FMO DATABASE

FMODB ID: G5Z81

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	OptHSide
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	-1253210.36787
FMO2-HF: Nuclear repulsion	1198943.48181
FMO2-HF: Total energy	-54266.88606
FMO2-MP2: Total energy	-54426.391313

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.
-331.114	-326.651	34.519	-17.379	-21.603	-0.2

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 : 0.807 / q_NPA : 0.894

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	-0.004	0.002	2.820	-9.712	-6.983	0.261	-1.085	-1.906	0.000
4	A	6	ALA	0	0.023	0.027	4.856	6.192	6.256	-0.001	-0.008	-0.055	0.000
5	A	7	ILE	0	0.013	0.006	8.432	-1.618	-1.618	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.046	-0.048	10.693	2.014	2.014	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.017	-0.008	13.546	0.444	0.444	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.784	0.877	16.684	14.898	14.898	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.023	0.034	20.129	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.015	-0.019	23.610	-0.097	-0.097	0.000	0.000	0.000	0.000
11	A	13	THR	0	-0.069	-0.030	26.725	0.411	0.411	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.023	-0.010	27.420	-0.368	-0.368	0.000	0.000	0.000	0.000
13	A	15	ASN	0	-0.033	-0.011	29.334	0.026	0.026	0.000	0.000	0.000	0.000
14	A	16	GLN	0	0.063	0.012	24.961	-0.394	-0.394	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.018	-0.009	28.055	-0.166	-0.166	0.000	0.000	0.000	0.000
16	A	18	GLU	-1	-0.895	-0.940	30.662	-9.055	-9.055	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.863	-0.911	25.671	-12.004	-12.004	0.000	0.000	0.000	0.000
18	A	20	GLY	0	-0.020	-0.005	26.281	0.017	0.017	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.038	-0.034	18.539	-0.380	-0.380	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.018	-0.004	22.531	-0.441	-0.441	0.000	0.000	0.000	0.000
21	A	23	ILE	0	-0.006	-0.027	19.613	-0.667	-0.667	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.875	-0.941	19.257	-14.335	-14.335	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.831	-0.877	19.817	-13.383	-13.383	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.077	-0.064	16.618	-1.665	-1.665	0.000	0.000	0.000	0.000
25	A	27	ILE	0	0.046	0.019	15.124	-1.448	-1.448	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.799	-0.855	14.890	-17.227	-17.227	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.920	0.959	15.397	16.386	16.386	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.023	-0.014	10.565	-1.076	-1.076	0.000	0.000	0.000	0.000
29	A	31	THR	0	-0.006	-0.010	10.636	-2.646	-2.646	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.823	0.888	10.798	15.181	15.181	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.032	-0.013	7.534	-1.041	-1.041	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.015	-0.004	6.563	-1.520	-1.520	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.926	-0.962	6.519	-23.521	-23.521	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.038	-0.015	8.885	0.705	0.705	0.000	0.000	0.000	0.000
35	A	37	MET	0	-0.117	-0.046	5.430	2.402	2.402	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.008	0.011	6.052	-2.245	-2.245	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.063	-0.044	2.710	-12.206	-8.090	3.150	-1.838	-5.428	-0.018
38	A	40	GLN	0	0.036	0.022	3.683	5.382	5.996	0.002	-0.150	-0.466	0.000
39	A	41	VAL	0	0.021	0.006	5.455	-4.288	-4.288	0.000	0.000	0.000	0.000
40	A	42	SER	0	-0.055	-0.029	7.522	1.199	1.199	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.832	-0.908	9.092	-17.317	-17.317	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.021	-0.013	11.177	-2.111	-2.111	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.103	-0.067	11.827	0.870	0.870	0.000	0.000	0.000	0.000
