FMO DATABASE

FMODB ID: VQJK1

Calculation Name: 3BN6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BN6

Chain ID: A

ChEMBL ID:

UniProt ID: Q95114

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1643184.902749
FMO2-HF: Nuclear repulsion	1580736.434171
FMO2-HF: Total energy	-62448.468578
FMO2-MP2: Total energy	-62633.449494

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:158:CYS)

Summations of interaction energy for fragment #1(A:158:CYS)

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.
-25.111	-19.203	24.326	-8.236	-21.998	0.024

Interaction energy analysis for fragmet #1(A:158:CYS)

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 : 0.026

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	3	GLU	-1	-0.907	-0.939	2.113	-7.601	-3.618	4.630	-3.874	-4.739	0.034
4	A	4	PRO	0	0.003	-0.012	3.298	-2.446	-1.709	0.219	-0.085	-0.872	0.000
5	A	5	LEU	0	-0.036	-0.027	2.716	0.224	0.875	1.595	-0.059	-2.187	0.006
6	A	6	GLY	0	0.071	0.039	6.170	0.180	0.180	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.067	-0.025	9.644	0.023	0.023	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.887	0.927	11.618	0.481	0.481	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.848	-0.901	11.406	0.550	0.550	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.073	-0.052	14.157	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.006	-0.002	10.804	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.028	0.018	9.517	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.044	0.020	13.232	-0.058	-0.058	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.081	0.018	16.991	-0.110	-0.110	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.962	0.982	18.865	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.082	-0.039	12.962	0.121	0.121	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.017	0.015	15.035	-0.137	-0.137	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.011	-0.011	17.534	0.085	0.085	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.007	-0.007	19.327	-0.093	-0.093	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.025	-0.016	21.797	0.031	0.031	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.011	-0.031	24.655	0.057	0.057	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.003	-0.014	25.058	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.011	0.014	26.746	0.034	0.034	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.921	0.968	29.328	0.229	0.229	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.031	0.020	32.232	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.000	-0.008	34.574	0.010	0.010	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.018	0.013	36.080	0.012	0.012	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.005	0.014	36.517	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.013	0.006	33.229	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.026	-0.005	32.594	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.013	-0.014	32.323	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.000	-0.011	28.757	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.029	-0.002	25.204	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.031	-0.011	23.941	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.050	0.017	20.666	-0.022	-0.022	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.009	0.006	18.656	-0.063	-0.063	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.028	-0.003	19.270	0.043	0.043	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.004	0.012	17.209	0.008	0.008	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.742	0.871	14.907	0.182	0.182	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.016	-0.024	12.025	0.092	0.092	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.792	-0.890	15.206	-0.389	-0.389	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.004	0.024	18.351	0.130	0.130	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.005	-0.016	20.224	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.002	-0.004	23.835	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.902	0.955	26.954	0.131	0.131	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.015	0.010	27.217	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.050	-0.027	22.966	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.056	0.014	20.968	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.016	0.001	20.243	0.014	0.014	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.007	-0.019	22.179	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.018	0.027	24.644	0.029	0.029	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.039	0.015	25.996	0.023	0.023	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.071	-0.038	29.152	0.028	0.028	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.020	-0.018	28.470	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.063	0.036	28.121	0.009	0.009	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.035	0.012	25.674	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.060	-0.034	25.218	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.781	-0.827	24.407	-0.447	-0.447	0.000	0.000	0.000	0.000
59	A	59	TRP	0	0.005	-0.022	19.695	-0.069	-0.069	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.020	0.019	16.193	0.071	0.071	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.020	-0.004	16.037	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.016	-0.002	10.998	0.130	0.130	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.772	-0.841	12.647	-0.770	-0.770	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.018	-0.004	6.352	0.118	0.118	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.028	-0.008	9.592	0.380	0.380	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.064	-0.044	7.629	0.471	0.471	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.025	0.009	6.396	-0.193	-0.193	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.896	0.967	2.669	-4.530	-2.276	0.550	-0.938	-1.865	0.007
69	A	69	ARG	1	0.984	0.987	1.842	-2.881	-6.290	12.948	-3.839	-5.701	0.016
70	A	70	VAL	0	0.017	0.002	2.063	-12.833	-15.699	3.730	2.221	-3.084	-0.033
71	A	71	THR	0	-0.012	-0.046	2.900	2.439	3.811	0.694	-0.056	-2.011	-0.001
72	A	72	GLY	0	0.028	0.010	4.735	2.138	2.279	-0.001	-0.015	-0.124	0.000
