FMO DATABASE

FMODB ID: YVJN2

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	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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1642515.735887
FMO2-HF: Nuclear repulsion	1580067.767045
FMO2-HF: Total energy	-62447.968842
FMO2-MP2: Total energy	-62633.007133

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:1:CYS)

Summations of interaction energy for fragment #1(A:1: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.
-72.659	-408.652	528.807	-147.674	-45.14	0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.911 / q_NPA : -0.940

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	-0.935	-0.960	3.340	25.484	28.798	-0.011	-1.699	-1.603	0.007
4	A	4	PRO	0	-0.037	-0.032	5.276	1.642	1.674	-0.001	-0.003	-0.028	0.000
5	A	5	LEU	0	-0.015	-0.010	5.957	-0.685	-0.685	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.060	0.024	9.392	-1.489	-1.489	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.077	-0.027	12.868	-1.996	-1.996	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.955	0.965	14.594	-21.105	-21.105	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.863	-0.907	13.997	20.427	20.427	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.055	-0.046	16.902	-0.343	-0.343	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.027	0.005	14.341	-0.218	-0.218	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.019	0.022	12.988	-0.588	-0.588	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.036	0.015	17.104	-1.050	-1.050	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.076	0.008	20.701	0.676	0.676	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.951	0.975	23.062	-13.356	-13.356	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.075	-0.038	16.973	-1.022	-1.022	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.001	0.026	18.523	0.721	0.721	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.005	-0.009	20.832	-0.720	-0.720	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.009	-0.012	22.590	0.593	0.593	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.029	-0.007	25.023	-0.175	-0.175	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.025	-0.033	27.729	-0.590	-0.590	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.002	-0.006	28.453	0.321	0.321	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.011	0.008	30.243	-0.465	-0.465	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.930	0.972	32.908	-8.968	-8.968	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.043	0.024	35.862	-0.111	-0.111	0.000	0.000	0.000	0.000
26	A	26	TRP	0	-0.001	-0.007	38.243	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.014	0.010	39.661	-0.163	-0.163	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.009	0.008	40.175	-0.041	-0.041	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.016	-0.001	37.182	0.314	0.314	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.023	0.019	36.232	0.263	0.263	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.033	-0.024	36.042	0.104	0.104	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.008	-0.022	32.479	0.018	0.018	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.042	-0.011	28.878	0.310	0.310	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.020	-0.012	27.566	0.206	0.206	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.047	0.014	24.119	0.271	0.271	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.026	0.015	22.229	0.516	0.516	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.026	-0.002	22.892	0.217	0.217	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.001	0.007	20.864	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.752	0.881	18.385	-15.632	-15.632	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.000	-0.013	14.712	-0.909	-0.909	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.843	-0.929	18.232	15.655	15.655	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.047	0.001	20.886	-0.833	-0.833	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.008	-0.019	23.077	-0.826	-0.826	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.011	-0.011	26.481	-0.120	-0.120	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.895	0.954	30.016	-9.461	-9.461	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.028	0.016	30.685	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.039	-0.013	26.012	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.062	0.011	24.701	0.540	0.540	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.014	