FMO DATABASE

FMODB ID: 9G5M2

Calculation Name: 1MBY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MBY

Chain ID: A

ChEMBL ID:

UniProt ID: Q64702

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-390381.603095
FMO2-HF: Nuclear repulsion	361378.317563
FMO2-HF: Total energy	-29003.285532
FMO2-MP2: Total energy	-29088.056597

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:845:SER)

Summations of interaction energy for fragment #1(A:845:SER)

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.
1.571	4.111	-0.001	-1.208	-1.33	0.004

Interaction energy analysis for fragmet #1(A:845:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.011

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	847	PHE	0	-0.029	-0.024	3.231	0.287	2.693	0.000	-1.142	-1.264	0.004
4	A	848	VAL	0	0.015	0.005	5.716	0.022	0.022	0.000	0.000	0.000	0.000
5	A	849	LYS	1	0.938	0.981	9.360	0.886	0.886	0.000	0.000	0.000	0.000
6	A	850	ASN	0	0.000	-0.008	11.200	0.074	0.074	0.000	0.000	0.000	0.000
7	A	851	VAL	0	0.020	0.017	14.407	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	852	GLY	0	0.008	0.006	16.829	0.010	0.010	0.000	0.000	0.000	0.000
9	A	853	TRP	0	-0.023	-0.011	20.578	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	854	ALA	0	-0.007	-0.001	23.409	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	855	THR	0	-0.010	-0.008	26.772	0.005	0.005	0.000	0.000	0.000	0.000
12	A	856	GLN	0	0.026	0.009	29.242	0.004	0.004	0.000	0.000	0.000	0.000
13	A	857	LEU	0	-0.015	0.009	32.969	0.000	0.000	0.000	0.000	0.000	0.000
14	A	858	THR	0	0.017	0.002	33.377	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	859	SER	0	0.017	0.014	30.503	0.003	0.003	0.000	0.000	0.000	0.000
16	A	860	GLY	0	0.018	0.005	27.743	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	861	ALA	0	-0.017	0.006	25.326	0.009	0.009	0.000	0.000	0.000	0.000
18	A	862	VAL	0	0.012	0.003	18.982	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	863	TRP	0	-0.030	-0.028	17.834	0.002	0.002	0.000	0.000	0.000	0.000
20	A	864	VAL	0	0.017	0.000	13.126	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	865	GLN	0	0.013	0.018	13.253	0.045	0.045	0.000	0.000	0.000	0.000
22	A	866	PHE	0	0.033	0.007	8.618	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	867	ASN	0	-0.016	-0.006	3.688	0.963	1.097	-0.001	-0.066	-0.066	0.000
24	A	868	ASP	-1	-0.831	-0.872	7.046	-1.119	-1.119	0.000	0.000	0.000	0.000
25	A	869	GLY	0	-0.028	-0.009	8.526	0.307	0.307	0.000	0.000	0.000	0.000
26	A	870	SER	0	-0.069	-0.061	10.811	0.248	0.248	0.000	0.000	0.000	0.000
27	A	871	GLN	0	0.012	-0.026	13.346	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	872	LEU	0	-0.004	0.019	14.425	0.062	0.062	0.000	0.000	0.000	0.000
29	A	873	VAL	0	0.011	0.000	17.419	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	874	MET	0	-0.037	-0.019	18.788	0.030	0.030	0.000	0.000	0.000	0.000
31	A	875	GLN	0	-0.003	0.003	22.617	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	876	ALA	0	-0.001	-0.001	24.898	0.011	0.011	0.000	0.000	0.000	0.000
33	A	877	GLY	0	0.039	0.000	26.932	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	878	VAL	0	-0.047	-0.010	29.735	0.004	0.004	0.000	0.000	0.000	0.000
35	A	879	SER	0	0.066	0.040	31.293	0.001	0.001	0.000	0.000	0.000	0.000
36	A	880	SER	0	-0.116	-0.068	33.456	0.006	0.006	0.000	0.000	0.000	0.000
37	A	881	ILE	0	0.030	0.021	34.101	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	882	SER	0	0.025	0.013	36.083	0.005	0.005	0.000	0.000	0.000	0.000
39	A	883	TYR	0	0.008	-0.007	37.306	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	884	THR	0	0.019	0.004	39.764	0.003	0.003	0.000	0.000	0.000	0.000
41	A	885	SER	0	-0.019	-0.002	41.443	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	886	PRO	0	-0.014	-0.025	44.221	0.000	0.000	0.000	0.000	0.000	0.000
43	A	887	ASP	-1	-0.920	-0.964	45.299	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	888	GLY	0	0.019	0.015	44.737	0.002	0.002	0.000	0.000	0.000	0.000
45	A	889	GLN	0	-0.020	0.006	45.228	0.002	0.002	0.000	0.000	0.000	0.000
46	A	890	THR	0	0.006	-0.003	40.401	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	891	THR	0	-0.040	-0.011	42.589	0.003	0.003	0.000	0.000	0.000	0.000
48	A	892	ARG	1	0.951	0.970	37.493	0.016	0.016	0.000	0.000	0.000	0.000
49	A	893	TYR	0	-0.003	-0.008	39.733	0.001	0.001	0.000	0.000	0.000	0.000
50	A	894	GLY	0	-0.047	-0.045	38.642	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	895	GLU	-1	-0.888	-0.949	34.537	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	896	ASN	0	-0.049	-0.020	38.086	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	897	GLU	-1	-0.863	-0.909	41.483	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	898	LYS	1	0.939	0.968	42.528	0.033	0.033	0.000	0.000	0.000	0.000
55	A	899	LEU	0	0.033	0.016	38.891	0.001	0.001	0.000	0.000	0.000	0.000
56	A	900	PRO	0	-0.004	0.005	43.618	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	901	GLU	-1	-0.826	-0.951	44.453	-0.054	-0.054	0.000	0.000	0.000	0.000
58	A	902	TYR	0	0.012	0.010	44.546	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	903	ILE	0	-0.002	0.006	39.902	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	904	LYS	1	0.898	0.962	40.110	0.046	0.046	0.000	0.000	0.000	0.000
61	A	905	GLN	0	0.004	-0.005	39.884	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	906	LYS	1	0.950	0.974	38.915	0.050	0.050	0.000	0.000	0.000	0.000
63	A	907	LEU	0	-0.012	0.001	34.970	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	908	GLN	0	0.000	-0.012	35.222	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	909	LEU	0	-0.054	-0.011	36.113	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	910	LEU	0	-0.027	-0.019	31.073	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	911	SER	0	-0.065	-0.024	30.884	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	912	SER	0	0.006	0.010	28.109	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	913	ILE	0	0.031	0.015	26.724	0.000	0.000	0.000	0.000	0.000	0.000
70	A	914	LEU	0	-0.033	0.007	20.584	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	915	LEU	0	-0.009	-0.015	21.354	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	916	MET	0	0.000	0.005	16.863	0.004	0.004	0.000	0.000	0.000	0.000
73	A	917	PHE	0	0.013	-0.010	16.276	-0.033	-0.033	0.000	0.000	0.000	0.000
74	A	918	SER	0	-0.026	-0.010	12.158	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	919	ASN	0	-0.024	-0.008	14.408	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:845:SER)