FMO DATABASE

FMODB ID: 853NY

Calculation Name: 1P8C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1P8C

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1V5

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-846963.406631
FMO2-HF: Nuclear repulsion	802574.313676
FMO2-HF: Total energy	-44389.092955
FMO2-MP2: Total energy	-44517.055365

3D Structure Molmil

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:10:ARG)

Summations of interaction energy for fragment #1(A:10:ARG)

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.
-127.024	-117.66	9.463	-7.7	-11.127	-0.071

Interaction energy analysis for fragmet #1(A:10:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.960 / 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

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	12	GLU	-1	-0.768	-0.858	2.957	-27.793	-25.634	0.078	-0.895	-1.343	0.002
4	A	13	LEU	0	0.023	0.009	2.354	1.154	3.155	2.004	-1.364	-2.640	0.000
5	A	14	ASN	0	0.004	-0.002	4.185	0.798	1.162	0.000	-0.144	-0.220	0.000
6	A	15	GLU	-1	-0.794	-0.878	6.173	-21.888	-21.888	0.000	0.000	0.000	0.000
7	A	16	LYS	1	0.794	0.875	5.931	27.815	27.815	0.000	0.000	0.000	0.000
8	A	17	VAL	0	-0.007	-0.005	7.768	2.029	2.029	0.000	0.000	0.000	0.000
9	A	18	LEU	0	-0.001	0.002	9.823	1.937	1.937	0.000	0.000	0.000	0.000
10	A	19	SER	0	-0.080	-0.037	11.591	1.620	1.620	0.000	0.000	0.000	0.000
11	A	20	ARG	1	0.930	0.952	12.756	16.544	16.544	0.000	0.000	0.000	0.000
12	A	21	GLY	0	0.065	0.060	14.160	0.416	0.416	0.000	0.000	0.000	0.000
13	A	22	THR	0	0.005	0.002	15.130	0.913	0.913	0.000	0.000	0.000	0.000
14	A	23	LEU	0	0.042	0.005	17.782	-0.616	-0.616	0.000	0.000	0.000	0.000
15	A	24	ASN	0	0.041	0.003	19.687	-0.180	-0.180	0.000	0.000	0.000	0.000
16	A	25	THR	0	0.024	0.028	13.436	0.075	0.075	0.000	0.000	0.000	0.000
17	A	26	LYS	1	0.900	0.945	15.223	14.519	14.519	0.000	0.000	0.000	0.000
18	A	27	ARG	1	0.950	0.983	16.353	11.709	11.709	0.000	0.000	0.000	0.000
19	A	28	PHE	0	0.025	0.019	13.641	0.111	0.111	0.000	0.000	0.000	0.000
20	A	29	PHE	0	0.040	0.003	8.675	-0.478	-0.478	0.000	0.000	0.000	0.000
21	A	30	ASN	0	-0.056	-0.031	13.564	-0.421	-0.421	0.000	0.000	0.000	0.000
22	A	31	LEU	0	-0.003	-0.005	16.282	0.197	0.197	0.000	0.000	0.000	0.000
23	A	32	ASP	-1	-0.857	-0.905	11.859	-22.527	-22.527	0.000	0.000	0.000	0.000
24	A	33	SER	0	0.026	0.022	13.237	0.198	0.198	0.000	0.000	0.000	0.000
25	A	34	ALA	0	-0.038	-0.024	14.468	0.394	0.394	0.000	0.000	0.000	0.000
26	A	35	VAL	0	-0.007	0.001	16.839	0.544	0.544	0.000	0.000	0.000	0.000
27	A	36	TYR	0	-0.003	-0.027	13.432	0.605	0.605	0.000	0.000	0.000	0.000
28	A	37	ARG	1	0.903	0.959	16.254	16.469	16.469	0.000	0.000	0.000	0.000
29	A	38	PRO	0	0.046	0.023	19.940	0.388	0.388	0.000	0.000	0.000	0.000
30	A	39	GLY	0	0.001	-0.002	23.334	0.189	0.189	0.000	0.000	0.000	0.000
31	A	40	LYS	1	0.904	0.954	26.553	9.797	9.797	0.000	0.000	0.000	0.000
32	A	41	LEU	0	0.012	0.018	24.162	0.244	0.244	0.000	0.000	0.000	0.000
