FMO DATABASE

FMODB ID: VRNV1

Calculation Name: 2B2A-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B2A

Chain ID: B

ChEMBL ID:

UniProt ID: O77448

Base Structure: X-ray

Registration Date: 2023-03-13

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1674420.330119
FMO2-HF: Nuclear repulsion	1609113.249796
FMO2-HF: Total energy	-65307.080323
FMO2-MP2: Total energy	-65501.404494

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(B:14:LEU)

Summations of interaction energy for fragment #1(B:14:LEU)

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.
-7.585	-1.507	8.146	-5.176	-9.046	-0.025

Interaction energy analysis for fragmet #1(B:14:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.025

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	B	16	ARG	1	0.929	0.993	3.784	0.441	2.110	-0.030	-0.773	-0.866	0.002
4	B	17	LYS	1	0.991	0.984	6.337	0.424	0.424	0.000	0.000	0.000	0.000
5	B	18	GLU	-1	-0.843	-0.941	9.218	-0.442	-0.442	0.000	0.000	0.000	0.000
6	B	19	ASP	-1	-0.861	-0.936	8.363	-0.651	-0.651	0.000	0.000	0.000	0.000
7	B	20	LEU	0	-0.031	-0.011	7.372	0.140	0.140	0.000	0.000	0.000	0.000
8	B	21	LEU	0	-0.006	-0.020	9.352	0.093	0.093	0.000	0.000	0.000	0.000
9	B	22	THR	0	-0.007	-0.004	12.871	0.048	0.048	0.000	0.000	0.000	0.000
10	B	23	VAL	0	-0.004	-0.003	10.747	0.037	0.037	0.000	0.000	0.000	0.000
11	B	24	LEU	0	-0.026	-0.031	11.676	0.033	0.033	0.000	0.000	0.000	0.000
12	B	25	LYN	0	-0.023	0.017	14.553	0.003	0.003	0.000	0.000	0.000	0.000
13	B	26	GLN	0	-0.067	-0.032	16.680	-0.038	-0.038	0.000	0.000	0.000	0.000
14	B	27	ILE	0	-0.031	0.000	14.524	0.002	0.002	0.000	0.000	0.000	0.000
15	B	28	SER	0	0.006	0.001	18.667	0.007	0.007	0.000	0.000	0.000	0.000
16	B	29	ALA	0	-0.022	-0.010	20.465	-0.008	-0.008	0.000	0.000	0.000	0.000
17	B	30	LEU	0	-0.024	-0.006	15.616	0.008	0.008	0.000	0.000	0.000	0.000
18	B	31	LYS	1	0.921	0.969	19.715	-0.142	-0.142	0.000	0.000	0.000	0.000
19	B	32	TYR	0	-0.046	-0.004	19.855	-0.025	-0.025	0.000	0.000	0.000	0.000
20	B	33	VAL	0	0.047	0.013	15.297	0.034	0.034	0.000	0.000	0.000	0.000
21	B	34	SER	0	-0.026	-0.014	17.014	-0.040	-0.040	0.000	0.000	0.000	0.000
22	B	35	ASN	0	-0.006	0.018	15.695	0.039	0.039	0.000	0.000	0.000	0.000
23	B	36	LEU	0	0.052	0.009	15.696	0.003	0.003	0.000	0.000	0.000	0.000
24	B	37	TYR	0	-0.007	-0.007	17.639	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	38	GLU	-1	-0.881	-0.966	20.111	0.023	0.023	0.000	0.000	0.000	0.000
26	B	39	PHE	0	-0.019	0.011	20.411	0.002	0.002	0.000	0.000	0.000	0.000
