FMO DATABASE

FMODB ID: JLL39

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

Total energy (hartree)

FMO2-HF: Electronic energy	-816475.327257
FMO2-HF: Nuclear repulsion	775785.279792
FMO2-HF: Total energy	-40690.047464
FMO2-MP2: Total energy	-40810.618931

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.
-1.167	0.951	0.04	-1.002	-1.156	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 : -0.032 / q_NPA : -0.023

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

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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	-0.007	-0.010	3.308	-2.533	-0.513	0.041	-0.995	-1.066
4	A	9	LYS	1	0.853	0.935	4.377	1.686	1.784	-0.001	-0.007	-0.090
5	A	10	PRO	0	0.019	-0.001	8.394	0.044	0.044	0.000	0.000	0.000
6	A	11	GLY	0	0.061	0.026	12.104	0.009	0.009	0.000	0.000	0.000
7	A	12	ASP	-1	-0.816	-0.885	7.979	-0.917	-0.917	0.000	0.000	0.000
8	A	13	LEU	0	-0.022	0.002	11.181	0.054	0.054	0.000	0.000	0.000
9	A	14	ILE	0	-0.047	-0.030	8.024	-0.110	-0.110	0.000	0.000	0.000
10	A	15	GLU	-1	-0.691	-0.806	10.562	-0.118	-0.118	0.000	0.000	0.000
11	A	16	ILE	0	0.004	-0.015	10.851	0.020	0.020	0.000	0.000	0.000
12	A	17	PHE	0	-0.045	-0.029	10.941	-0.015	-0.015	0.000	0.000	0.000
13	A	18	ARG	1	0.912	0.959	14.797	-0.061	-0.061	0.000	0.000	0.000
14	A	19	PRO	0	-0.016	-0.017	17.381	-0.023	-0.023	0.000	0.000	0.000
15	A	20	PHE	0	-0.049	-0.029	20.463	-0.007	-0.007	0.000	0.000	0.000
16	A	21	TYR	0	-0.024	0.010	20.437	-0.010	-0.010	0.000	0.000	0.000
17	A	22	ARG	1	0.767	0.871	16.565	0.108	0.108	0.000	0.000	0.000
18	A	23	HIS	0	-0.016	-0.008	16.326	-0.007	-0.007	0.000	0.000	0.000
19	A	24	TRP	0	-0.038	-0.028	13.172	-0.018	-0.018	0.000	0.000	0.000
20	A	25	ALA	0	-0.008	-0.002	13.514	0.028	0.028	0.000	0.000	0.000
21	A	26	ILE	0	-0.008	0.002	13.643	-0.047	-0.047	0.000	0.000	0.000
22	A	27	TYR	0	-0.029	-0.058	9.037	0.073	0.073	0.000	0.000	0.000
23	A	28	VAL	0	-0.013	-0.021	12.164	-0.017	-0.017	0.000	0.000	0.000
24	A	29	GLY	0	0.032	0.022	11.889	-0.012	-0.012	0.000	0.000	0.000
25	A	30	ASP	-1	-0.941	-0.964	12.430	-0.024	-0.024	0.000	0.000	0.000
26	A	31	GLY	0	0.026	0.021	10.413	0.066	0.066	0.000	0.000	0.000
27	A	32	TYR	0	-0.048	-0.029	11.463	0.063	0.063	0.000	0.000	0.000
28	A	33	VAL	0	-0.018	-0.012	12.077	-0.079	-0.079	0.000	0.000	0.000
29	A	34	VAL	0	-0.004	0.000	14.670	0.033	0.033	0.000	0.000	0.000
30	A	35	HIS	0	-0.033	-0.031	17.107	-0.027	-0.027	0.000	0.000	0.000
31	A	36	LEU	0	0.044	0.040	19.176	0.008	0.008	0.000	0.000	0.000
32	A	37	ALA	0	0.012	-0.005	21.674	0.007	0.007	0.000	0.000	0.000
33	A	38	PRO	0	0.020	-0.002	23.529	-0.005	-0.005	0.000	0.000	0.000
34	A	39	PRO	0	-0.003	0.012	26.310	0.007	0.007	0.000	0.000	0.000
35	A	58	ALA	0	-0.007	0.004	27.164	0.002	0.002	0.000	0.000	0.000
36	A	59	ILE	0	0.004	-0.014	26.806	-0.004	-0.004	0.000	0.000	0.000
37	A	60	VAL	0	0.020	0.014	22.693	0.001	0.001	0.000	0.000	0.000
38	A	61	LYS	1	0.834	0.926	21.613	-0.033	-0.033	0.000	0.000	0.000
39	A	62	LYS	1	0.854	0.912	17.486	0.040	0.040	0.000	0.000	0.000
40	A	63	GLU	-1	-0.821	-0.893	18.095	0.068	0.068	0.000	0.000	0.000
41	A	64	LEU	0	0.017	0.009	14.081	-0.022	-0.022	0.000	0.000	0.000
42	A	65	LEU	0	-0.007	-0.012	7.532	-0.021	-0.021	0.000	0.000	0.000
43	A	66	TYR	0	-0.027	-0.007	11.955	0.073	0.073	0.000	0.000	0.000
44	A	67	ASP	-1	-0.840	-0.933	12.812	0.230	0.230	0.000	0.000	0.000
45	A	68	VAL	0	-0.044	-0.013	14.435	-0.017	-0.017	0.000	0.000	0.000
46	A	69	ALA	0	-0.014	0.005	11.199	-0.037	-0.037	0.000	0.000	0.000
47	A	70	GLY	0	0.025	0.014	13.263	-0.027	-0.027	0.000	0.000	0.000
48	A	71	SER	0	-0.073	-0.055	14.091	0.071	0.071	0.000	0.000	0.000
49	A	72	ASP	-1	-0.890	-0.930	14.034	0.215	0.215	0.000	0.000	0.000
50	A	73	LYS	1	0.946	0.962	10.380	-0.161	-0.161	0.000	0.000	0.000
51	A	74	TYR	0	0.018	0.008	5.581	-0.054	-0.054	0.000	0.000	0.000
52	A	75	GLN	0	-0.055	-0.030	6.168	0.061	0.061	0.000	0.000	0.000
53	A	76	VAL	0	0.015	0.009	5.628	0.064	0.064	0.000	0.000	0.000
54	A	77	ASN	0	-0.082	-0.060	7.731	-0.004	-0.004	0.000	0.000	0.000
55	A	78	ASN	0	0.028	0.001	10.328	0.102	0.102	0.000	0.000	0.000
56	A	79	LYS	1	0.799	0.886	13.128	0.200	0.200	0.000	0.000	0.000
57	A	80	HIS	0	0.054	0.044	15.728	0.013	0.013	0.000	0.000	0.000
58	A	81	ASP	-1	-0.715	-0.809	14.350	-0.351	-0.351	0.000	0.000	0.000
59	A	82	ASP	-1	-0.881	-0.914	17.174	-0.189	-0.189	0.000	0.000	0.000
60	A	83	LYS	1	0.738	0.841	18.943	0.187	0.187	0.000	0.000	0.000
61	A	84	TYR	0	-0.001	0.005	20.916	0.019	0.019	0.000	0.000	0.000
62	A	85	SER	0	0.000	-0.003	20.149	-0.014	-0.014	0.000	0.000	0.000
63	A	86	PRO	0	-0.005	0.017	16.063	0.015	0.015	0.000	0.000	0.000
64	A	87	LEU	0	-0.021	-0.011	18.780	0.013	0.013	0.000	0.000	0.000
65	A	88	PRO	0	-0.018	-0.024	18.593	-0.019	-0.019	0.000	0.000	0.000
66	A	89	CYS	0	0.048	0.018	13.819	0.018	0.018	0.000	0.000	0.000
67	A	90	SER	0	-0.013	0.000	17.151	0.005	0.005	0.000	0.000	0.000
