FMO DATABASE

FMODB ID: Q1GVY

Calculation Name: 3PUF-O-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: O

ChEMBL ID:

UniProt ID: O75792

Base Structure: X-ray

Registration Date: 2023-06-19

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-744910.363163
FMO2-HF: Nuclear repulsion	701480.436739
FMO2-HF: Total energy	-43429.926424
FMO2-MP2: Total energy	-43557.615119

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(O:9:ILE)

Summations of interaction energy for fragment #1(O:9:ILE)

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.
-14.702	-8.701	4.799	-4.705	-6.095	-0.01

Interaction energy analysis for fragmet #1(O:9:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.005

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	O	11	ARG	1	0.949	0.974	3.394	-9.100	-5.452	0.103	-1.760	-1.992	0.008
4	O	12	HIS	0	-0.017	-0.003	2.517	-4.471	-2.488	4.694	-2.895	-3.781	-0.018
5	O	13	ARG	1	0.922	0.967	3.674	-0.274	0.096	0.002	-0.050	-0.322	0.000
6	O	14	VAL	0	0.043	0.021	5.735	0.251	0.251	0.000	0.000	0.000	0.000
7	O	15	HIS	0	-0.015	-0.008	5.765	0.004	0.004	0.000	0.000	0.000	0.000
8	O	16	LEU	0	0.050	0.037	10.545	0.072	0.072	0.000	0.000	0.000	0.000
9	O	25	VAL	0	0.003	-0.007	27.812	0.000	0.000	0.000	0.000	0.000	0.000
10	O	26	PRO	0	0.003	0.006	30.187	-0.001	-0.001	0.000	0.000	0.000	0.000
11	O	27	ALA	0	0.011	0.008	30.302	0.005	0.005	0.000	0.000	0.000	0.000
12	O	28	THR	0	-0.036	-0.017	32.269	-0.003	-0.003	0.000	0.000	0.000	0.000
13	O	29	LEU	0	0.018	0.007	28.973	0.005	0.005	0.000	0.000	0.000	0.000
14	O	30	HIS	0	0.050	0.015	33.623	-0.003	-0.003	0.000	0.000	0.000	0.000
15	O	31	LEU	0	-0.001	0.013	31.645	0.004	0.004	0.000	0.000	0.000	0.000
16	O	32	LEU	0	0.014	-0.006	34.881	-0.003	-0.003	0.000	0.000	0.000	0.000
17	O	33	PRO	0	-0.002	0.013	36.525	0.002	0.002	0.000	0.000	0.000	0.000
18	O	34	CYS	0	-0.059	-0.039	37.890	0.000	0.000	0.000	0.000	0.000	0.000
19	O	35	GLU	-1	-0.900	-0.939	33.364	0.061	0.061	0.000	0.000	0.000	0.000
20	O	36	VAL	0	-0.082	-0.051	34.755	-0.001	-0.001	0.000	0.000	0.000	0.000
21	O	37	ALA	0	0.023	0.002	34.201	0.002	0.002	0.000	0.000	0.000	0.000
22	O	38	VAL	0	-0.084	-0.032	33.225	0.005	0.005	0.000	0.000	0.000	0.000
23	O	39	ASP	-1	-0.806	-0.898	28.186	0.090	0.090	0.000	0.000	0.000	0.000
24	O	40	GLY	0	-0.034	-0.018	30.893	0.006	0.006	0.000	0.000	0.000	0.000
25	O	41	PRO	0	-0.042	-0.016	31.808	-0.007	-0.007	0.000	0.000	0.000	0.000
26	O	42	ALA	0	0.077	0.028	34.672	0.001	0.001	0.000	0.000	0.000	0.000
27	O	43	PRO	0	-0.054	-0.014	37.731	-0.003	-0.003	0.000	0.000	0.000	0.000
28	O	44	VAL	0	0.066	0.019	37.025	-0.002	-0.002	0.000	0.000	0.000	0.000
29	O	45	GLY	0	0.034	0.021	40.198	-0.002	-0.002	0.000	0.000	0.000	0.000
30	O	46	ARG	1	0.925	0.958	41.968	-0.029	-0.029	0.000	0.000	0.000	0.000
31	O	47	PHE	0	-0.006	-0.008	43.822	-0.001	-0.001	0.000	0.000	0.000	0.000
32	O	48	PHE	0	0.013	0.011	41.101	-0.001	-0.001	0.000	0.000	0.000	0.000
33	O	49	THR	0	0.016	-0.024	40.811	-0.002	-0.002	0.000	0.000	0.000	0.000
