FMO DATABASE

FMODB ID: V5241

Calculation Name: 2DUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DUD

Chain ID: A

ChEMBL ID:

UniProt ID: Q04837

Base Structure: X-ray

Registration Date: 2023-06-21

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737375.062624
FMO2-HF: Nuclear repulsion	697031.834811
FMO2-HF: Total energy	-40343.227813
FMO2-MP2: Total energy	-40463.040292

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:12:ARG)

Summations of interaction energy for fragment #1(A:12: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.
81.348	83.843	-0.034	-1.449	-1.012	0.001

Interaction energy analysis for fragmet #1(A:12:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.015 / q_NPA : 1.002

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	14	LEU	0	-0.002	0.018	3.734	-5.430	-2.935	-0.034	-1.449	-1.012	0.001
4	A	15	ASN	0	-0.005	0.004	6.377	4.326	4.326	0.000	0.000	0.000	0.000
5	A	16	ARG	1	0.907	0.947	8.920	26.980	26.980	0.000	0.000	0.000	0.000
6	A	17	VAL	0	0.014	0.035	10.839	1.114	1.114	0.000	0.000	0.000	0.000
7	A	18	HIS	0	-0.009	-0.017	12.706	-0.696	-0.696	0.000	0.000	0.000	0.000
8	A	19	LEU	0	0.014	0.006	17.223	0.403	0.403	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.030	0.014	20.670	-0.183	-0.183	0.000	0.000	0.000	0.000
10	A	21	GLY	0	-0.007	0.000	23.749	0.249	0.249	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.895	0.952	26.904	9.440	9.440	0.000	0.000	0.000	0.000
12	A	23	VAL	0	0.019	0.001	26.954	-0.109	-0.109	0.000	0.000	0.000	0.000
13	A	24	GLY	0	0.016	0.021	29.463	0.281	0.281	0.000	0.000	0.000	0.000
14	A	25	GLN	0	-0.003	-0.030	31.257	0.534	0.534	0.000	0.000	0.000	0.000
15	A	26	ASP	-1	-0.867	-0.927	31.173	-9.135	-9.135	0.000	0.000	0.000	0.000
16	A	27	PRO	0	-0.036	-0.018	27.943	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	28	VAL	0	0.021	0.035	28.724	0.269	0.269	0.000	0.000	0.000	0.000
18	A	29	LEU	0	0.020	-0.002	26.023	-0.422	-0.422	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.929	0.964	25.796	11.431	11.431	0.000	0.000	0.000	0.000
20	A	31	GLN	0	-0.005	0.003	26.550	-0.640	-0.640	0.000	0.000	0.000	0.000
21	A	32	VAL	0	0.050	0.023	29.050	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.849	-0.932	30.290	-9.484	-9.484	0.000	0.000	0.000	0.000
23	A	34	GLY	0	0.014	0.031	29.109	-0.291	-0.291	0.000	0.000	0.000	0.000
24	A	35	LYS	1	0.835	0.909	25.490	11.110	11.110	0.000	0.000	0.000	0.000
25	A	36	ASN	0	0.000	-0.007	21.793	0.400	0.400	0.000	0.000	0.000	0.000
26	A	37	PRO	0	0.005	0.016	23.136	-0.483	-0.483	0.000	0.000	0.000	0.000
27	A	38	VAL	0	0.001	-0.002	20.901	-0.624	-0.624	0.000	0.000	0.000	0.000
28	A	39	THR	0	0.028	0.001	22.875	0.629	0.629	0.000	0.000	0.000	0.000
29	A	40	ILE	0	-0.054	-0.030	23.132	-0.648	-0.648	0.000	0.000	0.000	0.000
30	A	41	PHE	0	0.012	0.011	22.780	0.574	0.574	0.000	0.000	0.000	0.000
31	A	42	SER	0	-0.021	-0.021	25.489	-0.216	-0.216	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.082	0.029	23.007	0.244	0.244	0.000	0.000	0.000	0.000
33	A	44	ALA	0	-0.033	-0.012	26.422	-0.157	-0.157	0.000	0.000	0.000	0.000
34	A	45	THR	0	-0.022	0.033	24.170	0.016	0.016	0.000	0.000	0.000	0.000
35	A	46	ASN	0	0.047	-0.003	27.354	0.449	0.449	0.000	0.000	0.000	0.000
36	A	47	GLU	-1	-0.894	-0.940	27.802	-11.496	-11.496	0.000	0.000	0.000	0.000
37	A	48	MET	0	-0.041	-0.041	30.487	0.352	0.352	0.000	0.000	0.000	0.000
38	A	49	TRP	0	0.040	0.038	33.023	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	62	VAL	0	0.016	0.014	38.481	0.025	0.025	0.000	0.000	0.000	0.000
40	A	63	SER	0	-0.036	-0.009	37.818	0.105	0.105	0.000	0.000	0.000	0.000
41	A	64	GLN	0	-0.053	-0.090	34.488	0.022	0.022	0.000	0.000	0.000	0.000
42	A	65	LYS	1	1.007	1.024	30.008	10.324	10.324	0.000	0.000	0.000	0.000
43	A	66	THR	0	-0.071	-0.021	30.791	-0.215	-0.215	0.000	0.000	0.000	0.000
44	A	67	THR	0	0.042	0.024	25.498	0.154	0.154	0.000	0.000	0.000	0.000
45	A	68	TRP	0	0.042	0.007	27.634	-0.211	-0.211	0.000	0.000	0.000	0.000
46	A	69	HIS	0	-0.053	-0.025	21.944	0.001	0.001	0.000	0.000	0.000	0.000
