FMO DATABASE

FMODB ID: VRY21

Calculation Name: 3B8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8F

Chain ID: A

ChEMBL ID:

UniProt ID: A0A1Q4

Base Structure: X-ray

Registration Date: 2023-03-14

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1317028.755595
FMO2-HF: Nuclear repulsion	1259390.791239
FMO2-HF: Total energy	-57637.964356
FMO2-MP2: Total energy	-57803.843669

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-30.951	-26.934	15.926	-8.723	-11.218	0

Interaction energy analysis for fragmet #1(A:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.002

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	4	GLU	-1	-0.879	-0.957	3.133	-5.202	-3.198	0.023	-0.793	-1.233	0.001
4	A	5	GLN	0	-0.006	-0.003	1.982	-13.689	-13.062	10.114	-4.904	-5.837	-0.037
5	A	6	GLN	0	-0.015	-0.006	1.976	-11.050	-9.812	5.790	-3.015	-4.012	0.036
6	A	7	LEU	0	-0.009	-0.002	5.011	0.169	0.317	-0.001	-0.011	-0.136	0.000
7	A	8	TYR	0	0.015	0.000	7.219	0.186	0.186	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.892	-0.942	6.686	-1.166	-1.166	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.019	0.014	8.557	0.279	0.279	0.000	0.000	0.000	0.000
10	A	11	VAL	0	0.007	0.000	10.538	0.110	0.110	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.894	0.952	11.842	1.222	1.222	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.042	-0.033	9.763	0.324	0.324	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.012	0.008	14.058	0.092	0.092	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.035	-0.018	16.396	0.046	0.046	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.924	-0.962	15.733	-0.777	-0.777	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.011	0.005	18.221	0.024	0.024	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.796	0.895	20.032	0.124	0.124	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.013	-0.014	21.384	0.037	0.037	0.000	0.000	0.000	0.000
19	A	20	PRO	0	-0.002	0.011	22.912	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.101	-0.058	23.872	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.880	-0.929	26.830	-0.201	-0.201	0.000	0.000	0.000	0.000
22	A	23	TRP	0	-0.020	-0.009	23.646	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.039	0.010	22.325	0.020	0.020	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.010	-0.010	19.952	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.039	-0.012	17.386	0.055	0.055	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.001	0.004	16.186	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.009	0.002	12.406	0.052	0.052	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.015	-0.006	14.224	-0.061	-0.061	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.926	0.972	7.992	-2.797	-2.797	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.038	0.010	12.333	-0.198	-0.198	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.906	-0.976	12.490	1.312	1.312	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.864	-0.905	12.839	1.742	1.742	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.054	-0.032	9.585	0.301	0.301	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.064	-0.048	9.349	0.278	0.278	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.011	-0.010	7.466	-0.113	-0.113	0.000	0.000	0.000	0.000
36	A	37	TYR	0	-0.015	-0.001	11.906	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.035	0.007	14.030	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.072	-0.046	16.576	0.042	0.042	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.041	0.015	19.613	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.005	0.000	22.306	0.033	0.033	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.060	-0.015	25.524	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	43	ASP	-1	-0.800	-0.901	28.466	-0.081	-0.081	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.042	-0.022	30.878	0.017	0.017	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.013	0.000	34.321	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.005	-0.006	37.867	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.093	0.058	35.856	0.006	0.006	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.058	-0.030	35.401	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.094	-0.071	34.580	0.008	0.008	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.899	-0.932	30.501	-0.066	-0.066	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.052	-0.031	27.673	0.016	0.016	0.000	0.000	0.000	0.000
51	A	52	CYS	0	-0.018	-0.019	21.946	0.023	0.023	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.081	0.046	20.654	0.019	0.019	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.823	-0.919	18.466	-0.044	-0.044	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.053	-0.036	20.646	0.062	0.062	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.032	0.008	23.025	0.031	0.031	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.056	0.032	17.612	0.044	0.044	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.021	-0.017	19.582	0.075	0.075	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.003	-0.005	21.322	0.033	0.033	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.926	-0.961	19.333	0.486	0.486	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.009	0.001	18.853	0.044	0.044	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.021	-0.016	20.318	0.021	0.021	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.912	0.972	23.671	-0.380	-0.380	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.067	-0.045	20.129	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.023	0.006	22.286	0.003	0.003	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.869	0.950	16.648	-1.007	-1.007	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.931	0.983	18.377	-0.724	-0.724	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.012	-0.004	15.835	0.151	0.151	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.029	-0.044	11.480	0.053	0.053	0.000	0.000	0.000	0.000
