FMO DATABASE

FMODB ID: 66VYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-743552.275962
FMO2-HF: Nuclear repulsion	700319.594079
FMO2-HF: Total energy	-43232.681883
FMO2-MP2: Total energy	-43359.727607

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.
-156.867	-159.414	31.048	-13.698	-14.803	0.097

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 : -0.827 / q_NPA : -0.913

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	0.051	0.016	2.151	-7.455	-6.830	5.978	-2.876	-3.727	-0.007
4	R	13	ARG	1	0.853	0.918	1.729	-125.230	-128.489	25.072	-10.804	-11.010	0.104
5	R	14	VAL	0	0.020	0.017	4.571	-1.786	-1.805	-0.001	-0.013	0.034	0.000
6	R	15	HIS	0	0.023	0.013	4.689	-6.553	-6.447	-0.001	-0.005	-0.100	0.000
7	R	16	LEU	0	0.040	0.022	9.061	-1.993	-1.993	0.000	0.000	0.000	0.000
8	R	17	ARG	1	0.961	0.990	12.884	-20.954	-20.954	0.000	0.000	0.000	0.000
9	R	25	VAL	0	-0.002	-0.020	30.119	-0.010	-0.010	0.000	0.000	0.000	0.000
10	R	26	PRO	0	-0.016	0.003	30.329	0.301	0.301	0.000	0.000	0.000	0.000
11	R	27	ALA	0	0.007	0.007	28.992	-0.266	-0.266	0.000	0.000	0.000	0.000
12	R	28	THR	0	-0.045	-0.030	30.950	-0.210	-0.210	0.000	0.000	0.000	0.000
13	R	29	LEU	0	0.019	0.013	28.593	0.045	0.045	0.000	0.000	0.000	0.000
14	R	30	HIS	0	0.036	0.019	32.748	-0.276	-0.276	0.000	0.000	0.000	0.000
15	R	31	LEU	0	0.002	0.013	31.761	0.123	0.123	0.000	0.000	0.000	0.000
16	R	32	LEU	0	0.025	0.004	34.764	-0.261	-0.261	0.000	0.000	0.000	0.000
17	R	33	PRO	0	-0.012	0.010	36.410	0.172	0.172	0.000	0.000	0.000	0.000
18	R	34	CYS	0	-0.098	-0.058	37.845	-0.157	-0.157	0.000	0.000	0.000	0.000
19	R	35	GLU	-1	-0.854	-0.915	32.289	9.605	9.605	0.000	0.000	0.000	0.000
20	R	36	VAL	0	-0.075	-0.038	34.858	-0.321	-0.321	0.000	0.000	0.000	0.000
21	R	37	ALA	0	0.009	-0.001	34.334	0.149	0.149	0.000	0.000	0.000	0.000
22	R	38	VAL	0	-0.062	-0.036	32.852	0.025	0.025	0.000	0.000	0.000	0.000
23	R	39	ASP	-1	-0.861	-0.916	28.095	10.577	10.577	0.000	0.000	0.000	0.000
24	R	40	GLY	0	-0.009	-0.011	29.374	0.217	0.217	0.000	0.000	0.000	0.000
25	R	41	PRO	0	-0.036	-0.016	31.351	-0.016	-0.016	0.000	0.000	0.000	0.000
26	R	42	ALA	0	0.068	0.027	33.112	-0.240	-0.240	0.000	0.000	0.000	0.000
27	R	43	PRO	0	0.002	0.021	36.124	0.079	0.079	0.000	0.000	0.000	0.000
28	R	44	VAL	0	0.027	-0.014	35.688	-0.259	-0.259	0.000	0.000	0.000	0.000
29	R	45	GLY	0	0.040	0.024	38.670	-0.151	-0.151	0.000	0.000	0.000	0.000
30	R	46	ARG	1	0.913	0.946	40.316	-6.994	-6.994	0.000	0.000	0.000	0.000
31	R	47	PHE	0	-0.060	-0.033	42.266	-0.239	-0.239	0.000	0.000	0.000	0.000
32	R	48	PHE	0	0.024	0.016	39.763	-0.127	-0.127	0.000	0.000	0.000	0.000
33	R	49	THR	0	0.065	0.015	39.770	-0.043	-0.043	0.000	0.000	0.000	0.000
34	R	50	PRO	0	-0.032	-0.003	42.667	-0.089	-0.089	0.000	0.000	0.000	0.000
35	R	51	ALA	0	0.001	-0.001	45.835	-0.167	-0.167	0.000	0.000	0.000	0.000
36	R	52	ILE	0	-0.017	0.008	41.644	-0.075	-0.075	0.000	0.000	0.000	0.000
