FMO DATABASE

FMODB ID: N991Q

Calculation Name: 4DOT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DOT

Chain ID: A

ChEMBL ID:

UniProt ID: P53816

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	OptHSide
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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817661.858077
FMO2-HF: Nuclear repulsion	776972.201597
FMO2-HF: Total energy	-40689.65648
FMO2-MP2: Total energy	-40810.367502

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:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
-0.844	1.301	0.011	-0.997	-1.16	0

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.025

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].
3	A	8	PRO	0	-0.046	-0.029	3.496	-1.996	0.036	0.012	-0.986	-1.059
4	A	9	LYS	1	0.894	0.959	4.043	1.305	1.418	-0.001	-0.011	-0.101
5	A	10	PRO	0	0.037	-0.002	8.269	0.064	0.064	0.000	0.000	0.000
6	A	11	GLY	0	0.005	-0.006	11.867	-0.010	-0.010	0.000	0.000	0.000
7	A	12	ASP	-1	-0.821	-0.883	8.019	-0.570	-0.570	0.000	0.000	0.000
8	A	13	LEU	0	-0.020	-0.002	11.133	0.049	0.049	0.000	0.000	0.000
9	A	14	ILE	0	-0.038	-0.020	8.001	-0.019	-0.019	0.000	0.000	0.000
10	A	15	GLU	-1	-0.748	-0.841	10.423	0.070	0.070	0.000	0.000	0.000
11	A	16	ILE	0	0.010	-0.012	11.112	0.094	0.094	0.000	0.000	0.000
12	A	17	PHE	0	-0.050	-0.031	10.919	-0.069	-0.069	0.000	0.000	0.000
13	A	18	ARG	1	0.919	0.971	15.048	-0.168	-0.168	0.000	0.000	0.000
14	A	19	PRO	0	0.013	0.002	17.986	-0.021	-0.021	0.000	0.000	0.000
15	A	20	PHE	0	-0.074	-0.045	20.727	-0.011	-0.011	0.000	0.000	0.000
16	A	21	TYR	0	-0.046	-0.016	20.887	-0.012	-0.012	0.000	0.000	0.000
17	A	22	ARG	1	0.815	0.902	16.577	-0.055	-0.055	0.000	0.000	0.000
18	A	23	HIS	0	-0.017	-0.010	16.635	-0.025	-0.025	0.000	0.000	0.000
19	A	24	TRP	0	-0.045	-0.017	13.251	0.026	0.026	0.000	0.000	0.000
20	A	25	ALA	0	-0.006	-0.007	13.640	-0.002	-0.002	0.000	0.000	0.000
21	A	26	ILE	0	-0.003	0.009	13.655	-0.013	-0.013	0.000	0.000	0.000
22	A	27	TYR	0	-0.037	-0.059	8.940	0.071	0.071	0.000	0.000	0.000
23	A	28	VAL	0	-0.030	-0.033	12.449	-0.027	-0.027	0.000	0.000	0.000
24	A	29	GLY	0	0.024	0.022	11.656	-0.009	-0.009	0.000	0.000	0.000
25	A	30	ASP	-1	-0.926	-0.962	12.065	-0.087	-0.087	0.000	0.000	0.000
26	A	31	GLY	0	0.013	0.012	10.542	0.046	0.046	0.000	0.000	0.000
27	A	32	TYR	0	-0.038	-0.012	11.567	0.082	0.082	0.000	0.000	0.000
28	A	33	VAL	0	-0.014	-0.007	12.449	-0.040	-0.040	0.000	0.000	0.000
