FMO DATABASE

FMODB ID: VRG51

Calculation Name: 3PUF-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: L

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-788190.549075
FMO2-HF: Nuclear repulsion	743501.707816
FMO2-HF: Total energy	-44688.84126
FMO2-MP2: Total energy	-44820.113091

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(L:10:GLU)

Summations of interaction energy for fragment #1(L: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.
-126.97	-124.777	24.503	-13.179	-13.516	0.113

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.814 / q_NPA : -0.904

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	L	12	HIS	0	0.026	0.019	2.585	-10.593	-6.338	2.970	-2.891	-4.334	-0.003
4	L	13	ARG	1	0.849	0.914	1.662	-107.792	-110.338	21.532	-10.062	-8.924	0.114
5	L	14	VAL	0	0.032	0.021	3.808	0.222	0.186	-0.001	0.017	0.021	0.000
6	L	15	HIS	0	-0.001	0.007	3.615	-9.659	-9.139	0.002	-0.243	-0.279	0.002
7	L	16	LEU	0	0.046	0.025	8.505	-2.687	-2.687	0.000	0.000	0.000	0.000
8	L	17	ARG	1	0.928	0.978	12.166	-17.806	-17.806	0.000	0.000	0.000	0.000
9	L	18	SER	0	-0.005	-0.004	14.909	-0.195	-0.195	0.000	0.000	0.000	0.000
10	L	19	ALA	0	-0.014	-0.032	15.689	-0.348	-0.348	0.000	0.000	0.000	0.000
11	L	20	THR	0	0.017	0.022	18.643	-0.684	-0.684	0.000	0.000	0.000	0.000
12	L	21	LEU	0	0.021	0.014	21.066	-0.638	-0.638	0.000	0.000	0.000	0.000
13	L	22	ARG	1	0.781	0.874	21.308	-13.483	-13.483	0.000	0.000	0.000	0.000
14	L	23	ASP	-1	-0.887	-0.925	24.129	10.966	10.966	0.000	0.000	0.000	0.000
15	L	24	ALA	0	-0.012	-0.006	27.269	-0.154	-0.154	0.000	0.000	0.000	0.000
16	L	25	VAL	0	-0.004	0.003	29.287	-0.051	-0.051	0.000	0.000	0.000	0.000
17	L	26	PRO	0	-0.033	-0.021	30.313	0.270	0.270	0.000	0.000	0.000	0.000
18	L	27	ALA	0	0.013	0.009	28.598	-0.264	-0.264	0.000	0.000	0.000	0.000
19	L	28	THR	0	-0.016	-0.015	30.643	-0.065	-0.065	0.000	0.000	0.000	0.000
20	L	29	LEU	0	-0.012	0.000	27.629	-0.048	-0.048	0.000	0.000	0.000	0.000
21	L	30	HIS	0	0.059	0.027	32.121	-0.354	-0.354	0.000	0.000	0.000	0.000
22	L	31	LEU	0	-0.005	0.005	31.287	0.264	0.264	0.000	0.000	0.000	0.000
23	L	32	LEU	0	0.023	0.006	33.949	-0.300	-0.300	0.000	0.000	0.000	0.000
24	L	33	PRO	0	-0.021	0.001	35.184	0.193	0.193	0.000	0.000	0.000	0.000
25	L	34	CYS	0	-0.073	-0.050	36.302	-0.218	-0.218	0.000	0.000	0.000	0.000
26	L	35	GLU	-1	-0.842	-0.907	31.213	10.046	10.046	0.000	0.000	0.000	0.000
27	L	36	VAL	0	-0.091	-0.065	32.629	-0.358	-0.358	0.000	0.000	0.000	0.000
28	L	37	ALA	0	0.028	0.029	30.810	0.257	0.257	0.000	0.000	0.000	0.000
29	L	38	VAL	0	-0.073	-0.047	29.772	-0.014	-0.014	0.000	0.000	0.000	0.000
30	L	39	ASP	-1	-0.867	-0.912	25.045	11.994	11.994	0.000	0.000	0.000	0.000
31	L	40	GLY	0	-0.013	-0.019	27.050	0.043	0.043	0.000	0.000	0.000	0.000
32	L	41	PRO	0	-0.042	-0.007	27.803	-0.082	-0.082	0.000	0.000	0.000	0.000
33	L	42	ALA	0	0.074	0.023	30.100	-0.250	-0.250	0.000	0.000	0.000	0.000
34	L	43	PRO	0	-0.012	0.006	33.650	0.032	0.032	0.000	0.000	0.000	0.000
35	L	44	VAL	0	0.043	0.010	34.258	-0.286	-0.286	0.000	0.000	0.000	0.000
36	L	45	GLY	0	0.037	0.005	37.122	-0.213	-0.213	0.000	0.000	0.000	0.000
