FMO DATABASE

FMODB ID: 39RZL

Calculation Name: 5D4L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D4L

Chain ID: A

ChEMBL ID:

UniProt ID: D5X329

Base Structure: X-ray

Registration Date: 2023-09-19

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-700897.890556
FMO2-HF: Nuclear repulsion	662140.145342
FMO2-HF: Total energy	-38757.745214
FMO2-MP2: Total energy	-38871.48301

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-1.146	2.651	0.671	-1.764	-2.706	0.001

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.005

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	5	LYS	1	0.972	0.991	3.817	-0.494	1.026	-0.029	-0.744	-0.747	0.001
4	A	6	LEU	0	0.007	-0.001	6.735	-0.036	-0.036	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.040	-0.016	9.012	-0.162	-0.162	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.013	0.012	13.164	0.040	0.040	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.025	-0.013	16.673	-0.033	-0.033	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.926	0.962	19.269	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.827	0.912	21.968	-0.090	-0.090	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.031	0.017	23.653	0.006	0.006	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.843	-0.929	26.889	0.069	0.069	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.010	0.004	29.121	0.000	0.000	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.012	0.009	32.238	0.000	0.000	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.042	0.013	34.938	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.847	-0.931	37.875	0.011	0.011	0.000	0.000	0.000	0.000
16	A	18	GLY	0	-0.003	-0.010	38.245	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	ALA	0	-0.035	-0.018	39.316	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	HIS	0	0.005	0.007	40.013	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.947	0.977	33.807	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.940	-0.989	35.820	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	23	PHE	0	0.071	0.046	37.064	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.013	0.001	34.565	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.026	-0.016	31.890	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.848	-0.921	32.640	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.109	-0.046	34.516	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.027	-0.022	28.826	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.878	-0.935	29.997	-0.045	-0.045	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.862	0.930	30.748	0.019	0.019	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.024	0.004	30.828	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	32	GLY	0	-0.022	-0.004	28.114	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.063	-0.034	25.130	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.913	0.943	20.021	0.119	0.119	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.014	0.012	23.433	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	36	TYR	0	-0.008	0.005	24.346	0.007	0.007	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.048	-0.019	23.016	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.015	-0.005	25.950	0.002	0.002	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.012	0.017	27.944	0.002	0.002	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.024	-0.003	30.382	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	ASN	0	-0.053	-0.043	33.963	0.003	0.003	0.000	0.000	0.000	0.000
40	A	42	LEU	0	0.027	0.032	32.617	0.004	0.004	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.014	0.016	36.836	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.021	-0.006	39.073	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.918	0.953	41.246	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.002	0.008	43.104	0.002	0.002	0.000	0.000	0.000	0.000
45	A	47	SER	0	0.001	-0.002	43.276	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.046	0.007	35.653	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.018	0.000	37.829	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.069	-0.009	39.211	0.000	0.000	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.028	0.014	40.961	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.940	-0.983	43.981	0.019	0.019	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.002	-0.005	47.341	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	54	HIS	0	-0.070	-0.033	41.298	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.025	0.004	45.667	0.001	0.001	0.000	0.000	0.000	0.000
54	A	56	MET	0	-0.062	-0.025	44.456	0.002	0.002	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.019	0.021	38.435	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.042	-0.043	44.253	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.942	-0.998	45.365	0.026	0.026	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.976	-0.961	46.510	0.016	0.016	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.803	-0.879	42.872	0.016	0.016	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.059	-0.034	41.177	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.024	-0.016	37.776	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.046	-0.024	33.836	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	MET	0	0.001	0.001	29.436	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	ILE	0	-0.008	-0.007	29.151	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.008	-0.004	23.754	0.005	0.005	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.047	0.017	24.507	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.043	-0.020	19.908	0.010	0.010	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.017	-0.002	21.848	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.053	0.011	20.976	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.918	-0.976	22.221	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.899	-0.941	23.630	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.022	-0.021	25.354	0.001	0.001	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.027	-0.011	26.436	0.004	0.004	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.011	0.007	29.100	0.002	0.002	0.000	0.000	0.000	0.000
75	A	77	PRO	0	0.063	0.016	30.854	0.002	0.002	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.002	0.005	28.640	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.033	-0.018	32.255	0.003	0.003	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.959	-0.973	34.790	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.025	-0.009	36.178	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	PHE	0	-0.028	-0.034	32.846	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.015	0.026	37.933	0.002	0.002	0.000	0.000	0.000	0.000
82	A	84	PRO	0	0.026	0.009	40.607	0.001	0.001	0.000	0.000	0.000	0.000
83	A	85	PHE	0	-0.057	-0.016	39.995	0.001	0.001	0.000	0.000	0.000	0.000
84	A	86	PHE	0	-0.005	-0.021	36.595	0.001	0.001	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.918	-0.952	42.427	0.003	0.003	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.043	-0.014	45.598	0.000	0.000	0.000	0.000	0.000	0.000
87	A	89	HIS	1	0.824	0.904	43.138	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.077	0.056	43.141	0.000	0.000	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.015	-0.009	39.136	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.027	0.005	35.059	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.019	0.000	31.250	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	94	PHE	0	-0.039	0.005	30.203	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.033	0.002	27.120	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.033	-0.011	24.047	0.014	0.014	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.868	-0.917	21.183	0.051	0.051	0.000	0.000	0.000	0.000
96	A	98	ILE	0	-0.025	-0.018	18.278	0.021	0.021	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.007	-0.021	13.756	0.032	0.032	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.009	0.019	13.235	0.038	0.038	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.004	0.001	8.981	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.962	0.972	7.721	0.767	0.767	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.007	-0.002	4.014	-0.462	-0.259	0.000	-0.089	-0.115	0.000
102	A	104	ILE	0	-0.041	-0.032	2.419	-0.880	1.194	0.700	-0.931	-1.844	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)