FMO DATABASE

FMODB ID: 5JJJZ

Calculation Name: 4DPO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DPO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PWK2

Base Structure: X-ray

Registration Date: 2023-09-21

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817031.596011
FMO2-HF: Nuclear repulsion	773758.103309
FMO2-HF: Total energy	-43273.492701
FMO2-MP2: Total energy	-43397.078771

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:-5:ASN)

Summations of interaction energy for fragment #1(A:-5:ASN)

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.
-23.365	-15.413	9.89	-6.81	-11.032	0.039

Interaction energy analysis for fragmet #1(A:-5:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.090 / q_NPA : 0.041

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	-3	TYR	0	-0.002	0.002	2.026	-12.650	-8.959	7.763	-5.078	-6.376	0.047
4	A	-2	PHE	0	0.021	-0.012	2.590	-10.488	-6.764	2.125	-1.614	-4.235	-0.008
5	A	-1	GLN	0	0.069	0.043	3.758	0.972	1.509	0.002	-0.118	-0.421	0.000
6	A	0	SER	0	-0.013	0.002	6.278	0.144	0.144	0.000	0.000	0.000	0.000
7	A	1	MET	0	-0.070	-0.037	6.525	-0.359	-0.359	0.000	0.000	0.000	0.000
8	A	2	LEU	0	-0.057	-0.019	8.901	-0.071	-0.071	0.000	0.000	0.000	0.000
9	A	3	ALA	0	0.035	0.030	10.426	0.043	0.043	0.000	0.000	0.000	0.000
10	A	4	ILE	0	-0.042	-0.017	12.385	0.027	0.027	0.000	0.000	0.000	0.000
11	A	5	ARG	1	0.819	0.891	16.082	-0.183	-0.183	0.000	0.000	0.000	0.000
12	A	6	VAL	0	-0.003	0.002	19.034	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	7	VAL	0	-0.018	-0.003	22.545	0.030	0.030	0.000	0.000	0.000	0.000
14	A	8	ALA	0	0.021	-0.008	25.543	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	9	LYS	1	0.899	0.946	28.576	0.012	0.012	0.000	0.000	0.000	0.000
16	A	10	ASN	0	0.032	0.019	31.704	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	11	GLN	0	-0.030	-0.010	34.891	0.007	0.007	0.000	0.000	0.000	0.000
18	A	12	VAL	0	-0.003	-0.002	37.761	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	13	LYS	1	0.909	0.957	40.434	0.022	0.022	0.000	0.000	0.000	0.000
20	A	14	PRO	0	0.043	0.019	43.895	0.001	0.001	0.000	0.000	0.000	0.000
21	A	15	GLU	-1	-0.923	-0.965	45.366	0.008	0.008	0.000	0.000	0.000	0.000
22	A	16	LYS	1	0.759	0.855	42.737	0.017	0.017	0.000	0.000	0.000	0.000
23	A	17	VAL	0	0.033	0.030	39.827	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	18	GLN	0	0.015	0.014	40.165	0.003	0.003	0.000	0.000	0.000	0.000
25	A	19	GLU	-1	-0.821	-0.915	40.626	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	20	PHE	0	0.071	0.030	33.897	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	21	MET	0	0.013	0.002	35.993	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	22	ASN	0	-0.102	-0.065	35.827	0.000	0.000	0.000	0.000	0.000	0.000
29	A	23	LEU	0	0.022	0.020	35.851	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	24	CYS	0	0.029	0.009	31.793	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	25	LYS	1	0.909	0.972	31.254	0.001	0.001	0.000	0.000	0.000	0.000
32	A	26	SER	0	-0.016	-0.037	31.532	0.004	0.004	0.000	0.000	0.000	0.000
33	A	27	LEU	0	0.049	0.044	28.542	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	28	ILE	0	-0.011	0.018	26.321	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	29	GLU	-1	-0.886	-0.924	26.352	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	30	GLU	-1	-0.864	-0.932	26.805	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	31	THR	0	-0.039	-0.033	22.903	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	32	LEU	0	-0.028	-0.034	21.848	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	33	LYS	1	0.717	0.856	21.203	0.041	0.041	0.000	0.000	0.000	0.000
40	A	34	GLU	-1	-0.805	-0.880	20.671	-0.182	-0.182	0.000	0.000	0.000	0.000
41	A	35	GLU	-1	-0.897	-0.951	14.616	-0.352	-0.352	0.000	0.000	0.000	0.000
42	A	36	GLY	0	-0.015	-0.020	14.305	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	37	CYS	0	-0.018	0.003	15.385	0.015	0.015	0.000	0.000	0.000	0.000
44	A	38	ILE	0	-0.113	-0.050	11.943	0.003	0.003	0.000	0.000	0.000	0.000
45	A	39	ASP	-1	-0.884	-0.950	16.144	0.203	0.203	0.000	0.000	0.000	0.000
46	A	40	TYR	0	-0.041	-0.058	19.539	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	41	GLY	0	0.011	0.027	22.929	0.012	0.012	0.000	0.000	0.000	0.000