29	A	34	VAL	0	0.006	0.007	14.967	0.009	0.009	0.000	0.000	0.000
30	A	35	HIS	0	-0.048	-0.039	17.346	0.005	0.005	0.000	0.000	0.000
31	A	36	LEU	0	0.029	0.037	19.336	-0.004	-0.004	0.000	0.000	0.000
32	A	37	ALA	0	0.019	0.002	21.782	0.013	0.013	0.000	0.000	0.000
33	A	38	PRO	0	0.043	0.013	23.734	-0.009	-0.009	0.000	0.000	0.000
34	A	39	PRO	0	0.007	0.013	26.877	0.006	0.006	0.000	0.000	0.000
35	A	58	ALA	0	-0.001	0.002	26.869	0.002	0.002	0.000	0.000	0.000
36	A	59	ILE	0	-0.025	-0.027	26.961	-0.004	-0.004	0.000	0.000	0.000
37	A	60	VAL	0	0.017	0.014	22.744	0.007	0.007	0.000	0.000	0.000
38	A	61	LYS	1	0.894	0.963	21.874	-0.065	-0.065	0.000	0.000	0.000
39	A	62	LYS	1	0.846	0.907	17.802	0.037	0.037	0.000	0.000	0.000
40	A	63	GLU	-1	-0.887	-0.940	18.037	0.090	0.090	0.000	0.000	0.000
41	A	64	LEU	0	0.046	0.031	14.020	-0.011	-0.011	0.000	0.000	0.000
42	A	65	LEU	0	0.007	-0.005	8.185	0.007	0.007	0.000	0.000	0.000
43	A	66	TYR	0	-0.058	-0.022	11.376	0.078	0.078	0.000	0.000	0.000
44	A	67	ASP	-1	-0.843	-0.936	12.473	0.182	0.182	0.000	0.000	0.000
45	A	68	VAL	0	-0.070	-0.026	14.729	0.002	0.002	0.000	0.000	0.000
46	A	69	ALA	0	-0.031	-0.019	11.297	-0.009	-0.009	0.000	0.000	0.000
47	A	70	GLY	0	0.067	0.047	13.319	-0.030	-0.030	0.000	0.000	0.000
48	A	71	SER	0	-0.063	-0.037	13.552	0.057	0.057	0.000	0.000	0.000
49	A	72	ASP	-1	-0.902	-0.950	14.277	0.263	0.263	0.000	0.000	0.000
50	A	73	LYS	1	0.945	0.956	10.632	-0.232	-0.232	0.000	0.000	0.000
51	A	74	TYR	0	0.010	0.003	5.557	-0.200	-0.200	0.000	0.000	0.000
52	A	75	GLN	0	-0.059	-0.024	6.347	0.280	0.280	0.000	0.000	0.000
53	A	76	VAL	0	0.034	0.014	5.356	-0.063	-0.063	0.000	0.000	0.000
54	A	77	ASN	0	-0.090	-0.067	7.448	-0.034	-0.034	0.000	0.000	0.000
55	A	78	ASN	0	0.005	-0.003	10.480	0.061	0.061	0.000	0.000	0.000
56	A	79	LYS	1	0.865	0.910	12.766	-0.010	-0.010	0.000	0.000	0.000
57	A	80	HIS	0	0.017	0.012	15.301	-0.006	-0.006	0.000	0.000	0.000
58	A	81	ASP	-1	-0.729	-0.813	14.841	-0.175	-0.175	0.000	0.000	0.000
59	A	82	ASP	-1	-0.862	-0.905	17.315	-0.073	-0.073	0.000	0.000	0.000
60	A	83	LYS	1	0.785	0.880	19.125	0.068	0.068	0.000	0.000	0.000
61	A	84	TYR	0	-0.021	-0.013	20.850	0.009	0.009	0.000	0.000	0.000
62	A	85	SER	0	-0.011	-0.007	20.118	-0.008	-0.008	0.000	0.000	0.000
63	A	86	PRO	0	-0.001	0.017	16.470	0.010	0.010	0.000	0.000	0.000
64	A	87	LEU	0	-0.016	-0.019	19.170	0.004	0.004	0.000	0.000	0.000
65	A	88	PRO	0	-0.018	-0.022	19.003	-0.013	-0.013	0.000	0.000	0.000
66	A	89	CYS	0	0.069	0.022	14.077	0.011	0.011	0.000	0.000	0.000
