FMO DATABASE

FMODB ID: R5G88

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

Total energy (hartree)

FMO2-HF: Electronic energy	-747220.300216
FMO2-HF: Nuclear repulsion	703987.077928
FMO2-HF: Total energy	-43233.222288
FMO2-MP2: Total energy	-43360.310757

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.
-156.477	-159.606	31.378	-14.043	-14.205	0.105

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 : -0.815 / 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	0.074	0.038	2.085	-8.948	-8.514	7.817	-3.645	-4.605	-0.007
4	R	13	ARG	1	0.874	0.941	1.697	-122.798	-126.518	23.563	-10.380	-9.464	0.112
5	R	14	VAL	0	0.039	0.024	4.561	-2.767	-2.809	-0.001	-0.008	0.051	0.000
6	R	15	HIS	0	0.006	0.014	4.266	-6.127	-5.928	-0.001	-0.010	-0.187	0.000
7	R	16	LEU	0	0.045	0.020	9.285	-2.228	-2.228	0.000	0.000	0.000	0.000
8	R	17	ARG	1	0.945	0.995	10.944	-22.410	-22.410	0.000	0.000	0.000	0.000
9	R	25	VAL	0	-0.010	-0.022	30.260	-0.014	-0.014	0.000	0.000	0.000	0.000
10	R	26	PRO	0	-0.008	-0.001	30.349	0.271	0.271	0.000	0.000	0.000	0.000
11	R	27	ALA	0	0.007	0.010	28.998	-0.290	-0.290	0.000	0.000	0.000	0.000
12	R	28	THR	0	-0.018	-0.020	30.977	-0.065	-0.065	0.000	0.000	0.000	0.000
13	R	29	LEU	0	0.012	0.011	28.509	-0.097	-0.097	0.000	0.000	0.000	0.000
14	R	30	HIS	0	0.027	0.011	32.590	-0.326	-0.326	0.000	0.000	0.000	0.000
15	R	31	LEU	0	-0.007	0.006	32.335	0.195	0.195	0.000	0.000	0.000	0.000
16	R	32	LEU	0	0.028	0.007	34.872	-0.256	-0.256	0.000	0.000	0.000	0.000
17	R	33	PRO	0	-0.015	0.002	36.574	0.191	0.191	0.000	0.000	0.000	0.000
18	R	34	CYS	0	-0.072	-0.050	37.946	-0.206	-0.206	0.000	0.000	0.000	0.000
19	R	35	GLU	-1	-0.832	-0.897	32.758	9.587	9.587	0.000	0.000	0.000	0.000
20	R	36	VAL	0	-0.082	-0.057	34.671	-0.347	-0.347	0.000	0.000	0.000	0.000
21	R	37	ALA	0	-0.015	-0.002	33.845	0.231	0.231	0.000	0.000	0.000	0.000
22	R	38	VAL	0	-0.041	-0.032	32.651	-0.051	-0.051	0.000	0.000	0.000	0.000
23	R	39	ASP	-1	-0.878	-0.913	27.858	10.788	10.788	0.000	0.000	0.000	0.000
24	R	40	GLY	0	-0.015	-0.020	29.960	0.103	0.103	0.000	0.000	0.000	0.000
25	R	41	PRO	0	-0.036	-0.020	31.220	-0.054	-0.054	0.000	0.000	0.000	0.000
26	R	42	ALA	0	0.071	0.035	33.257	-0.241	-0.241	0.000	0.000	0.000	0.000
27	R	43	PRO	0	0.002	0.018	36.421	0.101	0.101	0.000	0.000	0.000	0.000
28	R	44	VAL	0	0.044	0.002	35.937	-0.255	-0.255	0.000	0.000	0.000	0.000
29	R	45	GLY	0	0.041	0.017	38.721	-0.162	-0.162	0.000	0.000	0.000	0.000
30	R	46	ARG	1	0.897	0.939	40.329	-7.027	-7.027	0.000	0.000	0.000	0.000
31	R	47	PHE	0	-0.046	-0.032	42.567	-0.240	-0.240	0.000	0.000	0.000	0.000
32	R	48	PHE	0	0.024	0.029	39.903	-0.108	-0.108	0.000	0.000	0.000	0.000
33	R	49	THR	0	0.077	0.025	39.904	-0.068	-0.068	0.000	0.000	0.000	0.000
34	R	50	PRO	0	-0.043	-0.010	42.791	-0.100	-0.100	0.000	0.000	0.000	0.000
35	R	51	ALA	0	-0.019	-0.006	45.772	-0.185	-0.185	0.000	0.000	0.000	0.000
