FMO DATABASE

FMODB ID: ZY5VN

Calculation Name: 3PUF-R-Xray372

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: 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	OptHSide
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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-744411.100196
FMO2-HF: Nuclear repulsion	701178.163948
FMO2-HF: Total energy	-43232.936248
FMO2-MP2: Total energy	-43360.034585

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:10:GLU)

Summations of interaction energy for fragment #1(R:10:GLU)

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.
-154.794	-157.226	30.518	-13.625	-14.461	0.101

Interaction energy analysis for fragmet #1(R:10:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.826 / q_NPA : -0.918

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	R	12	HIS	0	0.059	0.020	2.142	-7.696	-7.195	6.392	-3.037	-3.856	-0.007
4	R	13	ARG	1	0.861	0.922	1.725	-122.680	-125.736	24.128	-10.567	-10.505	0.108
5	R	14	VAL	0	0.019	0.022	4.491	-1.858	-1.881	-0.001	-0.014	0.038	0.000
6	R	15	HIS	0	0.015	0.008	4.496	-6.316	-6.170	-0.001	-0.007	-0.138	0.000
7	R	16	LEU	0	0.046	0.024	9.042	-2.028	-2.028	0.000	0.000	0.000	0.000
8	R	17	ARG	1	0.954	0.990	11.884	-21.753	-21.753	0.000	0.000	0.000	0.000
9	R	25	VAL	0	-0.013	-0.023	30.148	0.000	0.000	0.000	0.000	0.000	0.000
10	R	26	PRO	0	-0.009	0.002	30.309	0.285	0.285	0.000	0.000	0.000	0.000
11	R	27	ALA	0	0.000	0.007	28.939	-0.263	-0.263	0.000	0.000	0.000	0.000
12	R	28	THR	0	-0.029	-0.021	30.917	-0.138	-0.138	0.000	0.000	0.000	0.000
13	R	29	LEU	0	0.010	0.008	28.543	0.049	0.049	0.000	0.000	0.000	0.000
14	R	30	HIS	0	0.035	0.017	32.698	-0.258	-0.258	0.000	0.000	0.000	0.000
15	R	31	LEU	0	0.006	0.014	32.051	0.120	0.120	0.000	0.000	0.000	0.000
16	R	32	LEU	0	0.024	0.002	34.734	-0.261	-0.261	0.000	0.000	0.000	0.000
17	R	33	PRO	0	-0.019	0.002	36.403	0.175	0.175	0.000	0.000	0.000	0.000
18	R	34	CYS	0	-0.076	-0.047	37.856	-0.220	-0.220	0.000	0.000	0.000	0.000
19	R	35	GLU	-1	-0.858	-0.921	32.197	9.642	9.642	0.000	0.000	0.000	0.000
20	R	36	VAL	0	-0.090	-0.039	34.818	-0.328	-0.328	0.000	0.000	0.000	0.000
21	R	37	ALA	0	0.015	0.001	34.312	0.150	0.150	0.000	0.000	0.000	0.000
22	R	38	VAL	0	-0.055	-0.034	32.827	0.025	0.025	0.000	0.000	0.000	0.000
23	R	39	ASP	-1	-0.860	-0.915	28.028	10.655	10.655	0.000	0.000	0.000	0.000
24	R	40	GLY	0	-0.010	-0.014	29.335	0.217	0.217	0.000	0.000	0.000	0.000
25	R	41	PRO	0	-0.040	-0.020	31.315	-0.024	-0.024	0.000	0.000	0.000	0.000
26	R	42	ALA	0	0.068	0.028	33.083	-0.240	-0.240	0.000	0.000	0.000	0.000
27	R	43	PRO	0	-0.001	0.022	36.090	0.078	0.078	0.000	0.000	0.000	0.000
28	R	44	VAL	0	0.032	-0.012	35.589	-0.257	-0.257	0.000	0.000	0.000	0.000
29	R	45	GLY	0	0.043	0.024	38.645	-0.152	-0.152	0.000	0.000	0.000	0.000
30	R	46	ARG	1	0.912	0.945	40.287	-7.021	-7.021	0.000	0.000	0.000	0.000
31	R	47	PHE	0	-0.062	-0.034	42.230	-0.241	-0.241	0.000	0.000	0.000	0.000
32	R	48	PHE	0	0.031	0.023	40.028	-0.126	-0.126	0.000	0.000	0.000	0.000