44	A	46	THR	0	0.035	0.000	15.910	-0.477	-0.477	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.779	-0.862	18.896	-14.641	-14.641	0.000	0.000	0.000	0.000
46	A	48	ALA	0	0.007	-0.014	21.619	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.021	-0.001	24.358	0.416	0.416	0.000	0.000	0.000	0.000
48	A	50	PHE	0	0.043	0.014	24.071	0.262	0.262	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.035	0.012	24.872	-0.449	-0.449	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.025	0.009	22.819	-0.345	-0.345	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.067	-0.032	23.482	-0.271	-0.271	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.884	0.926	25.365	11.586	11.586	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.069	0.032	19.936	-0.388	-0.388	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.854	-0.896	22.372	-12.541	-12.541	0.000	0.000	0.000	0.000
55	A	57	ARG	1	0.781	0.873	19.098	15.965	15.965	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.007	0.013	22.146	-0.538	-0.538	0.000	0.000	0.000	0.000
57	A	59	ALA	0	0.023	0.013	18.404	-0.429	-0.429	0.000	0.000	0.000	0.000
58	A	60	MET	0	0.002	0.010	16.129	-1.378	-1.378	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.012	-0.017	17.846	-1.086	-1.086	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.841	0.925	15.687	17.748	17.748	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.006	0.004	11.379	-0.546	-0.546	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.038	-0.029	14.505	-1.221	-1.221	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.024	-0.020	16.344	-0.232	-0.232	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.843	-0.898	14.034	-18.849	-18.849	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.019	-0.007	10.760	-1.628	-1.628	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.999	-0.991	12.286	-19.212	-19.212	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.030	-0.016	13.445	1.761	1.761	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.875	0.937	9.941	23.965	23.965	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.017	0.023	9.025	-0.729	-0.729	0.000	0.000	0.000	0.000
70	A	72	PHE	0	-0.024	-0.018	6.013	-0.105	-0.105	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.814	-0.903	1.662	-116.982	-120.892	18.533	-8.049	-6.574	-0.099
72	A	74	THR	0	-0.009	-0.012	2.307	-22.281	-22.299	5.820	-2.180	-3.622	-0.023
73	A	75	VAL	0	-0.001	0.019	4.263	6.756	6.895	0.000	-0.070	-0.069	0.000
74	A	76	LEU	0	0.015	0.004	5.316	-0.632	-0.632	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.012	-0.009	8.390	2.970	2.970	0.000	0.000	0.000	0.000
76	A	78	TYR	0	0.041	0.023	12.088	-0.539	-0.539	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.906	0.932	14.494	14.830	14.830	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.076	0.044	14.985	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.861	-0.907	16.781	-14.521	-14.521	0.000	0.000	0.000	0.000
80	A	82	ARG	1	0.815	0.902	16.643	15.591	15.591	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.030	0.032	13.337	0.375	0.375	0.000	0.000	0.000	0.000
82	A	84	SER	0	0.036	0.006	16.859	0.942	0.942	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.922	0.968	20.125	11.991	11.991	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.010	-0.020	22.358	0.688	0.688	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.083	0.047	21.438	-0.790	-0.790	0.000	0.000	0.000	0.000
86	A	88	ARG	1	1.002	0.997	21.018	11.277	11.277	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.830	-0.893	21.065	-14.036	-14.036	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.016	-0.026	16.411	-1.010	-1.010	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.021	-0.011	16.445	-1.296	-1.296	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.004	0.012	17.169	-0.720	-0.720	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.015	0.002	14.853	-0.697	-0.697	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.025	0.010	11.002	-1.344	-1.344	0.000	0.000	0.000	0.000
