FMO DATABASE

FMODB ID: GNVQ1

Calculation Name: 3B8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1321571.768822
FMO2-HF: Nuclear repulsion	1263932.865419
FMO2-HF: Total energy	-57638.903403
FMO2-MP2: Total energy	-57804.825258

3D Structure Molmil

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.
-41.715	-47.142	30.388	-12.083	-12.877	-0.054

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 : -0.008 / q_NPA : -0.020

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	-0.811	-0.922	1.837	-15.677	-17.020	9.675	-4.433	-3.898	-0.051
4	A	5	GLN	0	-0.004	0.000	1.845	-12.823	-14.097	10.661	-4.236	-5.151	-0.037
5	A	6	GLN	0	-0.024	-0.016	1.815	-11.838	-14.772	10.053	-3.408	-3.712	0.034
6	A	7	LEU	0	0.000	-0.003	5.609	-0.156	-0.032	-0.001	-0.006	-0.116	0.000
7	A	8	TYR	0	0.006	0.003	7.538	0.155	0.155	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.865	-0.930	7.231	-0.376	-0.376	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.005	0.007	9.057	0.183	0.183	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.004	-0.003	10.960	0.041	0.041	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.842	0.903	11.443	0.857	0.857	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.050	-0.034	10.229	0.205	0.205	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.023	-0.001	14.501	0.052	0.052	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.031	-0.017	16.796	0.017	0.017	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.850	-0.913	15.377	-0.582	-0.582	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.058	-0.026	18.612	0.042	0.042	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.758	0.856	20.411	0.024	0.024	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.006	-0.002	21.798	0.019	0.019	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.013	0.024	22.903	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.098	-0.068	23.924	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.894	-0.937	26.825	-0.162	-0.162	0.000	0.000	0.000	0.000
22	A	23	TRP	0	-0.031	-0.009	23.854	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.027	-0.006	22.809	0.033	0.033	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.014	-0.015	20.263	-0.066	-0.066	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.033	-0.011	17.670	0.068	0.068	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.001	0.001	16.355	-0.099	-0.099	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.006	0.003	12.690	0.101	0.101	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.013	-0.007	14.017	-0.132	-0.132	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.862	0.954	8.065	-2.552	-2.552	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.041	0.012	12.204	-0.270	-0.270	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.826	-0.921	12.770	1.185	1.185	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.776	-0.846	12.458	1.835	1.835	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.011	-0.007	9.794	0.323	0.323	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.078	-0.057	9.735	0.290	0.290	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.005	-0.007	7.486	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	37	TYR	0	-0.006	0.010	11.961	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.039	-0.005	13.961	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.098	-0.057	16.527	0.039	0.039	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.063	0.028	19.714	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.021	0.017	22.519	0.025	0.025	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.044	-0.007	25.733	0.006	0.006	0.000	0.000	0.000	0.000
42	A	43	ASP	-1	-0.750	-0.846	28.903	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.050	-0.022	31.177	0.016	0.016	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.010	-0.003	34.658	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.014	-0.022	37.643	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.103	0.053	35.612	0.008	0.008	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.091	-0.041	34.983	0.000	0.000	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.054	-0.026	34.531	0.011	0.011	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.890	-0.931	30.694	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.049	-0.036	27.280	0.012	0.012	0.000	0.000	0.000	0.000
51	A	52	CYS	0	-0.055	-0.018	21.556	0.034	0.034	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.076	0.058	21.047	0.034	0.034	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.750	-0.892	18.667	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.018	-0.037	20.231	0.065	0.065	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.023	0.017	22.769	0.029	0.029	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.028	0.011	17.260	0.052	0.052	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.012	-0.009	19.256	0.074	0.074	0.000	0.000	0.000	0.000
58	A	59	LEU	0	0.026	0.009	20.932	0.035	0.035	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.810	-0.889	19.689	0.545	0.545	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.006	0.000	18.539	0.050	0.050	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.015	-0.012	20.215	0.017	0.017	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.766	0.887	22.269	-0.504	-0.504	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.063	-0.038	20.430	0.005	0.005	0.000	0.000	0.000	0.000
64	A	65	GLN	0	-0.029	-0.008	22.492	0.010	0.010	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.824	0.906	16.584	-1.151	-1.151	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.855	0.923	17.449	-0.725	-0.725	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.002	-0.002	15.067	0.153	0.153	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.049	-0.035	10.654	0.080	0.080	0.000	0.000	0.000	0.000
