FMO DATABASE

FMODB ID: V5Y91

Calculation Name: 5M97-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5M97

Chain ID: B

ChEMBL ID:

UniProt ID: Q10113

Base Structure: X-ray

Registration Date: 2023-06-22

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-353446.016159
FMO2-HF: Nuclear repulsion	324659.545622
FMO2-HF: Total energy	-28786.470536
FMO2-MP2: Total energy	-28868.217453

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:6:GLN)

Summations of interaction energy for fragment #1(B:6:GLN)

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.
-5.692	-1.647	0.348	-1.661	-2.732	-0.002

Interaction energy analysis for fragmet #1(B:6:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.004

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	B	8	GLN	0	0.064	0.023	3.511	-3.221	-1.395	-0.005	-0.789	-1.031	0.002
4	B	9	GLN	0	-0.004	0.020	2.697	-3.333	-1.512	0.354	-0.699	-1.477	-0.004
5	B	10	GLN	0	0.006	0.002	4.050	0.789	1.187	-0.001	-0.173	-0.224	0.000
6	B	11	ILE	0	0.019	0.021	5.953	0.473	0.473	0.000	0.000	0.000	0.000
7	B	12	THR	0	0.051	0.017	7.905	0.142	0.142	0.000	0.000	0.000	0.000
8	B	13	SER	0	-0.095	-0.046	8.320	0.125	0.125	0.000	0.000	0.000	0.000
9	B	14	LEU	0	0.008	0.000	9.745	0.195	0.195	0.000	0.000	0.000	0.000
10	B	15	GLU	-1	-0.920	-0.965	11.962	-0.240	-0.240	0.000	0.000	0.000	0.000
11	B	16	THR	0	-0.053	-0.032	12.607	0.076	0.076	0.000	0.000	0.000	0.000
12	B	17	GLN	0	0.029	0.017	14.101	0.071	0.071	0.000	0.000	0.000	0.000
13	B	18	LEU	0	-0.025	-0.015	15.850	0.082	0.082	0.000	0.000	0.000	0.000
14	B	19	TYR	0	-0.079	-0.047	17.589	0.065	0.065	0.000	0.000	0.000	0.000
15	B	20	GLU	-1	-0.857	-0.941	17.265	-0.657	-0.657	0.000	0.000	0.000	0.000
16	B	21	VAL	0	-0.026	-0.007	19.670	0.042	0.042	0.000	0.000	0.000	0.000
17	B	22	ASN	0	-0.036	-0.027	21.156	0.066	0.066	0.000	0.000	0.000	0.000
18	B	23	GLU	-1	-0.880	-0.912	23.529	-0.309	-0.309	0.000	0.000	0.000	0.000
19	B	24	THR	0	-0.053	-0.036	23.927	0.018	0.018	0.000	0.000	0.000	0.000
20	B	25	MET	0	-0.039	-0.011	25.814	0.024	0.024	0.000	0.000	0.000	0.000
21	B	26	PHE	0	0.046	0.002	26.299	0.019	0.019	0.000	0.000	0.000	0.000
22	B	27	GLY	0	-0.034	-0.001	29.192	0.012	0.012	0.000	0.000	0.000	0.000
23	B	28	LEU	0	0.038	0.016	29.006	0.014	0.014	0.000	0.000	0.000	0.000
24	B	29	GLU	-1	-0.900	-0.921	31.847	-0.088	-0.088	0.000	0.000	0.000	0.000
25	B	30	ARG	1	0.928	0.943	29.985	0.187	0.187	0.000	0.000	0.000	0.000
26	B	31	GLU	-1	-0.930	-0.956	34.280	-0.168	-0.168	0.000	0.000	0.000	0.000
27	B	32	ARG	1	0.723	0.823	35.257	0.102	0.102	0.000	0.000	0.000	0.000
28	B	33	ASP	-1	-0.813	-0.892	38.007	-0.080	-0.080	0.000	0.000	0.000	0.000
29	B	34	PHE	0	-0.014	0.012	39.623	0.007	0.007	0.000	0.000	0.000	0.000
30	B	35	TYR	0	-0.014	-0.021	38.527	0.007	0.007	0.000	0.000	0.000	0.000
