FMO DATABASE

FMODB ID: MV8QZ

Calculation Name: 3LBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LBX

Chain ID: A

ChEMBL ID:

UniProt ID: P02549

Base Structure: X-ray

Registration Date: 2023-06-22

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1142496.160805
FMO2-HF: Nuclear repulsion	1084049.10762
FMO2-HF: Total energy	-58447.053184
FMO2-MP2: Total energy	-58618.73336

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:19:GLU)

Summations of interaction energy for fragment #1(A:19:GLU)

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.
-4.699	-7.28	20.784	-9.994	-8.209	-0.001

Interaction energy analysis for fragmet #1(A:19:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.906 / q_NPA : -0.946

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	21	ALA	0	-0.020	-0.019	3.508	-4.453	-2.847	-0.012	-0.725	-0.869	0.001
4	A	22	GLU	-1	-0.811	-0.922	2.450	43.333	45.893	3.024	-2.831	-2.753	-0.032
5	A	23	GLU	-1	-0.939	-0.960	5.451	19.967	19.967	0.000	0.000	0.000	0.000
6	A	24	ILE	0	-0.031	-0.022	8.107	-1.053	-1.053	0.000	0.000	0.000	0.000
7	A	25	GLN	0	0.033	0.022	1.853	-18.818	-25.565	17.772	-6.438	-4.587	0.030
8	A	26	GLU	-1	-0.860	-0.923	5.874	22.745	22.745	0.000	0.000	0.000	0.000
9	A	27	ARG	1	0.924	0.954	6.498	-31.462	-31.462	0.000	0.000	0.000	0.000
10	A	28	ARG	1	0.904	0.945	6.510	-35.188	-35.188	0.000	0.000	0.000	0.000
11	A	29	GLN	0	-0.025	-0.026	8.596	-0.191	-0.191	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-0.855	-0.933	11.928	16.582	16.582	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.094	-0.024	10.222	-0.956	-0.956	0.000	0.000	0.000	0.000
14	A	32	LEU	0	-0.027	-0.002	12.815	-0.974	-0.974	0.000	0.000	0.000	0.000
15	A	33	THR	0	0.024	-0.003	14.603	-1.486	-1.486	0.000	0.000	0.000	0.000
16	A	34	ARG	1	0.959	0.982	16.913	-18.566	-18.566	0.000	0.000	0.000	0.000
17	A	35	TYR	0	0.012	0.000	18.390	-1.212	-1.212	0.000	0.000	0.000	0.000
18	A	36	GLN	0	0.041	0.028	20.260	-0.471	-0.471	0.000	0.000	0.000	0.000
19	A	37	SER	0	-0.001	-0.007	21.748	-0.556	-0.556	0.000	0.000	0.000	0.000
20	A	38	PHE	0	-0.055	-0.033	22.734	-0.497	-0.497	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.938	0.970	24.438	-13.133	-13.133	0.000	0.000	0.000	0.000
22	A	40	GLU	-1	-0.872	-0.936	25.710	11.294	11.294	0.000	0.000	0.000	0.000
23	A	41	ARG	1	0.963	0.977	25.109	-12.375	-12.375	0.000	0.000	0.000	0.000
24	A	42	VAL	0	-0.046	-0.014	27.986	-0.352	-0.352	0.000	0.000	0.000	0.000
25	A	43	ALA	0	0.009	0.005	30.328	-0.378	-0.378	0.000	0.000	0.000	0.000
26	A	44	GLU	-1	-0.880	-0.927	31.786	9.466	9.466	0.000	0.000	0.000	0.000
27	A	45	ARG	1	0.943	0.963	32.861	-9.664	-9.664	0.000	0.000	0.000	0.000
28	A	46	GLY	0	0.015	0.005	34.546	-0.253	-0.253	0.000	0.000	0.000	0.000
29	A	47	GLN	0	-0.010	-0.013	36.503	-0.156	-0.156	0.000	0.000	0.000	0.000