27	B	40	LEU	0	0.009	-0.002	20.401	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	41	LEU	0	-0.003	0.011	23.525	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	42	ALA	0	-0.016	0.003	25.652	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	43	THR	0	-0.076	-0.053	24.960	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	44	GLU	-1	-0.977	-0.992	27.601	0.049	0.049	0.000	0.000	0.000	0.000
32	B	45	LYS	1	0.733	0.870	24.876	-0.104	-0.104	0.000	0.000	0.000	0.000
33	B	46	ILE	0	-0.041	-0.017	23.542	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	47	VAL	0	0.041	0.006	27.603	0.000	0.000	0.000	0.000	0.000	0.000
35	B	48	GLN	0	0.016	0.002	28.157	0.001	0.001	0.000	0.000	0.000	0.000
36	B	49	THR	0	-0.070	-0.045	28.705	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	50	SER	0	0.007	0.018	27.362	0.000	0.000	0.000	0.000	0.000	0.000
38	B	51	GLU	-1	-0.947	-0.963	27.778	0.011	0.011	0.000	0.000	0.000	0.000
39	B	52	LEU	0	-0.021	-0.025	22.604	0.007	0.007	0.000	0.000	0.000	0.000
40	B	53	ASP	-1	-0.834	-0.921	20.889	-0.040	-0.040	0.000	0.000	0.000	0.000
41	B	54	THR	0	0.006	-0.005	20.657	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	55	GLN	0	0.003	0.014	15.546	-0.027	-0.027	0.000	0.000	0.000	0.000
43	B	56	PHE	0	0.000	-0.011	16.573	0.002	0.002	0.000	0.000	0.000	0.000
44	B	57	GLN	0	0.015	0.013	17.830	0.004	0.004	0.000	0.000	0.000	0.000
45	B	58	GLU	-1	-0.905	-0.956	14.186	-0.150	-0.150	0.000	0.000	0.000	0.000
46	B	59	PHE	0	-0.017	-0.001	11.652	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	60	LEU	0	-0.017	0.012	13.998	0.032	0.032	0.000	0.000	0.000	0.000
48	B	61	THR	0	-0.007	0.004	16.292	0.010	0.010	0.000	0.000	0.000	0.000
49	B	62	THR	0	-0.122	-0.061	10.880	-0.005	-0.005	0.000	0.000	0.000	0.000
50	B	63	THR	0	-0.005	-0.004	11.201	0.017	0.017	0.000	0.000	0.000	0.000
51	B	64	ILE	0	-0.032	-0.008	10.576	-0.042	-0.042	0.000	0.000	0.000	0.000
52	B	65	ILE	0	-0.009	-0.001	12.217	0.098	0.098	0.000	0.000	0.000	0.000
53	B	66	ALA	0	0.016	0.000	14.696	-0.047	-0.047	0.000	0.000	0.000	0.000
54	B	67	SER	0	0.038	0.014	16.302	0.039	0.039	0.000	0.000	0.000	0.000
55	B	68	GLU	-1	-0.839	-0.901	19.313	0.233	0.233	0.000	0.000	0.000	0.000
56	B	69	GLN	0	0.024	-0.009	21.791	-0.022	-0.022	0.000	0.000	0.000	0.000
57	B	70	ASN	0	-0.027	0.005	23.407	0.012	0.012	0.000	0.000	0.000	0.000
58	B	71	LEU	0	0.044	0.019	22.656	-0.008	-0.008	0.000	0.000	0.000	0.000
59	B	72	VAL	0	0.026	0.016	25.279	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	73	GLU	-1	-0.860	-0.943	26.938	0.069	0.069	0.000	0.000	0.000	0.000
