FMO DATABASE

FMODB ID: R5NY8

Calculation Name: 3PUF-R-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: R

ChEMBL ID:

UniProt ID: O75792

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	121
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-757355.02347
FMO2-HF: Nuclear repulsion	713609.485842
FMO2-HF: Total energy	-43745.537628
FMO2-MP2: Total energy	-43874.208132

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(R:9:ACE )

Summations of interaction energy for fragment #1(R:9: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.
2.331	4.629	2.929	-2.573	-2.655	-0.014

Interaction energy analysis for fragmet #1(R:9:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.013

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

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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	R	11	ARG	1	0.948	0.975	3.744	0.969	2.133	-0.004	-0.579	-0.581	-0.001
4	R	12	HIS	0	0.021	0.015	2.558	-1.119	-0.673	2.840	-1.747	-1.540	-0.012
5	R	13	ARG	1	0.826	0.919	3.311	2.301	2.989	0.093	-0.247	-0.534	-0.001
6	R	14	VAL	0	0.027	0.016	6.405	0.047	0.047	0.000	0.000	0.000	0.000
7	R	15	HIS	0	0.028	0.017	8.385	0.207	0.207	0.000	0.000	0.000	0.000
8	R	16	LEU	0	0.031	0.017	12.133	0.054	0.054	0.000	0.000	0.000	0.000
9	R	17	ARG	1	0.914	0.955	15.719	0.227	0.227	0.000	0.000	0.000	0.000
10	R	18	NME	0	0.069	0.044	18.731	0.022	0.022	0.000	0.000	0.000	0.000
11	R	24	ACE	0	0.007	-0.007	32.380	-0.001	-0.001	0.000	0.000	0.000	0.000
12	R	25	VAL	0	-0.004	-0.019	32.776	0.004	0.004	0.000	0.000	0.000	0.000
13	R	26	PRO	0	-0.022	0.010	32.658	-0.003	-0.003	0.000	0.000	0.000	0.000
14	R	27	ALA	0	0.010	0.008	31.281	0.002	0.002	0.000	0.000	0.000	0.000
15	R	28	THR	0	-0.044	-0.029	33.207	0.003	0.003	0.000	0.000	0.000	0.000
16	R	29	LEU	0	0.016	0.011	30.191	0.000	0.000	0.000	0.000	0.000	0.000
17	R	30	HIS	0	0.038	0.020	34.403	0.003	0.003	0.000	0.000	0.000	0.000
18	R	31	LEU	0	0.000	0.011	32.701	0.000	0.000	0.000	0.000	0.000	0.000
19	R	32	LEU	0	0.026	0.005	35.807	0.001	0.001	0.000	0.000	0.000	0.000
20	R	33	PRO	0	-0.011	0.011	37.415	0.001	0.001	0.000	0.000	0.000	0.000
21	R	34	CYS	0	-0.098	-0.058	38.916	0.001	0.001	0.000	0.000	0.000	0.000
22	R	35	GLU	-1	-0.853	-0.915	33.393	-0.002	-0.002	0.000	0.000	0.000	0.000
23	R	36	VAL	0	-0.076	-0.039	36.184	0.000	0.000	0.000	0.000	0.000	0.000
24	R	37	ALA	0	0.010	0.000	35.733	0.001	0.001	0.000	0.000	0.000	0.000
25	R	38	VAL	0	-0.062	-0.036	34.604	0.000	0.000	0.000	0.000	0.000	0.000
26	R	39	ASP	-1	-0.859	-0.915	30.063	-0.016	-0.016	0.000	0.000	0.000	0.000
27	R	40	GLY	0	-0.009	-0.012	31.650	-0.003	-0.003	0.000	0.000	0.000	0.000
28	R	41	PRO	0	-0.039	-0.018	33.779	0.000	0.000	0.000	0.000	0.000	0.000
29	R	42	ALA	0	0.071	0.027	35.773	0.003	0.003	0.000	0.000	0.000	0.000
30	R	43	PRO	0	-0.023	0.009	38.597	-0.002	-0.002	0.000	0.000	0.000	0.000
31	R	44	VAL	0	0.038	-0.008	37.874	0.002	0.002	0.000	0.000	0.000	0.000
32	R	45	GLY	0	0.035	0.021	41.096	0.001	0.001	0.000	0.000	0.000	0.000
33	R	46	ARG	1	0.933	0.962	42.871	0.023	0.023	0.000	0.000	0.000	0.000
34	R	47	PHE	0	-0.047	-0.027	44.686	0.001	0.001	0.000	0.000	0.000	0.000
