FMO DATABASE

FMODB ID: GNR41

Calculation Name: 2D1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1H

Chain ID: A

ChEMBL ID:

UniProt ID: F9VNN8

Base Structure: X-ray

Registration Date: 2023-03-13

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-788315.432264
FMO2-HF: Nuclear repulsion	746143.422536
FMO2-HF: Total energy	-42172.009728
FMO2-MP2: Total energy	-42291.449429

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:1:MET)

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

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.
-30.511	-43.804	45.988	-14.269	-18.425	0.03

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.076

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	3	LYS	1	1.017	0.997	3.878	0.324	3.461	-0.019	-1.770	-1.348	0.004
4	A	4	GLU	-1	-0.915	-0.964	6.770	0.056	0.056	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.965	0.999	4.368	-0.887	-0.749	-0.001	-0.010	-0.127	0.000
6	A	6	LEU	0	-0.008	0.009	2.997	0.799	1.352	0.086	-0.111	-0.528	-0.001
7	A	7	GLU	-1	-0.791	-0.889	6.034	0.882	0.882	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.093	-0.067	7.605	0.153	0.153	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.887	0.910	2.048	-19.430	-38.637	34.190	-9.690	-5.293	0.072
10	A	10	LYS	1	0.893	0.942	8.320	-0.862	-0.862	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.843	-0.920	10.371	0.930	0.930	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.872	-0.939	8.169	2.647	2.647	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.017	-0.013	5.683	-0.348	-0.348	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.917	0.965	8.579	-1.055	-1.055	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.023	-0.014	12.267	-0.203	-0.203	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.154	-0.071	9.587	-0.260	-0.260	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.105	-0.089	7.114	-0.180	-0.180	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.892	0.958	12.268	-0.559	-0.559	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.045	-0.007	11.607	-0.093	-0.093	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.005	-0.026	15.790	0.063	0.063	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.854	-0.948	16.172	0.495	0.495	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.011	-0.003	17.091	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.801	-0.902	15.242	0.091	0.091	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.008	-0.006	11.153	-0.067	-0.067	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.017	0.016	12.923	-0.039	-0.039	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.002	0.003	15.319	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.015	0.003	8.350	-0.098	-0.098	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.019	-0.023	8.752	-0.154	-0.154	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.868	0.931	11.534	0.061	0.061	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.032	-0.034	13.782	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.028	-0.013	8.233	-0.140	-0.140	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.918	-0.951	11.336	-0.363	-0.363	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.042	-0.002	13.446	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.964	-0.959	13.196	-1.106	-1.106	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.963	0.980	15.520	0.377	0.377	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.048	-0.024	18.221	0.018	0.018	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.010	0.008	18.844	0.029	0.029	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.030	-0.026	21.423	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.012	-0.036	23.124	0.011	0.011	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.870	-0.940	24.140	-0.147	-0.147	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.827	-0.893	23.782	-0.251	-0.251	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.020	-0.003	18.604	0.018	0.018	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.020	-0.008	22.574	0.028	0.028	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.906	-0.945	25.538	-0.058	-0.058	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.046	-0.026	20.645	0.013	0.013	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.054	-0.036	17.710	0.022	0.022	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.898	0.972	23.798	0.050	0.050	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.008	0.009	22.846	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.028	0.006	26.913	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.996	0.967	26.744	0.110	0.110	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.013	0.010	26.251	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.007	0.010	23.642	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.047	0.027	21.446	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.888	-0.959	21.414	-0.134	-0.134	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.064	-0.028	22.230	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.030	0.031	18.067	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.039	-0.029	17.644	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.924	0.959	17.936	0.048	0.048	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.906	0.963	15.698	-0.118	-0.118	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.046	0.004	12.174	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.061	-0.018	13.743	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.895	-0.935	15.923	-0.055	-0.055	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.024	0.001	11.492	0.019	0.019	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.025	-0.021	11.640	-0.084	-0.084	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.033	-0.002	7.809	-0.233	-0.233	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.003	0.000	10.985	-0.120	-0.120	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.030	0.017	14.291	0.056	0.056	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.904	0.967	17.396	0.238	0.238	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.021	-0.003	20.951	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.927	0.970	23.648	0.234	0.234	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.022	0.008	26.327	0.001	0.001	0.000	0.000	0.000	0.000
72	A	79	PRO	0	0.026	-0.008	32.785	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	80	LYS	1	0.929	0.987	28.241	0.232	0.232	0.000	0.000	0.000	0.000
74	A	81	TYR	0	0.030	-0.001	25.452	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	82	TYR	0	0.008	0.015	22.361	0.025	0.025	0.000	0.000	0.000	0.000
76	A	83	TYR	0	-0.003	-0.009	18.527	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	84	SER	0	0.013	0.001	16.572	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	85	ILE	0	0.047	0.029	9.841	0.044	0.044	0.000	0.000	0.000	0.000
79	A	86	SER	0	-0.022	-0.026	10.767	0.025	0.025	0.000	0.000	0.000	0.000
80	A	87	SER	0	0.045	0.006	10.746	-0.270	-0.270	0.000	0.000	0.000	0.000
81	A	88	ASN	0	-0.014	0.003	8.788	-0.272	-0.272	0.000	0.000	0.000	0.000
82	A	89	ILE	0	0.067	0.032	6.277	-0.317	-0.317	0.000	0.000	0.000	0.000
83	A	90	LEU	0	-0.015	-0.014	2.656	-1.255	0.164	0.393	-0.356	-1.456	-0.001
84	A	91	GLU	-1	-0.832	-0.926	2.290	-10.259	-9.334	2.771	-1.541	-2.154	-0.023
85	A	92	LYS	1	0.825	0.946	4.846	1.773	1.877	-0.001	-0.005	-0.097	0.000
86	A	93	ILE	0	0.074	0.030	2.083	0.100	0.122	1.787	-0.353	-1.456	-0.004
87	A	94	ARG	1	0.930	0.966	2.179	-3.068	-1.938	6.540	-2.574	-5.096	-0.013
88	A	95	ASN	0	0.003	-0.018	3.058	3.859	1.883	0.212	2.239	-0.475	-0.003
89	A	96	ASP	-1	-0.816	-0.867	6.085	0.081	0.081	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.028	-0.020	3.723	-0.013	0.449	0.030	-0.098	-0.395	-0.001
91	A	98	LEU	0	0.005	0.015	6.442	-0.045	-0.045	0.000	0.000	0.000	0.000
92	A	99	ASN	0	0.019	0.006	8.658	-0.209	-0.209	0.000	0.000	0.000	0.000
93	A	101	ALA	0	0.043	0.011	10.285	-0.137	-0.137	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.838	0.915	12.089	-0.902	-0.902	0.000	0.000	0.000	0.000
95	A	103	ARG	1	0.924	0.953	12.343	-0.804	-0.804	0.000	0.000	0.000	0.000
96	A	104	MET	0	-0.005	0.002	14.270	-0.056	-0.056	0.000	0.000	0.000	0.000
97	A	105	GLU	-1	-0.830	-0.898	16.245	0.796	0.796	0.000	0.000	0.000	0.000
98	A	106	LEU	0	-0.021	-0.035	17.940	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	107	ALA	0	-0.048	-0.007	19.796	-0.067	-0.067	0.000	0.000	0.000	0.000
100	A	108	ALA	0	-0.037	-0.008	20.931	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	109	THR	0	-0.046	-0.009	22.672	-0.034	-0.034	0.000	0.000	0.000	0.000

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