000	0.000
8	B	11	ASP	-1	-0.876	-0.940	17.384	-12.845	-12.845	0.000	0.000	0.000	0.000
9	B	12	TRP	0	0.046	0.002	17.186	0.983	0.983	0.000	0.000	0.000	0.000
10	B	13	VAL	0	-0.036	-0.004	22.554	0.264	0.264	0.000	0.000	0.000	0.000
11	B	14	ALA	0	0.080	0.048	23.878	0.449	0.449	0.000	0.000	0.000	0.000
12	B	15	PHE	0	-0.043	-0.022	22.656	0.274	0.274	0.000	0.000	0.000	0.000
13	B	16	GLY	0	-0.046	-0.036	24.789	0.269	0.269	0.000	0.000	0.000	0.000
14	B	17	GLU	-1	-0.936	-0.964	27.702	-9.570	-9.570	0.000	0.000	0.000	0.000
15	B	18	ILE	0	-0.016	-0.003	24.792	0.241	0.241	0.000	0.000	0.000	0.000
16	B	19	ILE	0	-0.071	-0.018	26.170	0.072	0.072	0.000	0.000	0.000	0.000
17	B	20	PRO	0	0.040	0.016	30.199	0.303	0.303	0.000	0.000	0.000	0.000
18	B	21	ARG	1	1.047	1.008	32.937	7.748	7.748	0.000	0.000	0.000	0.000
19	B	22	ASN	0	-0.043	-0.015	34.795	-0.069	-0.069	0.000	0.000	0.000	0.000
20	B	23	GLN	0	0.008	-0.009	30.754	-0.188	-0.188	0.000	0.000	0.000	0.000
21	B	24	LYS	1	0.964	0.992	30.056	8.734	8.734	0.000	0.000	0.000	0.000
22	B	25	ALA	0	-0.012	0.004	29.506	-0.273	-0.273	0.000	0.000	0.000	0.000
23	B	26	VAL	0	0.070	0.029	26.327	-0.269	-0.269	0.000	0.000	0.000	0.000
24	B	27	ALA	0	0.045	0.035	25.446	-0.399	-0.399	0.000	0.000	0.000	0.000
25	B	28	ASN	0	-0.029	-0.031	24.699	-0.068	-0.068	0.000	0.000	0.000	0.000
26	B	29	SER	0	0.012	0.012	24.612	-0.564	-0.564	0.000	0.000	0.000	0.000
27	B	30	LEU	0	0.040	0.011	21.125	-0.463	-0.463	0.000	0.000	0.000	0.000
28	B	31	LYS	1	0.903	0.963	20.234	11.789	11.789	0.000	0.000	0.000	0.000
29	B	32	SER	0	0.037	0.026	20.173	-0.513	-0.513	0.000	0.000	0.000	0.000
30	B	33	TRP	0	0.002	0.019	18.002	-0.465	-0.465	0.000	0.000	0.000	0.000
31	B	34	ASN	0	0.041	0.021	14.917	-0.845	-0.845	0.000	0.000	0.000	0.000
32	B	35	GLU	-1	-0.841	-0.901	15.725	-14.647	-14.647	0.000	0.000	0.000	0.000
33	B	36	THR	0	-0.016	-0.004	17.009	-0.428	-0.428	0.000	0.000	0.000	0.000
34	B	37	LEU	0	-0.048	-0.032	13.700	-0.661	-0.661	0.000	0.000	0.000	0.000
35	B	38	THR	0	-0.037	-0.043	12.185	-1.564	-1.564	0.000	0.000	0.000	0.000
36	B	39	SER	0	-0.034	-0.042	13.061	-0.618	-0.618	0.000	0.000	0.000	0.000
37	B	40	ARG	1	0.904	0.962	14.139	17.134	17.134	0.000	0.000	0.000	0.000
38	B	41	LEU	0	0.014	-0.009	7.736	-0.095	-0.095	0.000	0.000	0.000	0.000
39	B	42	ALA	0	-0.021	0.016	10.609	-1.616	-1.616	0.000	0.000	0.000	0.000
40	B	43	THR	0	-0.117	-0.053	12.526	0.538	0.538	0.000	0.000	0.000	0.000
41	B	44	LEU	0	-0.037	-0.036	12.360	0.931	0.931	0.000	0.000	0.000	0.000
42	B	45	PRO	0	-0.004	0.010	10.638	-1.819	-1.819	0.000	0.000	0.000	0.000
43	B	46	GLU	-1	-0.934	-0.963	4.967	-48.846	-48.753	-0.001	-0.001	-0.091	0.000
44	B	47	LYS	1	0.901	0.952	7.694	32.183	32.183	0.000	0.000	0.000	0.000
45	B	48	PRO	0	0.020	0.012	10.846	0.334	0.334	0.000	0.000	0.000	0.000