35	R	48	PHE	0	0.008	0.006	41.376	0.001	0.001	0.000	0.000	0.000	0.000
36	R	49	THR	0	0.056	0.010	42.020	0.000	0.000	0.000	0.000	0.000	0.000
37	R	50	PRO	0	-0.023	0.001	44.800	0.001	0.001	0.000	0.000	0.000	0.000
38	R	51	ALA	0	0.006	0.002	47.798	0.001	0.001	0.000	0.000	0.000	0.000
39	R	52	ILE	0	-0.025	0.004	43.426	0.001	0.001	0.000	0.000	0.000	0.000
40	R	53	ARG	1	0.874	0.939	47.901	0.013	0.013	0.000	0.000	0.000	0.000
41	R	54	GLN	0	0.018	0.004	48.403	0.001	0.001	0.000	0.000	0.000	0.000
42	R	55	GLY	0	0.030	0.023	51.527	0.000	0.000	0.000	0.000	0.000	0.000
43	R	56	PRO	0	-0.032	-0.009	53.358	0.000	0.000	0.000	0.000	0.000	0.000
44	R	57	GLU	-1	-0.851	-0.915	51.941	-0.004	-0.004	0.000	0.000	0.000	0.000
45	R	58	GLY	0	0.044	0.025	48.315	0.001	0.001	0.000	0.000	0.000	0.000
46	R	59	LEU	0	-0.021	-0.008	44.516	0.000	0.000	0.000	0.000	0.000	0.000
47	R	60	GLU	-1	-0.880	-0.936	47.732	-0.005	-0.005	0.000	0.000	0.000	0.000
48	R	61	VAL	0	-0.010	0.001	44.693	-0.001	-0.001	0.000	0.000	0.000	0.000
49	R	62	SER	0	0.023	0.016	48.157	0.001	0.001	0.000	0.000	0.000	0.000
50	R	63	PHE	0	0.008	-0.004	41.619	-0.001	-0.001	0.000	0.000	0.000	0.000
51	R	64	ARG	1	0.916	0.944	43.169	0.009	0.009	0.000	0.000	0.000	0.000
52	R	65	GLY	0	0.035	0.025	47.840	0.001	0.001	0.000	0.000	0.000	0.000
53	R	66	ARG	1	0.965	0.993	47.249	0.001	0.001	0.000	0.000	0.000	0.000
54	R	67	CYS	0	0.036	0.017	48.498	-0.001	-0.001	0.000	0.000	0.000	0.000
55	R	68	LEU	0	-0.031	-0.015	43.207	0.001	0.001	0.000	0.000	0.000	0.000
56	R	69	ARG	1	0.833	0.898	46.676	0.004	0.004	0.000	0.000	0.000	0.000
57	R	70	GLY	0	0.012	-0.013	43.590	0.001	0.001	0.000	0.000	0.000	0.000
58	R	71	GLU	-1	-0.884	-0.938	42.037	-0.010	-0.010	0.000	0.000	0.000	0.000
59	R	72	GLU	-1	-0.908	-0.939	39.966	-0.020	-0.020	0.000	0.000	0.000	0.000
60	R	73	VAL	0	-0.038	-0.021	35.441	0.001	0.001	0.000	0.000	0.000	0.000
61	R	74	ALA	0	-0.023	-0.019	35.935	-0.002	-0.002	0.000	0.000	0.000	0.000
62	R	75	VAL	0	-0.016	-0.007	29.582	0.002	0.002	0.000	0.000	0.000	0.000
63	R	76	PRO	0	0.018	0.012	30.510	0.000	0.000	0.000	0.000	0.000	0.000
64	R	77	PRO	0	0.015	0.000	31.483	-0.003	-0.003	0.000	0.000	0.000	0.000
65	R	78	GLY	0	0.013	0.007	29.168	0.002	0.002	0.000	0.000	0.000	0.000
66	R	79	LEU	0	-0.029	-0.012	25.658	0.000	0.000	0.000	0.000	0.000	0.000
67	R	80	VAL	0	-0.017	-0.006	24.802	-0.001	-0.001	0.000	0.000	0.000	0.000
68	R	81	GLY	0	0.024	0.027	25.236	0.001	0.001	0.000	0.000	0.000	0.000
69	R	82	TYR	0	-0.001	-0.017	22.686	-0.009	-0.009	0.000	0.000	0.000	0.000
70	R	83	VAL	0	0.009	0.007	24.720	0.007	0.007	0.000	0.000	0.000	0.000
71	R	84	MET	0	-0.009	-0.006	18.881	-0.008	-0.008	0.000	0.000	0.000	0.000
72	R	85	VAL	0	0.019	0.012	21.622	0.012	0.012	0.000	0.000	0.000	0.000
73	R	86	THR	0	-0.047	-0.030	20.642	-0.018	-0.018	0.000	0.000	0.000	0.000
74	R	87	NME	0	0.023	0.023	17.008	0.008	0.008	0.000	0.000	0.000	0.000
75	R	116	ACE	0	0.030	0.001	11.633	0.014	0.014	0.000	0.000	0.000	0.000
76	R	117	ASP	-1	-0.865	-0.935	8.697	-0.810	-0.810	0.000	0.000	0.000	0.000
77	R	118	ARG	1	0.812	0.916	8.729	0.391	0.391	0.000	0.000	0.000	0.000
78	R	119	PHE	0	0.014	-0.014	11.502	-0.047	-0.047	0.000	0.000	0.000	0.000