37	R	53	ARG	1	0.871	0.938	46.175	-6.446	-6.446	0.000	0.000	0.000	0.000
38	R	54	GLN	0	0.019	0.005	47.117	0.123	0.123	0.000	0.000	0.000	0.000
39	R	55	GLY	0	0.027	0.022	50.243	-0.137	-0.137	0.000	0.000	0.000	0.000
40	R	56	PRO	0	-0.028	-0.008	52.327	0.035	0.035	0.000	0.000	0.000	0.000
41	R	57	GLU	-1	-0.850	-0.915	51.289	6.008	6.008	0.000	0.000	0.000	0.000
42	R	58	GLY	0	0.045	0.026	47.538	0.105	0.105	0.000	0.000	0.000	0.000
43	R	59	LEU	0	-0.020	-0.008	43.193	-0.122	-0.122	0.000	0.000	0.000	0.000
44	R	60	GLU	-1	-0.881	-0.936	46.676	6.214	6.214	0.000	0.000	0.000	0.000
45	R	61	VAL	0	-0.014	-0.001	43.236	0.006	0.006	0.000	0.000	0.000	0.000
46	R	62	SER	0	0.026	0.017	46.720	-0.061	-0.061	0.000	0.000	0.000	0.000
47	R	63	PHE	0	0.007	-0.004	40.008	0.043	0.043	0.000	0.000	0.000	0.000
48	R	64	ARG	1	0.917	0.945	41.401	-7.367	-7.367	0.000	0.000	0.000	0.000
49	R	65	GLY	0	0.033	0.023	46.342	-0.077	-0.077	0.000	0.000	0.000	0.000
50	R	66	ARG	1	0.966	0.994	46.095	-6.769	-6.769	0.000	0.000	0.000	0.000
51	R	67	CYS	0	0.034	0.016	47.287	0.157	0.157	0.000	0.000	0.000	0.000
52	R	68	LEU	0	-0.032	-0.015	42.054	0.099	0.099	0.000	0.000	0.000	0.000
53	R	69	ARG	1	0.835	0.898	45.693	-6.366	-6.366	0.000	0.000	0.000	0.000
54	R	70	GLY	0	0.015	-0.013	42.679	0.133	0.133	0.000	0.000	0.000	0.000
55	R	71	GLU	-1	-0.889	-0.939	41.418	7.228	7.228	0.000	0.000	0.000	0.000
56	R	72	GLU	-1	-0.908	-0.939	38.956	8.207	8.207	0.000	0.000	0.000	0.000
57	R	73	VAL	0	-0.034	-0.020	34.926	-0.098	-0.098	0.000	0.000	0.000	0.000
58	R	74	ALA	0	-0.026	-0.020	35.105	0.228	0.228	0.000	0.000	0.000	0.000
59	R	75	VAL	0	-0.015	-0.006	28.783	0.008	0.008	0.000	0.000	0.000	0.000
60	R	76	PRO	0	0.018	0.012	30.348	-0.155	-0.155	0.000	0.000	0.000	0.000
61	R	77	PRO	0	0.015	-0.001	31.174	0.296	0.296	0.000	0.000	0.000	0.000
62	R	78	GLY	0	0.012	0.007	28.794	0.049	0.049	0.000	0.000	0.000	0.000
63	R	79	LEU	0	-0.028	-0.012	25.501	0.514	0.514	0.000	0.000	0.000	0.000
64	R	80	VAL	0	-0.017	-0.005	23.743	-0.329	-0.329	0.000	0.000	0.000	0.000
65	R	81	GLY	0	0.022	0.027	24.301	0.393	0.393	0.000	0.000	0.000	0.000
66	R	82	TYR	0	0.000	-0.016	20.969	0.048	0.048	0.000	0.000	0.000	0.000
67	R	83	VAL	0	0.009	0.008	23.018	-0.157	-0.157	0.000	0.000	0.000	0.000
68	R	84	MET	0	-0.014	-0.010	17.065	0.367	0.367	0.000	0.000	0.000	0.000
69	R	85	VAL	0	0.016	0.017	18.997	-0.630	-0.630	0.000	0.000	0.000	0.000
70	R	86	THR	0	-0.014	-0.006	15.642	0.920	0.920	0.000	0.000	0.000	0.000
71	R	117	ASP	-1	-0.827	-0.887	5.578	38.314	38.314	0.000	0.000	0.000	0.000
72	R	118	ARG	1	0.781	0.901	6.303	-33.986	-33.986	0.000	0.000	0.000	0.000
73	R	119	PHE	0	0.005	-0.017	7.327	1.502	1.502	0.000	0.000	0.000	0.000
74	R	120	ILE	0	0.004	0.026	10.935	-1.673	-1.673	0.000	0.000	0.000	0.000
75	R	121	GLY	0	0.008	-0.006	13.773	0.718	0.718	0.000	0.000	0.000	0.000
76	R	122	ALA	0	-0.020	-0.012	16.775	-0.541	-0.541	0.000	0.000	0.000	0.000