30	A	48	LYS	1	0.879	0.924	35.237	-9.195	-9.195	0.000	0.000	0.000	0.000
31	A	49	LEU	0	-0.073	-0.030	37.398	-0.161	-0.161	0.000	0.000	0.000	0.000
32	A	50	GLU	-1	-0.821	-0.897	40.646	7.209	7.209	0.000	0.000	0.000	0.000
33	A	51	ASP	-1	-0.836	-0.899	42.344	7.274	7.274	0.000	0.000	0.000	0.000
34	A	52	SER	0	-0.044	-0.016	43.411	-0.262	-0.262	0.000	0.000	0.000	0.000
35	A	53	TYR	0	-0.008	-0.003	44.774	-0.204	-0.204	0.000	0.000	0.000	0.000
36	A	54	HIS	0	-0.032	-0.049	45.714	-0.318	-0.318	0.000	0.000	0.000	0.000
37	A	55	LEU	0	-0.035	0.001	47.946	-0.154	-0.154	0.000	0.000	0.000	0.000
38	A	56	GLN	0	-0.015	-0.020	47.386	-0.267	-0.267	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.037	-0.006	50.644	-0.136	-0.136	0.000	0.000	0.000	0.000
40	A	58	PHE	0	0.001	0.004	52.524	-0.128	-0.128	0.000	0.000	0.000	0.000
41	A	59	LYS	1	0.826	0.896	52.007	-6.336	-6.336	0.000	0.000	0.000	0.000
42	A	60	ARG	1	0.838	0.901	54.034	-6.039	-6.039	0.000	0.000	0.000	0.000
43	A	61	ASP	-1	-0.805	-0.879	56.665	5.680	5.680	0.000	0.000	0.000	0.000
44	A	62	ALA	0	0.007	-0.001	58.339	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	63	ASP	-1	-0.810	-0.896	59.082	5.366	5.366	0.000	0.000	0.000	0.000
46	A	64	ASP	-1	-0.876	-0.943	60.144	5.371	5.371	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.064	-0.024	62.546	-0.115	-0.115	0.000	0.000	0.000	0.000
48	A	66	GLY	0	0.040	0.011	63.871	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.750	0.856	60.411	-5.500	-5.500	0.000	0.000	0.000	0.000
50	A	68	TRP	0	0.046	0.015	66.731	-0.070	-0.070	0.000	0.000	0.000	0.000
51	A	69	ILE	0	-0.010	-0.007	67.282	-0.089	-0.089	0.000	0.000	0.000	0.000
52	A	70	MET	0	0.006	0.006	69.456	-0.088	-0.088	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.958	-0.973	70.354	4.642	4.642	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.811	0.888	72.792	-4.552	-4.552	0.000	0.000	0.000	0.000
55	A	73	VAL	0	0.024	0.010	73.727	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	74	ASN	0	0.004	0.007	73.574	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	75	ILE	0	0.058	0.032	76.536	-0.072	-0.072	0.000	0.000	0.000	0.000
58	A	76	LEU	0	-0.053	-0.019	77.815	-0.085	-0.085	0.000	0.000	0.000	0.000
59	A	77	THR	0	-0.009	-0.006	79.250	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	78	ASP	-1	-0.918	-0.938	80.380	4.047	4.047	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.896	0.938	83.061	-3.703	-3.703	0.000	0.000	0.000	0.000
62	A	80	SER	0	-0.050	-0.027	84.872	-0.079	-0.079	0.000	0.000	0.000	0.000
63	A	81	TYR	0	0.001	-0.003	85.666	0.028	0.028	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.874	-0.924	84.074	3.899	3.899	0.000	0.000	0.000	0.000
65	A	83	ASP	-1	-0.910	-0.966	88.539	3.578	3.578	0.000	0.000	0.000	0.000
66	A	84	PRO	0	-0.069	-0.023	88.872	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	85	THR	0	0.041	-0.005	92.028	0.011	0.011	0.000	0.000	0.000	0.000