61	B	74	ASN	0	-0.078	-0.039	27.320	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	75	TYR	0	-0.027	-0.061	23.061	0.006	0.006	0.000	0.000	0.000	0.000
63	B	76	LYS	1	0.848	0.948	27.346	-0.070	-0.070	0.000	0.000	0.000	0.000
64	B	77	GLN	0	0.011	0.020	29.896	0.004	0.004	0.000	0.000	0.000	0.000
65	B	87	MET	0	-0.012	-0.008	26.768	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	88	THR	0	-0.057	-0.008	22.859	-0.004	-0.004	0.000	0.000	0.000	0.000
67	B	89	ILE	0	0.043	0.007	18.144	0.004	0.004	0.000	0.000	0.000	0.000
68	B	90	LYS	1	0.964	0.964	20.012	-0.108	-0.108	0.000	0.000	0.000	0.000
69	B	91	GLN	0	0.060	0.030	21.198	0.007	0.007	0.000	0.000	0.000	0.000
70	B	92	VAL	0	0.038	0.033	22.232	0.006	0.006	0.000	0.000	0.000	0.000
71	B	93	ILE	0	-0.015	-0.014	16.507	0.014	0.014	0.000	0.000	0.000	0.000
72	B	94	ASP	-1	-0.884	-0.935	20.369	0.229	0.229	0.000	0.000	0.000	0.000
73	B	95	ASP	-1	-0.885	-0.959	22.539	0.158	0.158	0.000	0.000	0.000	0.000
74	B	96	SER	0	-0.104	-0.054	20.483	0.012	0.012	0.000	0.000	0.000	0.000
75	B	97	ILE	0	-0.001	-0.018	17.852	0.015	0.015	0.000	0.000	0.000	0.000
76	B	98	ILE	0	-0.015	0.010	21.421	0.000	0.000	0.000	0.000	0.000	0.000
77	B	99	LEU	0	-0.055	-0.023	24.376	-0.009	-0.009	0.000	0.000	0.000	0.000
78	B	100	LEU	0	-0.071	-0.014	18.997	0.001	0.001	0.000	0.000	0.000	0.000
79	B	101	GLY	0	-0.007	0.000	23.610	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	102	ASN	0	-0.052	-0.029	25.534	0.013	0.013	0.000	0.000	0.000	0.000
81	B	103	LYS	1	0.939	0.981	22.840	-0.224	-0.224	0.000	0.000	0.000	0.000
82	B	104	GLN	0	0.007	-0.004	20.593	0.014	0.014	0.000	0.000	0.000	0.000
83	B	105	ASN	0	-0.004	-0.004	16.702	0.014	0.014	0.000	0.000	0.000	0.000
84	B	106	TYR	0	0.046	0.048	15.549	0.054	0.054	0.000	0.000	0.000	0.000
85	B	107	VAL	0	0.015	0.000	9.369	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	108	GLN	0	0.005	-0.017	12.481	0.087	0.087	0.000	0.000	0.000	0.000
87	B	109	GLN	0	0.007	-0.008	14.512	-0.027	-0.027	0.000	0.000	0.000	0.000
88	B	110	ILE	0	-0.036	-0.007	11.077	-0.041	-0.041	0.000	0.000	0.000	0.000
89	B	111	GLY	0	-0.013	-0.007	14.874	-0.014	-0.014	0.000	0.000	0.000	0.000
90	B	112	THR	0	0.024	0.009	16.608	-0.052	-0.052	0.000	0.000	0.000	0.000
91	B	113	THR	0	-0.022	-0.001	19.375	0.001	0.001	0.000	0.000	0.000	0.000
92	B	114	THR	0	0.001	-0.005	22.850	-0.007	-0.007	0.000	0.000	0.000	0.000
93	B	115	ILE	0	-0.014	-0.005	25.198	-0.007	-0.007	0.000	0.000	0.000	0.000
94	B	116	GLY	0	-0.009	-0.002	28.947	-0.008	-0.008	0.000	0.000	0.000	0.000
