FMO DATABASE

FMODB ID: 53ZNZ

Calculation Name: 3PU6-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PU6

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MR08

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	149
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1362567.180098
FMO2-HF: Nuclear repulsion	1305640.951139
FMO2-HF: Total energy	-56926.228959
FMO2-MP2: Total energy	-57092.290484

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:ACE )

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

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.
-0.18	0.704	-0.006	-0.417	-0.462	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.022

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	LYS	1	0.831	0.918	3.837	1.768	2.652	-0.006	-0.417	-0.462	-0.001
4	A	3	LYS	1	0.894	0.976	5.752	0.736	0.736	0.000	0.000	0.000	0.000
5	A	4	VAL	0	0.023	0.005	9.415	0.136	0.136	0.000	0.000	0.000	0.000
6	A	5	LEU	0	0.007	0.004	12.806	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.047	-0.024	16.035	0.026	0.026	0.000	0.000	0.000	0.000
8	A	7	CYS	0	-0.044	-0.007	19.172	0.001	0.001	0.000	0.000	0.000	0.000
9	A	8	VAL	0	-0.010	-0.003	22.180	0.006	0.006	0.000	0.000	0.000	0.000
10	A	9	GLY	0	0.062	0.032	25.598	0.001	0.001	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.019	-0.013	29.027	0.006	0.006	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.774	-0.892	28.669	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.019	-0.004	32.173	0.003	0.003	0.000	0.000	0.000	0.000
14	A	13	ARG	1	0.849	0.936	34.895	0.029	0.029	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.071	0.042	35.904	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.782	-0.886	33.018	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.861	-0.955	31.831	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	17	GLY	0	0.032	0.025	29.437	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.015	-0.003	27.335	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	ALA	0	0.034	0.013	24.056	0.000	0.000	0.000	0.000	0.000	0.000
21	A	20	ILE	0	-0.019	0.000	23.354	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	21	ALA	0	-0.009	-0.016	24.011	0.005	0.005	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.010	-0.005	20.299	0.005	0.005	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.047	0.005	19.597	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.848	0.900	19.299	0.019	0.019	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.016	0.012	20.640	0.011	0.011	0.000	0.000	0.000	0.000
27	A	26	VAL	0	-0.018	-0.014	14.511	0.011	0.011	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.924	-0.966	15.486	0.028	0.028	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-1.011	-0.984	16.506	0.050	0.050	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.017	-0.017	16.874	0.016	0.016	0.000	0.000	0.000	0.000
31	A	30	MET	0	-0.114	-0.043	12.350	0.015	0.015	0.000	0.000	0.000	0.000
32	A	31	PRO	0	0.073	0.029	11.260	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.983	-0.998	5.899	0.449	0.449	0.000	0.000	0.000	0.000
34	A	33	TRP	0	-0.054	-0.016	8.009	-0.167	-0.167	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.028	-0.007	10.686	0.059	0.059	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.016	0.003	12.529	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	36	PHE	0	-0.071	-0.039	14.602	0.013	0.013	0.000	0.000	0.000	0.000
38	A	37	PHE	0	0.018	0.003	18.513	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.039	0.017	22.188	0.003	0.003	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.027	-0.005	24.167	0.006	0.006	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.867	-0.936	27.191	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	41	THR	0	-0.081	-0.032	28.206	0.001	0.001	0.000	0.000	0.000	0.000