68	A	86	ASN	0	-0.054	-0.016	93.608	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	87	ILE	0	0.072	0.035	92.674	0.047	0.047	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.073	0.043	91.938	0.072	0.072	0.000	0.000	0.000	0.000
71	A	89	GLY	0	0.036	0.014	90.760	0.041	0.041	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.825	0.911	88.350	-3.590	-3.590	0.000	0.000	0.000	0.000
73	A	91	TYR	0	0.071	0.040	86.820	0.047	0.047	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.014	-0.001	86.670	0.019	0.019	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.881	0.936	83.996	-3.740	-3.740	0.000	0.000	0.000	0.000
76	A	94	HIS	0	-0.027	0.004	82.605	0.045	0.045	0.000	0.000	0.000	0.000
77	A	95	GLN	0	0.026	0.011	82.139	0.042	0.042	0.000	0.000	0.000	0.000
78	A	96	SER	0	-0.035	-0.017	79.481	0.045	0.045	0.000	0.000	0.000	0.000
79	A	97	LEU	0	0.009	0.013	76.800	0.063	0.063	0.000	0.000	0.000	0.000
80	A	98	GLU	-1	-0.819	-0.925	77.394	4.027	4.027	0.000	0.000	0.000	0.000
81	A	99	ALA	0	-0.035	-0.012	77.325	0.053	0.053	0.000	0.000	0.000	0.000
82	A	100	GLU	-1	-0.826	-0.895	73.878	4.509	4.509	0.000	0.000	0.000	0.000
83	A	101	VAL	0	-0.002	0.008	72.888	0.087	0.087	0.000	0.000	0.000	0.000
84	A	102	GLN	0	0.024	0.003	72.604	0.094	0.094	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.092	-0.064	71.292	0.075	0.075	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.879	0.957	66.290	-4.822	-4.822	0.000	0.000	0.000	0.000
87	A	105	SER	0	0.045	0.018	67.828	0.067	0.067	0.000	0.000	0.000	0.000
88	A	106	ARG	1	0.758	0.860	62.871	-5.057	-5.057	0.000	0.000	0.000	0.000
89	A	107	LEU	0	0.010	-0.002	61.736	0.070	0.070	0.000	0.000	0.000	0.000
90	A	108	MET	0	0.041	0.036	63.134	0.127	0.127	0.000	0.000	0.000	0.000
91	A	109	SER	0	0.028	0.002	63.352	0.055	0.055	0.000	0.000	0.000	0.000
92	A	110	GLU	-1	-0.882	-0.902	59.982	5.378	5.378	0.000	0.000	0.000	0.000
93	A	111	LEU	0	0.009	0.020	58.289	0.139	0.139	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.846	-0.932	58.723	5.101	5.101	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.838	0.898	57.379	-5.528	-5.528	0.000	0.000	0.000	0.000
96	A	114	THR	0	-0.035	-0.033	54.214	0.137	0.137	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.883	0.951	54.400	-5.546	-5.546	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-0.993	-1.007	54.710	5.463	5.463	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.859	-0.908	53.669	5.812	5.812	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.888	0.954	46.499	-6.591	-6.591	0.000	0.000	0.000	0.000
101	A	119	PHE	0	-0.023	-0.003	49.203	0.174	0.174	0.000	0.000	0.000	0.000
102	A	120	THR	0	0.061	0.050	49.910	-0.141	-0.141	0.000	0.000	0.000	0.000
103	A	121	MET	0	-0.003	-0.010	50.583	0.120	0.120	0.000	0.000	0.000	0.000