37	L	46	ARG	1	0.881	0.942	38.982	-7.629	-7.629	0.000	0.000	0.000	0.000
38	L	47	PHE	0	-0.027	-0.021	40.370	-0.173	-0.173	0.000	0.000	0.000	0.000
39	L	48	PHE	0	0.034	0.027	39.047	-0.142	-0.142	0.000	0.000	0.000	0.000
40	L	49	THR	0	0.053	0.007	38.743	-0.099	-0.099	0.000	0.000	0.000	0.000
41	L	50	PRO	0	-0.035	-0.017	41.532	-0.106	-0.106	0.000	0.000	0.000	0.000
42	L	51	ALA	0	-0.005	0.013	44.488	-0.183	-0.183	0.000	0.000	0.000	0.000
43	L	52	ILE	0	-0.035	-0.011	40.600	-0.078	-0.078	0.000	0.000	0.000	0.000
44	L	53	ARG	1	0.797	0.884	45.257	-6.627	-6.627	0.000	0.000	0.000	0.000
45	L	54	GLN	0	-0.019	-0.031	45.841	-0.038	-0.038	0.000	0.000	0.000	0.000
46	L	55	GLY	0	0.014	0.019	48.794	-0.092	-0.092	0.000	0.000	0.000	0.000
47	L	56	PRO	0	0.024	-0.007	50.177	0.097	0.097	0.000	0.000	0.000	0.000
48	L	57	GLU	-1	-0.940	-0.956	50.429	6.172	6.172	0.000	0.000	0.000	0.000
49	L	58	GLY	0	-0.011	-0.019	47.063	0.117	0.117	0.000	0.000	0.000	0.000
50	L	59	LEU	0	-0.012	0.019	42.288	-0.084	-0.084	0.000	0.000	0.000	0.000
51	L	60	GLU	-1	-0.780	-0.872	45.719	6.545	6.545	0.000	0.000	0.000	0.000
52	L	61	VAL	0	0.013	0.019	42.285	0.014	0.014	0.000	0.000	0.000	0.000
53	L	62	SER	0	0.013	0.002	45.398	-0.109	-0.109	0.000	0.000	0.000	0.000
54	L	63	PHE	0	0.006	0.004	37.657	0.081	0.081	0.000	0.000	0.000	0.000
55	L	64	ARG	1	0.920	0.948	38.504	-7.923	-7.923	0.000	0.000	0.000	0.000
56	L	65	GLY	0	0.026	0.021	44.076	-0.063	-0.063	0.000	0.000	0.000	0.000
57	L	66	ARG	1	0.946	0.989	44.391	-6.944	-6.944	0.000	0.000	0.000	0.000
58	L	67	CYS	0	-0.041	-0.004	46.204	0.064	0.064	0.000	0.000	0.000	0.000
59	L	68	LEU	0	-0.009	-0.010	40.749	0.089	0.089	0.000	0.000	0.000	0.000
60	L	69	ARG	1	0.915	0.937	44.606	-6.492	-6.492	0.000	0.000	0.000	0.000
61	L	70	GLY	0	0.020	-0.005	41.937	0.144	0.144	0.000	0.000	0.000	0.000
62	L	71	GLU	-1	-0.812	-0.862	40.246	7.495	7.495	0.000	0.000	0.000	0.000
63	L	72	GLU	-1	-0.793	-0.865	38.381	8.594	8.594	0.000	0.000	0.000	0.000
64	L	73	VAL	0	-0.018	-0.002	34.929	-0.121	-0.121	0.000	0.000	0.000	0.000
65	L	74	ALA	0	-0.006	-0.009	35.082	0.232	0.232	0.000	0.000	0.000	0.000
66	L	75	VAL	0	-0.021	-0.015	28.879	0.062	0.062	0.000	0.000	0.000	0.000
67	L	76	PRO	0	0.006	0.013	30.259	-0.215	-0.215	0.000	0.000	0.000	0.000
68	L	77	PRO	0	0.017	-0.017	31.013	0.319	0.319	0.000	0.000	0.000	0.000
69	L	78	GLY	0	0.016	0.018	29.609	-0.036	-0.036	0.000	0.000	0.000	0.000
70	L	79	LEU	0	-0.040	-0.009	26.037	0.509	0.509	0.000	0.000	0.000	0.000
71	L	80	VAL	0	-0.013	-0.013	24.738	-0.375	-0.375	0.000	0.000	0.000	0.000
72	L	81	GLY	0	0.016	0.023	24.809	0.420	0.420	0.000	0.000	0.000	0.000
73	L	82	TYR	0	-0.010	-0.025	21.216	0.042	0.042	0.000	0.000	0.000	0.000
74	L	83	VAL	0	0.016	0.005	22.788	-0.118	-0.118	0.000	0.000	0.000	0.000
75	L	84	MET	0	-0.033	-0.023	17.273	0.130	0.130	0.000	0.000	0.000	0.000
76	L	85	VAL	0	-0.009	0.009	17.465	-0.489	-0.489	0.000	0.000	0.000	0.000
77	L	86	THR	0	-0.027	-0.040	13.082	1.279	1.279	0.000	0.000	0.000	0.000
78	L	87	GLU	-1	-0.896	-0.917	12.329	20.573	20.573	0.000	0.000	0.000	0.000
79	L	120	ILE	0	0.031	0.010	11.166	-0.099	-0.099	0.000	0.000	0.000	0.000