77	R	123	THR	0	-0.014	-0.006	19.349	-0.207	-0.207	0.000	0.000	0.000	0.000
78	R	124	ALA	0	0.035	0.020	22.779	-0.338	-0.338	0.000	0.000	0.000	0.000
79	R	125	ASN	0	-0.007	-0.009	23.933	0.169	0.169	0.000	0.000	0.000	0.000
80	R	126	PHE	0	-0.003	-0.001	26.122	-0.457	-0.457	0.000	0.000	0.000	0.000
81	R	127	SER	0	0.026	0.010	28.794	0.175	0.175	0.000	0.000	0.000	0.000
82	R	128	ARG	1	0.875	0.916	31.578	-8.441	-8.441	0.000	0.000	0.000	0.000
83	R	129	PHE	0	-0.017	-0.003	31.986	0.196	0.196	0.000	0.000	0.000	0.000
84	R	130	THR	0	0.024	0.026	34.084	-0.204	-0.204	0.000	0.000	0.000	0.000
85	R	131	LEU	0	-0.036	-0.007	36.060	0.191	0.191	0.000	0.000	0.000	0.000
86	R	132	TRP	0	-0.019	-0.030	37.888	-0.288	-0.288	0.000	0.000	0.000	0.000
87	R	133	GLY	0	0.023	0.002	39.790	0.161	0.161	0.000	0.000	0.000	0.000
88	R	134	LEU	0	-0.023	-0.017	42.558	-0.110	-0.110	0.000	0.000	0.000	0.000
89	R	135	GLU	-1	-0.955	-0.980	44.999	6.110	6.110	0.000	0.000	0.000	0.000
90	R	136	THR	0	-0.020	-0.013	46.908	-0.165	-0.165	0.000	0.000	0.000	0.000
91	R	137	ILE	0	-0.009	0.010	43.548	0.174	0.174	0.000	0.000	0.000	0.000
92	R	138	PRO	0	-0.002	-0.002	39.932	-0.059	-0.059	0.000	0.000	0.000	0.000
93	R	139	GLY	0	0.119	0.069	42.430	0.051	0.051	0.000	0.000	0.000	0.000
94	R	140	PRO	0	-0.021	-0.038	41.503	0.219	0.219	0.000	0.000	0.000	0.000
95	R	141	ASP	-1	-0.917	-0.947	40.489	7.501	7.501	0.000	0.000	0.000	0.000
96	R	142	ALA	0	0.020	0.023	38.100	0.153	0.153	0.000	0.000	0.000	0.000
97	R	143	LYS	1	1.005	0.988	29.968	-9.823	-9.823	0.000	0.000	0.000	0.000
98	R	144	VAL	0	-0.011	-0.018	32.991	0.280	0.280	0.000	0.000	0.000	0.000
99	R	145	ARG	1	0.869	0.931	33.367	-7.635	-7.635	0.000	0.000	0.000	0.000
100	R	146	GLY	0	0.037	0.028	34.714	0.060	0.060	0.000	0.000	0.000	0.000
101	R	147	ALA	0	-0.069	-0.043	29.264	0.161	0.161	0.000	0.000	0.000	0.000
102	R	148	LEU	0	0.019	0.006	29.681	0.364	0.364	0.000	0.000	0.000	0.000
103	R	149	THR	0	0.032	0.027	31.483	0.045	0.045	0.000	0.000	0.000	0.000
104	R	150	TRP	0	0.008	0.022	23.912	-0.055	-0.055	0.000	0.000	0.000	0.000
105	R	151	PRO	0	0.023	0.010	26.269	0.144	0.144	0.000	0.000	0.000	0.000
106	R	152	SER	0	-0.040	-0.031	27.613	0.096	0.096	0.000	0.000	0.000	0.000
107	R	153	LEU	0	0.006	0.010	30.299	-0.080	-0.080	0.000	0.000	0.000	0.000
108	R	154	ALA	0	-0.001	-0.016	25.036	0.055	0.055	0.000	0.000	0.000	0.000
109	R	155	ALA	0	0.007	-0.001	26.342	0.253	0.253	0.000	0.000	0.000	0.000
110	R	156	ALA	0	0.002	0.008	27.348	0.054	0.054	0.000	0.000	0.000	0.000
111	R	157	ILE	0	-0.047	-0.015	26.994	-0.057	-0.057	0.000	0.000	0.000	0.000
112	R	158	HIS	0	-0.028	-0.021	23.176	0.221	0.221	0.000	0.000	0.000	0.000
113	R	159	ALA	0	-0.007	0.021	24.873	0.544	0.544	0.000	0.000	0.000	0.000
114	R	160	GLN	0	-0.054	-0.033	23.798	-0.194	-0.194	0.000	0.000	0.000	0.000
115	R	161	VAL	0	-0.004	0.007	26.971	-0.353	-0.353	0.000	0.000	0.000	0.000

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