104	A	122	GLY	0	0.007	0.000	47.089	0.072	0.072	0.000	0.000	0.000	0.000
105	A	123	HIS	0	-0.013	-0.002	45.762	0.084	0.084	0.000	0.000	0.000	0.000
106	A	124	SER	0	-0.008	-0.024	43.614	-0.107	-0.107	0.000	0.000	0.000	0.000
107	A	125	ALA	0	0.024	0.022	46.712	-0.062	-0.062	0.000	0.000	0.000	0.000
108	A	126	HIS	0	-0.028	-0.010	49.904	-0.218	-0.218	0.000	0.000	0.000	0.000
109	A	127	GLU	-1	-0.812	-0.911	52.203	5.731	5.731	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.836	-0.899	51.173	6.245	6.245	0.000	0.000	0.000	0.000
111	A	129	THR	0	-0.010	-0.027	52.598	-0.117	-0.117	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.793	0.881	55.370	-5.852	-5.852	0.000	0.000	0.000	0.000
113	A	131	ALA	0	-0.017	0.010	57.682	-0.109	-0.109	0.000	0.000	0.000	0.000
114	A	132	HIS	0	-0.006	-0.028	56.033	0.039	0.039	0.000	0.000	0.000	0.000
115	A	133	ILE	0	-0.007	0.004	59.252	-0.070	-0.070	0.000	0.000	0.000	0.000
116	A	134	GLU	-1	-0.812	-0.891	61.613	4.838	4.838	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.893	-0.939	60.832	5.309	5.309	0.000	0.000	0.000	0.000
118	A	136	LEU	0	-0.018	-0.009	61.901	-0.086	-0.086	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.879	0.931	65.123	-4.918	-4.918	0.000	0.000	0.000	0.000
120	A	138	HIS	0	-0.023	-0.021	66.858	-0.137	-0.137	0.000	0.000	0.000	0.000
121	A	139	LEU	0	-0.030	-0.015	66.519	-0.076	-0.076	0.000	0.000	0.000	0.000
122	A	140	TRP	0	-0.003	-0.009	69.233	-0.043	-0.043	0.000	0.000	0.000	0.000
123	A	141	ASP	-1	-0.890	-0.947	71.119	4.443	4.443	0.000	0.000	0.000	0.000
124	A	142	LEU	0	-0.005	0.010	73.462	-0.073	-0.073	0.000	0.000	0.000	0.000
125	A	143	LEU	0	-0.012	-0.008	72.520	-0.064	-0.064	0.000	0.000	0.000	0.000
126	A	144	LEU	0	-0.018	-0.011	74.035	-0.069	-0.069	0.000	0.000	0.000	0.000
127	A	145	GLU	-1	-0.938	-0.959	77.021	4.067	4.067	0.000	0.000	0.000	0.000
128	A	146	LEU	0	0.016	0.000	77.492	-0.070	-0.070	0.000	0.000	0.000	0.000
129	A	147	THR	0	-0.091	-0.052	78.095	-0.045	-0.045	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.012	0.008	80.745	-0.061	-0.061	0.000	0.000	0.000	0.000
131	A	149	GLU	-1	-0.931	-0.967	83.037	3.789	3.789	0.000	0.000	0.000	0.000
132	A	150	LYS	1	0.768	0.883	83.416	-4.000	-4.000	0.000	0.000	0.000	0.000
133	A	151	GLY	0	0.047	0.017	84.931	-0.045	-0.045	0.000	0.000	0.000	0.000
134	A	152	ASP	-1	-0.792	-0.885	86.415	3.618	3.618	0.000	0.000	0.000	0.000
135	A	153	GLN	0	-0.055	-0.026	87.434	-0.080	-0.080	0.000	0.000	0.000	0.000
136	A	154	LEU	0	-0.043	-0.022	87.382	-0.056	-0.056	0.000	0.000	0.000	0.000
137	A	155	LEU	0	-0.006	0.003	88.655	-0.050	-0.050	0.000	0.000	0.000	0.000
138	A	156	ARG	1	0.751	0.849	90.835	-3.635	-3.635	0.000	0.000	0.000	0.000
139	A	157	ALA	0	-0.018	0.014	94.438	-0.047	-0.047	0.000	0.000	0.000	0.000
140	A	158	LEU	0	-0.083	-0.043	94.695	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLU)