FMO DATABASE

FMODB ID: LZY59

Calculation Name: 5MJ0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJ0

Chain ID: B

ChEMBL ID:

UniProt ID: Q01151

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	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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-466971.649292
FMO2-HF: Nuclear repulsion	436451.459846
FMO2-HF: Total energy	-30520.189446
FMO2-MP2: Total energy	-30609.225474

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(B:19:GLY)

Summations of interaction energy for fragment #1(B:19:GLY)

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.
-2.004	-0.865	-0.016	-0.509	-0.615	0

Interaction energy analysis for fragmet #1(B:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.012

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	B	21	PRO	0	0.024	0.020	3.811	-0.472	0.667	-0.016	-0.509	-0.615
4	B	22	GLU	-1	-0.865	-0.927	6.623	0.498	0.498	0.000	0.000	0.000
5	B	23	VAL	0	0.006	0.002	9.294	-0.067	-0.067	0.000	0.000	0.000
6	B	24	LYS	1	0.927	0.962	13.046	0.196	0.196	0.000	0.000	0.000
7	B	25	VAL	0	0.045	0.018	15.791	-0.021	-0.021	0.000	0.000	0.000
8	B	26	ALA	0	0.019	0.029	19.333	0.017	0.017	0.000	0.000	0.000
9	B	27	SER	0	0.008	-0.031	22.799	0.002	0.002	0.000	0.000	0.000
10	B	28	SER	0	-0.082	-0.044	24.613	-0.003	-0.003	0.000	0.000	0.000
11	B	29	GLU	-1	-0.914	-0.937	23.605	-0.067	-0.067	0.000	0.000	0.000
12	B	30	ASP	-1	-0.804	-0.896	24.125	-0.044	-0.044	0.000	0.000	0.000
13	B	31	VAL	0	-0.036	-0.022	17.800	-0.014	-0.014	0.000	0.000	0.000
14	B	32	ASP	-1	-0.813	-0.901	19.744	-0.085	-0.085	0.000	0.000	0.000
15	B	33	LEU	0	-0.031	-0.012	14.167	-0.037	-0.037	0.000	0.000	0.000
16	B	34	PRO	0	0.011	0.018	12.301	0.022	0.022	0.000	0.000	0.000
17	B	35	CYS	0	0.018	0.053	13.043	-0.028	-0.028	0.000	0.000	0.000
18	B	36	THR	0	-0.015	-0.033	8.239	0.014	0.014	0.000	0.000	0.000
19	B	37	ALA	0	0.000	0.004	9.170	-0.115	-0.115	0.000	0.000	0.000
20	B	38	PRO	0	-0.008	-0.004	9.345	-0.014	-0.014	0.000	0.000	0.000
21	B	39	TRP	0	-0.048	-0.026	11.809	0.036	0.036	0.000	0.000	0.000
22	B	40	ASP	-1	-0.852	-0.922	15.457	-0.138	-0.138	0.000	0.000	0.000
23	B	41	PRO	0	-0.044	-0.024	18.607	0.005	0.005	0.000	0.000	0.000
24	B	42	GLN	0	-0.010	-0.026	21.072	0.004	0.004	0.000	0.000	0.000
25	B	43	VAL	0	0.025	0.026	20.743	0.012	0.012	0.000	0.000	0.000
26	B	44	PRO	0	-0.023	-0.014	22.849	-0.008	-0.008	0.000	0.000	0.000
27	B	45	TYR	0	-0.005	0.007	18.125	0.002	0.002	0.000	0.000	0.000
28	B	46	THR	0	0.010	0.018	22.560	-0.003	-0.003	0.000	0.000	0.000
29	B	47	VAL	0	0.000	-0.010	18.484	0.000	0.000	0.000	0.000	0.000
30	B	48	SER	0	-0.005	0.010	19.634	0.014	0.014	0.000	0.000	0.000
31	B	49	TRP	0	0.008	-0.008	14.109	0.008	0.008	0.000	0.000	0.000
32	B	50	VAL	0	0.004	0.008	16.661	0.011	0.011	0.000	0.000	0.000
33	B	51	LYS	1	0.887	0.944	16.660	-0.118	-0.118	0.000	0.000	0.000
34	B	52	LEU	0	-0.070	-0.042	11.864	0.022	0.022	0.000	0.000	0.000
