FMO DATABASE

FMODB ID: VR811

Calculation Name: 3VJZ-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VJZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K0P4

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	165
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1668561.310236
FMO2-HF: Nuclear repulsion	1604245.133641
FMO2-HF: Total energy	-64316.176594
FMO2-MP2: Total energy	-64506.25608

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:0:HIS )

Summations of interaction energy for fragment #1(A:0:HIS )

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.
-46.066	-39.325	7.707	-6.52	-7.929	-0.069

Interaction energy analysis for fragmet #1(A:0:HIS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.082 / q_NPA : -0.049

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	2	THR	0	0.021	0.025	3.857	-2.185	-0.950	-0.008	-0.511	-0.717	0.002
4	A	3	ALA	0	-0.007	-0.010	6.083	1.235	1.235	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.012	0.029	8.843	-0.519	-0.519	0.000	0.000	0.000	0.000
6	A	5	THR	0	-0.042	-0.026	11.385	0.435	0.435	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.031	-0.013	14.134	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.062	0.031	16.154	0.152	0.152	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.873	-0.952	18.487	-0.490	-0.490	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.880	-0.949	21.743	-0.688	-0.688	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.062	0.039	18.787	0.033	0.033	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.769	0.884	23.153	0.531	0.531	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.096	-0.056	26.076	0.074	0.074	0.000	0.000	0.000	0.000
14	A	13	GLN	0	0.052	0.057	22.526	0.032	0.032	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.900	-0.950	27.928	-0.383	-0.383	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.012	-0.020	29.166	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.014	-0.019	29.055	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.062	0.045	26.411	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.036	0.035	24.143	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.057	-0.040	24.117	-0.057	-0.057	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.018	-0.001	22.424	-0.061	-0.061	0.000	0.000	0.000	0.000
22	A	21	THR	0	0.051	0.019	19.590	-0.110	-0.110	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.047	-0.022	19.480	-0.128	-0.128	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.046	-0.023	19.610	-0.087	-0.087	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.017	0.001	18.117	-0.058	-0.058	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.009	0.010	15.300	-0.184	-0.184	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.038	-0.028	14.799	-0.130	-0.130	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.001	0.010	15.656	-0.079	-0.079	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.818	-0.924	10.010	-3.205	-3.205	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.082	-0.038	9.645	0.063	0.063	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.043	-0.041	11.153	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.027	-0.016	13.204	0.086	0.086	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.006	-0.005	6.655	-0.210	-0.210	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.007	0.022	6.805	-0.383	-0.383	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.024	-0.006	8.752	0.435	0.435	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.786	-0.884	12.229	-0.512	-0.512	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.879	-0.927	7.918	-0.281	-0.281	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.122	-0.064	11.380	0.219	0.219	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.030	-0.001	13.043	0.145	0.145	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.093	-0.043	15.942	0.120	0.120	0.000	0.000	0.000	0.000
41	A	40	CYS	0	-0.095	-0.048	18.157	0.057	0.057	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.013	-0.012	16.834	0.040	0.040	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.022	0.006	17.714	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.853	-0.939	14.419	-0.824	-0.824	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.868	-0.946	16.456	-0.623	-0.623	0.000	0.000	0.000	0.000
46	A	45	GLN	0	-0.028	-0.023	19.088	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	46	HIS	0	-0.044	-0.022	12.683	-0.248	-0.248	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.030	-0.015	14.810	-0.200	-0.200	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.049	-0.028	15.949	-0.054	-0.054	0.000	0.000	0.000	0.000
50	A	49	THR	0	-0.007	-0.002	14.441	0.032	0.032	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.032	0.028	12.565	-0.073	-0.073	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.036	-0.030	14.138	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	52	CYS	0	0.002	0.001	17.292	0.083	0.083	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.010	0.003	11.625	0.187	0.187	0.000	0.000	0.000	0.000
55	A	54	LEU	0	-0.026	-0.024	15.424	0.010	0.010	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.809	-0.893	16.348	-0.729	-0.729	0.000	0.000	0.000	0.000
57	A	56	SER	0	-0.021	-0.021	18.765	0.044	0.044	0.000	0.000	0.000	0.000
58	A	57	GLN	0	0.007	0.019	15.394	0.063	0.063	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.079	-0.043	17.734	0.080	0.080	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.884	-0.944	20.239	-0.583	-0.583	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.990	-0.989	22.682	-0.564	-0.564	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.032	0.016	21.300	0.058	0.058	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.072	-0.030	20.698	0.013	0.013	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.000	-0.046	15.911	-0.142	-0.142	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.024	0.000	15.648	-0.176	-0.176	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.031	0.019	15.594	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	66	LEU	0	0.002	0.027	11.858	-0.151	-0.151	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.063	-0.055	10.561	-0.337	-0.337	0.000	0.000	0.000	0.000
69	A	68	ALA	0	-0.052	-0.024	10.938	-0.269	-0.269	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.039	-0.020	12.361	0.025	0.025	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.065	0.023	9.042	-0.139	-0.139	0.000	0.000	0.000	0.000
72	A	71	TYR	0	-0.027	-0.061	6.686	-0.053	-0.053	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.079	0.041	7.722	0.210	0.210	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.906	-0.952	2.170	-30.711	-27.064	7.553	-5.325	-5.875	-0.066
75	A	74	TYR	0	0.009	-0.009	2.922	-3.037	-1.178	0.162	-0.684	-1.337	-0.005
76	A	75	ILE	0	-0.007	0.012	6.854	1.121	1.121	0.000	0.000	0.000	0.000
77	A	76	PHE	0	-0.020	-0.018	9.543	0.629	0.629	0.000	0.000	0.000	0.000
78	A	77	ARG	1	0.825	0.900	5.253	1.398	1.398	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.080	0.067	5.508	0.249	0.249	0.000	0.000	0.000	0.000
80	A	79	PRO	0	0.016	0.004	8.103	0.187	0.187	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.074	0.054	11.770	0.177	0.177	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.042	0.013	13.528	0.173	0.173	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.920	-0.978	15.264	-0.322	-0.322	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.035	-0.029	14.546	0.125	0.125	0.000	0.000	0.000	0.000
85	A	84	LEU	0	0.074	0.047	17.205	0.079	0.079	0.000	0.000	0.000	0.000
86	A	85	ARG	1	0.816	0.883	18.139	0.557	0.557	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.878	0.920	19.251	0.346	0.346	0.000	0.000	0.000	0.000
88	A	87	TRP	0	0.033	0.026	20.022	0.036	0.036	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.788	0.883	23.971	0.309	0.309	0.000	0.000	0.000	0.000
90	A	89	ILE	0	0.100	0.096	22.529	0.022	0.022	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.852	0.908	22.917	0.341	0.341	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.011	0.005	23.668	0.001	0.001	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.125	0.060	19.443	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.022	-0.011	18.711	-0.046	-0.046	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.887	0.951	19.152	0.378	0.378	0.000	0.000	0.000	0.000
96	A	95	VAL	0	0.019	0.017	20.185	0.024	0.024	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.019	0.018	15.114	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.841	-0.898	16.172	-0.594	-0.594	0.000	0.000	0.000	0.000
99	A	98	LYS	1	0.803	0.919	17.501	0.397	0.397	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.058	0.024	16.793	0.028	0.028	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.926	0.967	9.983	0.877	0.877	0.000	0.000	0.000	0.000
102	A	101	ALA	0	-0.041	-0.017	13.931	0.013	0.013	0.000	0.000	0.000	0.000
103	A	102	LEU	0	0.020	0.015	16.238	0.056	0.056	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.072	-0.052	7.159	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.942	-0.988	9.951	-0.669	-0.669	0.000	0.000	0.000	0.000