95	B	117	PHE	0	-0.007	-0.023	28.853	0.008	0.008	0.000	0.000	0.000	0.000
96	B	118	TYR	0	-0.010	0.003	27.518	-0.003	-0.003	0.000	0.000	0.000	0.000
97	B	119	VAL	0	0.040	0.017	20.984	0.008	0.008	0.000	0.000	0.000	0.000
98	B	120	GLU	-1	-0.955	-0.968	23.127	0.142	0.142	0.000	0.000	0.000	0.000
99	B	121	TYR	0	0.026	-0.011	18.242	0.028	0.028	0.000	0.000	0.000	0.000
100	B	122	GLU	-1	-0.909	-0.953	19.704	0.141	0.141	0.000	0.000	0.000	0.000
101	B	123	ASN	0	-0.032	-0.010	19.434	0.004	0.004	0.000	0.000	0.000	0.000
102	B	124	ILE	0	-0.027	-0.008	15.993	-0.009	-0.009	0.000	0.000	0.000	0.000
103	B	125	ASN	0	-0.073	-0.041	14.388	0.000	0.000	0.000	0.000	0.000	0.000
104	B	126	LEU	0	-0.024	0.029	12.647	0.023	0.023	0.000	0.000	0.000	0.000
105	B	127	SER	0	-0.007	-0.035	14.228	-0.072	-0.072	0.000	0.000	0.000	0.000
106	B	128	ARG	1	0.988	1.004	7.199	-0.740	-0.740	0.000	0.000	0.000	0.000
107	B	129	GLN	0	0.044	0.009	9.264	0.088	0.088	0.000	0.000	0.000	0.000
108	B	130	THR	0	-0.004	0.002	7.772	-0.003	-0.003	0.000	0.000	0.000	0.000
109	B	131	LEU	0	0.021	0.031	10.324	-0.061	-0.061	0.000	0.000	0.000	0.000
110	B	132	TYR	0	0.035	0.012	13.503	-0.036	-0.036	0.000	0.000	0.000	0.000
111	B	133	SER	0	-0.044	-0.030	12.770	-0.047	-0.047	0.000	0.000	0.000	0.000
112	B	134	SER	0	0.022	-0.006	14.869	0.011	0.011	0.000	0.000	0.000	0.000
113	B	135	ASN	0	0.061	0.035	12.751	-0.006	-0.006	0.000	0.000	0.000	0.000
114	B	136	PHE	0	0.083	0.021	11.175	0.010	0.010	0.000	0.000	0.000	0.000
115	B	137	ARG	1	0.927	0.980	16.316	-0.085	-0.085	0.000	0.000	0.000	0.000
116	B	138	ASN	0	-0.013	-0.003	19.322	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	139	LEU	0	-0.003	0.007	16.429	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	140	LEU	0	-0.011	-0.002	19.892	0.002	0.002	0.000	0.000	0.000	0.000
119	B	141	ASN	0	-0.046	-0.035	21.820	0.000	0.000	0.000	0.000	0.000	0.000
120	B	142	ILE	0	-0.023	0.005	22.248	-0.006	-0.006	0.000	0.000	0.000	0.000
121	B	143	PHE	0	-0.023	-0.006	19.552	0.000	0.000	0.000	0.000	0.000	0.000
122	B	144	GLY	0	0.070	0.045	24.535	-0.005	-0.005	0.000	0.000	0.000	0.000
123	B	145	GLU	-1	-0.926	-0.998	25.389	0.128	0.128	0.000	0.000	0.000	0.000
124	B	146	GLU	-1	-0.949	-0.984	25.337	0.129	0.129	0.000	0.000	0.000	0.000
125	B	147	ASP	-1	-0.743	-0.861	24.893	0.136	0.136	0.000	0.000	0.000	0.000
126	B	148	PHE	0	-0.023	-0.013	17.408	0.024	0.024	0.000	0.000	0.000	0.000
127	B	149	LYS	1	0.945	0.967	20.714	-0.123	-0.123	0.000	0.000	0.000	0.000
128	B	150	TYR	0	0.038	0.019	21.540	0.022	0.022	0.000	0.000	0.000	0.000