68	A	91	LYS	1	0.980	0.979	19.772	0.119	0.119	0.000	0.000	0.000
69	A	92	ILE	0	-0.010	0.028	16.444	0.009	0.009	0.000	0.000	0.000
70	A	93	ILE	0	0.007	0.004	14.803	0.009	0.009	0.000	0.000	0.000
71	A	94	GLN	0	-0.066	-0.032	18.835	0.013	0.013	0.000	0.000	0.000
72	A	95	ARG	1	0.893	0.935	22.576	0.082	0.082	0.000	0.000	0.000
73	A	96	ALA	0	0.019	0.000	19.295	0.010	0.010	0.000	0.000	0.000
74	A	97	GLU	-1	-0.785	-0.905	18.821	-0.063	-0.063	0.000	0.000	0.000
75	A	98	GLU	-1	-0.879	-0.917	22.638	-0.059	-0.059	0.000	0.000	0.000
76	A	99	LEU	0	-0.021	-0.010	24.282	0.008	0.008	0.000	0.000	0.000
77	A	100	VAL	0	-0.047	-0.009	22.364	0.007	0.007	0.000	0.000	0.000
78	A	101	GLY	0	-0.016	-0.006	25.294	0.003	0.003	0.000	0.000	0.000
79	A	102	GLN	0	-0.070	-0.030	28.027	0.003	0.003	0.000	0.000	0.000
80	A	103	GLU	-1	-0.935	-0.967	28.202	-0.005	-0.005	0.000	0.000	0.000
81	A	104	VAL	0	-0.036	-0.018	27.089	-0.005	-0.005	0.000	0.000	0.000
82	A	105	LEU	0	-0.004	-0.008	30.125	0.003	0.003	0.000	0.000	0.000
83	A	106	TYR	0	-0.023	0.001	25.627	0.003	0.003	0.000	0.000	0.000
84	A	107	LYS	1	0.962	0.983	29.060	0.017	0.017	0.000	0.000	0.000
85	A	108	LEU	0	0.061	0.027	24.080	-0.006	-0.006	0.000	0.000	0.000
86	A	109	THR	0	-0.075	-0.069	24.870	0.004	0.004	0.000	0.000	0.000
87	A	110	SER	0	0.019	-0.005	20.772	-0.001	-0.001	0.000	0.000	0.000
88	A	111	GLU	-1	-0.824	-0.907	21.302	-0.047	-0.047	0.000	0.000	0.000
89	A	112	ASN	0	-0.021	-0.014	23.469	-0.014	-0.014	0.000	0.000	0.000
90	A	113	CYS	0	-0.033	-0.008	19.736	-0.003	-0.003	0.000	0.000	0.000
91	A	114	GLU	-1	-0.688	-0.819	18.563	-0.141	-0.141	0.000	0.000	0.000
92	A	115	HIS	0	-0.056	-0.030	19.903	-0.022	-0.022	0.000	0.000	0.000
93	A	116	PHE	0	0.034	0.017	20.233	-0.010	-0.010	0.000	0.000	0.000
94	A	117	VAL	0	-0.006	0.003	16.269	-0.008	-0.008	0.000	0.000	0.000
95	A	118	ASN	0	-0.024	-0.044	18.102	-0.039	-0.039	0.000	0.000	0.000
96	A	119	GLU	-1	-0.858	-0.920	19.885	-0.084	-0.084	0.000	0.000	0.000
97	A	120	LEU	0	-0.026	-0.004	19.595	0.002	0.002	0.000	0.000	0.000
98	A	121	ARG	1	0.735	0.836	12.044	0.422	0.422	0.000	0.000	0.000
99	A	122	TYR	0	-0.042	-0.069	16.412	-0.007	-0.007	0.000	0.000	0.000
100	A	123	GLY	0	0.015	0.026	21.548	0.011	0.011	0.000	0.000	0.000
101	A	124	VAL	0	-0.032	-0.018	24.729	-0.002	-0.002	0.000	0.000	0.000
102	A	125	ALA	0	-0.045	-0.014	25.556	0.004	0.004	0.000	0.000	0.000

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