FMO DATABASE

FMODB ID: N96QQ

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1168841.526939
FMO2-HF: Nuclear repulsion	1118127.121396
FMO2-HF: Total energy	-50714.405543
FMO2-MP2: Total energy	-50866.141279

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.
-11.186	-11.902	16.069	-7.92	-7.434	-0.048

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 : 0.015 / q_NPA : -0.018

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	3	THR	0	-0.016	-0.007	3.866	-0.051	1.442	-0.009	-0.801	-0.683	0.003
4	A	4	PHE	0	-0.001	-0.002	6.628	0.597	0.597	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.791	-0.913	9.660	-0.808	-0.808	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.799	-0.863	13.239	-0.666	-0.666	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.006	0.032	16.118	0.084	0.084	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.057	-0.039	18.756	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.084	-0.050	19.322	0.038	0.038	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.004	-0.021	24.537	0.005	0.005	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.005	-0.004	25.984	0.019	0.019	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.038	-0.015	21.178	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.843	0.913	24.464	0.189	0.189	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.777	-0.876	21.871	-0.143	-0.143	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.013	0.017	17.679	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.021	-0.025	17.698	0.063	0.063	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.012	0.003	14.089	-0.062	-0.062	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.830	-0.898	11.677	0.085	0.085	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.041	0.016	14.017	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.052	0.036	15.011	0.032	0.032	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.033	-0.019	16.843	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.870	-0.927	18.356	0.271	0.271	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.060	-0.040	13.270	0.038	0.038	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.022	-0.009	11.268	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.027	-0.005	11.634	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.012	0.004	9.653	0.109	0.109	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.023	-0.002	9.244	-0.165	-0.165	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.071	-0.038	10.204	0.079	0.079	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.802	0.891	12.368	0.238	0.238	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.009	0.010	15.189	0.052	0.052	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.027	-0.010	18.246	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.051	0.000	16.714	0.035	0.035	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.775	-0.858	23.178	-0.164	-0.164	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.030	0.005	25.618	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.036	-0.033	27.891	0.015	0.015	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.028	0.020	30.974	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.056	-0.020	29.790	0.014	0.014	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.009	-0.021	27.112	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.000	0.007	20.832	0.010	0.010	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.039	-0.013	19.874	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.049	0.038	16.791	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.872	-0.930	11.695	-0.928	-0.928	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.880	-0.952	13.562	-0.336	-0.336	0.000	0.000	0.000	0.000
44	A	44	HIS	1	0.823	0.909	8.968	0.927	0.927	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.956	0.970	9.346	0.245	0.245	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.026	0.016	6.857	-0.117	-0.117	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.050	-0.019	2.409	0.569	0.557	2.721	-1.320	-1.390	-0.005
48	A	48	ILE	0	-0.026	-0.004	7.186	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.014	-0.004	10.507	-0.153	-0.153	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.016	0.013	13.676	0.068	0.068	0.000	0.000	0.000	0.000
51	A	51	PHE	0	-0.057	-0.030	10.608	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.911	0.952	16.364	-0.080	-0.080	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.013	-0.001	17.669	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.047	-0.010	18.451	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.822	0.897	19.535	0.113	0.113	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.001	0.004	20.986	0.019	0.019	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.024	-0.009	23.699	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.003	0.009	24.763	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.758	-0.845	28.042	-0.095	-0.095	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.027	0.006	28.780	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.054	-0.040	30.949	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.036	-0.045	32.644	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.780	-0.856	29.117	-0.110	-0.110	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.001	-0.012	28.100	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.020	-0.018	22.030	0.010	0.010	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.002	-0.002	26.097	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.837	-0.899	23.860	-0.099	-0.099	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.020	0.009	18.028	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.009	-0.019	20.144	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.003	-0.004	17.813	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.004	0.004	16.904	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.008	0.009	12.056	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.025	-0.003	13.052	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.841	0.916	12.228	-0.587	-0.587	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.018	0.010	11.025	-0.129	-0.129	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.899	-0.954	10.989	1.701	1.701	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.012	0.017	12.241	0.091	0.091	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.028	0.020	6.459	0.195	0.195	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.050	-0.036	8.758	-0.187	-0.187	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.034	0.029	6.731	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.020	0.005	9.104	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.846	0.930	11.551	-0.304	-0.304	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.061	-0.040	14.050	0.012	0.012	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.024	0.002	13.939	-0.038	-0.038	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.001	0.004	17.604	0.038	0.038	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.012	0.011	16.795	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.904	0.938	22.520	0.114	0.114	0.000	0.000	0.000	0.000
88	A	88	THR	0	0.024	-0.012	26.163	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.019	-0.008	28.650	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.771	0.885	31.395	0.101	0.101	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.029	-0.018	29.143	0.012	0.012	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.004	-0.003	26.077	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	93	TYR	0	-0.033	-0.028	24.159	0.012	0.012	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.035	0.018	22.952	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.025	-0.009	21.983	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	TYR	0	0.005	-0.003	19.147	0.011	0.011	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.029	0.030	17.205	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.031	-0.010	17.078	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.002	-0.003	18.000	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.046	-0.027	19.002	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.001	-0.004	17.645	0.028	0.028	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.009	-0.007	17.361	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.017	0.021	18.001	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.024	-0.016	15.384	-0.017	-0.017	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.012	-0.018	19.774	0.013	0.013	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.026	0.002	20.057	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.025	-0.001	22.434	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.055	-0.023	23.417	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.957	-0.966	27.511	-0.101	-0.101	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.001	-0.019	30.399	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.014	0.013	28.738	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.016	-0.011	26.859	0.007	0.007	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.012	0.000	20.319	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.023	-0.013	22.192	0.012	0.012	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.060	0.018	19.263	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.023	-0.006	14.106	0.034	0.034	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.932	0.984	12.109	1.000	1.000	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.008	-0.016	8.802	0.244	0.244	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.075	-0.042	2.366	-0.776	0.245	0.261	-0.793	-0.489	0.005
120	A	120	ILE	0	-0.028	-0.009	4.056	0.698	1.062	0.001	-0.129	-0.236	0.000
121	A	121	GLY	0	0.090	0.064	2.234	-2.590	-1.413	3.561	-3.084	-1.654	-0.007
122	A	122	TYR	0	-0.024	-0.015	2.682	0.892	-1.266	0.362	1.917	-0.121	-0.001
123	A	123	TRP	0	0.023	0.004	5.745	-0.422	-0.422	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.030	0.023	5.731	-0.264	-0.264	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.790	-0.872	1.877	-10.923	-13.524	9.172	-3.710	-2.861	-0.043
126	A	126	TYR	0	-0.008	-0.023	5.135	0.557	0.557	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.001	-0.007	7.952	-0.319	-0.319	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.062	-0.034	10.690	0.078	0.078	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.014	0.012	14.041	-0.036	-0.036	0.000	0.000	0.000	0.000
130	A	130	TYR	0	-0.057	-0.037	16.402	0.053	0.053	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.003	-0.010	20.003	0.022	0.022	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.009	-0.007	23.527	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.023	0.028	27.031	0.004	0.004	0.000	0.000	0.000	0.000

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