31	B	36	PHE	0	-0.027	-0.011	42.155	0.007	0.007	0.000	0.000	0.000	0.000
32	B	37	ASN	0	-0.015	-0.029	42.875	0.011	0.011	0.000	0.000	0.000	0.000
33	B	38	LYS	1	0.890	0.959	44.688	0.100	0.100	0.000	0.000	0.000	0.000
34	B	39	LEU	0	-0.031	-0.015	45.569	0.004	0.004	0.000	0.000	0.000	0.000
35	B	40	ARG	1	0.945	0.976	47.792	0.052	0.052	0.000	0.000	0.000	0.000
36	B	41	GLU	-1	-0.883	-0.956	49.060	-0.069	-0.069	0.000	0.000	0.000	0.000
37	B	42	ILE	0	-0.011	-0.007	51.474	0.004	0.004	0.000	0.000	0.000	0.000
38	B	43	GLU	-1	-0.901	-0.949	51.635	-0.042	-0.042	0.000	0.000	0.000	0.000
39	B	44	ILE	0	0.000	0.004	52.273	0.004	0.004	0.000	0.000	0.000	0.000
40	B	45	LEU	0	-0.029	0.011	55.795	0.003	0.003	0.000	0.000	0.000	0.000
41	B	46	VAL	0	0.012	-0.004	57.564	0.002	0.002	0.000	0.000	0.000	0.000
42	B	47	GLN	0	-0.022	-0.023	55.690	0.005	0.005	0.000	0.000	0.000	0.000
43	B	48	THR	0	-0.013	0.006	59.247	0.003	0.003	0.000	0.000	0.000	0.000
44	B	49	HIS	0	0.002	0.012	61.739	0.002	0.002	0.000	0.000	0.000	0.000
45	B	50	LEU	0	-0.037	-0.025	61.750	0.002	0.002	0.000	0.000	0.000	0.000
46	B	51	THR	0	-0.081	-0.048	63.278	0.002	0.002	0.000	0.000	0.000	0.000
47	B	52	THR	0	-0.042	-0.033	63.846	0.001	0.001	0.000	0.000	0.000	0.000
48	B	53	SER	0	-0.025	-0.018	64.445	0.000	0.000	0.000	0.000	0.000	0.000
49	B	54	PRO	0	-0.027	0.011	65.289	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	55	MET	0	-0.009	0.016	61.690	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	56	SER	0	0.035	0.012	66.892	0.000	0.000	0.000	0.000	0.000	0.000
52	B	57	MET	0	0.033	0.000	64.086	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	58	GLU	-1	-0.928	-0.960	63.690	-0.051	-0.051	0.000	0.000	0.000	0.000
54	B	59	ASN	0	0.009	-0.010	62.672	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	60	MET	0	0.016	-0.001	60.114	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	61	LEU	0	0.026	0.006	59.240	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	62	GLU	-1	-0.825	-0.856	58.327	-0.067	-0.067	0.000	0.000	0.000	0.000
58	B	63	ARG	1	0.846	0.883	55.742	0.059	0.059	0.000	0.000	0.000	0.000
59	B	64	ILE	0	0.017	0.005	54.405	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	65	GLN	0	-0.043	-0.033	53.497	-0.006	-0.006	0.000	0.000	0.000	0.000
61	B	66	ALA	0	-0.020	-0.004	52.777	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	67	ILE	0	-0.027	-0.001	50.044	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	68	LEU	0	-0.044	-0.022	49.142	-0.005	-0.005	0.000	0.000	0.000	0.000
64	B	69	TYR	0	-0.028	-0.025	47.974	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	70	SER	0	-0.007	0.023	48.195	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	71	THR	0	0.033	0.011	43.756	0.000	0.000	0.000	0.000	0.000	0.000
67	B	72	GLU	-1	-1.009	-0.999	43.184	-0.101	-0.101	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:GLN)