73	A	73	ILE	0	-0.029	0.010	6.292	-0.726	-0.726	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.003	0.000	8.814	0.340	0.340	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.012	-0.014	11.489	0.017	0.017	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.006	0.001	14.860	0.053	0.053	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.045	0.035	18.315	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.011	-0.018	21.568	0.008	0.008	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.861	0.919	24.322	0.306	0.306	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.832	-0.914	28.087	-0.260	-0.260	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.019	0.006	30.736	0.008	0.008	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.018	-0.006	33.178	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.032	-0.007	32.406	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.047	-0.023	27.120	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.032	0.015	26.337	0.020	0.020	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.038	0.018	22.331	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.008	0.018	19.888	0.036	0.036	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.005	-0.005	20.816	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.019	0.021	20.267	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.005	0.008	13.768	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.919	0.976	17.568	0.728	0.728	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.006	-0.009	11.387	-0.050	-0.050	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.020	0.021	14.807	0.106	0.106	0.000	0.000	0.000	0.000
94	A	94	TYR	0	0.004	-0.008	11.521	-0.208	-0.208	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.087	0.039	12.973	0.195	0.195	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.812	-0.924	10.637	-1.218	-1.218	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.771	-0.856	13.336	-0.451	-0.451	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.024	0.004	16.247	0.053	0.053	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.087	-0.060	17.523	0.023	0.023	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.081	-0.049	19.142	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	TRP	0	-0.009	-0.020	14.885	-0.139	-0.139	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.000	0.016	15.772	0.126	0.126	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.816	-0.880	16.229	-0.937	-0.937	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.015	-0.016	11.498	-0.034	-0.034	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.898	0.948	15.642	0.836	0.836	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.785	-0.873	16.572	-1.222	-1.222	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.029	-0.011	15.901	0.078	0.078	0.000	0.000	0.000	0.000
108	A	108	GLY	0	-0.010	-0.001	18.669	0.029	0.029	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.023	0.011	21.214	0.044	0.044	0.000	0.000	0.000	0.000
110	A	110	SER	0	0.040	0.005	23.065	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.978	-0.983	23.995	-0.513	-0.513	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.076	-0.076	19.585	-0.037	-0.037	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.800	0.905	15.645	1.292	1.292	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.012	-0.010	18.293	-0.064	-0.064	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.026	-0.017	13.434	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	116	PRO	0	0.013	0.012	16.987	0.074	0.074	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.023	-0.004	17.447	-0.136	-0.136	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.064	-0.039	17.996	-0.040	-0.040	0.000	0.000	0.000	0.000
119	A	119	MET	0	0.057	0.020	20.610	0.010	0.010	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.782	-0.862	23.342	-0.475	-0.475	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.025	0.012	23.233	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.008	-0.025	21.847	-0.023	-0.023	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.006	-0.013	20.510	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.083	-0.052	15.073	-0.150	-0.150	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.861	0.932	15.692	1.313	1.313	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.953	0.979	9.316	1.927	1.927	0.000	0.000	0.000	0.000
127	A	127	ASN	0	-0.037	-0.008	11.235	0.334	0.334	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.024	-0.003	7.803	-0.473	-0.473	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.036	-0.013	7.161	0.631	0.631	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.852	-0.927	9.028	-1.483	-1.483	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.028	-0.009	10.339	0.286	0.286	0.000	0.000	0.000	0.000
132	A	132	PRO	0	-0.044	-0.027	5.907	-0.031	-0.031	0.000	0.000	0.000	0.000
133	A	133	PHE	0	0.025	0.030	7.791	0.584	0.584	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.078	-0.047	5.940	-0.814	-0.814	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.001	0.003	6.756	0.386	0.386	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.853	0.908	7.265	-0.080	-0.080	0.000	0.000	0.000	0.000
137	A	137	PHE	0	-0.034	-0.012	9.481	-0.021	-0.021	0.000	0.000	0.000	0.000
138	A	138	VAL	0	0.024	0.008	8.815	-0.159	-0.159	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.840	0.937	12.307	1.014	1.014	0.000	0.000	0.000	0.000
140	A	140	ILE	0	0.004	0.004	12.610	-0.100	-0.100	0.000	0.000	0.000	0.000
141	A	141	GLN	0	-0.025	-0.036	15.930	0.088	0.088	0.000	0.000	0.000	0.000
142	A	142	PRO	0	-0.019	-0.013	19.377	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	143	VAL	0	-0.014	-0.006	21.354	0.045	0.045	0.000	0.000	0.000	0.000
144	A	144	ALA	0	0.024	0.017	23.363	0.060	0.060	0.000	0.000	0.000	0.000
145	A	145	TRP	0	-0.028	-0.024	23.761	-0.065	-0.065	0.000	0.000	0.000	0.000
146	A	146	HIS	0	0.046	0.045	25.825	0.026	0.026	0.000	0.000	0.000	0.000
147	A	147	ASN	0	-0.018	-0.011	27.950	0.005	0.005	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.865	0.924	27.787	0.361	0.361	0.000	0.000	0.000	0.000
149	A	149	ILE	0	-0.010	0.024	22.833	-0.034	-0.034	0.000	0.000	0.000	0.000
150	A	150	THR	0	-0.008	-0.009	22.900	0.035	0.035	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.019	-0.011	16.927	-0.049	-0.049	0.000	0.000	0.000	0.000
152	A	152	ARG	1	0.823	0.931	17.208	0.573	0.573	0.000	0.000	0.000	0.000
153	A	153	VAL	0	-0.025	-0.026	11.245	-0.076	-0.076	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.726	-0.865	8.132	-0.844	-0.844	0.000	0.000	0.000	0.000
155	A	155	LEU	0	-0.010	-0.001	6.164	-0.223	-0.223	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.033	-0.014	3.780	-1.242	1.803	-0.039	-1.591	-1.415	-0.005

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Interactive mode: IFIE and PIEDA for fragment #1(A:158:CYS)