FMO DATABASE

FMODB ID: M3K9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-390214.213031
FMO2-HF: Nuclear repulsion	361210.657607
FMO2-HF: Total energy	-29003.555425
FMO2-MP2: Total energy	-29088.268917

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.
1.393	4.25	-0.003	-1.387	-1.468	0.005

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 : 0.037 / q_NPA : 0.017

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	847	PHE	0	-0.025	-0.022	3.313	-0.028	2.584	-0.002	-1.244	-1.366	0.005
4	A	848	VAL	0	0.014	0.004	5.993	-0.027	-0.027	0.000	0.000	0.000	0.000
5	A	849	LYS	1	0.938	0.982	9.573	0.786	0.786	0.000	0.000	0.000	0.000
6	A	850	ASN	0	-0.011	-0.011	11.394	0.051	0.051	0.000	0.000	0.000	0.000
7	A	851	VAL	0	0.029	0.023	14.677	0.003	0.003	0.000	0.000	0.000	0.000
8	A	852	GLY	0	0.016	0.007	17.086	0.003	0.003	0.000	0.000	0.000	0.000
9	A	853	TRP	0	-0.020	-0.004	20.838	0.002	0.002	0.000	0.000	0.000	0.000
10	A	854	ALA	0	-0.007	0.002	23.687	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	855	THR	0	-0.003	-0.007	26.789	0.007	0.007	0.000	0.000	0.000	0.000
12	A	856	GLN	0	0.022	0.006	29.325	0.004	0.004	0.000	0.000	0.000	0.000
13	A	857	LEU	0	-0.015	0.013	33.003	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	858	THR	0	0.021	0.000	32.982	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	859	SER	0	0.029	0.021	30.178	0.004	0.004	0.000	0.000	0.000	0.000
16	A	860	GLY	0	0.011	0.003	27.659	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	861	ALA	0	-0.018	0.006	25.206	0.010	0.010	0.000	0.000	0.000	0.000
18	A	862	VAL	0	0.003	-0.004	19.086	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	863	TRP	0	-0.029	-0.025	18.166	0.006	0.006	0.000	0.000	0.000	0.000
20	A	864	VAL	0	0.015	0.002	13.323	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	865	GLN	0	0.004	0.012	13.333	0.042	0.042	0.000	0.000	0.000	0.000
22	A	866	PHE	0	0.036	0.008	8.656	-0.040	-0.040	0.000	0.000	0.000	0.000
23	A	867	ASN	0	-0.023	-0.017	3.698	1.084	1.329	-0.001	-0.143	-0.102	0.000
24	A	868	ASP	-1	-0.825	-0.880	6.928	-0.886	-0.886	0.000	0.000	0.000	0.000
25	A	869	GLY	0	-0.028	-0.006	8.372	0.273	0.273	0.000	0.000	0.000	0.000
26	A	870	SER	0	-0.071	-0.051	10.824	0.217	0.217	0.000	0.000	0.000	0.000
27	A	871	GLN	0	0.023	-0.019	13.207	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	872	LEU	0	-0.004	0.019	14.200	0.059	0.059	0.000	0.000	0.000	0.000
29	A	873	VAL	0	0.008	-0.004	17.419	-0.030	-0.030	0.000	0.000	0.000	0.000
30	A	874	MET	0	-0.036	-0.015	17.849	0.034	0.034	0.000	0.000	0.000	0.000
31	A	875	GLN	0	0.000	0.002	22.299	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	876	ALA	0	-0.005	-0.005	24.443	0.011	0.011	0.000	0.000	0.000	0.000
33	A	877	GLY	0	0.044	0.003	26.503	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	878	VAL	0	-0.053	-0.015	29.244	0.003	0.003	0.000	0.000	0.000	0.000
35	A	879	SER	0	0.056	0.033	31.001	0.001	0.001	0.000	0.000	0.000	0.000
36	A	880	SER	0	-0.066	-0.043	32.907	0.005	0.005	0.000	0.000	0.000	0.000
37	A	881	ILE	0	0.006	0.014	33.564	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	882	SER	0	0.030	0.014	35.549	0.005	0.005	0.000	0.000	0.000	0.000
39	A	883	TYR	0	0.018	0.009	36.782	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	884	THR	0	0.040	0.021	39.254	0.004	0.004	0.000	0.000	0.000	0.000
41	A	885	SER	0	-0.055	-0.044	40.933	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	886	PRO	0	-0.007	-0.021	43.715	0.000	0.000	0.000	0.000	0.000	0.000
43	A	887	ASP	-1	-0.878	-0.916	44.786	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	888	GLY	0	0.005	0.010	44.258	0.002	0.002	0.000	0.000	0.000	0.000
45	A	889	GLN	0	-0.012	0.016	44.756	0.002	0.002	0.000	0.000	0.000	0.000
46	A	890	THR	0	-0.016	-0.032	39.898	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	891	THR	0	-0.047	-0.018	42.083	0.003	0.003	0.000	0.000	0.000	0.000
48	A	892	ARG	1	0.843	0.916	38.104	0.014	0.014	0.000	0.000	0.000	0.000
49	A	893	TYR	0	-0.020	-0.022	39.200	0.001	0.001	0.000	0.000	0.000	0.000
50	A	894	GLY	0	0.009	-0.012	38.120	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	895	GLU	-1	-0.911	-0.959	34.182	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	896	ASN	0	-0.056	-0.023	37.592	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	897	GLU	-1	-0.798	-0.877	41.017	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	898	LYS	1	0.970	0.985	41.996	0.030	0.030	0.000	0.000	0.000	0.000
55	A	899	LEU	0	0.035	0.014	38.394	0.001	0.001	0.000	0.000	0.000	0.000
56	A	900	PRO	0	-0.010	0.004	43.087	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	901	GLU	-1	-0.766	-0.898	44.033	-0.046	-0.046	0.000	0.000	0.000	0.000
58	A	902	TYR	0	0.025	0.016	44.139	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	903	ILE	0	-0.006	0.003	39.363	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	904	LYS	1	0.833	0.907	39.749	0.041	0.041	0.000	0.000	0.000	0.000
61	A	905	GLN	0	-0.007	-0.011	39.694	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	906	LYS	1	0.939	0.961	38.655	0.050	0.050	0.000	0.000	0.000	0.000
63	A	907	LEU	0	0.000	0.003	34.567	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	908	GLN	0	-0.018	-0.011	35.077	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	909	LEU	0	-0.055	-0.015	36.178	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	910	LEU	0	-0.023	-0.017	31.257	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	911	SER	0	-0.064	-0.031	30.902	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	912	SER	0	0.007	0.008	28.564	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	913	ILE	0	0.006	-0.004	26.933	0.001	0.001	0.000	0.000	0.000	0.000
70	A	914	LEU	0	-0.035	0.008	21.038	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	915	LEU	0	0.002	-0.009	21.583	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	916	MET	0	-0.005	0.002	17.222	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	917	PHE	0	0.015	-0.008	16.448	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	918	SER	0	-0.022	-0.009	12.308	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	919	ASN	0	-0.024	-0.008	14.524	0.018	0.018	0.000	0.000	0.000	0.000

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