FMO DATABASE

FMODB ID: 82V5Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-866882.973122
FMO2-HF: Nuclear repulsion	819355.282014
FMO2-HF: Total energy	-47527.691108
FMO2-MP2: Total energy	-47667.521736

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.
-21.513	-23.994	12.748	-5.028	-5.24	0.036

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 : 0.032 / q_NPA : 0.014

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	-0.765	-0.857	2.932	-1.180	1.252	0.143	-1.137	-1.438	0.002
4	C	11	ARG	1	0.864	0.932	1.956	-22.321	-27.234	12.605	-3.891	-3.802	0.034
5	C	12	HIS	0	0.023	0.022	6.511	-0.065	-0.065	0.000	0.000	0.000	0.000
6	C	13	ARG	1	0.803	0.875	5.692	0.221	0.221	0.000	0.000	0.000	0.000
7	C	14	VAL	0	0.019	0.015	9.523	0.236	0.236	0.000	0.000	0.000	0.000
8	C	15	HIS	0	-0.016	0.000	7.667	-0.213	-0.213	0.000	0.000	0.000	0.000
9	C	16	LEU	0	0.032	0.012	12.907	0.026	0.026	0.000	0.000	0.000	0.000
10	C	17	ARG	1	0.946	0.961	16.434	-0.377	-0.377	0.000	0.000	0.000	0.000
11	C	18	SER	0	0.036	0.011	18.683	-0.015	-0.015	0.000	0.000	0.000	0.000
12	C	19	ALA	0	-0.034	-0.010	20.652	-0.013	-0.013	0.000	0.000	0.000	0.000
13	C	20	THR	0	0.004	-0.028	22.743	-0.007	-0.007	0.000	0.000	0.000	0.000
14	C	21	LEU	0	0.004	0.011	22.032	-0.003	-0.003	0.000	0.000	0.000	0.000
15	C	22	ARG	1	0.794	0.884	25.561	-0.082	-0.082	0.000	0.000	0.000	0.000
16	C	23	ASP	-1	-0.844	-0.876	27.486	0.081	0.081	0.000	0.000	0.000	0.000
17	C	24	ALA	0	-0.002	0.001	28.186	0.008	0.008	0.000	0.000	0.000	0.000
18	C	25	VAL	0	0.013	0.004	30.147	-0.008	-0.008	0.000	0.000	0.000	0.000
19	C	26	PRO	0	-0.008	-0.014	33.255	0.004	0.004	0.000	0.000	0.000	0.000
20	C	27	ALA	0	0.016	0.016	33.819	0.001	0.001	0.000	0.000	0.000	0.000
21	C	28	THR	0	-0.024	-0.019	35.796	-0.003	-0.003	0.000	0.000	0.000	0.000
22	C	29	LEU	0	0.017	0.018	32.397	0.003	0.003	0.000	0.000	0.000	0.000
23	C	30	HIS	0	0.034	0.020	36.575	-0.006	-0.006	0.000	0.000	0.000	0.000
24	C	31	LEU	0	-0.006	0.002	36.026	0.004	0.004	0.000	0.000	0.000	0.000
25	C	32	LEU	0	0.033	0.013	38.757	-0.004	-0.004	0.000	0.000	0.000	0.000
26	C	33	PRO	0	-0.008	0.005	40.198	0.001	0.001	0.000	0.000	0.000	0.000
27	C	34	CYS	0	-0.074	-0.049	41.227	-0.002	-0.002	0.000	0.000	0.000	0.000
28	C	35	GLU	-1	-0.851	-0.911	35.309	0.075	0.075	0.000	0.000	0.000	0.000
29	C	36	VAL	0	-0.088	-0.063	37.236	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	37	ALA	0	0.013	0.023	35.183	0.004	0.004	0.000	0.000	0.000	0.000
