FMO DATABASE

FMODB ID: GN261

Calculation Name: 3PUF-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: C

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	127
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-863326.575945
FMO2-HF: Nuclear repulsion	815799.365267
FMO2-HF: Total energy	-47527.210678
FMO2-MP2: Total energy	-47667.040932

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(C:8:ALA)

Summations of interaction energy for fragment #1(C:8:ALA)

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.
-20.981	-21.047	10.002	-4.545	-5.39	0.031

Interaction energy analysis for fragmet #1(C:8:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / 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

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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	C	10	GLU	-1	-0.752	-0.844	2.743	-0.940	1.892	0.142	-1.357	-1.616	0.002
4	C	11	ARG	1	0.876	0.938	2.058	-21.154	-24.052	9.860	-3.188	-3.774	0.029
5	C	12	HIS	0	0.037	0.023	6.370	-0.137	-0.137	0.000	0.000	0.000	0.000
6	C	13	ARG	1	0.778	0.866	5.772	-0.283	-0.283	0.000	0.000	0.000	0.000
7	C	14	VAL	0	0.028	0.021	9.534	0.271	0.271	0.000	0.000	0.000	0.000
8	C	15	HIS	0	-0.029	-0.013	8.303	-0.288	-0.288	0.000	0.000	0.000	0.000
9	C	16	LEU	0	0.041	0.009	13.454	0.008	0.008	0.000	0.000	0.000	0.000
10	C	17	ARG	1	0.943	0.962	17.207	-0.425	-0.425	0.000	0.000	0.000	0.000
11	C	18	SER	0	0.053	0.020	19.310	-0.016	-0.016	0.000	0.000	0.000	0.000
12	C	19	ALA	0	-0.045	-0.023	21.317	-0.018	-0.018	0.000	0.000	0.000	0.000
13	C	20	THR	0	0.015	-0.011	22.968	-0.001	-0.001	0.000	0.000	0.000	0.000
14	C	21	LEU	0	0.001	0.028	22.387	-0.006	-0.006	0.000	0.000	0.000	0.000
15	C	22	ARG	1	0.785	0.871	25.913	-0.124	-0.124	0.000	0.000	0.000	0.000
16	C	23	ASP	-1	-0.838	-0.881	28.032	0.109	0.109	0.000	0.000	0.000	0.000
17	C	24	ALA	0	0.014	0.007	29.059	0.009	0.009	0.000	0.000	0.000	0.000
18	C	25	VAL	0	0.002	0.007	31.062	-0.009	-0.009	0.000	0.000	0.000	0.000
19	C	26	PRO	0	-0.043	-0.034	34.138	0.004	0.004	0.000	0.000	0.000	0.000
20	C	27	ALA	0	0.022	0.018	33.921	0.000	0.000	0.000	0.000	0.000	0.000
21	C	28	THR	0	-0.051	-0.026	35.871	-0.004	-0.004	0.000	0.000	0.000	0.000
22	C	29	LEU	0	0.013	0.010	33.090	0.004	0.004	0.000	0.000	0.000	0.000
23	C	30	HIS	0	0.056	0.030	37.282	-0.007	-0.007	0.000	0.000	0.000	0.000
24	C	31	LEU	0	-0.004	0.001	36.113	0.004	0.004	0.000	0.000	0.000	0.000
25	C	32	LEU	0	0.020	0.001	38.992	-0.005	-0.005	0.000	0.000	0.000	0.000
