FMO DATABASE

FMODB ID: JLRN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-185682.097135
FMO2-HF: Nuclear repulsion	165494.366243
FMO2-HF: Total energy	-20187.730891
FMO2-MP2: Total energy	-20246.860962

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.
24.632	29.623	0.329	-1.919	-3.403	0.006

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 : 0.942 / q_NPA : 0.957

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	C	32	LYS	1	1.012	1.004	2.971	29.260	32.237	0.048	-1.283	-1.742	0.003
4	C	33	ARG	1	0.989	0.993	2.833	32.930	34.944	0.281	-0.636	-1.661	0.003
5	C	34	GLN	0	0.008	0.015	4.849	2.781	2.781	0.000	0.000	0.000	0.000
6	C	35	VAL	0	0.011	0.019	6.682	1.626	1.626	0.000	0.000	0.000	0.000
7	C	36	SER	0	-0.032	-0.023	8.256	1.091	1.091	0.000	0.000	0.000	0.000
8	C	37	GLY	0	-0.047	-0.031	8.465	1.054	1.054	0.000	0.000	0.000	0.000
9	C	38	ASP	-1	-0.910	-0.937	9.976	-17.753	-17.753	0.000	0.000	0.000	0.000
10	C	39	GLU	-1	-0.836	-0.904	12.301	-13.614	-13.614	0.000	0.000	0.000	0.000
11	C	40	ALA	0	-0.077	-0.030	13.404	0.883	0.883	0.000	0.000	0.000	0.000
12	C	41	TYR	0	0.011	0.002	15.415	-0.218	-0.218	0.000	0.000	0.000	0.000
13	C	42	LEU	0	-0.061	-0.046	15.559	-0.163	-0.163	0.000	0.000	0.000	0.000
14	C	43	GLU	-1	-0.890	-0.933	19.451	-10.800	-10.800	0.000	0.000	0.000	0.000
15	C	44	ALA	0	-0.045	-0.019	20.984	0.057	0.057	0.000	0.000	0.000	0.000
16	C	45	ALA	0	-0.018	-0.018	23.120	0.297	0.297	0.000	0.000	0.000	0.000
17	C	46	PRO	0	0.023	0.013	25.957	-0.079	-0.079	0.000	0.000	0.000	0.000
18	C	47	LEU	0	-0.006	0.004	26.515	-0.026	-0.026	0.000	0.000	0.000	0.000
19	C	48	ALA	0	-0.018	-0.008	30.055	0.220	0.220	0.000	0.000	0.000	0.000
20	C	49	GLU	-1	-0.904	-0.948	33.429	-8.111	-8.111	0.000	0.000	0.000	0.000
21	C	50	LEU	0	-0.029	-0.010	35.013	0.117	0.117	0.000	0.000	0.000	0.000
22	C	51	HIS	0	-0.040	-0.026	36.919	0.221	0.221	0.000	0.000	0.000	0.000
23	C	52	ALA	0	0.038	0.010	40.343	-0.095	-0.095	0.000	0.000	0.000	0.000
24	C	53	PRO	0	-0.012	-0.006	42.276	0.129	0.129	0.000	0.000	0.000	0.000
25	C	54	ALA	0	0.020	0.012	45.538	0.014	0.014	0.000	0.000	0.000	0.000
26	C	55	GLY	0	-0.014	-0.009	49.019	0.012	0.012	0.000	0.000	0.000	0.000
27	C	56	MET	0	-0.044	-0.023	42.450	-0.014	-0.014	0.000	0.000	0.000	0.000
28	C	57	ILE	0	-0.016	-0.005	42.595	0.049	0.049	0.000	0.000	0.000	0.000
29	C	58	LEU	0	0.005	0.015	37.386	-0.063	-0.063	0.000	0.000	0.000	0.000
30	C	59	PRO	0	0.000	-0.013	36.282	0.093	0.093	0.000	0.000	0.000	0.000
31	C	60	VAL	0	0.012	0.009	36.170	0.029	0.029	0.000	0.000	0.000	0.000
32	C	61	THR	0	0.047	0.015	35.151	-0.147	-0.147	0.000	0.000	0.000	0.000
33	C	62	SER	0	-0.065	-0.003	31.464	-0.348	-0.348	0.000	0.000	0.000	0.000
34	C	63	GLY	0	0.003	-0.019	32.425	0.076	0.076	0.000	0.000	0.000	0.000
35	C	64	ASP	-1	-0.925	-0.955	27.633	-9.248	-9.248	0.000	0.000	0.000	0.000
36	C	65	TYR	0	-0.045	-0.032	22.357	-0.399	-0.399	0.000	0.000	0.000	0.000
37	C	66	ALA	0	0.012	0.007	27.119	0.171	0.171	0.000	0.000	0.000	0.000
38	C	67	ILE	0	-0.018	-0.008	25.216	-0.085	-0.085	0.000	0.000	0.000	0.000
39	C	68	PRO	0	0.005	0.014	29.224	0.229	0.229	0.000	0.000	0.000	0.000
40	C	69	VAL	0	0.033	0.009	31.299	-0.173	-0.173	0.000	0.000	0.000	0.000
41	C	70	THR	0	-0.046	-0.020	30.400	0.142	0.142	0.000	0.000	0.000	0.000
42	C	71	ASN	0	0.001	-0.004	32.718	-0.144	-0.144	0.000	0.000	0.000	0.000
43	C	72	GLY	0	0.000	0.006	34.011	-0.101	-0.101	0.000	0.000	0.000	0.000
44	C	73	SER	0	-0.018	-0.015	31.758	-0.230	-0.230	0.000	0.000	0.000	0.000
45	C	74	GLY	0	0.027	0.022	29.283	0.154	0.154	0.000	0.000	0.000	0.000
46	C	75	ALA	0	-0.009	-0.005	27.037	-0.052	-0.052	0.000	0.000	0.000	0.000
47	C	76	VAL	0	0.055	0.011	24.046	-0.220	-0.220	0.000	0.000	0.000	0.000
48	C	77	GLY	0	0.035	0.014	20.570	0.053	0.053	0.000	0.000	0.000	0.000
49	C	78	LYS	1	0.840	0.911	17.560	14.776	14.776	0.000	0.000	0.000	0.000
50	C	79	ALA	0	-0.028	-0.014	21.496	0.160	0.160	0.000	0.000	0.000	0.000
51	C	80	LEU	0	-0.073	-0.028	21.971	0.308	0.308	0.000	0.000	0.000	0.000
52	C	81	ASP	-1	-0.785	-0.869	22.434	-11.758	-11.758	0.000	0.000	0.000	0.000
53	C	82	ILE	0	-0.020	-0.009	16.950	0.222	0.222	0.000	0.000	0.000	0.000
54	C	83	ARG	1	0.830	0.891	20.586	10.672	10.672	0.000	0.000	0.000	0.000
55	C	84	PRO	0	-0.010	-0.011	21.165	0.301	0.301	0.000	0.000	0.000	0.000
56	C	85	PRO	0	-0.014	0.007	23.700	0.346	0.346	0.000	0.000	0.000	0.000

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