FMO DATABASE

FMODB ID: G67G1

Calculation Name: 3LLY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LLY

Chain ID: A

ChEMBL ID:

UniProt ID: P18674

Base Structure: X-ray

Registration Date: 2023-06-26

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1171158.799715
FMO2-HF: Nuclear repulsion	1120445.140994
FMO2-HF: Total energy	-50713.658721
FMO2-MP2: Total energy	-50865.44153

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-10.192	-8.413	10.946	-5.613	-7.109	-0.051

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.011

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	3	THR	0	-0.025	-0.022	3.794	-0.215	1.140	-0.011	-0.661	-0.683	0.003
4	A	4	PHE	0	0.011	0.004	6.432	0.624	0.624	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.818	-0.925	9.339	-0.905	-0.905	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.761	-0.801	12.874	-0.708	-0.708	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.017	0.039	15.501	0.092	0.092	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.058	-0.034	18.161	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.096	-0.064	18.542	0.044	0.044	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.006	-0.006	23.665	0.004	0.004	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.001	0.004	24.928	0.020	0.020	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.029	-0.017	20.504	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.817	0.906	23.571	0.208	0.208	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.854	-0.944	21.444	-0.162	-0.162	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.032	0.010	16.979	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.022	-0.009	17.270	0.058	0.058	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.003	-0.006	13.586	-0.062	-0.062	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.858	-0.916	11.878	0.087	0.087	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.021	0.011	13.476	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.062	0.038	14.937	0.009	0.009	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.042	-0.042	16.507	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.925	-0.944	18.292	0.230	0.230	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.001	-0.001	13.039	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.014	-0.012	10.995	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.023	-0.009	10.703	0.046	0.046	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.015	0.002	9.273	0.063	0.063	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.007	-0.006	9.075	-0.190	-0.190	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.028	-0.024	10.074	0.049	0.049	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.920	0.967	11.969	0.215	0.215	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.007	0.017	14.738	0.058	0.058	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.012	-0.004	17.375	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.013	-0.044	16.005	0.026	0.026	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.782	-0.875	22.489	-0.175	-0.175	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.033	0.006	25.042	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.035	-0.040	27.037	0.016	0.016	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.018	0.009	30.217	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.050	-0.023	29.305	0.016	0.016	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.009	-0.013	26.463	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.015	0.011	20.037	0.012	0.012	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.044	-0.017	19.226	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.034	0.030	16.094	0.004	0.004	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.932	-0.974	11.972	-0.846	-0.846	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.942	-1.005	12.830	-0.382	-0.382	0.000	0.000	0.000	0.000
44	A	44	HIS	1	0.802	0.911	8.205	0.997	0.997	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.986	0.989	9.083	0.184	0.184	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.026	0.013	6.636	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.049	-0.036	2.728	-0.160	0.577	0.837	-0.662	-0.911	-0.004
48	A	48	ILE	0	-0.031	-0.008	7.483	-0.073	-0.073	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.024	0.009	10.729	-0.153	-0.153	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.003	-0.005	13.843	0.054	0.054	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.067	-0.022	10.223	-0.039	-0.039	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.932	0.968	15.949	-0.046	-0.046	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.009	-0.007	17.109	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.039	-0.001	17.981	0.019	0.019	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.936	0.959	19.172	0.088	0.088	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.000	0.011	20.548	0.020	0.020	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.006	-0.004	22.831	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.036	-0.014	23.909	0.012	0.012	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.909	-0.966	27.090	-0.117	-0.117	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.029	0.013	28.261	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.016	-0.029	30.312	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.013	-0.013	31.956	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.781	-0.851	29.123	-0.135	-0.135	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.001	-0.011	27.427	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.004	-0.015	21.555	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.023	-0.016	25.714	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.894	-0.958	23.952	-0.155	-0.155	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.022	0.019	17.999	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.004	0.006	20.011	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.026	0.005	17.528	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.012	-0.002	16.811	0.012	0.012	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.009	0.017	12.261	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.001	-0.025	12.779	0.035	0.035	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.932	0.958	11.901	-0.319	-0.319	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.002	0.004	10.677	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.900	-0.956	10.699	1.559	1.559	0.000	0.000	0.000	0.000
77	A	77	GLY	0	-0.033	-0.017	11.625	0.138	0.138	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.007	0.016	6.214	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.067	-0.031	8.528	-0.107	-0.107	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.044	0.031	6.451	-0.149	-0.149	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.022	0.022	8.939	0.087	0.087	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.867	0.924	11.443	-0.127	-0.127	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.043	-0.016	13.893	0.028	0.028	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.031	0.013	13.642	-0.048	-0.048	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.014	0.005	17.731	0.045	0.045	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.014	0.008	16.657	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.994	1.012	22.446	0.145	0.145	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.024	0.004	26.086	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.024	-0.007	28.124	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.878	0.942	30.890	0.117	0.117	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.004	0.000	28.637	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.008	0.004	26.179	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.053	-0.045	23.528	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.021	0.021	22.572	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.028	-0.027	21.657	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.009	-0.001	18.677	0.019	0.019	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.013	-0.006	17.414	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.047	-0.015	16.917	0.005	0.005	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.019	-0.011	17.958	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.004	0.002	18.992	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.013	-0.005	17.953	0.006	0.006	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.028	-0.021	17.272	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.010	0.023	17.857	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.006	-0.005	15.107	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.013	-0.022	19.637	0.013	0.013	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.023	0.001	19.968	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.015	-0.003	22.453	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.049	-0.025	23.621	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.965	-0.967	27.432	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	110	ASN	0	-0.011	-0.027	30.365	0.011	0.011	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.020	0.000	28.639	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.022	-0.014	26.613	0.006	0.006	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.032	0.019	19.944	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.042	-0.027	22.012	0.014	0.014	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.074	0.018	18.643	0.002	0.002	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.006	0.001	13.690	0.027	0.027	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.963	0.997	11.717	1.177	1.177	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.029	-0.034	9.001	0.228	0.228	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.050	-0.014	2.733	-1.319	-0.684	0.098	-0.424	-0.309	0.001
120	A	120	ILE	0	-0.017	0.007	3.620	0.361	0.910	0.007	-0.219	-0.336	0.000
121	A	121	GLY	0	0.110	0.062	2.393	-0.456	-1.105	6.485	-3.722	-2.114	-0.013
122	A	122	TYR	0	-0.044	-0.005	2.679	1.658	-1.472	0.552	2.600	-0.022	-0.002
123	A	123	TRP	0	0.058	0.024	5.647	-0.448	-0.448	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.002	0.012	5.191	-0.506	-0.396	-0.001	-0.004	-0.104	0.000
125	A	125	ASP	-1	-0.809	-0.915	2.175	-10.980	-8.808	2.979	-2.521	-2.630	-0.036
126	A	126	TYR	0	-0.020	-0.040	5.475	0.670	0.670	0.000	0.000	0.000	0.000
127	A	127	PHE	0	-0.036	-0.023	8.233	-0.312	-0.312	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.057	-0.025	10.886	0.120	0.120	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.032	0.005	14.157	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	130	TYR	0	-0.072	-0.030	16.118	0.064	0.064	0.000	0.000	0.000	0.000
131	A	131	LEU	0	0.002	-0.006	20.142	0.024	0.024	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.007	-0.016	23.599	0.002	0.002	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.022	0.037	26.926	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:1:GLY)