FMO DATABASE

FMODB ID: 53VJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-785773.873093
FMO2-HF: Nuclear repulsion	741085.898504
FMO2-HF: Total energy	-44687.974589
FMO2-MP2: Total energy	-44819.225324

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.
-96.644	-88.652	11.115	-7.561	-11.544	0.059

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 : -0.882 / q_NPA : -0.965

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	0.022	0.018	2.464	-10.807	-8.138	4.329	-2.358	-4.639	0.004
4	L	13	ARG	1	0.908	0.966	2.088	-79.413	-74.358	6.787	-5.209	-6.632	0.055
5	L	14	VAL	0	0.036	0.023	3.664	2.060	2.112	0.000	0.038	-0.090	0.000
6	L	15	HIS	0	-0.007	-0.007	4.233	-8.489	-8.273	-0.001	-0.032	-0.183	0.000
7	L	16	LEU	0	0.028	0.024	7.795	-2.841	-2.841	0.000	0.000	0.000	0.000
8	L	17	ARG	1	0.928	0.985	11.508	-18.236	-18.236	0.000	0.000	0.000	0.000
9	L	18	SER	0	-0.022	-0.021	13.741	0.273	0.273	0.000	0.000	0.000	0.000
10	L	19	ALA	0	-0.012	-0.025	15.419	-0.177	-0.177	0.000	0.000	0.000	0.000
11	L	20	THR	0	0.030	0.036	18.394	-0.575	-0.575	0.000	0.000	0.000	0.000
12	L	21	LEU	0	0.036	0.020	20.832	-0.605	-0.605	0.000	0.000	0.000	0.000
13	L	22	ARG	1	0.812	0.906	20.514	-13.661	-13.661	0.000	0.000	0.000	0.000
14	L	23	ASP	-1	-0.927	-0.947	23.837	10.881	10.881	0.000	0.000	0.000	0.000
15	L	24	ALA	0	0.014	0.006	27.128	-0.195	-0.195	0.000	0.000	0.000	0.000
16	L	25	VAL	0	0.014	0.010	28.957	-0.086	-0.086	0.000	0.000	0.000	0.000
17	L	26	PRO	0	-0.021	-0.016	30.052	0.259	0.259	0.000	0.000	0.000	0.000
18	L	27	ALA	0	-0.004	-0.001	28.268	-0.245	-0.245	0.000	0.000	0.000	0.000
19	L	28	THR	0	-0.020	-0.016	30.243	-0.127	-0.127	0.000	0.000	0.000	0.000
20	L	29	LEU	0	-0.018	-0.001	27.573	0.092	0.092	0.000	0.000	0.000	0.000
21	L	30	HIS	0	0.080	0.046	32.020	-0.318	-0.318	0.000	0.000	0.000	0.000
22	L	31	LEU	0	-0.006	0.007	30.602	0.241	0.241	0.000	0.000	0.000	0.000
23	L	32	LEU	0	0.020	0.000	33.535	-0.298	-0.298	0.000	0.000	0.000	0.000
24	L	33	PRO	0	-0.010	0.010	35.001	0.177	0.177	0.000	0.000	0.000	0.000
25	L	34	CYS	0	-0.076	-0.048	36.212	-0.227	-0.227	0.000	0.000	0.000	0.000
26	L	35	GLU	-1	-0.892	-0.935	30.502	10.173	10.173	0.000	0.000	0.000	0.000
27	L	36	VAL	0	-0.088	-0.061	32.344	-0.353	-0.353	0.000	0.000	0.000	0.000
28	L	37	ALA	0	0.028	0.012	31.068	0.197	0.197	0.000	0.000	0.000	0.000
29	L	38	VAL	0	-0.067	-0.023	29.524	0.212	0.212	0.000	0.000	0.000	0.000
30	L	39	ASP	-1	-0.820	-0.894	25.255	11.767	11.767	0.000	0.000	0.000	0.000
31	L	40	GLY	0	-0.024	-0.024	27.059	0.174	0.174	0.000	0.000	0.000	0.000
32	L	41	PRO	0	-0.047	-0.019	27.988	-0.192	-0.192	0.000	0.000	0.000	0.000
33	L	42	ALA	0	0.079	0.023	30.635	-0.219	-0.219	0.000	0.000	0.000	0.000
34	L	43	PRO	0	-0.024	0.011	34.095	0.041	0.041	0.000	0.000	0.000	0.000
35	L	44	VAL	0	0.038	0.001	33.988	-0.297	-0.297	0.000	0.000	0.000	0.000
36	L	45	GLY	0	0.032	0.006	37.155	-0.189	-0.189	0.000	0.000	0.000	0.000
37	L	46	ARG	1	0.919	0.960	39.198	-7.722	-7.722	0.000	0.000	0.000	0.000
38	L	47	PHE	0	-0.036	-0.021	40.439	-0.187	-0.187	0.000	0.000	0.000	0.000