43	A	42	PRO	0	0.086	0.039	24.226	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.858	-0.949	23.666	-0.077	-0.077	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.110	-0.063	24.493	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.888	-0.944	20.133	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.033	-0.016	19.913	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.058	-0.017	20.008	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	48	LYS	1	1.007	0.985	17.193	0.033	0.033	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.021	0.027	15.526	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	ARG	1	0.873	0.926	15.473	0.073	0.073	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.976	-0.980	15.931	-0.097	-0.097	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.022	0.007	9.434	0.010	0.010	0.000	0.000	0.000	0.000
54	A	53	ALA	0	-0.012	-0.020	10.784	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	54	PRO	0	-0.001	0.006	9.825	-0.116	-0.116	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.832	-0.899	6.490	-2.100	-2.100	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.034	-0.039	9.730	0.127	0.127	0.000	0.000	0.000	0.000
58	A	57	ILE	0	0.007	0.016	11.780	0.035	0.035	0.000	0.000	0.000	0.000
59	A	58	VAL	0	0.000	0.007	14.857	0.015	0.015	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.025	-0.003	16.939	0.018	0.018	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.007	-0.006	20.359	0.003	0.003	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.848	-0.942	22.435	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.014	0.014	26.225	0.000	0.000	0.000	0.000	0.000	0.000
64	A	63	MET	0	-0.057	-0.013	29.451	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.025	0.018	31.722	0.002	0.002	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.045	0.027	35.354	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	66	PHE	0	-0.049	-0.037	38.388	0.003	0.003	0.000	0.000	0.000	0.000
68	A	67	LYS	1	0.843	0.902	38.065	0.036	0.036	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.834	-0.917	33.980	-0.058	-0.058	0.000	0.000	0.000	0.000
70	A	69	GLY	0	-0.056	-0.028	33.946	0.004	0.004	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.874	-0.931	30.328	-0.064	-0.064	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.085	-0.053	24.412	0.000	0.000	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.893	-0.934	26.482	-0.109	-0.109	0.000	0.000	0.000	0.000
74	A	73	PHE	0	-0.058	-0.036	17.511	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.001	0.006	22.582	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	75	ASP	-1	-0.802	-0.914	18.917	-0.310	-0.310	0.000	0.000	0.000	0.000
77	A	76	LEU	0	-0.022	-0.016	20.579	0.013	0.013	0.000	0.000	0.000	0.000
78	A	77	SER	0	0.026	0.009	18.356	0.003	0.003	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.886	-0.865	20.475	-0.152	-0.152	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.860	-0.939	23.233	-0.149	-0.149	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.937	0.963	26.215	0.116	0.116	0.000	0.000	0.000	0.000
82	A	81	THR	0	-0.033	-0.087	24.910	0.012	0.012	0.000	0.000	0.000	0.000
83	A	82	TYR	0	-0.014	-0.003	25.259	0.007	0.007	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.048	-0.015	26.977	0.011	0.011	0.000	0.000	0.000	0.000
85	A	84	TYR	0	-0.100	-0.042	30.458	0.008	0.008	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.005	-0.009	28.746	0.002	0.002	0.000	0.000	0.000	0.000
87	A	86	THR	0	-0.011	-0.015	30.817	0.004	0.004	0.000	0.000	0.000	0.000
88	A	87	HIS	0	-0.002	-0.007	33.708	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.033	-0.017	34.104	0.004	0.004	0.000	0.000	0.000	0.000
90	A	89	LEU	0	0.010	0.017	27.254	0.001	0.001	0.000	0.000	0.000	0.000
91	A	90	PRO	0	0.050	0.023	28.844	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	91	THR	0	0.042	0.028	26.297	0.001	0.001	0.000	0.000	0.000	0.000
93	A	92	PRO	0	0.029	0.034	27.669	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	93	ILE	0	0.020	-0.015	28.135	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	94	LEU	0	0.023	0.020	23.754	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	95	ILE	0	0.022	0.001	23.584	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	96	SER	0	-0.053	-0.032	23.394	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	97	TYR	0	0.004	0.012	21.258	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	98	LEU	0	0.002	-0.008	19.331	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.854	0.945	19.102	0.154	0.154	0.000	0.000	0.000	0.000
