FMO DATABASE

FMODB ID: M3QNZ

Calculation Name: 3PU6-A-Xray372

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: 2023-06-20

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	OptAll
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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1369377.878978
FMO2-HF: Nuclear repulsion	1312621.183909
FMO2-HF: Total energy	-56756.695069
FMO2-MP2: Total energy	-56922.227522

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:LEU)

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

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.
-12.099	-3.587	6.86	-5.037	-10.335	-0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.007

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	LYS	1	0.831	0.911	2.392	0.552	3.767	1.158	-1.249	-3.123	0.004
4	A	4	VAL	0	0.007	0.002	4.908	0.205	0.291	-0.001	-0.009	-0.076	0.000
5	A	5	LEU	0	0.008	0.002	8.556	0.077	0.077	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.017	0.000	11.473	0.047	0.047	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.061	-0.010	14.367	0.029	0.029	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.022	-0.014	17.599	0.010	0.010	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.056	0.033	20.803	0.003	0.003	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.068	-0.072	24.512	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.744	-0.865	25.534	-0.218	-0.218	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.025	0.007	28.426	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.859	0.925	30.642	0.133	0.133	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.044	0.024	31.388	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.718	-0.841	28.679	-0.139	-0.139	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.871	-0.931	26.971	-0.180	-0.180	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.004	0.001	25.511	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.011	-0.006	22.547	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.013	0.009	19.042	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.019	-0.003	19.023	-0.041	-0.041	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.006	-0.003	20.617	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.006	0.002	15.255	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.048	0.000	15.936	-0.034	-0.034	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.824	0.876	16.465	0.216	0.216	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.006	0.011	18.009	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.026	-0.025	11.628	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.930	-0.978	13.815	-0.474	-0.474	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.948	-0.969	15.498	-0.272	-0.272	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.045	-0.018	15.666	0.023	0.023	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.069	-0.019	9.272	0.062	0.062	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.056	0.009	10.359	-0.177	-0.177	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.879	-0.894	5.395	-1.279	-1.279	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.043	-0.032	6.224	-0.878	-0.878	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.010	-0.001	8.641	0.159	0.159	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.015	0.006	10.761	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.048	-0.031	12.666	0.012	0.012	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.016	0.004	15.357	0.017	0.017	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.015	0.007	18.706	0.020	0.020	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.024	-0.002	20.107	0.021	0.021	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.841	-0.913	22.883	-0.182	-0.182	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.024	0.004	24.291	0.020	0.020	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.031	0.022	19.326	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.884	-0.957	19.649	-0.236	-0.236	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.076	-0.044	21.545	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.748	-0.856	16.607	-0.416	-0.416	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.037	-0.027	16.931	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.037	-0.012	17.613	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.833	0.891	15.131	0.403	0.403	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.005	0.005	12.000	-0.074	-0.074	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.886	0.945	12.692	0.212	0.212	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.937	-0.969	13.427	-0.278	-0.278	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.049	-0.015	7.995	0.016	0.016	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.004	0.001	8.702	-0.158	-0.158	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.002	0.005	6.725	-0.063	-0.063	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.791	-0.872	2.530	-5.538	-2.886	3.917	-2.725	-3.845	-0.028
56	A	56	VAL	0	-0.024	-0.036	3.047	-0.553	0.330	0.132	-0.169	-0.846	-0.001
57	A	57	ILE	0	-0.016	-0.003	5.409	-0.249	-0.249	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.026	0.023	8.655	0.146	0.146	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.041	-0.020	10.864	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.000	-0.001	14.442	0.040	0.040	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.782	-0.918	16.831	-0.227	-0.227	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.017	0.033	20.565	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.095	-0.039	23.165	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.015	0.012	25.478	0.009	0.009	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.010	-0.008	29.131	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.048	-0.023	32.099	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.832	0.896	26.584	0.121	0.121	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.766	-0.875	27.914	-0.129	-0.129	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.050	-0.022	26.514	0.007	0.007	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.876	