106	A	105	GLN	0	-0.086	-0.033	12.860	0.138	0.138	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.045	-0.031	14.252	0.101	0.101	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.049	0.028	10.522	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	108	LYS	1	0.979	0.992	5.831	-0.527	-0.527	0.000	0.000	0.000	0.000
110	A	109	THR	0	-0.017	-0.004	9.062	0.082	0.082	0.000	0.000	0.000	0.000
111	A	110	ILE	0	0.031	0.012	12.364	0.036	0.036	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.816	-0.878	6.136	-3.943	-3.943	0.000	0.000	0.000	0.000
113	A	112	THR	0	-0.054	-0.032	9.512	0.207	0.207	0.000	0.000	0.000	0.000
114	A	113	LEU	0	-0.052	-0.033	10.816	0.107	0.107	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.009	0.010	12.274	0.080	0.080	0.000	0.000	0.000	0.000
116	A	115	ASP	-1	-0.971	-0.977	10.413	-0.698	-0.698	0.000	0.000	0.000	0.000
117	A	116	GLY	0	-0.051	-0.020	12.544	0.123	0.123	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.038	-0.021	15.564	0.082	0.082	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.085	-0.031	17.041	0.043	0.043	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.846	-0.924	18.124	-0.573	-0.573	0.000	0.000	0.000	0.000
121	A	120	ILE	0	0.072	0.014	17.402	0.005	0.005	0.000	0.000	0.000	0.000
122	A	121	PRO	0	0.001	0.004	20.468	0.021	0.021	0.000	0.000	0.000	0.000
123	A	122	SER	0	-0.036	-0.024	22.052	0.049	0.049	0.000	0.000	0.000	0.000
124	A	123	LEU	0	-0.020	-0.009	15.843	0.031	0.031	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.933	0.967	19.718	0.638	0.638	0.000	0.000	0.000	0.000
126	A	125	LYS	1	0.920	0.962	21.851	0.342	0.342	0.000	0.000	0.000	0.000
127	A	126	GLN	0	-0.080	-0.033	19.950	0.035	0.035	0.000	0.000	0.000	0.000
128	A	127	PHE	0	-0.032	-0.020	17.081	0.024	0.024	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.048	0.019	20.624	-0.056	-0.056	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.850	-0.928	20.521	-0.456	-0.456	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.040	-0.040	15.541	-0.021	-0.021	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.922	-0.951	21.299	-0.466	-0.466	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.965	-0.973	24.541	-0.350	-0.350	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.006	-0.034	21.278	0.018	0.018	0.000	0.000	0.000	0.000
135	A	134	ASP	-1	-0.745	-0.868	21.202	-0.816	-0.816	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.011	0.011	23.389	0.007	0.007	0.000	0.000	0.000	0.000
137	A	136	ALA	0	0.007	-0.005	24.757	0.012	0.012	0.000	0.000	0.000	0.000
138	A	137	TYR	0	-0.123	-0.096	20.388	-0.028	-0.028	0.000	0.000	0.000	0.000
139	A	138	TYR	0	0.013	0.030	23.769	0.011	0.011	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-0.946	-0.975	26.495	-0.341	-0.341	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.081	-0.046	24.584	0.021	0.021	0.000	0.000	0.000	0.000
142	A	141	ALA	0	0.042	0.012	24.248	0.016	0.016	0.000	0.000	0.000	0.000
143	A	142	GLU	-1	-0.904	-0.940	25.964	-0.371	-0.371	0.000	0.000	0.000	0.000
144	A	143	GLN	0	-0.107	-0.043	28.549	0.052	0.052	0.000	0.000	0.000	0.000
145	A	144	ASP	-1	-0.805	-0.948	24.791	-0.480	-0.480	0.000	0.000	0.000	0.000
146	A	145	LEU	0	0.020	0.032	24.268	-0.011	-0.011	0.000	0.000	0.000	0.000
147	A	146	PRO	0	-0.038	-0.025	26.943	0.009	0.009	0.000	0.000	0.000	0.000
148	A	147	LEU	0	-0.008	0.013	27.687	0.016	0.016	0.000	0.000	0.000	0.000
149	A	148	LEU	0	0.003	-0.005	22.511	0.010	0.010	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.000	0.002	26.038	0.004	0.004	0.000	0.000	0.000	0.000
151	A	150	GLU	-1	-0.953	-0.972	28.710	-0.279	-0.279	0.000	0.000	0.000	0.000
152	A	151	HIS	0	-0.007	-0.015	24.051	0.043	0.043	0.000	0.000	0.000	0.000
153	A	152	ILE	0	0.011	-0.003	24.451	0.019	0.019	0.000	0.000	0.000	0.000
154	A	153	GLN	0	-0.063	-0.043	27.709	0.007	0.007	0.000	0.000	0.000	0.000
155	A	154	SER	0	-0.073	-0.024	30.581	0.032	0.032	0.000	0.000	0.000	0.000
156	A	155	ASN	0	-0.103	-0.046	27.412	0.040	0.040	0.000	0.000	0.000	0.000
157	A	156	TRP	0	0.022	0.028	28.132	-0.030	-0.030	0.000	0.000	0.000	0.000
158	A	157	GLU	-1	-0.890	-0.967	29.010	-0.298	-0.298	0.000	0.000	0.000	0.000
159	A	158	THR	0	-0.048	-0.016	23.555	0.006	0.006	0.000	0.000	0.000	0.000
160	A	159	PHE	0	-0.021	-0.023	21.752	-0.041	-0.041	0.000	0.000	0.000	0.000
161	A	160	ALA	0	-0.028	0.005	25.736	-0.025	-0.025	0.000	0.000	0.000	0.000
162	A	161	HIS	0	-0.066	-0.026	26.773	0.013	0.013	0.000	0.000	0.000	0.000
163	A	162	ILE	0	0.041	0.024	23.565	-0.028	-0.028	0.000	0.000	0.000	0.000
164	A	163	GLY	0	-0.032	-0.026	24.814	0.026	0.026	0.000	0.000	0.000	0.000
165	A	164	NME	0	-0.012	0.018	22.983	0.012	0.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS )