FMO DATABASE

FMODB ID: R81J8

Calculation Name: 4PNH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PNH

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T109

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1427049.847441
FMO2-HF: Nuclear repulsion	1368697.854645
FMO2-HF: Total energy	-58351.992795
FMO2-MP2: Total energy	-58521.533287

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(A:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
-56.16	-54.16	-0.012	-0.771	-1.216	0.004

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.945 / q_NPA : 0.957

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	A	9	LEU	0	0.002	0.009	3.879	-1.235	0.251	-0.012	-0.711	-0.762	0.004
4	A	10	VAL	0	0.043	0.017	6.720	1.970	1.970	0.000	0.000	0.000	0.000
5	A	11	VAL	0	-0.016	0.004	10.349	-0.216	-0.216	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.009	0.008	13.059	1.067	1.067	0.000	0.000	0.000	0.000
7	A	13	ASP	-1	-0.767	-0.861	16.039	-13.456	-13.456	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.826	0.867	18.971	12.478	12.478	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.788	-0.874	20.710	-11.282	-11.282	0.000	0.000	0.000	0.000
10	A	16	GLY	0	-0.003	0.007	24.543	0.140	0.140	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.028	0.009	19.318	0.148	0.148	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.016	0.005	17.159	-0.194	-0.194	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.030	-0.013	21.271	-0.226	-0.226	0.000	0.000	0.000	0.000
14	A	20	VAL	0	0.024	0.028	24.742	0.121	0.121	0.000	0.000	0.000	0.000
15	A	28	SER	0	-0.010	-0.026	33.499	0.037	0.037	0.000	0.000	0.000	0.000
16	A	29	PRO	0	-0.003	-0.016	28.499	-0.176	-0.176	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.807	-0.914	28.214	-10.379	-10.379	0.000	0.000	0.000	0.000
18	A	31	GLU	-1	-0.916	-0.942	29.769	-8.620	-8.620	0.000	0.000	0.000	0.000
19	A	32	TRP	0	-0.049	-0.018	20.909	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.017	-0.001	26.741	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	34	ALA	0	0.010	0.005	22.158	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	35	LEU	0	0.013	0.001	23.633	0.466	0.466	0.000	0.000	0.000	0.000
23	A	36	PRO	0	0.043	0.002	22.867	-0.528	-0.528	0.000	0.000	0.000	0.000
24	A	37	GLY	0	0.032	0.025	22.469	-0.362	-0.362	0.000	0.000	0.000	0.000
25	A	38	SER	0	0.017	-0.017	19.783	-0.399	-0.399	0.000	0.000	0.000	0.000
26	A	39	LEU	0	-0.012	0.004	18.176	-0.824	-0.824	0.000	0.000	0.000	0.000
27	A	40	GLU	-1	-0.802	-0.879	17.718	-13.701	-13.701	0.000	0.000	0.000	0.000
28	A	41	ALA	0	-0.025	-0.013	17.037	-0.715	-0.715	0.000	0.000	0.000	0.000
29	A	42	ILE	0	-0.003	0.000	13.259	-1.097	-1.097	0.000	0.000	0.000	0.000
30	A	43	ALA	0	0.052	0.031	12.798	-1.366	-1.366	0.000	0.000	0.000	0.000
31	A	44	ARG	1	0.886	0.924	13.357	14.739	14.739	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.006	0.003	10.710	-0.979	-0.979	0.000	0.000	0.000	0.000
33	A	46	ASN	0	-0.013	-0.017	8.426	-0.544	-0.544	0.000	0.000	0.000	0.000
34	A	47	HIS	0	0.008	0.013	8.860	-1.965	-1.965	0.000	0.000	0.000	0.000
35	A	48	ALA	0	-0.011	0.005	10.036	-0.419	-0.419	0.000	0.000	0.000	0.000
36	A	49	GLY	0	-0.010	0.002	6.064	-1.425	-1.425	0.000	0.000	0.000	0.000
37	A	50	TYR	0	-0.052	-0.034	4.620	-6.532	-6.420	-0.001	-0.009	-0.102	0.000
38	A	51	ARG	1	0.874	0.922	3.683	44.022	44.424	0.001	-0.051	-0.352	0.000
39	A	52	VAL	0	0.032	0.012	6.034	0.594	0.594	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.011	0.009	8.920	1.017	1.017	0.000	0.000	0.000	0.000
41	A	54	VAL	0	-0.025	-0.014	11.296	1.043	1.043	0.000	0.000	0.000	0.000
42	A	55	ALA	0	0.047	0.024	15.009	0.355	0.355	0.000	0.000	0.000	0.000
43	A	56	THR	0	0.001	-0.003	17.251	0.846	0.846	0.000	0.000	0.000	0.000
44	A	57	ASN	0	0.056	0.048	20.889	0.052	0.052	0.000	0.000	0.000	0.000
45	A	58	GLN	0	0.051	0.010	23.685	0.250	0.250	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.028	-0.029	25.884	0.431	0.431	0.000	0.000	0.000	0.000
47	A	60	GLY	0	-0.017	-0.010	27.218	0.373	0.373	0.000	0.000	0.000	0.000
48	A	61	ILE	0	-0.009	-0.007	24.559	0.118	0.118	0.000	0.000	0.000	0.000
49	A	62	GLY	0	0.031	0.017	28.462	0.233	0.233	0.000	0.000	0.000	0.000
50	A	63	ARG	1	0.886	0.933	31.504	8.613	8.613	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.013	0.013	30.672	0.156	0.156	0.000	0.000	0.000	0.000
52	A	65	LEU	0	-0.057	-0.005	31.734	0.111	0.111	0.000	0.000	0.000	0.000
53	A	66	PHE	0	-0.005	-0.013	27.794	-0.109	-0.109	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.759	-0.847	32.007	-9.299	-9.299	0.000	0.000	0.000	0.000
55	A	68	MET	0	0.044	0.000	25.406	-0.289	-0.289	0.000	0.000	0.000	0.000
56	A	69	ALA	0	-0.007	0.016	28.382	-0.382	-0.382	0.000	0.000	0.000	0.000
57	A	70	THR	0	-0.011	-0.027	29.174	-0.244	-0.244	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.027	-0.016	23.793	-0.297	-0.297	0.000	0.000	0.000	0.000
59	A	72	ASN	0	-0.060	-0.038	24.530	-0.876	-0.876	0.000	0.000	0.000	0.000
60	A	73	ALA	0	-0.005	0.013	24.704	-0.396	-0.396	0.000	0.000	0.000	0.000
61	A	74	MET	0	0.033	0.028	24.259	-0.203	-0.203	0.000	0.000	0.000	0.000
62	A	75	HIS	0	0.028	0.002	17.104	-0.231	-0.231	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.023	-0.012	20.810	-0.516	-0.516	0.000	0.000	0.000	0.000
64	A	77	LYS	1	0.806	0.892	22.617	10.240	10.240	0.000	0.000	0.000	0.000
65	A	78	MET	0	-0.025	-0.010	18.747	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	79	HIS	0	0.001	0.004	15.598	-0.707	-0.707	0.000	0.000	0.000	0.000
67	A	80	ARG	1	0.947	0.965	18.739	11.051	11.051	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.011	0.004	21.033	0.090	0.090	0.000	0.000	0.000	0.000
69	A	82	ALA	0	0.014	0.010	15.582	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	83	ALA	0	0.025	0.007	17.579	-0.174	-0.174	0.000	0.000	0.000	0.000
71	A	84	ALA	0	-0.056	-0.021	18.486	0.088	0.088	0.000	0.000	0.000	0.000
72	A	85	VAL	0	-0.055	-0.020	17.516	0.445	0.445	0.000	0.000	0.000	0.000
73	A	86	GLY	0	-0.006	0.003	16.781	-0.350	-0.350	0.000	0.000	0.000	0.000
74	A	87	GLY	0	-0.017	0.002	13.638	-1.060	-1.060	0.000	0.000	0.000	0.000