31	C	38	VAL	0	-0.083	-0.049	34.200	0.003	0.003	0.000	0.000	0.000	0.000
32	C	39	ASP	-1	-0.868	-0.931	28.483	0.136	0.136	0.000	0.000	0.000	0.000
33	C	40	GLY	0	0.017	0.013	31.679	0.007	0.007	0.000	0.000	0.000	0.000
34	C	41	PRO	0	-0.041	-0.010	32.566	-0.006	-0.006	0.000	0.000	0.000	0.000
35	C	42	ALA	0	0.072	0.020	35.212	-0.003	-0.003	0.000	0.000	0.000	0.000
36	C	43	PRO	0	-0.021	0.002	38.716	-0.001	-0.001	0.000	0.000	0.000	0.000
37	C	44	VAL	0	0.065	0.015	39.114	-0.005	-0.005	0.000	0.000	0.000	0.000
38	C	45	GLY	0	0.031	0.006	42.187	-0.004	-0.004	0.000	0.000	0.000	0.000
39	C	46	ARG	1	0.883	0.944	44.092	-0.061	-0.061	0.000	0.000	0.000	0.000
40	C	47	PHE	0	-0.019	-0.022	45.520	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	48	PHE	0	0.025	0.028	43.554	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	49	THR	0	0.063	0.016	43.450	-0.002	-0.002	0.000	0.000	0.000	0.000
43	C	50	PRO	0	-0.015	0.001	46.261	-0.002	-0.002	0.000	0.000	0.000	0.000
44	C	51	ALA	0	-0.023	-0.005	49.250	-0.002	-0.002	0.000	0.000	0.000	0.000
45	C	52	ILE	0	-0.004	0.014	45.494	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	53	ARG	1	0.812	0.896	50.170	-0.035	-0.035	0.000	0.000	0.000	0.000
47	C	54	GLN	0	0.011	0.000	52.228	0.001	0.001	0.000	0.000	0.000	0.000
48	C	55	GLY	0	0.036	0.034	54.522	0.000	0.000	0.000	0.000	0.000	0.000
49	C	56	PRO	0	-0.067	-0.045	56.379	-0.001	-0.001	0.000	0.000	0.000	0.000
50	C	57	GLU	-1	-0.817	-0.897	53.337	0.022	0.022	0.000	0.000	0.000	0.000
51	C	58	GLY	0	0.012	0.008	51.570	-0.001	-0.001	0.000	0.000	0.000	0.000
52	C	59	LEU	0	-0.032	-0.005	47.869	0.000	0.000	0.000	0.000	0.000	0.000
53	C	60	GLU	-1	-0.860	-0.941	50.541	0.026	0.026	0.000	0.000	0.000	0.000
54	C	61	VAL	0	-0.019	-0.004	46.881	0.001	0.001	0.000	0.000	0.000	0.000
55	C	62	SER	0	0.008	0.014	50.222	-0.001	-0.001	0.000	0.000	0.000	0.000
56	C	63	PHE	0	0.006	-0.006	42.198	0.002	0.002	0.000	0.000	0.000	0.000
57	C	64	ARG	1	0.904	0.936	43.022	-0.059	-0.059	0.000	0.000	0.000	0.000
58	C	65	GLY	0	0.029	0.028	48.506	0.000	0.000	0.000	0.000	0.000	0.000
59	C	66	ARG	1	0.813	0.885	49.701	-0.034	-0.034	0.000	0.000	0.000	0.000
60	C	67	CYM	-1	-0.785	-0.842	50.592	0.032	0.032	0.000	0.000	0.000	0.000
61	C	68	LEU	0	-0.019	-0.011	44.939	0.001	0.001	0.000	0.000	0.000	0.000
62	C	69	ARG	1	0.825	0.851	48.987	-0.026	-0.026	0.000	0.000	0.000	0.000