-0.914	24.151	-0.108	-0.108	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.035	-0.018	18.487	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.771	-0.859	19.038	-0.128	-0.128	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.063	-0.049	11.194	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.017	0.008	15.262	0.024	0.024	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.742	-0.836	9.845	-0.223	-0.223	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.012	-0.005	12.356	0.045	0.045	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.019	-0.030	10.565	0.037	0.037	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.847	-0.894	12.717	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.791	-0.874	15.726	-0.093	-0.093	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.907	0.954	18.601	0.026	0.026	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.010	-0.037	17.213	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.003	-0.001	17.656	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.041	-0.019	19.408	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.091	-0.047	22.343	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.057	-0.034	20.996	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.003	-0.014	21.689	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.041	-0.019	22.794	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.037	-0.022	24.536	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.030	0.009	20.493	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.003	0.003	21.995	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	THR	0	0.010	0.016	21.033	0.004	0.004	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.012	0.003	21.485	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.003	0.009	21.977	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.024	0.025	17.525	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.035	0.015	16.990	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.047	-0.047	17.122	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.003	0.003	17.297	0.021	0.021	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.009	-0.006	13.453	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.784	0.860	13.446	0.109	0.109	0.000	0.000	0.000	0.000
100	A	100	GLY	0	-0.045	-0.008	14.118	0.028	0.028	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.087	-0.035	11.343	0.022	0.022	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.051	-0.011	7.157	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	103	SER	0	0.030	0.021	8.683	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.830	0.905	5.763	0.153	0.153	0.000	0.000	0.000	0.000
105	A	105	THR	0	0.035	0.010	8.368	-0.145	-0.145	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.041	-0.032	7.414	0.069	0.069	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.016	0.014	11.569	-0.038	-0.038	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.003	-0.003	13.791	0.010	0.010	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.039	0.022	16.321	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.035	0.000	18.948	0.015	0.015	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.096	-0.056	21.872	0.008	0.008	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.023	0.006	25.533	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.027	0.016	28.477	0.005	0.005	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.006	0.000	32.313	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.905	-0.967	34.004	-0.086	-0.086	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.037	-0.031	32.220	0.008	0.008	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.009	-0.003	29.913	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.081	-0.031	33.215	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.040	-0.012	36.034	0.007	0.007	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.063	-0.023	35.703	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.001	-0.016	34.293	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.918	-0.950	32.465	-0.131	-0.131	0.000	0.000	0.000	0.000
123	A	123	GLY	0	-0.008	-0.002	30.312	0.005	0.005	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.045	-0.013	25.187	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.048	-0.055	29.857	0.007	0.007	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.063	-0.061	29.732	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.007	0.020	29.033	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.087	0.037	26.484	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.009	-0.003	25.007	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.868	-0.928	24.356	-0.135	-0.135	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.020	-0.026	23.508	-0.007	-0.007	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.025	0.014	20.740	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	133	PHE	0	-0.013	-0.007	19.484	-0.027	-0.027	0.000	0.000	0.000	0.000
134	A	134	VAL	0	-0.031	-0.016	19.386	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.008	0.001	17.483	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.012	-0.013	14.622	-0.034	-0.034	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.019	-0.007	14.413	-0.025	-0.025	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.856	0.900	14.109	0.165	0.165	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.030	0.016	9.808	-0.014	-0.014	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.894	0.940	9.581	0.238	0.238	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.871	-0.901	10.510	-0.145	-0.145	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.016	-0.001	6.836	0.044	0.044	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.770	-0.873	5.669	-0.948	-0.948	0.000	0.000	0.000	0.000
144	A	144	GLY	0	-0.013	-0.002	6.082	0.067	0.067	0.000	0.000	0.000	0.000
145	A	145	MET	0	-0.072	-0.034	6.563	0.095	0.095	0.000	0.000	0.000	0.000
146	A	146	LEU	0	-0.041	-0.015	2.417	-0.874	-0.288	1.527	-0.411	-1.702	-0.001
147	A	147	LYS	1	0.725	0.845	3.136	-0.542	0.548	0.127	-0.474	-0.743	-0.004

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