48	A	42	VAL	0	-0.032	-0.021	26.170	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	43	TYR	0	-0.004	-0.003	24.339	0.019	0.019	0.000	0.000	0.000	0.000
50	A	44	GLN	0	-0.047	-0.027	30.526	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	45	GLU	-1	-0.953	-0.967	33.379	0.057	0.057	0.000	0.000	0.000	0.000
52	A	46	LEU	0	0.011	-0.002	32.988	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	47	GLU	-1	-0.961	-0.969	36.111	0.072	0.072	0.000	0.000	0.000	0.000
54	A	48	ASN	0	-0.076	-0.056	37.700	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	49	PRO	0	0.075	0.031	38.317	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	50	GLU	-1	-0.873	-0.932	39.359	0.024	0.024	0.000	0.000	0.000	0.000
57	A	51	ILE	0	-0.074	-0.031	34.302	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	52	LEU	0	0.032	0.016	34.121	0.009	0.009	0.000	0.000	0.000	0.000
59	A	53	THR	0	-0.043	-0.024	28.050	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	54	MET	0	-0.008	-0.002	26.963	0.008	0.008	0.000	0.000	0.000	0.000
61	A	55	LEU	0	-0.072	-0.029	23.641	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	56	GLU	-1	-0.758	-0.872	21.371	-0.083	-0.083	0.000	0.000	0.000	0.000
63	A	57	GLU	-1	-0.870	-0.928	13.890	0.253	0.253	0.000	0.000	0.000	0.000
64	A	58	TRP	0	0.016	0.019	16.055	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	59	LYS	1	0.889	0.934	8.378	0.591	0.591	0.000	0.000	0.000	0.000
66	A	60	ASP	-1	-0.875	-0.933	11.406	-0.918	-0.918	0.000	0.000	0.000	0.000
67	A	61	GLU	-1	-0.814	-0.902	13.536	-0.428	-0.428	0.000	0.000	0.000	0.000
68	A	62	GLY	0	0.033	0.019	15.962	0.064	0.064	0.000	0.000	0.000	0.000
69	A	63	SER	0	0.006	-0.015	14.877	0.061	0.061	0.000	0.000	0.000	0.000
70	A	64	LEU	0	-0.006	0.017	17.536	0.053	0.053	0.000	0.000	0.000	0.000
71	A	65	ASP	-1	-0.843	-0.890	19.958	-0.269	-0.269	0.000	0.000	0.000	0.000
72	A	66	GLN	0	-0.033	-0.039	17.879	0.048	0.048	0.000	0.000	0.000	0.000
73	A	67	HIS	1	0.855	0.923	21.625	0.162	0.162	0.000	0.000	0.000	0.000
74	A	68	ILE	0	-0.027	-0.012	23.396	0.021	0.021	0.000	0.000	0.000	0.000
75	A	69	ARG	1	0.747	0.850	25.021	0.269	0.269	0.000	0.000	0.000	0.000
76	A	70	SER	0	0.026	0.018	25.566	0.008	0.008	0.000	0.000	0.000	0.000
77	A	71	ASP	-1	-0.857	-0.934	27.441	-0.117	-0.117	0.000	0.000	0.000	0.000
78	A	72	HIS	0	0.046	0.023	25.514	0.009	0.009	0.000	0.000	0.000	0.000
79	A	73	PHE	0	-0.005	0.013	27.739	0.009	0.009	0.000	0.000	0.000	0.000
80	A	74	LYS	1	0.812	0.888	29.864	0.139	0.139	0.000	0.000	0.000	0.000
81	A	75	GLU	-1	-0.959	-0.979	32.457	-0.065	-0.065	0.000	0.000	0.000	0.000
82	A	76	ILE	0	-0.038	-0.030	31.971	0.008	0.008	0.000	0.000	0.000	0.000
83	A	77	PHE	0	-0.010	0.007	31.788	0.006	0.006	0.000	0.000	0.000	0.000
84	A	78	PRO	0	-0.014	-0.011	33.811	0.006	0.006	0.000	0.000	0.000	0.000
85	A	79	LEU	0	0.030	0.022	37.298	0.005	0.005	0.000	0.000	0.000	0.000
86	A	80	LEU	0	-0.017	-0.016	32.850	0.006	0.006	0.000	0.000	0.000	0.000
87	A	81	SER	0	0.005	-0.012	36.215	0.004	0.004	0.000	0.000	0.000	0.000
88	A	82	GLU	-1	-0.947	-0.955	38.158	-0.036	-0.036	0.000	0.000	0.000	0.000
89	A	83	CYS	0	-0.129	-0.049	39.336	0.006	0.006	0.000	0.000	0.000	0.000
90	A	84	LEU	0	-0.011	0.002	35.929	0.006	0.006	0.000	0.000	0.000	0.000
91	A	85	ASP	-1	-0.919	-0.946	40.605	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	86	LYS	1	0.807	0.900	35.626	0.028	0.028	0.000	0.000	0.000	0.000
93	A	87	GLU	-1	-0.854	-0.930	35.742	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	88	THR	0	-0.033	-0.028	32.605	0.005	0.005	0.000	0.000	0.000	0.000
95	A	89	GLU	-1	-0.862	-0.908	31.674	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	90	ILE	0	0.003	-0.009	26.484	0.009	0.009	0.000	0.000	0.000	0.000
97	A	91	ASN	0	-0.044	-0.010	25.412	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	92	ILE	0	0.050	0.027	20.144	0.011	0.011	0.000	0.000	0.000	0.000
99	A	93	TYR	0	-0.043	-0.021	19.496	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	94	ARG	1	0.890	0.914	13.712	0.571	0.571	0.000	0.000	0.000	0.000
101	A	95	LYS	1	0.913	0.974	10.234	-1.009	-1.009	0.000	0.000	0.000	0.000
102	A	96	LYS	1	0.980	0.992	12.945	0.231	0.231	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:ASN)