33	A	42	ASP	-1	-0.782	-0.870	22.240	-13.791	-13.791	0.000	0.000	0.000	0.000
34	A	43	VAL	0	0.046	0.010	18.284	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	44	LYS	1	0.862	0.931	17.881	13.557	13.557	0.000	0.000	0.000	0.000
36	A	45	THR	0	-0.014	-0.048	18.350	-0.508	-0.508	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.793	0.886	18.972	13.900	13.900	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.814	-0.890	13.159	-23.440	-23.440	0.000	0.000	0.000	0.000
39	A	48	LEU	0	0.049	0.030	14.629	-1.252	-1.252	0.000	0.000	0.000	0.000
40	A	49	MET	0	-0.041	-0.017	16.735	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	50	GLY	0	0.020	0.010	14.697	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	51	LEU	0	0.006	0.019	11.007	-1.380	-1.380	0.000	0.000	0.000	0.000
43	A	52	VAL	0	0.009	0.018	13.568	-0.413	-0.413	0.000	0.000	0.000	0.000
44	A	53	ALA	0	0.001	0.000	15.932	0.063	0.063	0.000	0.000	0.000	0.000
45	A	54	SER	0	-0.038	-0.045	10.847	-0.630	-0.630	0.000	0.000	0.000	0.000
46	A	55	THR	0	-0.010	-0.026	12.773	-1.194	-1.194	0.000	0.000	0.000	0.000
47	A	56	VAL	0	-0.023	-0.014	14.383	0.368	0.368	0.000	0.000	0.000	0.000
48	A	57	LEU	0	-0.058	-0.026	14.725	0.539	0.539	0.000	0.000	0.000	0.000
49	A	58	ARG	1	0.874	0.958	13.282	16.862	16.862	0.000	0.000	0.000	0.000
50	A	59	CYS	0	-0.012	0.006	4.710	-3.913	-3.863	-0.002	-0.005	-0.043	0.000
51	A	60	ASP	-1	-0.747	-0.859	7.253	-33.790	-33.790	0.000	0.000	0.000	0.000
52	A	61	ASP	-1	-0.829	-0.914	2.242	-111.321	-107.514	7.357	-5.022	-6.142	-0.073
53	A	63	ILE	0	0.009	0.011	7.638	1.105	1.105	0.000	0.000	0.000	0.000
54	A	64	ARG	1	0.844	0.910	3.351	53.565	54.351	0.027	-0.223	-0.590	0.000
55	A	65	TYR	0	-0.006	0.001	5.415	1.009	1.009	0.000	0.000	0.000	0.000
56	A	66	HIS	1	0.851	0.902	6.352	28.100	28.100	0.000	0.000	0.000	0.000
57	A	67	LEU	0	0.030	0.039	7.781	2.207	2.207	0.000	0.000	0.000	0.000
58	A	68	VAL	0	0.015	0.010	5.940	1.701	1.701	0.000	0.000	0.000	0.000
59	A	69	ARG	1	0.683	0.817	8.655	24.844	24.844	0.000	0.000	0.000	0.000
60	A	70	CYS	0	-0.035	-0.021	11.424	2.227	2.227	0.000	0.000	0.000	0.000
61	A	71	VAL	0	0.012	0.013	11.440	1.404	1.404	0.000	0.000	0.000	0.000
62	A	72	GLN	0	-0.005	-0.001	10.381	2.148	2.148	0.000	0.000	0.000	0.000
63	A	73	GLU	-1	-0.851	-0.908	14.342	-17.430	-17.430	0.000	0.000	0.000	0.000
64	A	74	GLY	0	-0.008	0.003	16.888	1.078	1.078	0.000	0.000	0.000	0.000
65	A	75	ALA	0	-0.064	-0.029	16.147	0.974	0.974	0.000	0.000	0.000	0.000
66	A	76	SER	0	-0.015	-0.031	17.215	-0.882	-0.882	0.000	0.000	0.000	0.000
67	A	77	ASP	-1	-0.757	-0.889	16.388	-18.504	-18.504	0.000	0.000	0.000	0.000
68	A	78	GLU	-1	-0.855	-0.915	18.258	-13.965	-13.965	0.000	0.000	0.000	0.000
69	A	79	GLU	-1	-0.791	-0.867	19.723	-14.232	-14.232	0.000	0.000	0.000	0.000
70	A	80	ILE	0	-0.012	-0.016	13.782	-0.372	-0.372	0.000	0.000	0.000	0.000
71	A	81	PHE	0	-0.013	-0.008	17.166	-0.551	-0.551	0.000	0.000	0.000	0.000