39	L	48	PHE	0	0.033	0.018	38.721	-0.141	-0.141	0.000	0.000	0.000	0.000
40	L	49	THR	0	0.032	-0.004	38.583	-0.110	-0.110	0.000	0.000	0.000	0.000
41	L	50	PRO	0	-0.017	-0.001	41.311	-0.098	-0.098	0.000	0.000	0.000	0.000
42	L	51	ALA	0	-0.003	0.014	44.408	-0.182	-0.182	0.000	0.000	0.000	0.000
43	L	52	ILE	0	-0.053	-0.020	40.459	-0.076	-0.076	0.000	0.000	0.000	0.000
44	L	53	ARG	1	0.810	0.889	45.128	-6.587	-6.587	0.000	0.000	0.000	0.000
45	L	54	GLN	0	-0.007	-0.030	45.088	-0.043	-0.043	0.000	0.000	0.000	0.000
46	L	55	GLY	0	-0.016	0.013	48.562	-0.040	-0.040	0.000	0.000	0.000	0.000
47	L	56	PRO	0	0.012	-0.003	49.917	0.102	0.102	0.000	0.000	0.000	0.000
48	L	57	GLU	-1	-0.942	-0.968	50.759	6.057	6.057	0.000	0.000	0.000	0.000
49	L	58	GLY	0	-0.013	-0.003	46.704	0.092	0.092	0.000	0.000	0.000	0.000
50	L	59	LEU	0	-0.001	0.008	42.138	-0.088	-0.088	0.000	0.000	0.000	0.000
51	L	60	GLU	-1	-0.789	-0.883	45.600	6.503	6.503	0.000	0.000	0.000	0.000
52	L	61	VAL	0	0.006	0.012	41.989	-0.020	-0.020	0.000	0.000	0.000	0.000
53	L	62	SER	0	0.007	0.009	45.092	-0.098	-0.098	0.000	0.000	0.000	0.000
54	L	63	PHE	0	0.010	0.001	37.461	0.099	0.099	0.000	0.000	0.000	0.000
55	L	64	ARG	1	0.919	0.947	38.504	-7.867	-7.867	0.000	0.000	0.000	0.000
56	L	65	GLY	0	0.019	0.013	43.802	-0.072	-0.072	0.000	0.000	0.000	0.000
57	L	66	ARG	1	0.953	0.995	44.042	-7.048	-7.048	0.000	0.000	0.000	0.000
58	L	67	CYS	0	-0.015	0.003	45.538	0.107	0.107	0.000	0.000	0.000	0.000
59	L	68	LEU	0	-0.022	-0.013	40.251	0.090	0.090	0.000	0.000	0.000	0.000
60	L	69	ARG	1	1.004	0.985	44.046	-6.466	-6.466	0.000	0.000	0.000	0.000
61	L	70	GLY	0	0.006	-0.004	41.477	0.105	0.105	0.000	0.000	0.000	0.000
62	L	71	GLU	-1	-0.943	-0.962	40.733	7.290	7.290	0.000	0.000	0.000	0.000
63	L	72	GLU	-1	-0.880	-0.939	37.673	8.600	8.600	0.000	0.000	0.000	0.000
64	L	73	VAL	0	-0.017	-0.005	34.624	-0.127	-0.127	0.000	0.000	0.000	0.000
65	L	74	ALA	0	-0.025	-0.016	34.850	0.228	0.228	0.000	0.000	0.000	0.000
66	L	75	VAL	0	-0.034	-0.019	28.799	0.015	0.015	0.000	0.000	0.000	0.000
67	L	76	PRO	0	-0.001	0.011	30.531	-0.172	-0.172	0.000	0.000	0.000	0.000
68	L	77	PRO	0	0.033	-0.004	31.151	0.292	0.292	0.000	0.000	0.000	0.000
69	L	78	GLY	0	0.012	0.012	29.502	0.023	0.023	0.000	0.000	0.000	0.000
70	L	79	LEU	0	-0.019	-0.006	26.521	0.482	0.482	0.000	0.000	0.000	0.000
71	L	80	VAL	0	-0.017	-0.009	24.328	-0.337	-0.337	0.000	0.000	0.000	0.000
72	L	81	GLY	0	0.033	0.034	24.465	0.437	0.437	0.000	0.000	0.000	0.000
73	L	82	TYR	0	-0.016	-0.022	20.778	0.066	0.066	0.000	0.000	0.000	0.000
74	L	83	VAL	0	0.023	0.015	22.471	-0.067	-0.067	0.000	0.000	0.000	0.000
75	L	84	MET	0	-0.040	-0.028	16.696	0.104	0.104	0.000	0.000	0.000	0.000
76	L	85	VAL	0	0.001	0.012	17.913	-0.319	-0.319	0.000	0.000	0.000	0.000
77	L	86	THR	0	0.000	-0.015	13.558	1.363	1.363	0.000	0.000	0.000	0.000
78	L	87	GLU	-1	-0.918	-0.945	12.899	20.504	20.504	0.000	0.000	0.000	0.000
79	L	120	ILE	0	0.019	0.008	11.234	-0.323	-0.323	0.000	0.000	0.000	0.000
80	L	121	GLY	0	0.031	-0.007	12.835	0.793	0.793	0.000	0.000	0.000	0.000