80	L	121	GLY	0	0.014	-0.009	13.185	-0.081	-0.081	0.000	0.000	0.000	0.000
81	L	122	ALA	0	-0.004	-0.021	16.153	-1.039	-1.039	0.000	0.000	0.000	0.000
82	L	123	THR	0	-0.001	0.008	18.748	-0.165	-0.165	0.000	0.000	0.000	0.000
83	L	124	ALA	0	0.023	0.015	21.955	-0.472	-0.472	0.000	0.000	0.000	0.000
84	L	125	ASN	0	0.049	0.024	23.628	0.930	0.930	0.000	0.000	0.000	0.000
85	L	126	PHE	0	-0.023	0.003	25.770	-0.410	-0.410	0.000	0.000	0.000	0.000
86	L	127	SER	0	0.042	0.013	28.751	0.229	0.229	0.000	0.000	0.000	0.000
87	L	128	ARG	1	0.838	0.898	31.545	-8.721	-8.721	0.000	0.000	0.000	0.000
88	L	129	PHE	0	-0.013	0.003	31.934	0.295	0.295	0.000	0.000	0.000	0.000
89	L	130	THR	0	0.008	0.000	34.056	-0.185	-0.185	0.000	0.000	0.000	0.000
90	L	131	LEU	0	-0.049	-0.019	35.778	0.216	0.216	0.000	0.000	0.000	0.000
91	L	132	TRP	0	-0.024	-0.029	37.322	-0.351	-0.351	0.000	0.000	0.000	0.000
92	L	133	GLY	0	0.031	-0.004	39.050	0.174	0.174	0.000	0.000	0.000	0.000
93	L	134	LEU	0	-0.040	-0.019	41.697	-0.100	-0.100	0.000	0.000	0.000	0.000
94	L	135	GLU	-1	-0.864	-0.939	44.127	6.415	6.415	0.000	0.000	0.000	0.000
95	L	136	THR	0	-0.014	0.002	45.854	-0.125	-0.125	0.000	0.000	0.000	0.000
96	L	137	ILE	0	0.027	0.021	42.528	0.174	0.174	0.000	0.000	0.000	0.000
97	L	138	PRO	0	-0.006	0.005	39.379	-0.097	-0.097	0.000	0.000	0.000	0.000
98	L	139	GLY	0	0.077	0.046	41.567	0.083	0.083	0.000	0.000	0.000	0.000
99	L	140	PRO	0	0.015	-0.020	41.360	0.203	0.203	0.000	0.000	0.000	0.000
100	L	141	ASP	-1	-0.831	-0.896	40.409	7.872	7.872	0.000	0.000	0.000	0.000
101	L	142	ALA	0	0.002	0.000	37.728	0.198	0.198	0.000	0.000	0.000	0.000
102	L	143	LYS	1	0.867	0.924	33.761	-8.022	-8.022	0.000	0.000	0.000	0.000
103	L	144	VAL	0	0.024	0.014	31.262	0.181	0.181	0.000	0.000	0.000	0.000
104	L	145	ARG	1	0.752	0.836	32.925	-7.667	-7.667	0.000	0.000	0.000	0.000
105	L	146	GLY	0	0.044	0.028	34.711	0.023	0.023	0.000	0.000	0.000	0.000
106	L	147	ALA	0	-0.008	-0.001	29.188	0.140	0.140	0.000	0.000	0.000	0.000
107	L	148	LEU	0	0.003	-0.005	29.754	0.342	0.342	0.000	0.000	0.000	0.000
108	L	149	THR	0	-0.038	-0.021	31.563	0.021	0.021	0.000	0.000	0.000	0.000
109	L	150	TRP	0	0.022	0.024	24.810	-0.093	-0.093	0.000	0.000	0.000	0.000
110	L	151	PRO	0	0.021	0.007	26.699	0.112	0.112	0.000	0.000	0.000	0.000
111	L	152	SER	0	0.014	-0.003	28.053	0.141	0.141	0.000	0.000	0.000	0.000
112	L	153	LEU	0	-0.028	-0.003	31.062	-0.079	-0.079	0.000	0.000	0.000	0.000
113	L	154	ALA	0	0.005	-0.006	25.849	0.021	0.021	0.000	0.000	0.000	0.000
114	L	155	ALA	0	-0.007	-0.011	27.240	0.197	0.197	0.000	0.000	0.000	0.000
115	L	156	ALA	0	-0.030	-0.007	28.209	-0.043	-0.043	0.000	0.000	0.000	0.000
116	L	157	ILE	0	-0.046	-0.025	27.845	-0.102	-0.102	0.000	0.000	0.000	0.000
117	L	158	HIS	0	-0.035	-0.016	24.635	0.107	0.107	0.000	0.000	0.000	0.000
118	L	159	ALA	0	-0.002	0.017	26.205	0.364	0.364	0.000	0.000	0.000	0.000
119	L	160	GLN	0	-0.042	-0.016	27.280	0.286	0.286	0.000	0.000	0.000	0.000
120	L	161	VAL	0	0.003	0.002	28.923	-0.430	-0.430	0.000	0.000	0.000	0.000

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