46	B	49	PRO	0	0.006	-0.007	14.033	-0.632	-0.632	0.000	0.000	0.000	0.000
47	B	50	ALA	0	-0.002	0.010	16.200	0.081	0.081	0.000	0.000	0.000	0.000
48	B	51	ILE	0	0.029	0.001	17.296	0.510	0.510	0.000	0.000	0.000	0.000
49	B	52	ASP	-1	-0.867	-0.925	20.974	-12.101	-12.101	0.000	0.000	0.000	0.000
50	B	53	TRP	0	0.059	0.021	20.458	0.968	0.968	0.000	0.000	0.000	0.000
51	B	54	ALA	0	-0.014	0.003	25.150	0.536	0.536	0.000	0.000	0.000	0.000
52	B	55	TYR	0	0.055	0.039	27.143	0.586	0.586	0.000	0.000	0.000	0.000
53	B	56	TYR	0	0.028	0.010	25.202	0.296	0.296	0.000	0.000	0.000	0.000
54	B	57	LYS	1	0.911	0.953	29.144	10.503	10.503	0.000	0.000	0.000	0.000
55	B	58	ALA	0	-0.066	-0.036	31.039	0.352	0.352	0.000	0.000	0.000	0.000
56	B	59	ASN	0	-0.103	-0.030	32.408	0.557	0.557	0.000	0.000	0.000	0.000
57	B	60	VAL	0	0.030	0.013	33.315	-0.097	-0.097	0.000	0.000	0.000	0.000
58	B	61	ALA	0	-0.014	-0.016	35.276	0.242	0.242	0.000	0.000	0.000	0.000
59	B	62	LYS	1	0.924	0.968	36.593	8.053	8.053	0.000	0.000	0.000	0.000
60	B	63	ALA	0	0.058	0.007	35.915	-0.195	-0.195	0.000	0.000	0.000	0.000
61	B	64	GLY	0	0.059	0.056	33.533	-0.160	-0.160	0.000	0.000	0.000	0.000
62	B	65	LEU	0	-0.030	-0.010	31.481	-0.148	-0.148	0.000	0.000	0.000	0.000
63	B	66	VAL	0	0.066	0.027	27.901	-0.312	-0.312	0.000	0.000	0.000	0.000
64	B	67	ASP	-1	-0.896	-0.940	27.763	-10.496	-10.496	0.000	0.000	0.000	0.000
65	B	68	ASP	-1	-0.897	-0.943	27.792	-10.714	-10.714	0.000	0.000	0.000	0.000
66	B	69	PHE	0	-0.027	-0.030	26.142	-0.312	-0.312	0.000	0.000	0.000	0.000
67	B	70	GLU	-1	-0.885	-0.956	22.516	-13.604	-13.604	0.000	0.000	0.000	0.000
68	B	71	LYS	1	0.887	0.925	22.746	10.163	10.163	0.000	0.000	0.000	0.000
69	B	72	LYS	1	0.847	0.907	23.035	10.154	10.154	0.000	0.000	0.000	0.000
70	B	73	PHE	0	-0.036	0.000	17.258	-0.407	-0.407	0.000	0.000	0.000	0.000
71	B	74	ASN	0	0.014	-0.001	18.514	-1.494	-1.494	0.000	0.000	0.000	0.000
72	B	75	ALA	0	-0.091	-0.048	18.290	0.410	0.410	0.000	0.000	0.000	0.000
73	B	76	LEU	0	0.060	0.060	18.716	0.631	0.631	0.000	0.000	0.000	0.000
74	B	77	LYS	1	0.868	0.918	14.541	18.262	18.262	0.000	0.000	0.000	0.000
75	B	78	VAL	0	0.035	0.017	13.655	0.840	0.840	0.000	0.000	0.000	0.000
76	B	79	PRO	0	-0.020	0.006	13.552	-1.105	-1.105	0.000	0.000	0.000	0.000
77	B	80	ILE	0	0.021	-0.003	8.857	-0.482	-0.482	0.000	0.000	0.000	0.000
78	B	81	PRO	0	-0.037	-0.020	11.351	0.958	0.958	0.000	0.000	0.000	0.000
79	B	82	GLU	-1	-0.918	-0.959	13.094	-15.254	-15.254	0.000	0.000	0.000	0.000
80	B	83	ASP	-1	-0.843	-0.920	13.197	-17.876	-17.876	0.000	0.000	0.000	0.000
81	B	84	LYS	1	0.915	0.951	15.114	13.992	13.992	0.000	0.000	0.000	0.000
82	B	85	TYR	0	-0.055	-0.042	15.938	1.147	1.147	0.000	0.000	0.000	0.000
83	B	86	THR	0	-0.002	0.008	15.980	0.397	0.397	0.000	0.000	0.000	0.000