63	C	70	GLY	0	0.030	-0.003	46.659	0.001	0.001	0.000	0.000	0.000	0.000
64	C	71	GLU	-1	-0.824	-0.884	44.844	0.022	0.022	0.000	0.000	0.000	0.000
65	C	72	GLU	-1	-0.882	-0.943	43.179	0.038	0.038	0.000	0.000	0.000	0.000
66	C	73	VAL	0	-0.014	0.004	39.461	-0.003	-0.003	0.000	0.000	0.000	0.000
67	C	74	ALA	0	-0.006	-0.015	39.718	0.003	0.003	0.000	0.000	0.000	0.000
68	C	75	VAL	0	-0.017	-0.011	33.888	0.000	0.000	0.000	0.000	0.000	0.000
69	C	76	PRO	0	-0.006	0.000	35.637	-0.002	-0.002	0.000	0.000	0.000	0.000
70	C	77	PRO	0	0.001	0.000	36.145	0.001	0.001	0.000	0.000	0.000	0.000
71	C	78	GLY	0	0.020	0.004	34.586	-0.003	-0.003	0.000	0.000	0.000	0.000
72	C	79	LEU	0	-0.054	-0.016	30.629	-0.001	-0.001	0.000	0.000	0.000	0.000
73	C	80	VAL	0	0.000	-0.010	29.862	0.000	0.000	0.000	0.000	0.000	0.000
74	C	81	GLY	0	0.010	0.023	29.797	0.002	0.002	0.000	0.000	0.000	0.000
75	C	82	TYR	0	-0.040	-0.052	26.242	-0.001	-0.001	0.000	0.000	0.000	0.000
76	C	83	VAL	0	0.001	0.006	27.618	0.000	0.000	0.000	0.000	0.000	0.000
77	C	84	MET	0	-0.015	-0.006	21.976	0.012	0.012	0.000	0.000	0.000	0.000
78	C	85	VAL	0	0.020	0.011	22.517	-0.004	-0.004	0.000	0.000	0.000	0.000
79	C	86	THR	0	-0.057	-0.049	17.273	0.027	0.027	0.000	0.000	0.000	0.000
80	C	87	GLU	-1	-0.790	-0.858	16.588	0.458	0.458	0.000	0.000	0.000	0.000
81	C	88	GLU	-1	-0.956	-0.967	18.812	0.330	0.330	0.000	0.000	0.000	0.000
82	C	117	ASP	-1	-0.948	-0.972	7.147	2.452	2.452	0.000	0.000	0.000	0.000
83	C	118	ARG	1	0.779	0.858	8.534	-0.989	-0.989	0.000	0.000	0.000	0.000
84	C	119	PHE	0	-0.008	-0.016	11.310	-0.073	-0.073	0.000	0.000	0.000	0.000
85	C	120	ILE	0	0.040	0.029	14.131	-0.019	-0.019	0.000	0.000	0.000	0.000
86	C	121	GLY	0	-0.011	-0.021	17.588	-0.001	-0.001	0.000	0.000	0.000	0.000
87	C	122	ALA	0	0.031	0.033	20.627	-0.004	-0.004	0.000	0.000	0.000	0.000
88	C	123	THR	0	-0.030	-0.008	24.065	0.004	0.004	0.000	0.000	0.000	0.000
89	C	124	ALA	0	0.024	0.019	26.945	-0.006	-0.006	0.000	0.000	0.000	0.000
90	C	125	ASN	0	-0.003	-0.008	29.061	-0.001	-0.001	0.000	0.000	0.000	0.000
91	C	126	PHE	0	-0.002	-0.003	30.376	-0.001	-0.001	0.000	0.000	0.000	0.000
92	C	127	SER	0	0.044	0.020	33.877	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	128	ARG	1	0.863	0.923	36.713	-0.036	-0.036	0.000	0.000	0.000	0.000
94	C	129	PHE	0	-0.004	0.006	36.589	0.005	0.005	0.000	0.000	0.000	0.000
95	C	130	THR	0	0.003	0.007	38.683	-0.003	-0.003	0.000	0.000	0.000	0.000