0.000	23.618	-0.261	-0.261	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.016	0.002	25.844	0.177	0.177	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.020	0.030	28.029	-0.186	-0.186	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.046	0.024	29.436	-0.102	-0.102	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.052	-0.030	32.428	-0.376	-0.376	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.025	-0.006	31.730	0.588	0.588	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.057	0.031	31.230	-0.176	-0.176	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.035	0.013	28.462	0.320	0.320	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.073	-0.036	27.841	0.252	0.252	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.804	-0.875	27.412	10.993	10.993	0.000	0.000	0.000	0.000
59	A	59	TRP	0	-0.012	-0.021	22.544	0.556	0.556	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.014	0.018	19.508	-0.443	-0.443	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.018	0.002	19.037	0.418	0.418	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.022	0.003	14.517	-0.584	-0.584	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.792	-0.848	15.611	19.738	19.738	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.028	-0.003	9.453	-0.510	-0.510	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.041	-0.013	13.445	0.414	0.414	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.064	-0.040	12.294	-0.260	-0.260	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.020	-0.029	10.853	1.191	1.191	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.907	0.966	6.660	-34.933	-34.933	0.000	0.000	0.000	0.000
69	A	69	ARG	1	1.030	1.003	2.874	-81.712	-78.476	3.852	-3.983	-3.106	0.014
70	A	70	VAL	0	0.008	0.001	4.077	9.198	9.733	0.084	-0.298	-0.321	-0.002
71	A	71	THR	0	0.008	-0.040	2.912	-14.530	-12.144	3.385	-3.760	-2.011	0.009
72	A	72	GLY	0	0.017	-0.001	5.907	-5.962	-5.913	-0.001	-0.017	-0.032	0.000
73	A	73	ILE	0	-0.032	0.005	8.862	0.433	0.433	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.008	0.002	11.503	-1.077	-1.077	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.003	-0.010	14.551	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.013	0.013	18.214	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.049	0.035	21.530	0.054	0.054	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.016	-0.026	24.979	0.244	0.244	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.906	0.950	27.731	-9.946	-9.946	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.832	-0.912	31.434	9.373	9.373	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.002	-0.002	34.271	-0.245	-0.245	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.026	-0.014	36.430	-0.180	-0.180	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.024	-0.004	35.796	-0.109	-0.109	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.037	-0.015	30.117	0.263	0.263	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.004	0.001	30.108	-0.524	-0.524	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.058	0.019	25.561	0.398	0.398	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.020	0.029	22.789	-0.445	-0.445	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.008	-0.005	23.850	0.416	0.416	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.012	0.016	22.792	0.238	0.238	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.004	0.008	15.705	-0.639	-0.639	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.987	1.015	19.683	-13.083	-13.083	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.003	-0.003	13.636	0.091	0.091	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.012	0.018	17.076	-0.366	-0.366	0.000	0.000	0.000	0.000
94	A	94	TYR	0	0.010	-0.007	13.490	0.723	0.723	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.081	0.033	15.268	-1.141	-1.141	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.804	-0.910	14.410	23.785	23.785	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.780	-0.853	16.901	14.914	14.914	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.024	0.000	19.606	-0.543	-0.543	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.100	-0.070	20.852	-0.653	-0.653	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.085	-0.054	21.952	-0.349	-0.349	0.000	0.000	0.000	0.000
