FMO DATABASE

FMODB ID: 394LL

Calculation Name: 5D0O-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0O

Chain ID: C

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-26

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-185609.80682
FMO2-HF: Nuclear repulsion	165421.900992
FMO2-HF: Total energy	-20187.905828
FMO2-MP2: Total energy	-20247.016325

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(C:30:ARG)

Summations of interaction energy for fragment #1(C:30:ARG)

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.
23.163	26.706	0.06	-1.244	-2.36	0.002

Interaction energy analysis for fragmet #1(C:30:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.949 / q_NPA : 0.954

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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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	C	32	LYS	1	1.002	0.998	3.457	29.104	31.147	0.002	-0.856	-1.190	0.001
4	C	33	ARG	1	0.993	0.996	3.150	32.516	33.798	0.059	-0.373	-0.969	0.001
5	C	34	GLN	0	0.020	0.015	5.299	0.905	1.123	-0.001	-0.015	-0.201	0.000
6	C	35	VAL	0	0.004	0.008	7.210	1.828	1.828	0.000	0.000	0.000	0.000
7	C	36	SER	0	-0.038	-0.034	8.535	1.037	1.037	0.000	0.000	0.000	0.000
8	C	37	GLY	0	-0.025	-0.009	8.970	1.084	1.084	0.000	0.000	0.000	0.000
9	C	38	ASP	-1	-0.864	-0.898	10.353	-17.283	-17.283	0.000	0.000	0.000	0.000
10	C	39	GLU	-1	-0.850	-0.916	13.063	-14.018	-14.018	0.000	0.000	0.000	0.000
11	C	40	ALA	0	-0.045	-0.021	13.600	0.895	0.895	0.000	0.000	0.000	0.000
12	C	41	TYR	0	-0.023	-0.004	15.574	-0.156	-0.156	0.000	0.000	0.000	0.000
13	C	42	LEU	0	-0.050	-0.037	15.953	-0.162	-0.162	0.000	0.000	0.000	0.000
14	C	43	GLU	-1	-0.880	-0.926	19.846	-10.969	-10.969	0.000	0.000	0.000	0.000
15	C	44	ALA	0	-0.040	-0.029	21.770	-0.098	-0.098	0.000	0.000	0.000	0.000
16	C	45	ALA	0	-0.016	-0.016	23.890	0.309	0.309	0.000	0.000	0.000	0.000
17	C	46	PRO	0	0.008	0.006	26.666	-0.103	-0.103	0.000	0.000	0.000	0.000
18	C	47	LEU	0	0.003	0.012	27.076	0.030	0.030	0.000	0.000	0.000	0.000
19	C	48	ALA	0	-0.004	-0.012	30.393	0.198	0.198	0.000	0.000	0.000	0.000
20	C	49	GLU	-1	-0.921	-0.949	33.903	-8.059	-8.059	0.000	0.000	0.000	0.000
21	C	50	LEU	0	0.001	0.005	35.190	0.154	0.154	0.000	0.000	0.000	0.000
22	C	51	HIS	0	-0.048	-0.031	37.041	0.217	0.217	0.000	0.000	0.000	0.000
23	C	52	ALA	0	0.026	0.009	40.865	-0.060	-0.060	0.000	0.000	0.000	0.000
24	C	53	PRO	0	-0.014	-0.010	42.334	0.129	0.129	0.000	0.000	0.000	0.000
25	C	54	ALA	0	0.028	0.010	45.579	0.025	0.025	0.000	0.000	0.000	0.000
26	C	55	GLY	0	-0.020	-0.012	49.190	0.005	0.005	0.000	0.000	0.000	0.000
27	C	56	MET	0	-0.051	-0.015	42.235	0.008	0.008	0.000	0.000	0.000	0.000
28	C	57	ILE	0	-0.010	-0.003	43.011	0.043	0.043	0.000	0.000	0.000	0.000
29	C	58	LEU	0	0.005	0.010	37.947	-0.059	-0.059	0.000	0.000	0.000	0.000
30	C	59	PRO	0	-0.008	-0.020	36.217	0.098	0.098	0.000	0.000	0.000	0.000
31	C	60	VAL	0	0.017	0.010	36.645	0.005	0.005	0.000	0.000	0.000	0.000
32	C	61	THR	0	0.041	0.009	35.564	-0.137	-0.137	0.000	0.000	0.000	0.000
33	C	62	SER	0	-0.071	-0.016	31.701	-0.338	-0.338	0.000	0.000	0.000	0.000
34	C	63	GLY	0	0.031	0.012	32.238	0.183	0.183	0.000	0.000	0.000	0.000
35	C	64	ASP	-1	-0.929	-0.969	27.861	-9.206	-9.206	0.000	0.000	0.000	0.000
36	C	65	TYR	0	-0.034	-0.023	22.929	-0.480	-0.480	0.000	0.000	0.000	0.000
37	C	66	ALA	0	-0.006	0.014	27.611	0.015	0.015	0.000	0.000	0.000	0.000
38	C	67	ILE	0	-0.002	-0.006	25.868	-0.186	-0.186	0.000	0.000	0.000	0.000
39	C	68	PRO	0	-0.011	0.004	29.633	0.256	0.256	0.000	0.000	0.000	0.000
40	C	69	VAL	0	0.036	0.009	31.696	-0.176	-0.176	0.000	0.000	0.000	0.000
41	C	70	THR	0	-0.035	-0.026	30.202	0.148	0.148	0.000	0.000	0.000	0.000
42	C	71	ASN	0	-0.024	-0.012	32.891	-0.162	-0.162	0.000	0.000	0.000	0.000
43	C	72	GLY	0	0.015	0.015	34.769	-0.010	-0.010	0.000	0.000	0.000	0.000
44	C	73	SER	0	-0.034	-0.022	32.352	-0.154	-0.154	0.000	0.000	0.000	0.000
45	C	74	GLY	0	0.027	0.010	29.985	0.140	0.140	0.000	0.000	0.000	0.000
46	C	75	ALA	0	-0.021	0.009	26.956	-0.058	-0.058	0.000	0.000	0.000	0.000
47	C	76	VAL	0	0.059	0.018	24.026	-0.197	-0.197	0.000	0.000	0.000	0.000
48	C	77	GLY	0	0.037	-0.003	20.947	-0.021	-0.021	0.000	0.000	0.000	0.000
49	C	78	LYS	1	0.774	0.867	17.109	15.428	15.428	0.000	0.000	0.000	0.000
50	C	79	ALA	0	-0.011	0.010	21.750	0.115	0.115	0.000	0.000	0.000	0.000
51	C	80	LEU	0	-0.071	-0.032	21.991	0.309	0.309	0.000	0.000	0.000	0.000
52	C	81	ASP	-1	-0.758	-0.845	22.596	-11.740	-11.740	0.000	0.000	0.000	0.000
53	C	82	ILE	0	-0.022	-0.010	17.382	0.203	0.203	0.000	0.000	0.000	0.000
54	C	83	ARG	1	0.809	0.873	20.772	10.668	10.668	0.000	0.000	0.000	0.000
55	C	84	PRO	0	0.022	0.005	21.123	0.337	0.337	0.000	0.000	0.000	0.000
56	C	85	PRO	0	-0.062	-0.017	23.838	0.603	0.603	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:30:ARG)