67	A	90	SER	0	-0.007	-0.005	17.412	0.003	0.003	0.000	0.000	0.000
68	A	91	LYS	1	0.969	0.979	19.901	0.073	0.073	0.000	0.000	0.000
69	A	92	ILE	0	0.005	0.032	16.644	0.007	0.007	0.000	0.000	0.000
70	A	93	ILE	0	0.007	0.008	14.787	0.010	0.010	0.000	0.000	0.000
71	A	94	GLN	0	-0.041	-0.020	18.787	0.008	0.008	0.000	0.000	0.000
72	A	95	ARG	1	0.888	0.946	22.493	0.037	0.037	0.000	0.000	0.000
73	A	96	ALA	0	0.017	-0.011	19.462	0.009	0.009	0.000	0.000	0.000
74	A	97	GLU	-1	-0.785	-0.902	18.767	-0.041	-0.041	0.000	0.000	0.000
75	A	98	GLU	-1	-0.893	-0.924	22.448	-0.028	-0.028	0.000	0.000	0.000
76	A	99	LEU	0	-0.028	-0.012	24.207	0.005	0.005	0.000	0.000	0.000
77	A	100	VAL	0	-0.033	-0.004	22.301	0.007	0.007	0.000	0.000	0.000
78	A	101	GLY	0	-0.036	-0.020	25.152	-0.002	-0.002	0.000	0.000	0.000
79	A	102	GLN	0	-0.060	-0.029	27.974	0.002	0.002	0.000	0.000	0.000
80	A	103	GLU	-1	-0.923	-0.956	28.158	0.021	0.021	0.000	0.000	0.000
81	A	104	VAL	0	-0.041	-0.013	26.890	-0.004	-0.004	0.000	0.000	0.000
82	A	105	LEU	0	-0.002	-0.012	29.814	0.003	0.003	0.000	0.000	0.000
83	A	106	TYR	0	-0.019	0.004	25.916	0.003	0.003	0.000	0.000	0.000
84	A	107	LYS	1	0.996	0.994	29.631	-0.030	-0.030	0.000	0.000	0.000
85	A	108	LEU	0	0.032	0.012	24.238	-0.002	-0.002	0.000	0.000	0.000
86	A	109	THR	0	-0.066	-0.060	25.317	0.002	0.002	0.000	0.000	0.000
87	A	110	SER	0	0.039	-0.010	20.610	-0.001	-0.001	0.000	0.000	0.000
88	A	111	GLU	-1	-0.832	-0.904	21.114	0.037	0.037	0.000	0.000	0.000
89	A	112	ASN	0	-0.023	-0.013	23.417	-0.009	-0.009	0.000	0.000	0.000
90	A	113	CYS	0	-0.022	0.005	19.902	-0.007	-0.007	0.000	0.000	0.000
91	A	114	GLU	-1	-0.730	-0.843	18.223	0.017	0.017	0.000	0.000	0.000
92	A	115	HIS	0	-0.075	-0.042	19.782	-0.012	-0.012	0.000	0.000	0.000
93	A	116	PHE	0	0.038	0.016	20.380	-0.008	-0.008	0.000	0.000	0.000
94	A	117	VAL	0	0.005	0.006	16.152	-0.009	-0.009	0.000	0.000	0.000
95	A	118	ASN	0	-0.016	-0.043	18.390	-0.029	-0.029	0.000	0.000	0.000
96	A	119	GLU	-1	-0.877	-0.916	19.840	-0.023	-0.023	0.000	0.000	0.000
97	A	120	LEU	0	-0.040	-0.011	19.479	-0.006	-0.006	0.000	0.000	0.000
98	A	121	ARG	1	0.773	0.860	12.684	0.197	0.197	0.000	0.000	0.000
99	A	122	TYR	0	-0.056	-0.074	16.077	-0.006	-0.006	0.000	0.000	0.000
100	A	123	GLY	0	-0.005	0.022	21.356	0.002	0.002	0.000	0.000	0.000
101	A	124	VAL	0	-0.021	-0.018	24.639	0.002	0.002	0.000	0.000	0.000
102	A	125	ALA	0	-0.029	0.001	25.385	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)