FMO DATABASE

FMODB ID: 7G8MK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-390776.120306
FMO2-HF: Nuclear repulsion	361772.407305
FMO2-HF: Total energy	-29003.713001
FMO2-MP2: Total energy	-29088.390809

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.
1.283	3.955	0.012	-1.35	-1.334	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 : 0.043 / q_NPA : 0.021

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	-0.019	-0.022	3.431	-0.140	2.317	0.013	-1.212	-1.258	0.004
4	A	848	VAL	0	0.010	0.007	5.936	-0.037	-0.037	0.000	0.000	0.000	0.000
5	A	849	LYS	1	0.925	0.975	9.708	0.761	0.761	0.000	0.000	0.000	0.000
6	A	850	ASN	0	-0.005	-0.012	11.386	0.031	0.031	0.000	0.000	0.000	0.000
7	A	851	VAL	0	0.021	0.012	14.858	0.007	0.007	0.000	0.000	0.000	0.000
8	A	852	GLY	0	0.020	0.005	17.217	0.000	0.000	0.000	0.000	0.000	0.000
9	A	853	TRP	0	-0.041	-0.021	20.998	0.003	0.003	0.000	0.000	0.000	0.000
10	A	854	ALA	0	-0.003	0.000	23.918	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	855	THR	0	-0.011	-0.005	26.896	0.005	0.005	0.000	0.000	0.000	0.000
12	A	856	GLN	0	0.006	-0.003	29.401	0.003	0.003	0.000	0.000	0.000	0.000
13	A	857	LEU	0	-0.026	-0.009	32.800	0.000	0.000	0.000	0.000	0.000	0.000
14	A	858	THR	0	0.022	-0.004	33.309	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	859	SER	0	0.019	0.010	30.287	0.003	0.003	0.000	0.000	0.000	0.000
16	A	860	GLY	0	0.027	0.009	27.925	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	861	ALA	0	-0.023	0.001	25.467	0.010	0.010	0.000	0.000	0.000	0.000
18	A	862	VAL	0	0.005	-0.004	19.274	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	863	TRP	0	-0.039	-0.023	18.320	0.006	0.006	0.000	0.000	0.000	0.000
20	A	864	VAL	0	0.019	0.004	13.316	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	865	GLN	0	-0.027	-0.004	13.618	0.046	0.046	0.000	0.000	0.000	0.000
22	A	866	PHE	0	0.037	0.020	8.421	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	867	ASN	0	-0.013	-0.019	4.022	1.052	1.267	-0.001	-0.138	-0.076	0.000
24	A	868	ASP	-1	-0.823	-0.883	7.218	-0.806	-0.806	0.000	0.000	0.000	0.000
25	A	869	GLY	0	-0.025	-0.001	8.656	0.254	0.254	0.000	0.000	0.000	0.000
26	A	870	SER	0	-0.045	-0.039	10.601	0.203	0.203	0.000	0.000	0.000	0.000
27	A	871	GLN	0	0.020	-0.013	13.186	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	872	LEU	0	-0.007	0.006	13.988	0.058	0.058	0.000	0.000	0.000	0.000
29	A	873	VAL	0	0.011	-0.002	17.420	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	874	MET	0	-0.030	-0.007	17.642	0.033	0.033	0.000	0.000	0.000	0.000
31	A	875	GLN	0	-0.007	-0.013	22.367	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	876	ALA	0	0.002	0.008	24.680	0.010	0.010	0.000	0.000	0.000	0.000
33	A	877	GLY	0	0.045	0.012	26.722	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	878	VAL	0	-0.035	-0.010	29.074	0.002	0.002	0.000	0.000	0.000	0.000
35	A	879	SER	0	0.057	0.031	31.071	0.000	0.000	0.000	0.000	0.000	0.000
36	A	880	SER	0	-0.058	-0.034	33.014	0.004	0.004	0.000	0.000	0.000	0.000
37	A	881	ILE	0	0.004	0.008	33.514	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	882	SER	0	0.029	0.004	35.500	0.005	0.005	0.000	0.000	0.000	0.000
39	A	883	TYR	0	0.038	0.020	37.095	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	884	THR	0	0.030	0.018	38.977	0.004	0.004	0.000	0.000	0.000	0.000
41	A	885	SER	0	-0.054	-0.037	40.863	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	886	PRO	0	-0.028	-0.034	43.779	0.001	0.001	0.000	0.000	0.000	0.000
43	A	887	ASP	-1	-0.849	-0.898	44.923	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	888	GLY	0	0.003	0.007	44.435	0.002	0.002	0.000	0.000	0.000	0.000
45	A	889	GLN	0	-0.007	0.004	44.477	0.002	0.002	0.000	0.000	0.000	0.000
46	A	890	THR	0	-0.028	-0.025	39.751	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	891	THR	0	-0.043	-0.014	42.141	0.003	0.003	0.000	0.000	0.000	0.000
48	A	892	ARG	1	0.796	0.859	38.266	0.011	0.011	0.000	0.000	0.000	0.000
49	A	893	TYR	0	0.000	-0.005	39.208	0.002	0.002	0.000	0.000	0.000	0.000
50	A	894	GLY	0	0.024	-0.002	37.671	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	895	GLU	-1	-0.928	-0.971	33.383	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	896	ASN	0	-0.046	-0.012	37.328	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	897	GLU	-1	-0.779	-0.846	40.847	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	898	LYS	1	0.862	0.927	42.007	0.028	0.028	0.000	0.000	0.000	0.000
55	A	899	LEU	0	0.052	0.028	38.031	0.000	0.000	0.000	0.000	0.000	0.000
56	A	900	PRO	0	0.009	0.014	42.732	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	901	GLU	-1	-0.735	-0.874	43.771	-0.040	-0.040	0.000	0.000	0.000	0.000
58	A	902	TYR	0	0.027	0.016	44.070	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	903	ILE	0	-0.023	-0.002	39.080	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	904	LYS	1	0.838	0.908	39.687	0.036	0.036	0.000	0.000	0.000	0.000
61	A	905	GLN	0	0.005	-0.010	39.671	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	906	LYS	1	0.929	0.958	38.591	0.045	0.045	0.000	0.000	0.000	0.000
63	A	907	LEU	0	0.002	0.006	34.427	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	908	GLN	0	-0.015	-0.007	35.062	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	909	LEU	0	-0.036	-0.013	36.012	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	910	LEU	0	-0.011	0.003	31.118	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	911	SER	0	-0.040	0.000	30.892	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	912	SER	0	-0.014	0.002	28.633	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	913	ILE	0	0.016	-0.002	27.448	0.002	0.002	0.000	0.000	0.000	0.000
70	A	914	LEU	0	-0.025	0.009	21.313	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	915	LEU	0	-0.003	-0.011	21.743	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	916	MET	0	0.001	0.006	17.176	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	917	PHE	0	0.018	-0.003	16.505	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	918	SER	0	-0.014	-0.011	12.363	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	919	ASN	0	-0.032	-0.007	14.645	0.020	0.020	0.000	0.000	0.000	0.000

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