79	R	120	ILE	0	0.008	0.025	14.422	0.041	0.041	0.000	0.000	0.000	0.000
80	R	121	GLY	0	-0.003	-0.008	16.711	-0.025	-0.025	0.000	0.000	0.000	0.000
81	R	122	ALA	0	-0.026	-0.014	19.915	0.018	0.018	0.000	0.000	0.000	0.000
82	R	123	THR	0	-0.014	-0.005	22.080	0.000	0.000	0.000	0.000	0.000	0.000
83	R	124	ALA	0	0.032	0.018	25.697	0.001	0.001	0.000	0.000	0.000	0.000
84	R	125	ASN	0	-0.010	-0.011	26.015	0.002	0.002	0.000	0.000	0.000	0.000
85	R	126	PHE	0	-0.004	0.000	27.631	0.004	0.004	0.000	0.000	0.000	0.000
86	R	127	SER	0	0.030	0.011	30.281	-0.001	-0.001	0.000	0.000	0.000	0.000
87	R	128	ARG	1	0.872	0.916	32.957	0.023	0.023	0.000	0.000	0.000	0.000
88	R	129	PHE	0	-0.018	-0.004	33.111	-0.002	-0.002	0.000	0.000	0.000	0.000
89	R	130	THR	0	0.025	0.026	35.264	0.002	0.002	0.000	0.000	0.000	0.000
90	R	131	LEU	0	-0.038	-0.008	36.747	0.000	0.000	0.000	0.000	0.000	0.000
91	R	132	TRP	0	-0.016	-0.029	38.722	0.001	0.001	0.000	0.000	0.000	0.000
92	R	133	GLY	0	0.022	0.001	40.634	0.001	0.001	0.000	0.000	0.000	0.000
93	R	134	LEU	0	-0.024	-0.017	43.372	-0.001	-0.001	0.000	0.000	0.000	0.000
94	R	135	GLU	-1	-0.957	-0.980	45.877	0.000	0.000	0.000	0.000	0.000	0.000
95	R	136	THR	0	-0.020	-0.014	47.667	0.000	0.000	0.000	0.000	0.000	0.000
96	R	137	ILE	0	-0.010	0.010	44.103	0.000	0.000	0.000	0.000	0.000	0.000
97	R	138	PRO	0	0.001	-0.002	40.581	0.001	0.001	0.000	0.000	0.000	0.000
98	R	139	GLY	0	0.118	0.068	42.854	-0.001	-0.001	0.000	0.000	0.000	0.000
99	R	140	PRO	0	-0.020	-0.037	41.642	0.000	0.000	0.000	0.000	0.000	0.000
100	R	141	ASP	-1	-0.918	-0.947	40.520	0.009	0.009	0.000	0.000	0.000	0.000
101	R	142	ALA	0	0.020	0.023	38.459	0.002	0.002	0.000	0.000	0.000	0.000
102	R	143	LYS	1	1.006	0.987	29.955	-0.022	-0.022	0.000	0.000	0.000	0.000
103	R	144	VAL	0	-0.010	-0.018	33.377	0.001	0.001	0.000	0.000	0.000	0.000
104	R	145	ARG	1	0.868	0.931	33.658	0.000	0.000	0.000	0.000	0.000	0.000
105	R	146	GLY	0	0.037	0.029	34.676	0.000	0.000	0.000	0.000	0.000	0.000
106	R	147	ALA	0	-0.069	-0.043	29.405	0.002	0.002	0.000	0.000	0.000	0.000
107	R	148	LEU	0	0.020	0.006	29.679	0.000	0.000	0.000	0.000	0.000	0.000
108	R	149	THR	0	0.032	0.026	31.476	-0.003	-0.003	0.000	0.000	0.000	0.000
109	R	150	TRP	0	0.009	0.022	23.329	0.000	0.000	0.000	0.000	0.000	0.000
110	R	151	PRO	0	0.022	0.009	26.100	0.002	0.002	0.000	0.000	0.000	0.000
111	R	152	SER	0	-0.039	-0.031	27.312	0.000	0.000	0.000	0.000	0.000	0.000
112	R	153	LEU	0	0.006	0.010	29.565	0.001	0.001	0.000	0.000	0.000	0.000
113	R	154	ALA	0	-0.002	-0.016	24.334	0.003	0.003	0.000	0.000	0.000	0.000
114	R	155	ALA	0	0.005	-0.002	25.562	0.003	0.003	0.000	0.000	0.000	0.000
115	R	156	ALA	0	0.005	0.009	26.584	0.000	0.000	0.000	0.000	0.000	0.000
116	R	157	ILE	0	-0.048	-0.016	25.719	0.002	0.002	0.000	0.000	0.000	0.000
117	R	158	HIS	0	-0.030	-0.021	21.934	0.006	0.006	0.000	0.000	0.000	0.000
118	R	159	ALA	0	-0.006	0.021	23.591	-0.002	-0.002	0.000	0.000	0.000	0.000
119	R	160	GLN	0	-0.063	-0.038	22.743	0.008	0.008	0.000	0.000	0.000	0.000
120	R	161	VAL	0	0.003	0.002	25.914	-0.004	-0.004	0.000	0.000	0.000	0.000
121	R	162	NME	0	-0.001	0.007	28.499	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:9:ACE )