101	A	100	GLY	0	-0.043	-0.007	20.283	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	101	ILE	0	-0.092	-0.037	15.869	0.001	0.001	0.000	0.000	0.000	0.000
103	A	102	CYS	0	-0.068	-0.026	13.341	-0.040	-0.040	0.000	0.000	0.000	0.000
104	A	103	SER	0	0.046	0.024	15.242	0.015	0.015	0.000	0.000	0.000	0.000
105	A	104	LYS	1	0.913	0.962	13.083	0.431	0.431	0.000	0.000	0.000	0.000
106	A	105	THR	0	0.012	0.007	15.139	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	106	ILE	0	-0.015	-0.019	15.215	0.019	0.019	0.000	0.000	0.000	0.000
108	A	107	PHE	0	-0.010	0.007	18.866	0.007	0.007	0.000	0.000	0.000	0.000
109	A	108	LEU	0	0.010	-0.005	19.770	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	109	GLY	0	0.014	0.003	22.684	0.008	0.008	0.000	0.000	0.000	0.000
111	A	110	ILE	0	0.019	0.001	24.140	0.002	0.002	0.000	0.000	0.000	0.000
112	A	111	SER	0	0.004	0.009	27.973	0.005	0.005	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.013	-0.013	31.524	0.004	0.004	0.000	0.000	0.000	0.000
114	A	113	LEU	0	0.018	0.004	34.005	0.000	0.000	0.000	0.000	0.000	0.000
115	A	114	LEU	0	0.051	0.008	37.790	0.001	0.001	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.978	-0.988	39.370	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	116	ASN	0	-0.020	-0.019	37.465	0.004	0.004	0.000	0.000	0.000	0.000
118	A	117	VAL	0	-0.023	0.004	35.174	0.000	0.000	0.000	0.000	0.000	0.000
119	A	118	LEU	0	-0.078	-0.032	37.884	0.000	0.000	0.000	0.000	0.000	0.000
120	A	119	HIS	0	-0.011	0.002	40.716	0.002	0.002	0.000	0.000	0.000	0.000
121	A	120	PHE	0	-0.059	-0.031	38.850	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	SER	0	-0.010	-0.023	38.231	0.002	0.002	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.918	-0.940	35.842	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	123	GLY	0	-0.011	-0.005	33.688	0.002	0.002	0.000	0.000	0.000	0.000
125	A	124	LEU	0	-0.055	-0.018	29.121	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	125	SER	0	-0.014	-0.030	33.806	0.003	0.003	0.000	0.000	0.000	0.000
127	A	126	GLN	0	-0.054	-0.044	33.692	0.001	0.001	0.000	0.000	0.000	0.000
128	A	127	GLY	0	0.036	0.020	33.515	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	128	ALA	0	0.056	0.034	31.599	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	129	SER	0	0.012	-0.009	29.810	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	130	ASP	-1	-0.892	-0.945	28.723	-0.023	-0.023	0.000	0.000	0.000	0.000
132	A	131	SER	0	-0.023	-0.023	28.172	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	132	ALA	0	0.030	0.022	25.320	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	133	PHE	0	0.004	0.000	23.839	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	134	VAL	0	-0.021	-0.008	23.615	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	135	ALA	0	0.012	0.003	22.659	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.011	-0.012	18.188	-0.014	-0.014	0.000	0.000	0.000	0.000
138	A	137	GLY	0	-0.040	-0.014	18.786	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	138	ARG	1	0.954	0.970	19.093	0.098	0.098	0.000	0.000	0.000	0.000
140	A	139	ILE	0	0.032	0.032	14.561	-0.027	-0.027	0.000	0.000	0.000	0.000
141	A	140	LYS	1	0.901	0.937	14.604	-0.012	-0.012	0.000	0.000	0.000	0.000
142	A	141	GLU	-1	-0.950	-0.976	14.793	-0.118	-0.118	0.000	0.000	0.000	0.000
143	A	142	LEU	0	-0.027	-0.014	13.139	-0.021	-0.021	0.000	0.000	0.000	0.000
144	A	143	ASP	-1	-0.859	-0.956	9.467	-0.341	-0.341	0.000	0.000	0.000	0.000
145	A	144	GLY	0	-0.049	-0.018	10.356	-0.055	-0.055	0.000	0.000	0.000	0.000
146	A	145	MET	0	-0.069	-0.026	12.307	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	146	LEU	0	-0.025	-0.011	8.701	-0.043	-0.043	0.000	0.000	0.000	0.000
148	A	147	LYS	1	0.886	0.957	6.798	-0.114	-0.114	0.000	0.000	0.000	0.000
149	A	148	NME	0	-0.007	0.005	9.335	0.056	0.056	0.000	0.000	0.000	0.000

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