36	R	52	ILE	0	-0.003	0.010	41.540	-0.093	-0.093	0.000	0.000	0.000	0.000
37	R	53	ARG	1	0.813	0.906	46.198	-6.597	-6.597	0.000	0.000	0.000	0.000
38	R	54	GLN	0	0.055	0.012	47.058	0.148	0.148	0.000	0.000	0.000	0.000
39	R	55	GLY	0	0.030	0.027	49.993	-0.140	-0.140	0.000	0.000	0.000	0.000
40	R	56	PRO	0	-0.028	-0.018	51.925	0.060	0.060	0.000	0.000	0.000	0.000
41	R	57	GLU	-1	-0.828	-0.906	51.216	6.075	6.075	0.000	0.000	0.000	0.000
42	R	58	GLY	0	0.021	0.020	47.318	0.131	0.131	0.000	0.000	0.000	0.000
43	R	59	LEU	0	-0.007	-0.003	42.723	-0.117	-0.117	0.000	0.000	0.000	0.000
44	R	60	GLU	-1	-0.869	-0.932	46.600	6.223	6.223	0.000	0.000	0.000	0.000
45	R	61	VAL	0	-0.023	0.001	43.417	0.012	0.012	0.000	0.000	0.000	0.000
46	R	62	SER	0	0.019	0.013	46.909	-0.091	-0.091	0.000	0.000	0.000	0.000
47	R	63	PHE	0	0.011	-0.005	39.608	0.073	0.073	0.000	0.000	0.000	0.000
48	R	64	ARG	1	0.908	0.942	40.894	-7.493	-7.493	0.000	0.000	0.000	0.000
49	R	65	GLY	0	0.044	0.033	46.133	-0.078	-0.078	0.000	0.000	0.000	0.000
50	R	66	ARG	1	0.841	0.905	46.897	-6.672	-6.672	0.000	0.000	0.000	0.000
51	R	67	CYS	0	0.015	0.011	47.643	0.131	0.131	0.000	0.000	0.000	0.000
52	R	68	LEU	0	-0.020	-0.011	41.852	0.102	0.102	0.000	0.000	0.000	0.000
53	R	69	ARG	1	0.803	0.878	45.343	-6.502	-6.502	0.000	0.000	0.000	0.000
54	R	70	GLY	0	0.011	-0.013	42.583	0.159	0.159	0.000	0.000	0.000	0.000
55	R	71	GLU	-1	-0.884	-0.931	41.206	7.290	7.290	0.000	0.000	0.000	0.000
56	R	72	GLU	-1	-0.865	-0.908	38.837	8.359	8.359	0.000	0.000	0.000	0.000
57	R	73	VAL	0	-0.044	-0.010	34.464	-0.077	-0.077	0.000	0.000	0.000	0.000
58	R	74	ALA	0	-0.002	-0.011	35.084	0.209	0.209	0.000	0.000	0.000	0.000
59	R	75	VAL	0	-0.015	-0.006	28.780	0.059	0.059	0.000	0.000	0.000	0.000
60	R	76	PRO	0	0.014	0.012	30.220	-0.202	-0.202	0.000	0.000	0.000	0.000
61	R	77	PRO	0	0.008	-0.008	30.746	0.344	0.344	0.000	0.000	0.000	0.000
62	R	78	GLY	0	0.034	0.013	28.414	-0.027	-0.027	0.000	0.000	0.000	0.000
63	R	79	LEU	0	-0.059	-0.016	25.296	0.606	0.606	0.000	0.000	0.000	0.000
64	R	80	VAL	0	-0.011	-0.008	23.881	-0.352	-0.352	0.000	0.000	0.000	0.000
65	R	81	GLY	0	0.014	0.027	24.577	0.414	0.414	0.000	0.000	0.000	0.000
66	R	82	TYR	0	-0.001	-0.019	21.406	0.057	0.057	0.000	0.000	0.000	0.000
67	R	83	VAL	0	-0.010	0.002	23.329	-0.197	-0.197	0.000	0.000	0.000	0.000
68	R	84	MET	0	-0.015	-0.018	17.230	0.755	0.755	0.000	0.000	0.000	0.000
69	R	85	VAL	0	0.014	0.019	19.271	-0.618	-0.618	0.000	0.000	0.000	0.000
70	R	86	THR	0	-0.002	-0.001	16.067	1.596	1.596	0.000	0.000	0.000	0.000
71	R	117	ASP	-1	-0.845	-0.899	5.243	38.818	38.818	0.000	0.000	0.000	0.000
72	R	118	ARG	1	0.768	0.868	6.234	-34.579	-34.579	0.000	0.000	0.000	0.000
73	R	119	PHE	0	0.001	-0.017	7.127	1.841	1.841	0.000	0.000	0.000	0.000
74	R	120	ILE	0	0.020	0.027	11.271	-1.451	-1.451	0.000	0.000	0.000	0.000
75	R	121	GLY	0	0.013	0.006	14.312	0.582	0.582	0.000	0.000	0.000	0.000
76	R	122	ALA	0	0.000	-0.013	17.498	-0.598	-0.598	0.000	0.000	0.000	0.000
