FMO DATABASE

FMODB ID: 1N85Z

Calculation Name: 3BVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q38184

Base Structure: X-ray

Registration Date: 2023-09-23

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1251318.754477
FMO2-HF: Nuclear repulsion	1197052.750893
FMO2-HF: Total energy	-54266.003584
FMO2-MP2: Total energy	-54425.487471

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:3:LYS)

Summations of interaction energy for fragment #1(A:3: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.
-262.957	-249.581	13.482	-8.949	-17.908	-0.091

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.925 / q_NPA : 0.968

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	5	VAL	0	0.007	0.008	2.689	-8.145	-5.447	0.274	-1.062	-1.910	0.001
4	A	6	ALA	0	0.025	0.030	5.194	6.005	6.055	-0.001	-0.003	-0.045	0.000
5	A	7	ILE	0	0.008	0.003	8.463	-2.082	-2.082	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.051	-0.061	10.664	2.398	2.398	0.000	0.000	0.000	0.000
7	A	9	THR	0	0.006	-0.005	13.646	0.067	0.067	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.801	0.892	16.587	15.350	15.350	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.005	0.027	19.952	-0.155	-0.155	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.004	-0.017	23.334	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	13	THR	0	-0.072	-0.026	26.433	0.467	0.467	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.023	-0.008	27.265	-0.355	-0.355	0.000	0.000	0.000	0.000
13	A	15	ASN	0	0.011	0.015	29.276	0.143	0.143	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.078	0.016	24.832	-0.356	-0.356	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.017	-0.007	27.662	-0.204	-0.204	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.946	-0.973	30.277	-9.285	-9.285	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.884	-0.922	25.148	-12.314	-12.314	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.024	-0.007	25.480	0.001	0.001	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.041	-0.035	17.795	-0.450	-0.450	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.019	0.009	22.008	-0.435	-0.435	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.031	-0.033	19.551	-0.747	-0.747	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.854	-0.933	19.098	-15.136	-15.136	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.853	-0.899	19.393	-14.096	-14.096	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.082	-0.066	16.230	-1.910	-1.910	0.000	0.000	0.000	0.000
25	A	27	ILE	0	0.042	0.018	14.928	-1.714	-1.714	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.895	-0.922	14.368	-18.651	-18.651	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.917	0.954	14.568	18.205	18.205	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.033	-0.016	10.086	-1.377	-1.377	0.000	0.000	0.000	0.000
29	A	31	THR	0	0.014	0.005	9.914	-3.322	-3.322	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.946	0.966	10.744	16.522	16.522	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.032	-0.009	5.955	-1.594	-1.594	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.013	-0.006	6.261	-2.225	-2.225	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.918	-0.961	6.585	-26.145	-26.145	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.040	-0.013	8.979	0.955	0.955	0.000	0.000	0.000	0.000
35	A	37	MET	0	-0.116	-0.049	5.273	3.079	3.079	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.014	0.009	6.304	-2.686	-2.686	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.064	-0.044	2.441	-19.658	-15.965	7.909	-2.981	-8.622	-0.033
38	A	40	GLN	0	0.009	-0.005	3.662	6.503	7.106	0.001	-0.149	-0.455	0.000
39	A	41	VAL	0	0.015	0.007	5.425	-4.587	-4.587	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.091	-0.046	7.425	2.787	2.787	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.826	-0.927	9.092	-17.007	-17.007	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.011	-0.001	11.496	-2.413	-2.413	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.086	-0.039	11.946	1.079	1.079	0.000	0.000	0.000	0.000
44	A	46	THR	0	0.026	0.000	15.860	-0.431	-0.431	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.762	-0.841	18.868	-14.630	-14.630	0.000	0.000	0.000	0.000
46	A	48	ALA	0	0.000	-0.019	21.687	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.025	-0.005	24.403	0.452	0.452	0.000	0.000	0.000	0.000
48	A	50	PHE	0	0.039	0.011	24.121	0.317	0.317	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.029	0.005	24.693	-0.482	-0.482	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.022	0.011	22.531	-0.326	-0.326	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.077	-0.039	23.084	-0.240	-0.240	0.000	0.000	0.000	0.000
52	A	54	LYS	1	1.002	1.002	25.134	11.017	11.017	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.083	0.036	19.954	-0.412	-0.412	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.936	-0.950	22.599	-12.864	-12.864	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.760	0.861	19.000	16.023	16.023	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.006	0.013	22.283	-0.483	-0.483	0.000	0.000	0.000	0.000
57	A	59	ALA	0	0.015	0.011	18.370	-0.366	-0.366	0.000	0.000	0.000	0.000
58	A	60	MET	0	0.004	0.011	16.157	-1.273	-1.273	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.002	-0.012	18.002	-0.862	-0.862	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.889	0.961	16.423	17.369	17.369	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.003	0.005	11.621	-0.489	-0.489	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.035	-0.028	14.730	-1.009	-1.009	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.023	-0.020	16.852	-0.200	-0.200	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.865	-0.930	14.065	-17.968	-17.968	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.032	-0.016	11.596	-1.441	-1.441	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.989	-0.987	12.931	-17.419	-17.419	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.026	-0.009	13.680	1.535	1.535	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.878	0.937	9.952	21.222	21.222	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.021	0.026	9.017	-0.615	-0.615	0.000	0.000	0.000	0.000