69	A	70	HIS	0	0.040	0.055	8.378	0.046	0.046	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.040	0.019	12.332	0.078	0.078	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.016	-0.015	10.157	-0.103	-0.103	0.000	0.000	0.000	0.000
72	A	73	CYS	0	0.001	0.012	13.602	0.076	0.076	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.010	0.001	12.199	-0.108	-0.108	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.056	0.007	16.620	0.085	0.085	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.904	0.972	19.763	0.442	0.442	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.948	-0.983	21.718	-0.305	-0.305	0.000	0.000	0.000	0.000
77	A	78	ASN	0	0.023	0.023	24.758	0.010	0.010	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.831	-0.924	23.097	-0.366	-0.366	0.000	0.000	0.000	0.000
79	A	80	HIS	0	-0.056	-0.020	23.100	-0.065	-0.065	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.054	-0.030	23.209	0.013	0.013	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.953	-0.982	18.099	-0.863	-0.863	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.053	-0.031	14.621	0.071	0.071	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.950	0.975	16.637	0.433	0.433	0.000	0.000	0.000	0.000
84	A	85	VAL	0	0.030	0.012	13.308	0.038	0.038	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.054	-0.019	16.337	0.057	0.057	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.039	0.005	17.835	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.054	0.060	17.337	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	CYS	0	-0.007	0.012	20.241	0.010	0.010	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.080	0.021	23.870	0.024	0.024	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.039	0.008	26.250	0.022	0.022	0.000	0.000	0.000	0.000
91	A	93	GLN	0	0.009	-0.003	21.373	0.061	0.061	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.780	-0.863	23.038	0.124	0.124	0.000	0.000	0.000	0.000
93	A	95	ARG	1	0.899	0.960	23.900	-0.083	-0.083	0.000	0.000	0.000	0.000
94	A	96	LEU	0	0.007	0.000	18.179	0.040	0.040	0.000	0.000	0.000	0.000
95	A	97	PHE	0	0.042	0.013	21.632	0.050	0.050	0.000	0.000	0.000	0.000
96	A	98	TYR	0	0.026	0.023	23.710	0.003	0.003	0.000	0.000	0.000	0.000
97	A	99	TRP	0	0.005	-0.011	20.249	0.019	0.019	0.000	0.000	0.000	0.000
98	A	100	GLY	0	0.023	0.023	21.361	0.043	0.043	0.000	0.000	0.000	0.000
99	A	101	PRO	0	0.002	-0.009	20.800	0.000	0.000	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.818	-0.905	17.198	0.249	0.249	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.002	0.021	15.858	0.073	0.073	0.000	0.000	0.000	0.000
102	A	104	GLN	0	-0.081	-0.034	11.343	-0.186	-0.186	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.009	-0.016	13.176	0.033	0.033	0.000	0.000	0.000	0.000
104	A	106	ALA	0	-0.005	0.015	11.458	-0.052	-0.052	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.028	-0.013	13.000	0.070	0.070	0.000	0.000	0.000	0.000
106	A	108	THR	0	0.025	0.002	15.358	-0.090	-0.090	0.000	0.000	0.000	0.000
107	A	109	ASN	0	-0.060	-0.051	14.241	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	110	ALA	0	-0.021	-0.027	18.084	-0.043	-0.043	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.936	0.964	16.018	0.673	0.673	0.000	0.000	0.000	0.000
110	A	112	GLN	0	0.047	0.052	15.356	-0.076	-0.076	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.890	-0.927	11.411	-1.604	-1.604	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.033	-0.022	7.695	0.219	0.219	0.000	0.000	0.000	0.000
113	A	115	ILE	0	0.010	0.005	8.796	-0.091	-0.091	0.000	0.000	0.000	0.000
114	A	116	PHE	0	-0.011	-0.014	6.686	0.148	0.148	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.932	0.972	11.370	0.287	0.287	0.000	0.000	0.000	0.000
116	A	118	PRO	0	0.030	0.029	14.798	0.039	0.039	0.000	0.000	0.000	0.000
117	A	119	LEU	0	0.024	0.008	16.703	-0.064	-0.064	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.863	0.911	19.543	-0.227	-0.227	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.954	-0.984	18.483	-0.078	-0.078	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.056	-0.026	17.513	-0.036	-0.036	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.092	-0.037	21.564	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	124	PRO	0	0.024	0.013	24.477	0.023	0.023	0.000	0.000	0.000	0.000
123	A	125	TYR	0	-0.011	-0.005	26.187	0.007	0.007	0.000	0.000	0.000	0.000
124	A	126	HIS	1	0.795	0.866	26.711	-0.099	-0.099	0.000	0.000	0.000	0.000
125	A	127	TRP	0	0.033	0.000	28.868	0.010	0.010	0.000	0.000	0.000	0.000
126	A	128	THR	0	0.007	0.018	28.303	0.001	0.001	0.000	0.000	0.000	0.000
127	A	129	GLU	-1	-0.984	-0.978	30.356	0.079	0.079	0.000	0.000	0.000	0.000
128	A	130	ALA	0	-0.014	-0.014	31.592	0.001	0.001	0.000	0.000	0.000	0.000
129	A	131	TYR	0	-0.046	-0.012	33.630	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	132	HIS	0	0.029	0.023	29.808	0.022	0.022	0.000	0.000	0.000	0.000
131	A	133	ASP	-1	-0.881	-0.945	31.475	0.173	0.173	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.913	-0.978	32.916	0.159	0.159	0.000	0.000	0.000	0.000
133	A	135	MET	0	-0.023	-0.022	29.046	0.019	0.019	0.000	0.000	0.000	0.000
134	A	136	VAL	0	-0.012	0.003	27.720	0.032	0.032	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.962	0.986	28.145	-0.190	-0.190	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.843	-0.903	28.560	0.291	0.291	0.000	0.000	0.000	0.000
137	A	139	TRP	0	-0.019	-0.024	24.383	0.025	0.025	0.000	0.000	0.000	0.000
138	A	140	SER	0	-0.148	-0.084	24.569	0.048	0.048	0.000	0.000	0.000	0.000
139	A	141	THR	0	-0.020	-0.003	26.038	0.025	0.025	0.000	0.000	0.000	0.000
140	A	142	ARG	1	0.750	0.890	21.887	-0.316	-0.316	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)