69	A	70	HIS	0	0.046	0.037	7.196	0.175	0.175	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.025	0.008	11.581	0.171	0.171	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.011	-0.001	10.233	-0.174	-0.174	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.010	-0.005	13.475	0.152	0.152	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.010	0.023	12.409	-0.139	-0.139	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.028	-0.001	16.829	0.106	0.106	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.900	0.973	19.880	0.320	0.320	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.834	-0.913	22.077	-0.389	-0.389	0.000	0.000	0.000	0.000
77	A	78	ASN	0	0.014	0.017	25.113	0.013	0.013	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.757	-0.887	23.110	-0.311	-0.311	0.000	0.000	0.000	0.000
79	A	80	HIS	0	-0.091	-0.035	22.676	-0.063	-0.063	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.081	-0.036	23.232	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.870	-0.944	18.332	-0.818	-0.818	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.018	-0.008	15.037	0.068	0.068	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.821	0.896	15.975	0.378	0.378	0.000	0.000	0.000	0.000
84	A	85	VAL	0	0.011	0.006	13.297	0.065	0.065	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.019	0.003	16.136	0.066	0.066	0.000	0.000	0.000	0.000
86	A	87	SER	0	0.045	0.004	17.253	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.001	0.024	16.650	0.040	0.040	0.000	0.000	0.000	0.000
88	A	89	CYS	0	-0.008	0.017	19.517	0.008	0.008	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.076	0.023	23.328	0.028	0.028	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.016	-0.002	25.653	0.022	0.022	0.000	0.000	0.000	0.000
91	A	93	GLN	0	0.003	0.001	20.949	0.055	0.055	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.766	-0.856	22.478	0.041	0.041	0.000	0.000	0.000	0.000
93	A	95	ARG	1	0.855	0.931	23.145	-0.059	-0.059	0.000	0.000	0.000	0.000
94	A	96	LEU	0	-0.002	-0.001	17.503	0.045	0.045	0.000	0.000	0.000	0.000
95	A	97	PHE	0	0.024	-0.003	20.901	0.039	0.039	0.000	0.000	0.000	0.000
96	A	98	TYR	0	0.023	0.027	23.158	0.013	0.013	0.000	0.000	0.000	0.000
97	A	99	TRP	0	-0.020	-0.017	19.545	0.019	0.019	0.000	0.000	0.000	0.000
98	A	100	GLY	0	0.060	0.033	21.113	0.028	0.028	0.000	0.000	0.000	0.000
99	A	101	PRO	0	-0.008	-0.003	19.921	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.789	-0.883	16.537	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.019	0.009	15.045	0.027	0.027	0.000	0.000	0.000	0.000
102	A	104	GLN	0	-0.029	-0.019	10.447	-0.244	-0.244	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.015	-0.003	12.118	0.028	0.028	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.000	0.002	11.365	-0.096	-0.096	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.018	-0.014	12.775	0.148	0.148	0.000	0.000	0.000	0.000
106	A	108	THR	0	-0.010	-0.021	15.285	-0.097	-0.097	0.000	0.000	0.000	0.000
107	A	109	ASN	0	-0.035	-0.034	14.070	0.025	0.025	0.000	0.000	0.000	0.000
108	A	110	ALA	0	-0.016	-0.022	18.198	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.919	0.963	16.024	0.878	0.878	0.000	0.000	0.000	0.000
110	A	112	GLN	0	0.011	0.020	15.239	-0.098	-0.098	0.000	0.000	0.000	0.000
111	A	113	ASP	-1	-0.874	-0.924	11.810	-1.922	-1.922	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.040	-0.018	7.459	0.240	0.240	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.016	-0.008	8.461	-0.248	-0.248	0.000	0.000	0.000	0.000
114	A	116	PHE	0	0.002	-0.011	6.081	0.276	0.276	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.844	0.899	10.782	0.483	0.483	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.009	0.019	14.043	0.060	0.060	0.000	0.000	0.000	0.000
117	A	119	LEU	0	0.013	0.001	15.960	-0.043	-0.043	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.838	0.889	18.674	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.862	-0.916	17.761	-0.345	-0.345	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.049	-0.016	16.909	-0.029	-0.029	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.065	-0.036	21.130	0.020	0.020	0.000	0.000	0.000	0.000
122	A	124	PRO	0	0.003	0.000	24.057	0.026	0.026	0.000	0.000	0.000	0.000
123	A	125	TYR	0	0.004	0.006	25.654	0.000	0.000	0.000	0.000	0.000	0.000
124	A	126	HIS	1	0.798	0.882	26.128	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	127	TRP	0	0.043	-0.007	28.285	0.014	0.014	0.000	0.000	0.000	0.000
126	A	128	THR	0	-0.012	0.004	27.747	0.003	0.003	0.000	0.000	0.000	0.000
127	A	129	GLU	-1	-0.966	-0.976	30.076	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	130	ALA	0	-0.043	-0.024	31.166	0.004	0.004	0.000	0.000	0.000	0.000
129	A	131	TYR	0	-0.033	-0.006	32.799	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	132	HIS	0	-0.002	-0.007	29.331	0.014	0.014	0.000	0.000	0.000	0.000
131	A	133	ASP	-1	-0.857	-0.916	30.566	0.108	0.108	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.910	-0.977	32.137	0.112	0.112	0.000	0.000	0.000	0.000
133	A	135	MET	0	-0.021	-0.009	28.297	0.020	0.020	0.000	0.000	0.000	0.000
134	A	136	VAL	0	0.010	0.007	26.577	0.025	0.025	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.946	0.989	27.184	-0.156	-0.156	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.801	-0.861	27.682	0.266	0.266	0.000	0.000	0.000	0.000
137	A	139	TRP	0	-0.008	-0.028	23.317	0.017	0.017	0.000	0.000	0.000	0.000
138	A	140	SER	0	-0.092	-0.051	23.589	0.041	0.041	0.000	0.000	0.000	0.000
139	A	141	THR	0	-0.073	-0.025	25.366	0.035	0.035	0.000	0.000	0.000	0.000
140	A	142	ARG	1	0.720	0.833	21.535	-0.285	-0.285	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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