35	B	53	LEU	0	0.024	0.020	15.895	0.022	0.022	0.000	0.000	0.000
36	B	87	GLU	-1	-0.839	-0.918	24.363	-0.098	-0.098	0.000	0.000	0.000
37	B	88	ARG	1	0.922	0.974	15.105	0.262	0.262	0.000	0.000	0.000
38	B	89	PRO	0	0.024	0.005	21.276	0.006	0.006	0.000	0.000	0.000
39	B	90	TYR	0	0.013	-0.004	18.383	-0.014	-0.014	0.000	0.000	0.000
40	B	91	SER	0	-0.036	-0.014	18.094	-0.017	-0.017	0.000	0.000	0.000
41	B	92	LEU	0	-0.028	-0.006	17.555	0.022	0.022	0.000	0.000	0.000
42	B	93	LYS	1	0.798	0.870	19.778	0.078	0.078	0.000	0.000	0.000
43	B	94	ILE	0	-0.054	-0.028	19.253	0.017	0.017	0.000	0.000	0.000
44	B	95	ARG	1	0.904	0.931	22.975	0.041	0.041	0.000	0.000	0.000
45	B	96	ASN	0	-0.027	-0.010	26.228	0.008	0.008	0.000	0.000	0.000
46	B	97	THR	0	-0.024	0.000	21.271	0.011	0.011	0.000	0.000	0.000
47	B	98	THR	0	0.078	0.040	23.926	0.003	0.003	0.000	0.000	0.000
48	B	99	SER	0	0.073	0.008	22.280	-0.001	-0.001	0.000	0.000	0.000
49	B	100	SER	0	-0.026	0.000	21.384	0.013	0.013	0.000	0.000	0.000
50	B	101	ASN	0	0.040	0.026	20.689	0.010	0.010	0.000	0.000	0.000
51	B	102	SER	0	0.043	0.037	17.114	-0.005	-0.005	0.000	0.000	0.000
52	B	103	GLY	0	-0.007	0.004	15.205	0.019	0.019	0.000	0.000	0.000
53	B	104	THR	0	-0.009	-0.002	10.266	0.039	0.039	0.000	0.000	0.000
54	B	105	TYR	0	-0.032	-0.040	12.575	0.009	0.009	0.000	0.000	0.000
55	B	106	ARG	1	0.951	0.965	12.031	-0.324	-0.324	0.000	0.000	0.000
56	B	108	THR	0	0.005	-0.009	13.967	0.020	0.020	0.000	0.000	0.000
57	B	109	LEU	0	-0.001	0.009	15.619	-0.005	-0.005	0.000	0.000	0.000
58	B	110	GLN	0	0.037	0.005	18.156	0.016	0.016	0.000	0.000	0.000
59	B	111	ASP	-1	-0.801	-0.905	21.072	-0.038	-0.038	0.000	0.000	0.000
60	B	112	PRO	0	-0.001	-0.007	22.659	0.009	0.009	0.000	0.000	0.000
61	B	113	ASP	-1	-0.810	-0.890	24.924	0.007	0.007	0.000	0.000	0.000
62	B	114	GLY	0	-0.029	-0.009	25.386	0.005	0.005	0.000	0.000	0.000
63	B	115	GLN	0	-0.083	-0.040	24.619	0.009	0.009	0.000	0.000	0.000
64	B	116	ARG	1	0.785	0.879	19.113	0.018	0.018	0.000	0.000	0.000
65	B	117	ASN	0	-0.039	-0.026	17.785	0.003	0.003	0.000	0.000	0.000
66	B	118	LEU	0	0.035	0.038	13.824	0.011	0.011	0.000	0.000	0.000
67	B	119	SER	0	-0.021	-0.053	12.025	0.002	0.002	0.000	0.000	0.000
68	B	120	GLY	0	0.000	0.013	8.767	-0.025	-0.025	0.000	0.000	0.000
69	B	121	LYS	1	0.896	0.951	6.379	-1.518	-1.518	0.000	0.000	0.000
70	B	122	VAL	0	0.024	0.014	8.051	-0.264	-0.264	0.000	0.000	0.000
71	B	123	ILE	0	-0.035	-0.005	7.749	0.157	0.157	0.000	0.000	0.000
72	B	124	LEU	0	0.029	0.031	10.898	-0.105	-0.105	0.000	0.000	0.000
73	B	125	ARG	1	0.814	0.872	11.084	-0.019	-0.019	0.000	0.000	0.000
74	B	126	VAL	0	0.038	0.034	15.968	-0.027	-0.027	0.000	0.000	0.000
75	B	127	THR	0	-0.072	-0.037	18.649	0.010	0.010	0.000	0.000	0.000
76	B	128	GLY	0	0.063	0.023	21.414	-0.006	-0.006	0.000	0.000	0.000
77	B	129	SER	0	0.008	0.007	25.042	0.002	0.002	0.000	0.000	0.000
78	B	130	PRO	0	-0.002	0.018	27.895	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:19:GLY)