26	C	33	PRO	0	-0.007	0.011	40.174	0.001	0.001	0.000	0.000	0.000	0.000
27	C	34	CYS	0	-0.086	-0.049	41.385	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	35	GLU	-1	-0.886	-0.938	34.884	0.082	0.082	0.000	0.000	0.000	0.000
29	C	36	VAL	0	-0.081	-0.046	37.398	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	37	ALA	0	0.025	0.001	35.339	0.004	0.004	0.000	0.000	0.000	0.000
31	C	38	VAL	0	-0.076	-0.026	33.962	0.005	0.005	0.000	0.000	0.000	0.000
32	C	39	ASP	-1	-0.841	-0.921	28.903	0.144	0.144	0.000	0.000	0.000	0.000
33	C	40	GLY	0	0.000	0.001	31.721	0.009	0.009	0.000	0.000	0.000	0.000
34	C	41	PRO	0	-0.039	-0.006	33.220	-0.005	-0.005	0.000	0.000	0.000	0.000
35	C	42	ALA	0	0.069	0.015	35.824	-0.005	-0.005	0.000	0.000	0.000	0.000
36	C	43	PRO	0	-0.035	-0.001	39.319	0.000	0.000	0.000	0.000	0.000	0.000
37	C	44	VAL	0	0.069	0.017	39.450	-0.005	-0.005	0.000	0.000	0.000	0.000
38	C	45	GLY	0	0.030	0.009	42.613	-0.004	-0.004	0.000	0.000	0.000	0.000
39	C	46	ARG	1	0.893	0.952	44.769	-0.069	-0.069	0.000	0.000	0.000	0.000
40	C	47	PHE	0	-0.029	-0.024	45.997	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	48	PHE	0	0.031	0.022	44.295	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	49	THR	0	0.059	0.013	44.186	-0.002	-0.002	0.000	0.000	0.000	0.000
43	C	50	PRO	0	-0.019	0.000	46.837	-0.002	-0.002	0.000	0.000	0.000	0.000
44	C	51	ALA	0	-0.011	0.003	49.845	-0.003	-0.003	0.000	0.000	0.000	0.000
45	C	52	ILE	0	-0.027	-0.001	45.929	-0.002	-0.002	0.000	0.000	0.000	0.000
46	C	53	ARG	1	0.868	0.921	50.605	-0.040	-0.040	0.000	0.000	0.000	0.000
47	C	54	GLN	0	-0.012	-0.002	52.963	0.002	0.002	0.000	0.000	0.000	0.000
48	C	55	GLY	0	0.032	0.035	55.046	-0.001	-0.001	0.000	0.000	0.000	0.000
49	C	56	PRO	0	-0.066	-0.041	57.002	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	57	GLU	-1	-0.868	-0.919	53.912	0.027	0.027	0.000	0.000	0.000	0.000
51	C	58	GLY	0	0.044	0.007	51.760	0.000	0.000	0.000	0.000	0.000	0.000
52	C	59	LEU	0	-0.049	-0.011	48.575	0.000	0.000	0.000	0.000	0.000	0.000
53	C	60	GLU	-1	-0.880	-0.953	50.891	0.031	0.031	0.000	0.000	0.000	0.000
54	C	61	VAL	0	-0.009	0.005	47.381	0.001	0.001	0.000	0.000	0.000	0.000
55	C	62	SER	0	0.020	0.025	50.692	-0.001	-0.001	0.000	0.000	0.000	0.000
56	C	63	PHE	0	0.003	-0.002	42.548	0.002	0.002	0.000	0.000	0.000	0.000
57	C	64	ARG	1	0.914	0.938	43.613	-0.062	-0.062	0.000	0.000	0.000	0.000
58	C	65	GLY	0	0.027	0.023	48.954	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	66	ARG	1	0.868	0.933	49.368	-0.038	-0.038	0.000	0.000	0.000	0.000