70	A	72	PHE	0	-0.050	-0.036	5.949	-0.691	-0.691	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.849	-0.930	2.392	-71.090	-67.933	2.619	-2.510	-3.266	-0.031
72	A	74	THR	0	-0.035	-0.021	2.510	-25.381	-23.227	2.662	-1.843	-2.973	-0.025
73	A	75	VAL	0	0.005	0.019	4.565	5.065	5.135	-0.001	-0.016	-0.052	0.000
74	A	76	LEU	0	0.013	-0.002	5.188	-1.538	-1.538	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.009	-0.003	7.997	3.579	3.579	0.000	0.000	0.000	0.000
76	A	78	TYR	0	0.028	0.015	11.204	-0.868	-0.868	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.964	0.964	13.642	15.463	15.463	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.069	0.046	14.027	0.036	0.036	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.889	-0.942	15.839	-15.173	-15.173	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.814	0.908	16.143	16.313	16.313	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.045	0.037	13.108	0.433	0.433	0.000	0.000	0.000	0.000
82	A	84	SER	0	0.042	0.012	16.448	1.091	1.091	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.923	0.967	19.642	12.240	12.240	0.000	0.000	0.000	0.000
84	A	86	SER	0	0.019	0.025	21.930	0.666	0.666	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.086	0.043	21.278	-0.733	-0.733	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.974	0.984	21.184	11.158	11.158	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.863	-0.934	21.163	-13.866	-13.866	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.046	-0.033	16.115	-0.956	-0.956	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.019	-0.013	16.807	-1.208	-1.208	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.011	0.017	17.896	-0.603	-0.603	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.018	-0.001	15.245	-0.575	-0.575	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.022	0.012	11.526	-1.089	-1.089	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.939	0.977	13.076	14.552	14.552	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.909	-0.963	15.521	-16.438	-16.438	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.042	-0.013	14.499	0.406	0.406	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.007	-0.002	9.961	-0.518	-0.518	0.000	0.000	0.000	0.000
97	A	99	THR	0	0.043	0.016	10.826	-1.306	-1.306	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.893	0.958	11.832	15.858	15.858	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.078	-0.047	12.768	1.738	1.738	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.868	0.931	9.736	22.125	22.125	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.004	0.026	7.033	-3.091	-3.091	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.894	-0.947	3.717	-56.561	-55.952	0.001	-0.268	-0.342	-0.002
103	A	105	PHE	0	-0.008	-0.023	5.855	0.500	0.500	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.034	0.007	3.073	-0.387	-0.045	0.018	-0.117	-0.243	-0.001
105	A	107	SER	0	-0.055	-0.048	7.249	2.021	2.021	0.000	0.000	0.000	0.000
106	A	108	LEU	0	-0.002	-0.014	9.475	0.868	0.868	0.000	0.000	0.000	0.000
107	A	109	ASN	0	-0.093	-0.047	11.408	1.172	1.172	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.789	-0.872	14.058	-18.562	-18.562	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.034	-0.021	11.430	0.785	0.785	0.000	0.000	0.000	0.000
110	A	112	ILE	0	-0.040	0.013	10.880	0.592	0.592	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.766	-0.890	5.437	-56.163	-56.163	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.009	0.007	7.766	1.617	1.617	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.013	0.005	4.922	2.467	2.467	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.044	-0.029	6.927	3.848	3.848	0.000	0.000	0.000	0.000
115	A	117	ALA	0	0.014	-0.012	9.424	1.669	1.669	0.000	0.000	0.000	0.000
116	A	118	MET	0	-0.005	-0.021	13.048	1.568	1.568	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.038	0.042	11.188	1.201	1.201	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.007	-0.004	11.715	1.755	1.755	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.005	-0.002	13.139	1.446	1.446	0.000	0.000	0.000	0.000
120	A	122	PHE	0	0.045	0.014	14.386	1.195	1.195	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.008	-0.003	12.630	1.012	1.012	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.043	-0.013	16.474	1.098	1.098	0.000	0.000	0.000	0.000
123	A	125	ILE	0	-0.003	0.000	18.974	0.951	0.951	0.000	0.000	0.000	0.000
124	A	126	LEU	0	-0.004	0.008	18.120	0.773	0.773	0.000	0.000	0.000	0.000
125	A	127	SER	0	-0.021	-0.030	20.212	0.567	0.567	0.000	0.000	0.000	0.000
126	A	128	ALA	0	-0.024	-0.002	21.946	0.573	0.573	0.000	0.000	0.000	0.000
127	A	129	ILE	0	0.009	0.001	24.404	0.581	0.581	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.030	0.020	24.200	0.367	0.367	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-1.006	-1.011	26.072	-11.400	-11.400	0.000	0.000	0.000	0.000
130	A	132	PHE	0	0.001	0.007	28.002	0.461	0.461	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.915	-0.974	27.606	-11.138	-11.138	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.881	0.932	26.772	11.737	11.737	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.969	-0.965	31.760	-9.134	-9.134	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.053	-0.021	34.028	0.341	0.341	0.000	0.000	0.000	0.000
135	A	137	GLU	-1	-1.005	-1.004	33.099	-9.323	-9.323	0.000	0.000	0.000	0.000
136	A	138	TYR	0	-0.102	-0.034	32.291	0.109	0.109	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)