34	O	50	PRO	0	-0.020	0.002	43.755	-0.002	-0.002	0.000	0.000	0.000	0.000
35	O	51	ALA	0	-0.005	0.012	46.877	-0.001	-0.001	0.000	0.000	0.000	0.000
36	O	52	ILE	0	-0.065	-0.023	42.615	0.000	0.000	0.000	0.000	0.000	0.000
37	O	53	ARG	1	0.845	0.921	47.257	-0.011	-0.011	0.000	0.000	0.000	0.000
38	O	54	GLN	0	-0.031	-0.025	48.873	0.000	0.000	0.000	0.000	0.000	0.000
39	O	55	GLY	0	0.063	0.043	50.769	0.000	0.000	0.000	0.000	0.000	0.000
40	O	56	PRO	0	-0.035	-0.026	51.977	-0.001	-0.001	0.000	0.000	0.000	0.000
41	O	57	GLU	-1	-0.871	-0.926	51.128	0.004	0.004	0.000	0.000	0.000	0.000
42	O	58	GLY	0	-0.005	-0.020	47.978	-0.001	-0.001	0.000	0.000	0.000	0.000
43	O	59	LEU	0	-0.012	0.014	43.938	0.001	0.001	0.000	0.000	0.000	0.000
44	O	60	GLU	-1	-0.852	-0.926	47.121	0.009	0.009	0.000	0.000	0.000	0.000
45	O	61	VAL	0	0.020	0.010	44.066	0.000	0.000	0.000	0.000	0.000	0.000
46	O	62	SER	0	0.001	0.011	47.066	0.000	0.000	0.000	0.000	0.000	0.000
47	O	63	PHE	0	0.006	0.000	40.500	0.001	0.001	0.000	0.000	0.000	0.000
48	O	64	ARG	1	0.927	0.950	41.903	-0.042	-0.042	0.000	0.000	0.000	0.000
49	O	65	GLY	0	0.026	0.017	46.481	0.001	0.001	0.000	0.000	0.000	0.000
50	O	66	ARG	1	0.948	0.987	45.570	-0.029	-0.029	0.000	0.000	0.000	0.000
51	O	67	CYS	0	0.018	0.015	47.417	0.000	0.000	0.000	0.000	0.000	0.000
52	O	68	LEU	0	-0.022	-0.010	41.972	0.001	0.001	0.000	0.000	0.000	0.000
53	O	69	ARG	1	0.946	0.962	45.421	-0.007	-0.007	0.000	0.000	0.000	0.000
54	O	70	GLY	0	0.024	-0.010	42.624	0.001	0.001	0.000	0.000	0.000	0.000
55	O	71	GLU	-1	-0.865	-0.940	40.683	-0.007	-0.007	0.000	0.000	0.000	0.000
56	O	72	GLU	-1	-0.935	-0.969	38.810	-0.009	-0.009	0.000	0.000	0.000	0.000
57	O	73	VAL	0	-0.019	-0.006	35.442	-0.002	-0.002	0.000	0.000	0.000	0.000
58	O	74	ALA	0	-0.023	-0.027	35.234	0.000	0.000	0.000	0.000	0.000	0.000
59	O	75	VAL	0	-0.017	-0.002	28.887	0.001	0.001	0.000	0.000	0.000	0.000
60	O	76	PRO	0	-0.007	0.000	29.818	-0.002	-0.002	0.000	0.000	0.000	0.000
61	O	77	PRO	0	0.023	0.005	30.559	-0.004	-0.004	0.000	0.000	0.000	0.000
62	O	78	GLY	0	0.015	0.008	28.858	-0.002	-0.002	0.000	0.000	0.000	0.000
63	O	79	LEU	0	-0.028	-0.010	25.471	-0.007	-0.007	0.000	0.000	0.000	0.000
64	O	80	VAL	0	-0.016	-0.011	24.300	0.004	0.004	0.000	0.000	0.000	0.000
65	O	81	GLY	0	0.015	0.031	24.545	-0.002	-0.002	0.000	0.000	0.000	0.000
66	O	82	TYR	0	0.007	-0.018	21.530	-0.001	-0.001	0.000	0.000	0.000	0.000
67	O	83	VAL	0	0.024	0.020	23.847	0.007	0.007	0.000	0.000	0.000	0.000
68	O	84	MET	0	-0.032	-0.018	18.410	-0.005	-0.005	0.000	0.000	0.000	0.000
69	O	85	VAL	0	0.027	0.029	20.809	0.013	0.013	0.000	0.000	0.000	0.000
70	O	86	THR	0	-0.002	-0.002	17.185	-0.006	-0.006	0.000	0.000	0.000	0.000
71	O	118	ARG	1	0.890	0.920	8.005	-0.933	-0.933	0.000	0.000	0.000	0.000
72	O	119	PHE	0	-0.047	-0.046	10.408	-0.120	-0.120	0.000	0.000	0.000	0.000
73	O	120	ILE	0	0.022	0.022	13.058	0.046	0.046	0.000	0.000	0.000	0.000
74	O	121	GLY	0	0.055	0.033	15.825	-0.043	-0.043	0.000	0.000	0.000	0.000
75	O	122	ALA	0	-0.027	-0.019	18.585	0.016	0.016	0.000	0.000	0.000	0.000