60	C	67	CYM	-1	-0.824	-0.870	50.612	0.036	0.036	0.000	0.000	0.000	0.000
61	C	68	LEU	0	-0.017	-0.019	45.321	0.000	0.000	0.000	0.000	0.000	0.000
62	C	69	ARG	1	0.872	0.881	49.417	-0.030	-0.030	0.000	0.000	0.000	0.000
63	C	70	GLY	0	0.002	-0.004	46.835	0.000	0.000	0.000	0.000	0.000	0.000
64	C	71	GLU	-1	-0.814	-0.899	45.537	0.030	0.030	0.000	0.000	0.000	0.000
65	C	72	GLU	-1	-0.945	-0.982	43.637	0.049	0.049	0.000	0.000	0.000	0.000
66	C	73	VAL	0	-0.014	0.000	40.067	-0.003	-0.003	0.000	0.000	0.000	0.000
67	C	74	ALA	0	-0.026	-0.024	40.353	0.004	0.004	0.000	0.000	0.000	0.000
68	C	75	VAL	0	-0.009	-0.004	34.081	-0.001	-0.001	0.000	0.000	0.000	0.000
69	C	76	PRO	0	-0.004	-0.001	36.017	-0.002	-0.002	0.000	0.000	0.000	0.000
70	C	77	PRO	0	0.019	0.009	36.399	0.002	0.002	0.000	0.000	0.000	0.000
71	C	78	GLY	0	0.005	-0.002	34.616	-0.003	-0.003	0.000	0.000	0.000	0.000
72	C	79	LEU	0	-0.045	-0.015	30.970	0.001	0.001	0.000	0.000	0.000	0.000
73	C	80	VAL	0	-0.001	-0.014	29.897	-0.001	-0.001	0.000	0.000	0.000	0.000
74	C	81	GLY	0	0.009	0.021	29.993	0.002	0.002	0.000	0.000	0.000	0.000
75	C	82	TYR	0	-0.035	-0.041	26.244	0.001	0.001	0.000	0.000	0.000	0.000
76	C	83	VAL	0	0.014	0.015	27.758	-0.001	-0.001	0.000	0.000	0.000	0.000
77	C	84	MET	0	-0.020	-0.010	22.156	0.012	0.012	0.000	0.000	0.000	0.000
78	C	85	VAL	0	0.019	0.009	23.082	-0.008	-0.008	0.000	0.000	0.000	0.000
79	C	86	THR	0	-0.057	-0.041	18.196	0.038	0.038	0.000	0.000	0.000	0.000
80	C	87	GLU	-1	-0.781	-0.846	17.159	0.494	0.494	0.000	0.000	0.000	0.000
81	C	88	GLU	-1	-0.953	-0.966	19.412	0.321	0.321	0.000	0.000	0.000	0.000
82	C	117	ASP	-1	-0.953	-0.974	8.220	2.260	2.260	0.000	0.000	0.000	0.000
83	C	118	ARG	1	0.779	0.857	9.337	-1.008	-1.008	0.000	0.000	0.000	0.000
84	C	119	PHE	0	-0.013	-0.028	11.866	-0.048	-0.048	0.000	0.000	0.000	0.000
85	C	120	ILE	0	0.023	0.018	14.891	-0.033	-0.033	0.000	0.000	0.000	0.000
86	C	121	GLY	0	-0.004	-0.009	18.184	-0.004	-0.004	0.000	0.000	0.000	0.000
87	C	122	ALA	0	0.009	0.005	21.266	-0.009	-0.009	0.000	0.000	0.000	0.000
88	C	123	THR	0	-0.019	-0.006	24.450	-0.007	-0.007	0.000	0.000	0.000	0.000
89	C	124	ALA	0	0.017	0.009	27.217	-0.009	-0.009	0.000	0.000	0.000	0.000
90	C	125	ASN	0	0.027	0.009	29.234	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	126	PHE	0	0.015	0.009	30.565	-0.002	-0.002	0.000	0.000	0.000	0.000
92	C	127	SER	0	0.013	0.013	34.338	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	128	ARG	1	0.934	0.962	37.171	-0.049	-0.049	0.000	0.000	0.000	0.000
94	C	129	PHE	0	-0.008	0.004	36.892	0.005	0.005	0.000	0.000	0.000	0.000