75	A	88	ARG	1	0.795	0.857	9.135	23.919	23.919	0.000	0.000	0.000	0.000
76	A	89	ILE	0	0.034	0.031	10.311	-1.459	-1.459	0.000	0.000	0.000	0.000
77	A	90	ASP	-1	-0.817	-0.887	8.736	-27.989	-27.989	0.000	0.000	0.000	0.000
78	A	91	ALA	0	-0.010	0.001	11.595	0.072	0.072	0.000	0.000	0.000	0.000
79	A	92	VAL	0	-0.039	-0.018	13.582	-0.355	-0.355	0.000	0.000	0.000	0.000
80	A	93	PHE	0	0.027	0.001	16.512	0.590	0.590	0.000	0.000	0.000	0.000
81	A	94	PHE	0	0.038	0.015	20.091	-0.266	-0.266	0.000	0.000	0.000	0.000
82	A	95	CYS	0	0.041	0.031	21.912	0.675	0.675	0.000	0.000	0.000	0.000
83	A	112	MET	0	-0.037	-0.015	19.732	0.435	0.435	0.000	0.000	0.000	0.000
84	A	113	MET	0	0.036	0.015	15.248	-0.632	-0.632	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.944	0.960	16.591	11.925	11.925	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.049	0.041	17.092	0.050	0.050	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.041	-0.021	12.541	-0.942	-0.942	0.000	0.000	0.000	0.000
88	A	117	ALA	0	-0.004	-0.011	12.027	-1.794	-1.794	0.000	0.000	0.000	0.000
89	A	118	GLU	-1	-0.936	-0.945	12.572	-18.400	-18.400	0.000	0.000	0.000	0.000
90	A	119	ARG	1	0.880	0.943	11.549	21.095	21.095	0.000	0.000	0.000	0.000
91	A	120	PHE	0	-0.053	-0.045	7.326	-1.097	-1.097	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.912	-0.945	5.637	-37.817	-37.817	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.072	-0.043	5.500	-7.408	-7.408	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.797	-0.891	7.388	-20.118	-20.118	0.000	0.000	0.000	0.000
95	A	124	PRO	0	-0.020	-0.015	10.137	-0.893	-0.893	0.000	0.000	0.000	0.000
96	A	125	ALA	0	0.027	0.026	12.789	0.378	0.378	0.000	0.000	0.000	0.000
97	A	126	ASP	-1	-0.960	-0.974	8.981	-25.715	-25.715	0.000	0.000	0.000	0.000
98	A	127	THR	0	-0.126	-0.067	9.395	-2.047	-2.047	0.000	0.000	0.000	0.000
99	A	128	PRO	0	-0.062	-0.019	11.032	1.840	1.840	0.000	0.000	0.000	0.000
100	A	129	VAL	0	-0.003	-0.003	13.697	-0.883	-0.883	0.000	0.000	0.000	0.000
101	A	130	VAL	0	-0.009	-0.006	15.617	0.904	0.904	0.000	0.000	0.000	0.000
102	A	131	GLY	0	0.039	0.005	18.285	-0.111	-0.111	0.000	0.000	0.000	0.000
103	A	132	ASP	-1	-0.714	-0.817	21.557	-11.201	-11.201	0.000	0.000	0.000	0.000
104	A	133	SER	0	-0.033	-0.028	24.951	0.536	0.536	0.000	0.000	0.000	0.000
105	A	134	LEU	0	0.043	0.032	25.359	-0.473	-0.473	0.000	0.000	0.000	0.000
106	A	135	ARG	1	0.765	0.864	22.018	12.631	12.631	0.000	0.000	0.000	0.000
107	A	136	ASP	-1	-0.759	-0.892	19.999	-14.621	-14.621	0.000	0.000	0.000	0.000
108	A	137	LEU	0	-0.021	0.007	20.964	-0.538	-0.538	0.000	0.000	0.000	0.000
109	A	138	GLN	0	0.054	0.017	22.197	-0.188	-0.188	0.000	0.000	0.000	0.000
110	A	139	ALA	0	-0.048	-0.031	22.371	-0.130	-0.130	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.012	0.003	18.643	-0.401	-0.401	0.000	0.000	0.000	0.000
112	A	141	ALA	0	0.041	0.025	18.713	-0.499	-0.499	0.000	0.000	0.000	0.000
113	A	142	ALA	0	-0.069	-0.034	20.843	0.020	0.020	0.000	0.000	0.000	0.000
114	A	143	LEU	0	-0.041	-0.028	16.323	0.185	0.185	0.000	0.000	0.000	0.000