77	R	123	THR	0	-0.004	-0.004	19.457	-0.215	-0.215	0.000	0.000	0.000	0.000
78	R	124	ALA	0	0.013	0.010	22.886	-0.541	-0.541	0.000	0.000	0.000	0.000
79	R	125	ASN	0	-0.003	-0.007	23.971	0.138	0.138	0.000	0.000	0.000	0.000
80	R	126	PHE	0	0.001	0.003	26.151	-0.467	-0.467	0.000	0.000	0.000	0.000
81	R	127	SER	0	0.036	0.008	28.753	0.224	0.224	0.000	0.000	0.000	0.000
82	R	128	ARG	1	0.828	0.887	31.509	-8.539	-8.539	0.000	0.000	0.000	0.000
83	R	129	PHE	0	-0.014	0.000	32.191	0.257	0.257	0.000	0.000	0.000	0.000
84	R	130	THR	0	0.022	0.020	34.318	-0.214	-0.214	0.000	0.000	0.000	0.000
85	R	131	LEU	0	-0.042	-0.011	36.112	0.182	0.182	0.000	0.000	0.000	0.000
86	R	132	TRP	0	-0.011	-0.025	37.898	-0.314	-0.314	0.000	0.000	0.000	0.000
87	R	133	GLY	0	0.016	-0.005	39.926	0.171	0.171	0.000	0.000	0.000	0.000
88	R	134	LEU	0	-0.034	-0.015	42.682	-0.083	-0.083	0.000	0.000	0.000	0.000
89	R	135	GLU	-1	-0.817	-0.890	45.135	6.381	6.381	0.000	0.000	0.000	0.000
90	R	136	THR	0	-0.029	-0.015	46.942	-0.182	-0.182	0.000	0.000	0.000	0.000
91	R	137	ILE	0	-0.002	0.016	43.864	0.172	0.172	0.000	0.000	0.000	0.000
92	R	138	PRO	0	0.005	0.005	40.269	-0.062	-0.062	0.000	0.000	0.000	0.000
93	R	139	GLY	0	0.098	0.068	42.726	0.030	0.030	0.000	0.000	0.000	0.000
94	R	140	PRO	0	-0.020	-0.025	41.912	0.235	0.235	0.000	0.000	0.000	0.000
95	R	141	ASP	-1	-0.872	-0.944	40.875	7.602	7.602	0.000	0.000	0.000	0.000
96	R	142	ALA	0	0.019	0.026	38.639	0.189	0.189	0.000	0.000	0.000	0.000
97	R	143	LYS	1	0.995	0.981	30.924	-9.769	-9.769	0.000	0.000	0.000	0.000
98	R	144	VAL	0	0.011	0.002	32.984	0.303	0.303	0.000	0.000	0.000	0.000
99	R	145	ARG	1	0.883	0.935	33.438	-7.677	-7.677	0.000	0.000	0.000	0.000
100	R	146	GLY	0	0.044	0.029	34.890	0.095	0.095	0.000	0.000	0.000	0.000
101	R	147	ALA	0	-0.081	-0.050	29.640	0.218	0.218	0.000	0.000	0.000	0.000
102	R	148	LEU	0	0.019	0.002	29.872	0.367	0.367	0.000	0.000	0.000	0.000
103	R	149	THR	0	0.003	0.012	31.637	0.022	0.022	0.000	0.000	0.000	0.000
104	R	150	TRP	0	-0.004	0.009	25.152	-0.043	-0.043	0.000	0.000	0.000	0.000
105	R	151	PRO	0	0.025	0.003	26.738	0.134	0.134	0.000	0.000	0.000	0.000
106	R	152	SER	0	-0.025	-0.013	28.058	0.127	0.127	0.000	0.000	0.000	0.000
107	R	153	LEU	0	0.013	0.010	30.918	-0.009	-0.009	0.000	0.000	0.000	0.000
108	R	154	ALA	0	-0.006	-0.005	25.464	0.106	0.106	0.000	0.000	0.000	0.000
109	R	155	ALA	0	0.006	-0.005	26.235	0.330	0.330	0.000	0.000	0.000	0.000
110	R	156	ALA	0	-0.014	-0.003	27.277	0.061	0.061	0.000	0.000	0.000	0.000
111	R	157	ILE	0	-0.043	-0.023	26.584	-0.077	-0.077	0.000	0.000	0.000	0.000
112	R	158	HIS	0	-0.018	-0.006	23.258	0.190	0.190	0.000	0.000	0.000	0.000
113	R	159	ALA	0	-0.008	0.014	24.748	0.506	0.506	0.000	0.000	0.000	0.000
114	R	160	GLN	0	-0.058	-0.032	23.215	-0.205	-0.205	0.000	0.000	0.000	0.000
115	R	161	VAL	0	-0.007	0.005	26.571	-0.377	-0.377	0.000	0.000	0.000	0.000

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