FMO DATABASE

FMODB ID: LZ4G9

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-700921.405119
FMO2-HF: Nuclear repulsion	662163.11196
FMO2-HF: Total energy	-38758.293159
FMO2-MP2: Total energy	-38872.049408

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.
-1.154	2.646	0.435	-1.688	-2.546	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 : 0.021 / q_NPA : 0.003

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	0.934	0.975	3.817	-0.602	0.923	-0.028	-0.747	-0.750	0.001
4	A	6	LEU	0	0.014	0.007	6.738	-0.027	-0.027	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.033	-0.024	9.133	-0.137	-0.137	0.000	0.000	0.000	0.000
6	A	8	PRO	0	0.019	0.014	13.164	0.039	0.039	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.026	-0.011	16.673	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.884	0.931	19.269	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.807	0.897	21.962	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.031	0.018	23.653	0.005	0.005	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.811	-0.897	26.972	0.075	0.075	0.000	0.000	0.000	0.000
12	A	14	ILE	0	0.006	-0.001	29.134	0.000	0.000	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.013	0.008	32.251	0.000	0.000	0.000	0.000	0.000	0.000
14	A	16	LEU	0	0.043	0.018	34.950	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.787	-0.904	37.886	0.013	0.013	0.000	0.000	0.000	0.000
16	A	18	GLY	0	-0.004	-0.009	38.257	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	ALA	0	-0.035	-0.018	39.328	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	20	HIS	0	-0.022	-0.012	39.964	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.949	0.978	34.071	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.945	-0.978	35.831	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	23	PHE	0	0.047	0.026	37.075	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.029	0.011	34.621	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.013	-0.021	31.533	0.000	0.000	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.796	-0.867	32.650	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.057	-0.012	34.598	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.026	-0.018	28.837	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.859	-0.936	30.065	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	30	ARG	1	0.776	0.859	30.874	0.015	0.015	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.038	-0.003	30.961	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	32	GLY	0	-0.027	-0.005	28.242	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.068	-0.039	25.330	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.913	0.944	20.287	0.100	0.100	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.014	0.012	23.491	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	36	TYR	0	-0.029	-0.002	24.356	0.007	0.007	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.058	-0.023	23.003	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.011	-0.007	25.961	0.001	0.001	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.009	0.017	27.923	0.002	0.002	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.030	0.002	30.393	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	ASN	0	-0.051	-0.041	33.974	0.002	0.002	0.000	0.000	0.000	0.000
40	A	42	LEU	0	0.024	0.031	32.627	0.004	0.004	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.006	0.008	36.848	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.015	-0.006	39.085	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.785	0.862	41.258	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.010	0.010	43.117	0.002	0.002	0.000	0.000	0.000	0.000
45	A	47	SER	0	0.000	-0.005	43.289	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	HIS	0	0.043	0.006	35.445	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.020	-0.001	37.840	0.002	0.002	0.000	0.000	0.000	0.000
48	A	50	MET	0	-0.061	-0.003	39.201	0.000	0.000	0.000	0.000	0.000	0.000
49	A	51	TYR	0	0.011	0.006	40.961	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.938	-0.979	43.981	0.021	0.021	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.004	-0.009	47.341	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	54	HIS	0	-0.052	-0.021	41.428	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.023	0.002	45.739	0.001	0.001	0.000	0.000	0.000	0.000
54	A	56	MET	0	-0.059	-0.025	44.469	0.002	0.002	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.006	0.015	38.335	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.091	-0.078	44.265	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.764	-0.868	45.377	0.028	0.028	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.946	-0.940	46.521	0.018	0.018	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.814	-0.899	42.881	0.019	0.019	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.040	-0.023	41.288	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.028	-0.015	37.713	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.046	-0.027	33.936	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	MET	0	0.009	0.003	29.367	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	ILE	0	-0.008	-0.007	29.098	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.008	-0.004	23.881	0.004	0.004	0.000	0.000	0.000	0.000
66	A	68	ALA	0	0.043	0.020	24.523	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.043	-0.020	19.858	0.009	0.009	0.000	0.000	0.000	0.000
68	A	70	VAL	0	-0.017	-0.006	21.859	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.051	0.014	20.852	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.933	-0.979	22.221	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.889	-0.941	23.508	-0.059	-0.059	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.016	-0.016	25.406	0.001	0.001	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.030	-0.014	26.401	0.004	0.004	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.017	0.011	29.100	0.002	0.002	0.000	0.000	0.000	0.000
75	A	77	PRO	0	0.072	0.019	30.861	0.002	0.002	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.004	0.004	28.701	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.035	-0.019	32.175	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.960	-0.975	34.790	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.022	-0.009	36.176	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	PHE	0	-0.026	-0.032	32.886	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLN	0	-0.049	-0.017	37.933	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	PRO	0	0.032	0.014	40.607	0.001	0.001	0.000	0.000	0.000	0.000
83	A	85	PHE	0	-0.052	-0.015	39.941	0.000	0.000	0.000	0.000	0.000	0.000
84	A	86	PHE	0	0.003	-0.011	36.447	0.001	0.001	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.866	-0.914	42.432	0.006	0.006	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.046	-0.018	45.601	0.000	0.000	0.000	0.000	0.000	0.000
87	A	89	HIS	1	0.813	0.908	43.056	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.045	0.041	43.167	0.000	0.000	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.006	-0.012	39.155	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.029	-0.002	35.165	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.013	-0.003	31.239	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	PHE	0	-0.033	0.004	30.301	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.029	0.003	27.083	0.000	0.000	0.000	0.000	0.000	0.000
94	A	96	HIS	0	-0.055	-0.029	24.171	0.015	0.015	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.828	-0.899	21.282	0.054	0.054	0.000	0.000	0.000	0.000
96	A	98	ILE	0	-0.018	-0.007	18.194	0.021	0.021	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.003	-0.020	13.722	0.027	0.027	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.017	0.021	13.261	0.037	0.037	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.002	0.001	8.995	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.929	0.963	7.481	0.813	0.813	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.019	0.006	4.161	-0.463	-0.259	0.000	-0.091	-0.113	0.000
102	A	104	ILE	0	-0.016	-0.018	2.529	-0.868	1.203	0.463	-0.850	-1.683	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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