84	B	87	ALA	0	0.018	-0.005	18.794	0.220	0.220	0.000	0.000	0.000	0.000
85	B	88	GLN	0	-0.092	-0.038	18.644	-0.266	-0.266	0.000	0.000	0.000	0.000
86	B	89	VAL	0	0.058	0.036	18.707	0.238	0.238	0.000	0.000	0.000	0.000
87	B	90	ASP	-1	-0.784	-0.876	21.429	-12.085	-12.085	0.000	0.000	0.000	0.000
88	B	91	ALA	0	-0.094	-0.062	25.019	0.440	0.440	0.000	0.000	0.000	0.000
89	B	92	GLU	-1	-0.986	-0.987	21.196	-13.166	-13.166	0.000	0.000	0.000	0.000
90	B	93	GLU	-1	-0.874	-0.926	24.898	-10.709	-10.709	0.000	0.000	0.000	0.000
91	B	94	LYS	1	0.861	0.930	26.608	9.706	9.706	0.000	0.000	0.000	0.000
92	B	95	GLU	-1	-0.938	-0.997	27.237	-9.960	-9.960	0.000	0.000	0.000	0.000
93	B	96	ASP	-1	-0.781	-0.897	26.215	-10.956	-10.956	0.000	0.000	0.000	0.000
94	B	97	VAL	0	-0.068	-0.043	29.592	0.402	0.402	0.000	0.000	0.000	0.000
95	B	98	LYS	1	0.814	0.911	32.233	8.574	8.574	0.000	0.000	0.000	0.000
96	B	99	SER	0	-0.010	0.004	29.605	0.325	0.325	0.000	0.000	0.000	0.000
97	B	100	CYS	0	0.046	0.011	29.553	0.248	0.248	0.000	0.000	0.000	0.000
98	B	101	ALA	0	0.028	0.034	31.543	0.255	0.255	0.000	0.000	0.000	0.000
99	B	102	GLU	-1	-0.885	-0.905	34.362	-7.407	-7.407	0.000	0.000	0.000	0.000
100	B	103	PHE	0	0.015	0.005	35.158	0.268	0.268	0.000	0.000	0.000	0.000
101	B	104	LEU	0	-0.038	-0.016	31.390	0.219	0.219	0.000	0.000	0.000	0.000
102	B	105	THR	0	-0.080	-0.077	36.096	0.148	0.148	0.000	0.000	0.000	0.000
103	B	106	GLN	0	-0.013	-0.014	38.864	0.214	0.214	0.000	0.000	0.000	0.000
104	B	107	SER	0	-0.046	-0.021	38.281	0.246	0.246	0.000	0.000	0.000	0.000
105	B	108	LYS	1	1.002	0.986	34.658	8.535	8.535	0.000	0.000	0.000	0.000
106	B	109	THR	0	0.010	0.019	40.711	0.152	0.152	0.000	0.000	0.000	0.000
107	B	110	ARG	1	0.983	0.981	41.471	7.236	7.236	0.000	0.000	0.000	0.000
108	B	111	ILE	0	-0.067	-0.003	40.913	0.110	0.110	0.000	0.000	0.000	0.000
109	B	112	GLN	0	0.023	0.007	43.607	0.225	0.225	0.000	0.000	0.000	0.000
110	B	113	GLU	-1	-0.925	-0.945	46.159	-6.175	-6.175	0.000	0.000	0.000	0.000
111	B	114	TYR	0	0.000	-0.011	45.312	0.086	0.086	0.000	0.000	0.000	0.000
112	B	115	GLU	-1	-0.897	-0.952	45.112	-6.724	-6.724	0.000	0.000	0.000	0.000
113	B	116	LYS	1	0.935	0.962	48.799	5.859	5.859	0.000	0.000	0.000	0.000
114	B	117	GLU	-1	-0.962	-1.001	51.562	-5.435	-5.435	0.000	0.000	0.000	0.000
115	B	118	LEU	0	-0.041	-0.030	49.025	0.101	0.101	0.000	0.000	0.000	0.000
116	B	119	GLU	-1	-0.985	-0.979	52.865	-5.705	-5.705	0.000	0.000	0.000	0.000
117	B	120	LYS	1	0.884	0.946	54.329	5.556	5.556	0.000	0.000	0.000	0.000
118	B	121	MET	0	-0.011	0.001	55.723	0.077	0.077	0.000	0.000	0.000	0.000
119	B	122	ARG	1	0.926	0.993	54.928	5.578	5.578	0.000	0.000	0.000	0.000
120	B	123	ASN	0	-0.075	-0.042	57.743	0.053	0.053	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:LYS)