33	R	49	THR	0	0.065	0.020	39.891	-0.033	-0.033	0.000	0.000	0.000	0.000
34	R	50	PRO	0	-0.054	-0.018	42.628	-0.085	-0.085	0.000	0.000	0.000	0.000
35	R	51	ALA	0	-0.006	-0.003	45.796	-0.158	-0.158	0.000	0.000	0.000	0.000
36	R	52	ILE	0	-0.006	0.016	41.466	-0.077	-0.077	0.000	0.000	0.000	0.000
37	R	53	ARG	1	0.858	0.930	46.127	-6.535	-6.535	0.000	0.000	0.000	0.000
38	R	54	GLN	0	0.036	0.012	47.187	0.120	0.120	0.000	0.000	0.000	0.000
39	R	55	GLY	0	0.026	0.022	50.191	-0.138	-0.138	0.000	0.000	0.000	0.000
40	R	56	PRO	0	-0.025	-0.009	52.269	0.037	0.037	0.000	0.000	0.000	0.000
41	R	57	GLU	-1	-0.846	-0.915	51.254	6.029	6.029	0.000	0.000	0.000	0.000
42	R	58	GLY	0	0.038	0.030	47.475	0.107	0.107	0.000	0.000	0.000	0.000
43	R	59	LEU	0	-0.017	-0.005	43.072	-0.126	-0.126	0.000	0.000	0.000	0.000
44	R	60	GLU	-1	-0.881	-0.939	46.615	6.229	6.229	0.000	0.000	0.000	0.000
45	R	61	VAL	0	-0.004	0.007	43.179	0.002	0.002	0.000	0.000	0.000	0.000
46	R	62	SER	0	0.013	0.010	46.664	-0.064	-0.064	0.000	0.000	0.000	0.000
47	R	63	PHE	0	0.009	0.000	39.783	0.040	0.040	0.000	0.000	0.000	0.000
48	R	64	ARG	1	0.923	0.946	41.203	-7.419	-7.419	0.000	0.000	0.000	0.000
49	R	65	GLY	0	0.034	0.026	46.286	-0.078	-0.078	0.000	0.000	0.000	0.000
50	R	66	ARG	1	0.894	0.943	46.530	-6.689	-6.689	0.000	0.000	0.000	0.000
51	R	67	CYS	0	0.006	0.005	47.246	0.147	0.147	0.000	0.000	0.000	0.000
52	R	68	LEU	0	-0.013	-0.008	41.898	0.095	0.095	0.000	0.000	0.000	0.000
53	R	69	ARG	1	0.819	0.885	45.690	-6.397	-6.397	0.000	0.000	0.000	0.000
54	R	70	GLY	0	0.017	-0.014	42.614	0.133	0.133	0.000	0.000	0.000	0.000
55	R	71	GLU	-1	-0.898	-0.945	41.412	7.248	7.248	0.000	0.000	0.000	0.000
56	R	72	GLU	-1	-0.887	-0.922	38.894	8.256	8.256	0.000	0.000	0.000	0.000
57	R	73	VAL	0	-0.042	-0.021	34.919	-0.102	-0.102	0.000	0.000	0.000	0.000
58	R	74	ALA	0	-0.026	-0.019	35.045	0.228	0.228	0.000	0.000	0.000	0.000
59	R	75	VAL	0	-0.014	-0.005	28.767	0.009	0.009	0.000	0.000	0.000	0.000
60	R	76	PRO	0	0.018	0.011	30.462	-0.149	-0.149	0.000	0.000	0.000	0.000
61	R	77	PRO	0	0.013	0.000	31.115	0.290	0.290	0.000	0.000	0.000	0.000
62	R	78	GLY	0	0.016	0.007	28.583	0.050	0.050	0.000	0.000	0.000	0.000
63	R	79	LEU	0	-0.029	-0.011	25.779	0.524	0.524	0.000	0.000	0.000	0.000
64	R	80	VAL	0	-0.023	-0.005	23.728	-0.332	-0.332	0.000	0.000	0.000	0.000
65	R	81	GLY	0	0.023	0.028	24.246	0.403	0.403	0.000	0.000	0.000	0.000
66	R	82	TYR	0	0.008	-0.016	20.919	0.005	0.005	0.000	0.000	0.000	0.000
67	R	83	VAL	0	0.003	0.008	22.974	-0.159	-0.159	0.000	0.000	0.000	0.000
68	R	84	MET	0	-0.013	-0.010	17.115	0.560	0.560	0.000	0.000	0.000	0.000
69	R	85	VAL	0	0.018	0.015	18.949	-0.643	-0.643	0.000	0.000	0.000	0.000
70	R	86	THR	0	-0.014	-0.002	16.320	1.571	1.571	0.000	0.000	0.000	0.000
71	R	117	ASP	-1	-0.828	-0.890	5.674	37.929	37.929	0.000	0.000	0.000	0.000
72	R	118	ARG	1	0.770	0.893	6.232	-34.249	-34.249	0.000	0.000	0.000	0.000
73	R	119	PHE	0	0.004	-0.023	7.362	1.740	1.740	0.000	0.000	0.000	0.000
74	R	120	ILE	0	0.015	0.030	10.924	-1.674	-1.674	0.000	0.000	0.000	0.000