81	L	122	ALA	0	-0.018	-0.021	15.572	-0.928	-0.928	0.000	0.000	0.000	0.000
82	L	123	THR	0	0.007	-0.004	18.611	-0.105	-0.105	0.000	0.000	0.000	0.000
83	L	124	ALA	0	0.014	0.010	21.831	-0.422	-0.422	0.000	0.000	0.000	0.000
84	L	125	ASN	0	-0.014	-0.003	23.737	0.509	0.509	0.000	0.000	0.000	0.000
85	L	126	PHE	0	0.017	0.011	25.537	-0.390	-0.390	0.000	0.000	0.000	0.000
86	L	127	SER	0	0.032	0.006	28.618	0.181	0.181	0.000	0.000	0.000	0.000
87	L	128	ARG	1	0.923	0.960	31.359	-8.640	-8.640	0.000	0.000	0.000	0.000
88	L	129	PHE	0	-0.012	0.004	31.375	0.242	0.242	0.000	0.000	0.000	0.000
89	L	130	THR	0	0.003	-0.011	33.609	-0.187	-0.187	0.000	0.000	0.000	0.000
90	L	131	LEU	0	-0.036	-0.008	35.407	0.202	0.202	0.000	0.000	0.000	0.000
91	L	132	TRP	0	-0.047	-0.045	36.933	-0.331	-0.331	0.000	0.000	0.000	0.000
92	L	133	GLY	0	0.023	0.006	38.619	0.153	0.153	0.000	0.000	0.000	0.000
93	L	134	LEU	0	-0.035	-0.018	41.391	-0.102	-0.102	0.000	0.000	0.000	0.000
94	L	135	GLU	-1	-0.898	-0.955	43.638	6.321	6.321	0.000	0.000	0.000	0.000
95	L	136	THR	0	-0.028	-0.022	45.870	-0.116	-0.116	0.000	0.000	0.000	0.000
96	L	137	ILE	0	0.036	0.028	42.111	0.169	0.169	0.000	0.000	0.000	0.000
97	L	138	PRO	0	-0.005	0.003	39.162	-0.098	-0.098	0.000	0.000	0.000	0.000
98	L	139	GLY	0	0.085	0.045	41.591	0.083	0.083	0.000	0.000	0.000	0.000
99	L	140	PRO	0	-0.009	-0.036	41.289	0.206	0.206	0.000	0.000	0.000	0.000
100	L	141	ASP	-1	-0.921	-0.945	40.699	7.506	7.506	0.000	0.000	0.000	0.000
101	L	142	ALA	0	-0.005	0.013	37.202	0.164	0.164	0.000	0.000	0.000	0.000
102	L	143	LYS	1	1.002	0.981	33.407	-8.760	-8.760	0.000	0.000	0.000	0.000
103	L	144	VAL	0	0.025	0.008	31.266	0.153	0.153	0.000	0.000	0.000	0.000
104	L	145	ARG	1	0.857	0.932	32.904	-7.667	-7.667	0.000	0.000	0.000	0.000
105	L	146	GLY	0	0.056	0.031	34.812	-0.005	-0.005	0.000	0.000	0.000	0.000
106	L	147	ALA	0	-0.030	0.000	29.317	0.140	0.140	0.000	0.000	0.000	0.000
107	L	148	LEU	0	0.003	-0.013	29.843	0.304	0.304	0.000	0.000	0.000	0.000
108	L	149	THR	0	-0.053	-0.025	31.349	0.058	0.058	0.000	0.000	0.000	0.000
109	L	150	TRP	0	0.049	0.019	24.777	-0.105	-0.105	0.000	0.000	0.000	0.000
110	L	151	PRO	0	0.020	0.000	26.681	0.066	0.066	0.000	0.000	0.000	0.000
111	L	152	SER	0	0.012	0.015	28.230	0.142	0.142	0.000	0.000	0.000	0.000
112	L	153	LEU	0	-0.033	-0.011	30.629	-0.076	-0.076	0.000	0.000	0.000	0.000
113	L	154	ALA	0	-0.020	-0.005	25.843	0.046	0.046	0.000	0.000	0.000	0.000
114	L	155	ALA	0	0.029	0.001	27.263	0.230	0.230	0.000	0.000	0.000	0.000
115	L	156	ALA	0	-0.029	-0.002	28.266	-0.065	-0.065	0.000	0.000	0.000	0.000
116	L	157	ILE	0	-0.033	-0.022	27.701	-0.110	-0.110	0.000	0.000	0.000	0.000
117	L	158	HIS	0	-0.050	-0.024	24.480	0.180	0.180	0.000	0.000	0.000	0.000
118	L	159	ALA	0	-0.002	0.029	25.917	0.397	0.397	0.000	0.000	0.000	0.000
119	L	160	GLN	0	-0.030	-0.019	27.274	0.241	0.241	0.000	0.000	0.000	0.000
120	L	161	VAL	0	-0.003	0.002	28.925	-0.389	-0.389	0.000	0.000	0.000	0.000

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