72	A	82	GLU	-1	-0.916	-0.947	19.156	-12.030	-12.030	0.000	0.000	0.000	0.000
73	A	83	ALA	0	-0.051	-0.020	17.709	0.209	0.209	0.000	0.000	0.000	0.000
74	A	84	LEU	0	-0.016	-0.023	13.569	-0.247	-0.247	0.000	0.000	0.000	0.000
75	A	85	ASP	-1	-0.868	-0.939	17.758	-13.835	-13.835	0.000	0.000	0.000	0.000
76	A	86	ILE	0	-0.042	-0.015	21.369	0.485	0.485	0.000	0.000	0.000	0.000
77	A	87	ALA	0	-0.008	-0.015	17.827	0.223	0.223	0.000	0.000	0.000	0.000
78	A	88	LEU	0	-0.035	-0.018	19.759	0.068	0.068	0.000	0.000	0.000	0.000
79	A	89	VAL	0	-0.047	-0.025	21.052	0.409	0.409	0.000	0.000	0.000	0.000
80	A	90	VAL	0	-0.048	-0.019	22.603	0.354	0.354	0.000	0.000	0.000	0.000
81	A	91	GLY	0	-0.013	-0.003	20.661	0.139	0.139	0.000	0.000	0.000	0.000
82	A	92	GLY	0	0.035	0.024	21.736	0.117	0.117	0.000	0.000	0.000	0.000
83	A	93	SER	0	0.034	-0.013	21.646	-0.718	-0.718	0.000	0.000	0.000	0.000
84	A	94	ILE	0	-0.011	-0.006	19.841	-0.589	-0.589	0.000	0.000	0.000	0.000
85	A	95	VAL	0	0.026	0.021	16.849	-0.976	-0.976	0.000	0.000	0.000	0.000
86	A	96	ILE	0	0.030	0.029	16.439	-1.057	-1.057	0.000	0.000	0.000	0.000
87	A	97	PRO	0	-0.072	-0.048	15.953	-0.546	-0.546	0.000	0.000	0.000	0.000
88	A	98	HIS	0	0.030	0.005	11.402	0.051	0.051	0.000	0.000	0.000	0.000
89	A	99	LEU	0	0.047	0.038	12.280	-1.516	-1.516	0.000	0.000	0.000	0.000
90	A	100	ARG	1	0.937	0.965	14.192	16.430	16.430	0.000	0.000	0.000	0.000
91	A	101	ARG	1	0.797	0.889	9.433	25.759	25.759	0.000	0.000	0.000	0.000
92	A	102	ALA	0	-0.011	-0.005	9.834	-1.948	-1.948	0.000	0.000	0.000	0.000
93	A	103	VAL	0	0.031	0.013	10.874	-0.560	-0.560	0.000	0.000	0.000	0.000
94	A	104	GLY	0	0.028	0.023	12.316	0.157	0.157	0.000	0.000	0.000	0.000
95	A	105	PHE	0	-0.027	-0.025	4.165	-3.554	-3.357	-0.001	-0.047	-0.149	0.000
96	A	106	LEU	0	-0.024	-0.003	9.059	-0.978	-0.978	0.000	0.000	0.000	0.000
97	A	107	GLU	-1	-0.901	-0.961	11.538	-17.940	-17.940	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-0.966	-0.980	7.239	-35.140	-35.140	0.000	0.000	0.000	0.000
99	A	109	LEU	0	-0.014	-0.018	6.838	-0.151	-0.151	0.000	0.000	0.000	0.000
100	A	110	ARG	1	0.736	0.834	10.516	19.718	19.718	0.000	0.000	0.000	0.000
101	A	111	GLU	-1	-0.918	-0.958	13.767	-15.298	-15.298	0.000	0.000	0.000	0.000
102	A	112	MET	0	-0.044	0.003	8.383	-1.255	-1.255	0.000	0.000	0.000	0.000
103	A	113	GLU	-1	-0.835	-0.911	12.718	-17.599	-17.599	0.000	0.000	0.000	0.000
104	A	114	LYS	1	0.874	0.955	14.725	15.551	15.551	0.000	0.000	0.000	0.000
105	A	115	ASN	0	-0.089	-0.055	15.762	1.898	1.898	0.000	0.000	0.000	0.000
106	A	116	GLY	0	-0.030	-0.002	17.112	0.277	0.277	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.937	-0.969	11.380	-23.795	-23.795	0.000	0.000	0.000	0.000
108	A	118	THR	0	-0.053	-0.036	12.240	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	119	ILE	0	0.047	0.030	8.173	-2.324	-2.324	0.000	0.000	0.000	0.000
110	A	120	SER	0	-0.044	-0.016	7.181	0.409	0.409	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ARG)