101	A	101	TRP	0	-0.023	-0.028	17.337	1.140	1.140	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.003	0.018	17.032	-0.942	-0.942	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.913	-0.951	17.598	14.742	14.742	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.016	-0.007	11.945	0.353	0.353	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.890	0.943	16.692	-15.571	-15.571	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.877	-0.913	16.748	18.840	18.840	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.010	-0.020	15.838	-0.858	-0.858	0.000	0.000	0.000	0.000
108	A	108	GLY	0	-0.015	-0.004	18.626	-0.490	-0.490	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.014	0.015	21.382	-0.772	-0.772	0.000	0.000	0.000	0.000
110	A	110	SER	0	0.006	-0.011	23.077	0.272	0.272	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.948	-0.972	24.626	11.451	11.451	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.088	-0.072	21.010	0.642	0.642	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.965	1.002	16.187	-18.151	-18.151	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.016	-0.009	19.949	0.285	0.285	0.000	0.000	0.000	0.000
115	A	115	PHE	0	-0.043	-0.031	14.527	0.118	0.118	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.007	0.003	18.645	-0.589	-0.589	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.036	0.002	19.749	0.940	0.940	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.053	-0.037	20.777	0.150	0.150	0.000	0.000	0.000	0.000
119	A	119	MET	0	0.038	0.019	23.454	-0.200	-0.200	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.804	-0.883	25.450	11.994	11.994	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.014	-0.008	26.172	0.196	0.196	0.000	0.000	0.000	0.000
122	A	122	ASN	0	-0.038	-0.034	24.556	0.415	0.415	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.018	0.003	22.567	0.451	0.451	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.070	-0.041	17.044	0.860	0.860	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.876	0.944	17.678	-17.456	-17.456	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.961	0.983	9.898	-24.965	-24.965	0.000	0.000	0.000	0.000
127	A	127	ASN	0	-0.071	-0.036	13.580	-1.410	-1.410	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.029	0.003	7.921	1.232	1.232	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.061	-0.027	8.596	-3.254	-3.254	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.915	-0.962	8.960	22.703	22.703	0.000	0.000	0.000	0.000
131	A	131	THR	0	-0.029	-0.011	10.278	0.126	0.126	0.000	0.000	0.000	0.000
132	A	132	PRO	0	-0.034	-0.019	5.838	-0.538	-0.484	-0.001	-0.006	-0.047	0.000
133	A	133	PHE	0	0.008	0.020	8.002	-2.627	-2.627	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.022	-0.009	7.765	3.036	3.036	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.012	-0.004	9.274	-3.444	-3.444	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.851	0.918	10.597	-16.404	-16.404	0.000	0.000	0.000	0.000
137	A	137	PHE	0	-0.043	-0.020	13.211	-0.279	-0.279	0.000	0.000	0.000	0.000
138	A	138	VAL	0	0.044	0.022	11.509	0.480	0.480	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.858	0.928	14.860	-15.764	-15.764	0.000	0.000	0.000	0.000
140	A	140	ILE	0	0.005	0.006	16.116	0.410	0.410	0.000	0.000	0.000	0.000
141	A	141	GLN	0	-0.003	-0.018	18.868	-0.455	-0.455	0.000	0.000	0.000	0.000
142	A	142	PRO	0	-0.018	-0.014	22.112	0.060	0.060	0.000	0.000	0.000	0.000
143	A	143	VAL	0	-0.009	0.001	23.903	-0.343	-0.343	0.000	0.000	0.000	0.000
144	A	144	ALA	0	0.021	0.012	26.102	-0.553	-0.553	0.000	0.000	0.000	0.000
145	A	145	TRP	0	-0.025	-0.019	26.663	0.619	0.619	0.000	0.000	0.000	0.000
146	A	146	HIS	0	0.036	0.043	28.855	-0.311	-0.311	0.000	0.000	0.000	0.000
147	A	147	ASN	0	-0.033	-0.024	31.233	-0.040	-0.040	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.866	0.923	31.278	-9.681	-9.681	0.000	0.000	0.000	0.000
149	A	149	ILE	0	0.007	0.032	26.025	0.335	0.335	0.000	0.000	0.000	0.000
150	A	150	THR	0	0.005	-0.013	26.346	-0.204	-0.204	0.000	0.000	0.000	0.000
151	A	151	LEU	0	-0.021	-0.019	20.253	0.260	0.260	0.000	0.000	0.000	0.000
152	A	152	ARG	1	0.823	0.937	20.597	-13.836	-13.836	0.000	0.000	0.000	0.000
153	A	153	VAL	0	-0.019	-0.021	14.843	0.133	0.133	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.725	-0.874	11.264	24.609	24.609	0.000	0.000	0.000	0.000
155	A	155	LEU	0	-0.022	-0.014	9.677	-0.467	-0.467	0.000	0.000	0.000	0.000
156	A	156	LEU	0	-0.055	-0.031	6.504	-1.383	-1.383	0.000	0.000	0.000	0.000
157	A	157	GLY	0	0.058	0.014	3.112	-4.850	-5.398	2.738	-0.982	-1.207	0.009
158	A	158	CYS	-1	-0.909	-0.918	2.108	53.824	-291.227	518.762	-136.926	-36.785	-0.027

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