47	A	70	ARG	1	1.008	1.019	22.537	12.031	12.031	0.000	0.000	0.000	0.000
48	A	71	ILE	0	0.005	0.013	20.164	-0.836	-0.836	0.000	0.000	0.000	0.000
49	A	72	SER	0	-0.007	-0.010	19.436	0.724	0.724	0.000	0.000	0.000	0.000
50	A	73	VAL	0	0.017	0.009	18.453	-1.004	-1.004	0.000	0.000	0.000	0.000
51	A	74	PHE	0	0.030	0.010	16.607	0.413	0.413	0.000	0.000	0.000	0.000
52	A	75	ARG	1	1.015	0.995	14.207	18.589	18.589	0.000	0.000	0.000	0.000
53	A	76	PRO	0	-0.003	-0.021	17.404	0.507	0.507	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.098	0.062	19.876	0.466	0.466	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.053	-0.023	17.052	0.511	0.511	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.922	1.006	20.731	13.465	13.465	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.831	-0.918	22.411	-11.279	-11.279	0.000	0.000	0.000	0.000
58	A	81	VAL	0	0.026	0.029	22.874	0.494	0.494	0.000	0.000	0.000	0.000
59	A	82	ALA	0	-0.063	-0.060	23.663	0.322	0.322	0.000	0.000	0.000	0.000
60	A	83	TYR	0	0.040	-0.013	25.279	0.257	0.257	0.000	0.000	0.000	0.000
61	A	84	GLN	0	-0.069	-0.025	27.884	0.238	0.238	0.000	0.000	0.000	0.000
62	A	85	TYR	0	-0.005	-0.009	27.729	0.336	0.336	0.000	0.000	0.000	0.000
63	A	86	VAL	0	-0.109	0.006	25.505	0.191	0.191	0.000	0.000	0.000	0.000
64	A	87	LYS	1	0.959	0.970	28.603	9.436	9.436	0.000	0.000	0.000	0.000
65	A	88	LYS	1	0.869	0.933	31.894	8.134	8.134	0.000	0.000	0.000	0.000
66	A	89	GLY	0	0.013	0.000	32.942	0.184	0.184	0.000	0.000	0.000	0.000
67	A	90	SER	0	0.020	0.045	29.106	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	91	ARG	1	0.883	0.940	28.294	10.221	10.221	0.000	0.000	0.000	0.000
69	A	92	ILE	0	-0.023	-0.004	23.435	0.031	0.031	0.000	0.000	0.000	0.000
70	A	93	TYR	0	0.113	0.053	16.371	0.614	0.614	0.000	0.000	0.000	0.000
71	A	94	LEU	0	-0.086	-0.037	17.603	0.041	0.041	0.000	0.000	0.000	0.000
72	A	95	GLU	-1	-0.791	-0.901	13.496	-21.376	-21.376	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.008	-0.002	12.788	0.175	0.175	0.000	0.000	0.000	0.000
74	A	97	LYS	1	0.865	0.950	9.391	24.826	24.826	0.000	0.000	0.000	0.000
75	A	98	ILE	0	-0.002	-0.027	12.312	1.652	1.652	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.878	-0.927	13.842	-18.342	-18.342	0.000	0.000	0.000	0.000
77	A	100	TYR	0	0.020	-0.008	15.358	1.014	1.014	0.000	0.000	0.000	0.000
78	A	101	GLY	0	0.011	0.000	18.903	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	102	GLU	-1	-0.910	-0.955	20.704	-12.627	-12.627	0.000	0.000	0.000	0.000
80	A	103	TYR	0	-0.111	-0.054	22.282	0.178	0.178	0.000	0.000	0.000	0.000
81	A	104	MET	0	0.067	0.051	25.953	0.074	0.074	0.000	0.000	0.000	0.000
82	A	105	ASP	-1	-0.675	-0.812	28.921	-9.189	-9.189	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.866	0.956	32.521	8.129	8.129	0.000	0.000	0.000	0.000
84	A	107	ASN	0	0.023	-0.029	31.478	0.089	0.089	0.000	0.000	0.000	0.000
85	A	108	ASN	0	-0.188	-0.110	30.004	-0.174	-0.174	0.000	0.000	0.000	0.000
86	A	109	VAL	0	0.102	0.075	24.694	0.080	0.080	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.933	0.942	26.458	9.601	9.601	0.000	0.000	0.000	0.000
88	A	111	ARG	1	0.964	0.957	20.728	12.880	12.880	0.000	0.000	0.000	0.000
89	A	112	GLN	0	-0.043	-0.003	23.422	0.207	0.207	0.000	0.000	0.000	0.000
90	A	113	ALA	0	-0.081	-0.012	20.593	-0.537	-0.537	0.000	0.000	0.000	0.000
91	A	114	THR	0	-0.082	-0.058	18.467	0.633	0.633	0.000	0.000	0.000	0.000
92	A	115	THR	0	0.032	0.013	16.640	-0.776	-0.776	0.000	0.000	0.000	0.000
93	A	116	ILE	0	-0.028	-0.015	14.054	0.537	0.537	0.000	0.000	0.000	0.000
94	A	117	ILE	0	-0.026	-0.038	14.019	-1.926	-1.926	0.000	0.000	0.000	0.000
95	A	118	ALA	0	-0.084	-0.026	11.522	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	119	ASP	-1	-0.873	-0.952	13.658	-16.747	-16.747	0.000	0.000	0.000	0.000
97	A	120	ASN	0	0.061	0.022	16.520	-0.526	-0.526	0.000	0.000	0.000	0.000
98	A	121	ILE	0	0.036	0.018	19.356	0.304	0.304	0.000	0.000	0.000	0.000
99	A	122	ILE	0	-0.010	-0.023	22.481	0.124	0.124	0.000	0.000	0.000	0.000
100	A	123	PHE	0	0.008	0.002	24.500	0.199	0.199	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:ARG)