76	O	123	THR	0	-0.036	-0.020	21.545	0.005	0.005	0.000	0.000	0.000	0.000
77	O	124	ALA	0	0.008	-0.003	25.007	-0.002	-0.002	0.000	0.000	0.000	0.000
78	O	125	ASN	0	0.006	0.012	25.910	-0.002	-0.002	0.000	0.000	0.000	0.000
79	O	126	PHE	0	-0.011	-0.020	26.664	0.005	0.005	0.000	0.000	0.000	0.000
80	O	127	SER	0	0.000	0.002	29.821	-0.003	-0.003	0.000	0.000	0.000	0.000
81	O	128	ARG	1	0.959	0.974	32.481	0.017	0.017	0.000	0.000	0.000	0.000
82	O	129	PHE	0	-0.025	0.004	32.018	0.003	0.003	0.000	0.000	0.000	0.000
83	O	130	THR	0	0.020	0.016	34.629	-0.002	-0.002	0.000	0.000	0.000	0.000
84	O	131	LEU	0	-0.023	0.000	36.063	0.004	0.004	0.000	0.000	0.000	0.000
85	O	132	TRP	0	-0.027	-0.029	37.963	-0.001	-0.001	0.000	0.000	0.000	0.000
86	O	133	GLY	0	0.014	0.003	39.811	0.002	0.002	0.000	0.000	0.000	0.000
87	O	134	LEU	0	-0.020	-0.012	42.513	0.000	0.000	0.000	0.000	0.000	0.000
88	O	135	GLU	-1	-0.902	-0.950	45.064	0.016	0.016	0.000	0.000	0.000	0.000
89	O	136	THR	0	-0.052	-0.035	46.884	-0.002	-0.002	0.000	0.000	0.000	0.000
90	O	137	ILE	0	-0.009	0.012	42.997	0.001	0.001	0.000	0.000	0.000	0.000
91	O	138	PRO	0	-0.031	-0.015	39.668	0.000	0.000	0.000	0.000	0.000	0.000
92	O	139	GLY	0	0.119	0.065	42.151	-0.002	-0.002	0.000	0.000	0.000	0.000
93	O	140	PRO	0	0.005	-0.025	41.218	0.000	0.000	0.000	0.000	0.000	0.000
94	O	141	ASP	-1	-0.917	-0.951	39.833	0.004	0.004	0.000	0.000	0.000	0.000
95	O	142	ALA	0	-0.009	0.007	37.710	0.002	0.002	0.000	0.000	0.000	0.000
96	O	143	LYS	1	1.007	0.977	33.178	-0.022	-0.022	0.000	0.000	0.000	0.000
97	O	144	VAL	0	0.013	0.007	31.784	-0.003	-0.003	0.000	0.000	0.000	0.000
98	O	145	ARG	1	0.802	0.919	32.610	0.000	0.000	0.000	0.000	0.000	0.000
99	O	146	GLY	0	0.046	0.032	33.946	-0.004	-0.004	0.000	0.000	0.000	0.000
100	O	147	ALA	0	-0.023	-0.008	28.670	-0.004	-0.004	0.000	0.000	0.000	0.000
101	O	148	LEU	0	-0.006	-0.014	28.944	-0.006	-0.006	0.000	0.000	0.000	0.000
102	O	149	THR	0	-0.021	-0.014	30.663	-0.006	-0.006	0.000	0.000	0.000	0.000
103	O	150	TRP	0	0.034	0.030	22.945	-0.006	-0.006	0.000	0.000	0.000	0.000
104	O	151	PRO	0	0.020	0.011	25.407	-0.006	-0.006	0.000	0.000	0.000	0.000
105	O	152	SER	0	-0.034	-0.022	26.610	-0.008	-0.008	0.000	0.000	0.000	0.000
106	O	153	LEU	0	0.022	0.015	29.444	-0.003	-0.003	0.000	0.000	0.000	0.000
107	O	154	ALA	0	-0.009	-0.012	23.877	-0.004	-0.004	0.000	0.000	0.000	0.000
108	O	155	ALA	0	0.001	-0.009	24.709	-0.010	-0.010	0.000	0.000	0.000	0.000
109	O	156	ALA	0	-0.018	0.000	25.752	-0.006	-0.006	0.000	0.000	0.000	0.000
110	O	157	ILE	0	-0.049	-0.024	26.068	-0.001	-0.001	0.000	0.000	0.000	0.000
111	O	158	HIS	0	-0.054	-0.030	21.565	-0.012	-0.012	0.000	0.000	0.000	0.000
112	O	159	ALA	0	-0.011	0.019	22.767	-0.015	-0.015	0.000	0.000	0.000	0.000
113	O	160	GLN	0	-0.011	-0.019	22.462	0.003	0.003	0.000	0.000	0.000	0.000
114	O	161	VAL	0	0.009	0.010	25.269	0.007	0.007	0.000	0.000	0.000	0.000
115	O	162	PRO	0	-0.053	-0.018	27.967	-0.007	-0.007	0.000	0.000	0.000	0.000
116	O	163	GLU	-1	-0.960	-0.977	28.221	-0.107	-0.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(O:9:ILE)