96	C	131	LEU	0	-0.031	-0.004	40.475	0.003	0.003	0.000	0.000	0.000	0.000
97	C	132	TRP	0	-0.022	-0.034	42.165	-0.003	-0.003	0.000	0.000	0.000	0.000
98	C	133	GLY	0	0.009	0.000	43.751	0.001	0.001	0.000	0.000	0.000	0.000
99	C	134	LEU	0	-0.035	-0.019	46.462	0.001	0.001	0.000	0.000	0.000	0.000
100	C	135	GLU	-1	-0.849	-0.912	48.661	0.028	0.028	0.000	0.000	0.000	0.000
101	C	136	THR	0	-0.029	-0.005	50.771	-0.002	-0.002	0.000	0.000	0.000	0.000
102	C	137	ILE	0	0.000	0.016	47.758	0.002	0.002	0.000	0.000	0.000	0.000
103	C	138	PRO	0	-0.022	-0.007	44.330	-0.001	-0.001	0.000	0.000	0.000	0.000
104	C	139	GLY	0	0.093	0.052	47.059	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	140	PRO	0	-0.002	-0.020	46.465	0.001	0.001	0.000	0.000	0.000	0.000
106	C	141	ASP	-1	-0.893	-0.945	45.110	0.012	0.012	0.000	0.000	0.000	0.000
107	C	142	ALA	0	-0.041	-0.004	42.787	0.001	0.001	0.000	0.000	0.000	0.000
108	C	143	LYS	1	0.988	0.966	38.153	-0.020	-0.020	0.000	0.000	0.000	0.000
109	C	144	VAL	0	0.012	0.021	36.972	-0.001	-0.001	0.000	0.000	0.000	0.000
110	C	145	ARG	1	0.805	0.876	37.770	-0.022	-0.022	0.000	0.000	0.000	0.000
111	C	146	GLY	0	0.032	0.022	39.494	-0.002	-0.002	0.000	0.000	0.000	0.000
112	C	147	ALA	0	-0.007	0.000	33.951	-0.003	-0.003	0.000	0.000	0.000	0.000
113	C	148	LEU	0	-0.001	-0.003	34.516	-0.001	-0.001	0.000	0.000	0.000	0.000
114	C	149	THR	0	-0.043	-0.030	36.220	-0.003	-0.003	0.000	0.000	0.000	0.000
115	C	150	TRP	0	0.010	0.011	29.338	-0.005	-0.005	0.000	0.000	0.000	0.000
116	C	151	PRO	0	0.023	0.000	31.074	-0.005	-0.005	0.000	0.000	0.000	0.000
117	C	152	SER	0	-0.007	0.009	32.438	-0.005	-0.005	0.000	0.000	0.000	0.000
118	C	153	LEU	0	0.023	0.010	35.556	-0.003	-0.003	0.000	0.000	0.000	0.000
119	C	154	ALA	0	-0.005	-0.007	30.205	-0.004	-0.004	0.000	0.000	0.000	0.000
120	C	155	ALA	0	-0.002	-0.005	31.528	-0.006	-0.006	0.000	0.000	0.000	0.000
121	C	156	ALA	0	-0.025	-0.004	32.523	-0.004	-0.004	0.000	0.000	0.000	0.000
122	C	157	ILE	0	-0.056	-0.033	31.586	-0.003	-0.003	0.000	0.000	0.000	0.000
123	C	158	HIS	0	-0.035	-0.015	28.420	-0.009	-0.009	0.000	0.000	0.000	0.000
124	C	159	ALA	0	-0.002	0.018	29.894	-0.005	-0.005	0.000	0.000	0.000	0.000
125	C	160	GLN	0	-0.041	-0.027	28.778	-0.006	-0.006	0.000	0.000	0.000	0.000
126	C	161	VAL	0	0.020	0.015	32.335	0.004	0.004	0.000	0.000	0.000	0.000
127	C	162	PRO	0	-0.022	-0.005	35.242	-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)