75	R	121	GLY	0	0.011	-0.003	13.746	0.707	0.707	0.000	0.000	0.000	0.000
76	R	122	ALA	0	-0.024	-0.015	16.758	-0.566	-0.566	0.000	0.000	0.000	0.000
77	R	123	THR	0	-0.012	-0.003	19.325	-0.216	-0.216	0.000	0.000	0.000	0.000
78	R	124	ALA	0	0.037	0.018	22.760	-0.333	-0.333	0.000	0.000	0.000	0.000
79	R	125	ASN	0	-0.017	-0.016	23.829	0.119	0.119	0.000	0.000	0.000	0.000
80	R	126	PHE	0	0.005	0.005	25.887	-0.460	-0.460	0.000	0.000	0.000	0.000
81	R	127	SER	0	0.030	0.012	28.751	0.173	0.173	0.000	0.000	0.000	0.000
82	R	128	ARG	1	0.857	0.900	31.532	-8.479	-8.479	0.000	0.000	0.000	0.000
83	R	129	PHE	0	-0.011	-0.001	31.942	0.193	0.193	0.000	0.000	0.000	0.000
84	R	130	THR	0	0.034	0.029	34.027	-0.190	-0.190	0.000	0.000	0.000	0.000
85	R	131	LEU	0	-0.052	-0.013	35.970	0.191	0.191	0.000	0.000	0.000	0.000
86	R	132	TRP	0	-0.017	-0.034	37.887	-0.299	-0.299	0.000	0.000	0.000	0.000
87	R	133	GLY	0	0.033	0.007	39.789	0.163	0.163	0.000	0.000	0.000	0.000
88	R	134	LEU	0	-0.027	-0.013	42.556	-0.105	-0.105	0.000	0.000	0.000	0.000
89	R	135	GLU	-1	-0.875	-0.927	44.993	6.276	6.276	0.000	0.000	0.000	0.000
90	R	136	THR	0	-0.030	-0.016	46.913	-0.166	-0.166	0.000	0.000	0.000	0.000
91	R	137	ILE	0	-0.006	0.011	43.585	0.170	0.170	0.000	0.000	0.000	0.000
92	R	138	PRO	0	0.003	-0.002	39.947	-0.061	-0.061	0.000	0.000	0.000	0.000
93	R	139	GLY	0	0.106	0.066	42.435	0.052	0.052	0.000	0.000	0.000	0.000
94	R	140	PRO	0	-0.020	-0.033	41.509	0.220	0.220	0.000	0.000	0.000	0.000
95	R	141	ASP	-1	-0.894	-0.942	40.497	7.539	7.539	0.000	0.000	0.000	0.000
96	R	142	ALA	0	0.011	0.018	38.176	0.155	0.155	0.000	0.000	0.000	0.000
97	R	143	LYS	1	1.008	0.985	30.060	-9.837	-9.837	0.000	0.000	0.000	0.000
98	R	144	VAL	0	-0.007	-0.012	33.010	0.279	0.279	0.000	0.000	0.000	0.000
99	R	145	ARG	1	0.872	0.932	33.375	-7.666	-7.666	0.000	0.000	0.000	0.000
100	R	146	GLY	0	0.036	0.026	34.723	0.060	0.060	0.000	0.000	0.000	0.000
101	R	147	ALA	0	-0.066	-0.042	29.313	0.167	0.167	0.000	0.000	0.000	0.000
102	R	148	LEU	0	0.018	0.004	29.694	0.363	0.363	0.000	0.000	0.000	0.000
103	R	149	THR	0	0.023	0.027	31.502	0.025	0.025	0.000	0.000	0.000	0.000
104	R	150	TRP	0	0.007	0.011	24.220	-0.046	-0.046	0.000	0.000	0.000	0.000
105	R	151	PRO	0	0.025	0.009	26.336	0.146	0.146	0.000	0.000	0.000	0.000
106	R	152	SER	0	-0.037	-0.023	27.635	0.097	0.097	0.000	0.000	0.000	0.000
107	R	153	LEU	0	0.001	0.009	30.464	-0.083	-0.083	0.000	0.000	0.000	0.000
108	R	154	ALA	0	-0.003	-0.014	25.074	0.061	0.061	0.000	0.000	0.000	0.000
109	R	155	ALA	0	0.004	-0.002	26.376	0.256	0.256	0.000	0.000	0.000	0.000
110	R	156	ALA	0	0.002	0.007	27.379	0.055	0.055	0.000	0.000	0.000	0.000
111	R	157	ILE	0	-0.042	-0.015	26.677	-0.068	-0.068	0.000	0.000	0.000	0.000
112	R	158	HIS	0	-0.022	-0.017	23.295	0.163	0.163	0.000	0.000	0.000	0.000
113	R	159	ALA	0	-0.009	0.021	24.615	0.557	0.557	0.000	0.000	0.000	0.000
114	R	160	GLN	0	-0.058	-0.038	23.517	-0.229	-0.229	0.000	0.000	0.000	0.000
115	R	161	VAL	0	0.001	0.010	26.737	-0.358	-0.358	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:10:GLU)