93	A	95	LYS	1	0.898	0.966	12.241	14.453	14.453	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.903	-0.967	14.493	-17.458	-17.458	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.039	-0.012	13.879	0.389	0.389	0.000	0.000	0.000	0.000
96	A	98	PHE	0	0.007	0.000	9.136	-0.677	-0.677	0.000	0.000	0.000	0.000
97	A	99	THR	0	0.042	0.005	9.708	-1.938	-1.938	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.904	0.967	10.731	16.744	16.744	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.075	-0.046	11.607	1.833	1.833	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.839	0.919	8.449	24.399	24.399	0.000	0.000	0.000	0.000
101	A	103	ILE	0	-0.001	0.023	5.792	-4.878	-4.878	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.850	-0.923	1.884	-99.508	-98.972	6.757	-3.988	-3.305	-0.060
103	A	105	PHE	0	-0.012	-0.025	5.042	1.734	1.765	-0.001	0.000	-0.030	0.000
104	A	106	ILE	0	0.033	0.008	4.167	1.034	1.136	-0.001	-0.007	-0.094	0.000
105	A	107	SER	0	-0.040	-0.035	8.436	1.552	1.552	0.000	0.000	0.000	0.000
106	A	108	LEU	0	-0.006	-0.014	10.894	0.841	0.841	0.000	0.000	0.000	0.000
107	A	109	ASN	0	-0.095	-0.059	12.573	1.102	1.102	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.768	-0.858	15.203	-17.678	-17.678	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.056	-0.019	12.385	0.642	0.642	0.000	0.000	0.000	0.000
110	A	112	ILE	0	-0.028	0.004	11.498	0.359	0.359	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.759	-0.872	5.960	-49.538	-49.538	0.000	0.000	0.000	0.000
112	A	114	THR	0	0.000	-0.001	7.257	1.310	1.310	0.000	0.000	0.000	0.000
113	A	115	SER	0	-0.030	-0.018	4.455	2.436	2.496	-0.001	-0.004	-0.054	0.000
114	A	116	SER	0	-0.027	-0.012	6.597	3.848	3.848	0.000	0.000	0.000	0.000
115	A	117	ALA	0	0.028	-0.001	9.717	1.341	1.341	0.000	0.000	0.000	0.000
116	A	118	MET	0	0.000	-0.015	13.170	1.497	1.497	0.000	0.000	0.000	0.000
117	A	119	GLY	0	0.031	0.036	11.363	1.164	1.164	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.005	-0.012	11.274	1.582	1.582	0.000	0.000	0.000	0.000
119	A	121	LEU	0	-0.023	-0.010	12.749	1.421	1.421	0.000	0.000	0.000	0.000
120	A	122	PHE	0	0.046	0.015	14.702	1.185	1.185	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.010	0.001	12.515	1.053	1.053	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.032	-0.015	16.085	1.014	1.014	0.000	0.000	0.000	0.000
123	A	125	ILE	0	0.001	0.001	18.443	0.979	0.979	0.000	0.000	0.000	0.000
124	A	126	LEU	0	0.000	0.010	18.170	0.780	0.780	0.000	0.000	0.000	0.000
125	A	127	SER	0	0.001	-0.008	19.506	0.505	0.505	0.000	0.000	0.000	0.000
126	A	128	ALA	0	-0.034	-0.007	21.407	0.593	0.593	0.000	0.000	0.000	0.000
127	A	129	ILE	0	0.019	0.002	24.000	0.596	0.596	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.008	0.015	24.041	0.302	0.302	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.869	-0.927	25.642	-11.788	-11.788	0.000	0.000	0.000	0.000
130	A	132	PHE	0	-0.010	0.001	27.428	0.475	0.475	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.889	-0.958	27.497	-11.241	-11.241	0.000	0.000	0.000	0.000
132	A	134	ARG	1	0.764	0.854	25.307	12.169	12.169	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.939	-0.953	31.360	-9.305	-9.305	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.043	0.020	33.601	0.378	0.378	0.000	0.000	0.000	0.000
135	A	137	GLU	-1	-0.949	-0.960	33.342	-9.354	-9.354	0.000	0.000	0.000	0.000
136	A	138	TYR	0	-0.213	-0.140	31.863	0.236	0.236	0.000	0.000	0.000	0.000

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