129	B	151	PHE	0	0.032	0.043	16.013	0.029	0.029	0.000	0.000	0.000	0.000
130	B	152	LEU	0	-0.072	-0.041	15.499	0.038	0.038	0.000	0.000	0.000	0.000
131	B	153	ILE	0	-0.055	-0.022	16.981	0.060	0.060	0.000	0.000	0.000	0.000
132	B	154	ASP	-1	-0.847	-0.900	19.296	0.236	0.236	0.000	0.000	0.000	0.000
133	B	155	PHE	0	-0.039	-0.024	16.361	-0.013	-0.013	0.000	0.000	0.000	0.000
134	B	156	LEU	0	-0.081	-0.008	12.341	0.060	0.060	0.000	0.000	0.000	0.000
135	B	157	VAL	0	0.001	-0.008	11.171	-0.067	-0.067	0.000	0.000	0.000	0.000
136	B	158	PHE	0	0.017	0.000	6.926	0.213	0.213	0.000	0.000	0.000	0.000
137	B	159	THR	0	0.029	0.001	7.072	-0.184	-0.184	0.000	0.000	0.000	0.000
138	B	160	LYS	1	0.929	0.972	5.807	0.481	0.481	0.000	0.000	0.000	0.000
139	B	161	VAL	0	-0.019	-0.018	2.843	-0.968	0.085	0.233	-0.211	-1.075	0.000
140	B	162	GLU	-1	-0.898	-0.940	3.390	-2.540	-1.692	0.039	-0.239	-0.648	-0.001
141	B	163	GLN	0	-0.031	-0.031	5.275	-0.038	0.054	-0.001	-0.002	-0.088	0.000
142	B	164	ASN	0	-0.040	-0.018	6.024	-0.073	-0.073	0.000	0.000	0.000	0.000
143	B	165	GLY	0	0.078	0.051	2.886	-0.877	-0.383	0.299	-0.196	-0.596	0.001
144	B	166	TYR	0	-0.101	-0.081	2.978	-0.620	0.306	0.421	-0.026	-1.321	-0.003
145	B	167	LEU	0	0.039	0.022	2.166	-2.306	-1.418	7.166	-3.728	-4.326	-0.024
146	B	168	GLN	0	-0.009	-0.006	3.584	-0.669	-0.561	0.019	-0.001	-0.126	0.000
147	B	169	VAL	0	-0.073	-0.055	7.114	0.173	0.173	0.000	0.000	0.000	0.000
148	B	170	ALA	0	0.007	0.000	9.107	-0.118	-0.118	0.000	0.000	0.000	0.000
149	B	171	GLY	0	0.138	0.078	12.395	0.061	0.061	0.000	0.000	0.000	0.000
150	B	172	VAL	0	-0.024	-0.007	14.084	0.093	0.093	0.000	0.000	0.000	0.000
151	B	173	CYS	0	-0.032	-0.023	11.951	0.104	0.104	0.000	0.000	0.000	0.000
152	B	174	LEU	0	0.051	0.015	8.973	-0.114	-0.114	0.000	0.000	0.000	0.000
153	B	175	ASN	0	-0.049	-0.025	10.964	-0.156	-0.156	0.000	0.000	0.000	0.000
154	B	176	GLN	0	-0.062	-0.022	12.573	-0.066	-0.066	0.000	0.000	0.000	0.000
155	B	177	TYR	0	-0.100	-0.070	15.220	-0.081	-0.081	0.000	0.000	0.000	0.000
156	B	186	LYS	1	0.957	0.970	39.688	-0.044	-0.044	0.000	0.000	0.000	0.000
157	B	187	TRP	0	0.038	0.007	39.964	-0.003	-0.003	0.000	0.000	0.000	0.000
158	B	188	TYR	0	0.071	0.040	33.745	0.000	0.000	0.000	0.000	0.000	0.000
159	B	189	LYS	1	0.923	0.952	40.542	-0.050	-0.050	0.000	0.000	0.000	0.000
160	B	190	ASN	0	-0.020	-0.002	43.970	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	191	ASN	0	0.032	0.032	46.839	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:14:LEU)