95	C	130	THR	0	0.043	0.029	39.011	-0.003	-0.003	0.000	0.000	0.000	0.000
96	C	131	LEU	0	-0.050	-0.016	40.667	0.004	0.004	0.000	0.000	0.000	0.000
97	C	132	TRP	0	-0.023	-0.038	42.348	-0.003	-0.003	0.000	0.000	0.000	0.000
98	C	133	GLY	0	0.028	0.012	43.849	0.001	0.001	0.000	0.000	0.000	0.000
99	C	134	LEU	0	-0.061	-0.028	46.583	0.001	0.001	0.000	0.000	0.000	0.000
100	C	135	GLU	-1	-0.883	-0.934	48.939	0.030	0.030	0.000	0.000	0.000	0.000
101	C	136	THR	0	-0.021	-0.012	51.108	-0.001	-0.001	0.000	0.000	0.000	0.000
102	C	137	ILE	0	0.003	0.014	47.710	0.002	0.002	0.000	0.000	0.000	0.000
103	C	138	PRO	0	-0.036	-0.016	44.202	-0.002	-0.002	0.000	0.000	0.000	0.000
104	C	139	GLY	0	0.084	0.039	46.870	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	140	PRO	0	-0.001	-0.010	46.345	0.002	0.002	0.000	0.000	0.000	0.000
106	C	141	ASP	-1	-0.900	-0.943	45.358	0.017	0.017	0.000	0.000	0.000	0.000
107	C	142	ALA	0	-0.042	0.000	42.825	0.001	0.001	0.000	0.000	0.000	0.000
108	C	143	LYS	1	1.017	0.973	38.057	-0.026	-0.026	0.000	0.000	0.000	0.000
109	C	144	VAL	0	0.007	0.011	36.974	0.000	0.000	0.000	0.000	0.000	0.000
110	C	145	ARG	1	0.826	0.895	37.817	-0.028	-0.028	0.000	0.000	0.000	0.000
111	C	146	GLY	0	0.026	0.023	39.470	-0.002	-0.002	0.000	0.000	0.000	0.000
112	C	147	ALA	0	-0.007	-0.005	33.962	-0.002	-0.002	0.000	0.000	0.000	0.000
113	C	148	LEU	0	0.010	0.001	34.531	0.000	0.000	0.000	0.000	0.000	0.000
114	C	149	THR	0	-0.062	-0.030	36.399	-0.002	-0.002	0.000	0.000	0.000	0.000
115	C	150	TRP	0	0.025	0.018	29.213	-0.006	-0.006	0.000	0.000	0.000	0.000
116	C	151	PRO	0	0.004	-0.011	31.091	-0.005	-0.005	0.000	0.000	0.000	0.000
117	C	152	SER	0	-0.009	0.010	32.604	-0.004	-0.004	0.000	0.000	0.000	0.000
118	C	153	LEU	0	0.037	0.017	35.677	-0.003	-0.003	0.000	0.000	0.000	0.000
119	C	154	ALA	0	-0.001	-0.010	30.216	-0.005	-0.005	0.000	0.000	0.000	0.000
120	C	155	ALA	0	-0.001	0.001	31.284	-0.005	-0.005	0.000	0.000	0.000	0.000
121	C	156	ALA	0	-0.029	-0.013	32.609	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	157	ILE	0	-0.070	-0.037	31.744	-0.003	-0.003	0.000	0.000	0.000	0.000
123	C	158	HIS	0	-0.015	-0.013	28.480	-0.009	-0.009	0.000	0.000	0.000	0.000
124	C	159	ALA	0	-0.012	0.026	29.905	-0.004	-0.004	0.000	0.000	0.000	0.000
125	C	160	GLN	0	-0.028	-0.021	28.926	-0.005	-0.005	0.000	0.000	0.000	0.000
126	C	161	VAL	0	0.022	0.014	32.430	0.004	0.004	0.000	0.000	0.000	0.000
127	C	162	PRO	0	-0.025	-0.006	35.169	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:8:ALA)