115	A	144	GLY	0	0.022	0.021	17.119	-0.716	-0.716	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.030	-0.013	12.162	-0.503	-0.503	0.000	0.000	0.000	0.000
117	A	146	ARG	1	0.983	0.998	14.024	20.146	20.146	0.000	0.000	0.000	0.000
118	A	147	PRO	0	-0.009	0.002	17.185	-0.488	-0.488	0.000	0.000	0.000	0.000
119	A	148	HIS	0	-0.043	-0.041	17.132	-0.360	-0.360	0.000	0.000	0.000	0.000
120	A	149	LEU	0	0.002	-0.002	20.536	-0.120	-0.120	0.000	0.000	0.000	0.000
121	A	150	VAL	0	-0.028	-0.012	21.026	0.084	0.084	0.000	0.000	0.000	0.000
122	A	151	LEU	0	-0.063	-0.026	23.856	0.351	0.351	0.000	0.000	0.000	0.000
123	A	152	THR	0	0.010	-0.004	24.916	0.360	0.360	0.000	0.000	0.000	0.000
124	A	153	GLY	0	0.017	0.003	27.398	-0.123	-0.123	0.000	0.000	0.000	0.000
125	A	154	LYS	1	0.755	0.854	26.454	11.505	11.505	0.000	0.000	0.000	0.000
126	A	155	GLY	0	0.074	0.043	27.945	0.209	0.209	0.000	0.000	0.000	0.000
127	A	156	LYS	1	0.857	0.909	28.615	9.864	9.864	0.000	0.000	0.000	0.000
128	A	157	LYS	1	0.948	0.982	31.968	8.880	8.880	0.000	0.000	0.000	0.000
129	A	158	THR	0	-0.032	-0.054	28.043	0.256	0.256	0.000	0.000	0.000	0.000
130	A	159	LEU	0	-0.004	-0.003	29.678	0.006	0.006	0.000	0.000	0.000	0.000
131	A	160	ALA	0	-0.039	-0.013	31.689	0.116	0.116	0.000	0.000	0.000	0.000
132	A	161	ALA	0	-0.048	-0.017	33.552	0.201	0.201	0.000	0.000	0.000	0.000
133	A	162	GLY	0	0.026	0.029	32.809	0.140	0.140	0.000	0.000	0.000	0.000
134	A	163	GLY	0	-0.012	-0.020	32.200	-0.119	-0.119	0.000	0.000	0.000	0.000
135	A	164	LEU	0	-0.048	-0.024	26.507	-0.260	-0.260	0.000	0.000	0.000	0.000
136	A	165	PRO	0	-0.003	-0.002	24.009	0.214	0.214	0.000	0.000	0.000	0.000
137	A	166	GLU	-1	-0.878	-0.922	26.146	-10.575	-10.575	0.000	0.000	0.000	0.000
138	A	167	GLY	0	-0.009	0.004	22.953	0.070	0.070	0.000	0.000	0.000	0.000
139	A	168	THR	0	-0.087	-0.062	22.478	-0.675	-0.675	0.000	0.000	0.000	0.000
140	A	169	ARG	1	0.854	0.895	19.731	14.796	14.796	0.000	0.000	0.000	0.000
141	A	170	VAL	0	0.022	0.003	23.238	0.012	0.012	0.000	0.000	0.000	0.000
142	A	171	HIS	0	0.038	0.029	20.990	-0.392	-0.392	0.000	0.000	0.000	0.000
143	A	172	ASP	-1	-0.802	-0.899	24.579	-9.983	-9.983	0.000	0.000	0.000	0.000
144	A	173	ASP	-1	-0.805	-0.917	23.490	-12.166	-12.166	0.000	0.000	0.000	0.000
145	A	174	LEU	0	0.032	0.016	16.839	-0.316	-0.316	0.000	0.000	0.000	0.000
146	A	175	ARG	1	0.824	0.887	19.078	11.556	11.556	0.000	0.000	0.000	0.000
147	A	176	ALA	0	-0.010	-0.008	20.422	-0.295	-0.295	0.000	0.000	0.000	0.000
148	A	177	PHE	0	0.020	0.016	14.251	-0.182	-0.182	0.000	0.000	0.000	0.000
149	A	178	ALA	0	-0.007	-0.003	16.046	-0.615	-0.615	0.000	0.000	0.000	0.000
150	A	179	LEU	0	-0.045	-0.009	16.769	-0.359	-0.359	0.000	0.000	0.000	0.000
151	A	180	ASP	-1	-0.825	-0.894	18.739	-14.593	-14.593	0.000	0.000	0.000	0.000
152	A	181	PHE	0	0.026	0.003	10.552	-0.364	-0.364	0.000	0.000	0.000	0.000
153	A	182	LEU	0	-0.093	-0.046	11.607	-1.060	-1.060	0.000	0.000	0.000	0.000
154	A	183	SER	0	-0.004	-0.002	14.806	0.574	0.574	0.000	0.000	0.000	0.000
155	A	184	LYN	0	-0.039	0.027	12.836	0.122	0.122	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)