FMO DATABASE

FMODB ID: N97KQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-185761.270254
FMO2-HF: Nuclear repulsion	165573.755019
FMO2-HF: Total energy	-20187.515235
FMO2-MP2: Total energy	-20246.664341

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.
26.261	31.538	1.046	-2.297	-4.027	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 : 0.955 / q_NPA : 0.962

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	1.017	1.004	3.031	29.394	32.490	0.050	-1.323	-1.823	0.002
4	C	33	ARG	1	0.972	0.984	2.416	33.901	36.082	0.996	-0.974	-2.204	0.000
5	C	34	GLN	0	0.022	0.016	4.865	3.373	3.373	0.000	0.000	0.000	0.000
6	C	35	VAL	0	0.027	0.036	6.690	1.651	1.651	0.000	0.000	0.000	0.000
7	C	36	SER	0	-0.055	-0.035	8.263	1.776	1.776	0.000	0.000	0.000	0.000
8	C	37	GLY	0	-0.055	-0.035	8.495	1.023	1.023	0.000	0.000	0.000	0.000
9	C	38	ASP	-1	-0.936	-0.945	9.996	-18.180	-18.180	0.000	0.000	0.000	0.000
10	C	39	GLU	-1	-0.872	-0.950	12.316	-13.738	-13.738	0.000	0.000	0.000	0.000
11	C	40	ALA	0	-0.096	-0.038	13.441	0.892	0.892	0.000	0.000	0.000	0.000
12	C	41	TYR	0	0.031	0.012	15.418	-0.215	-0.215	0.000	0.000	0.000	0.000
13	C	42	LEU	0	-0.074	-0.055	15.412	-0.147	-0.147	0.000	0.000	0.000	0.000
14	C	43	GLU	-1	-0.881	-0.929	19.451	-10.828	-10.828	0.000	0.000	0.000	0.000
15	C	44	ALA	0	-0.040	-0.015	21.022	0.067	0.067	0.000	0.000	0.000	0.000
16	C	45	ALA	0	-0.020	-0.021	23.120	0.293	0.293	0.000	0.000	0.000	0.000
17	C	46	PRO	0	0.017	0.011	25.957	-0.079	-0.079	0.000	0.000	0.000	0.000
18	C	47	LEU	0	-0.002	0.006	26.685	-0.019	-0.019	0.000	0.000	0.000	0.000
19	C	48	ALA	0	-0.015	-0.006	30.055	0.214	0.214	0.000	0.000	0.000	0.000
20	C	49	GLU	-1	-0.916	-0.955	33.429	-8.032	-8.032	0.000	0.000	0.000	0.000
21	C	50	LEU	0	-0.016	-0.006	34.022	0.115	0.115	0.000	0.000	0.000	0.000
22	C	51	HIS	0	-0.040	-0.024	36.917	0.196	0.196	0.000	0.000	0.000	0.000
23	C	52	ALA	0	0.036	0.010	40.324	-0.095	-0.095	0.000	0.000	0.000	0.000
24	C	53	PRO	0	-0.014	-0.007	42.247	0.130	0.130	0.000	0.000	0.000	0.000
25	C	54	ALA	0	0.025	0.014	45.521	0.012	0.012	0.000	0.000	0.000	0.000
26	C	55	GLY	0	-0.018	-0.009	49.002	0.013	0.013	0.000	0.000	0.000	0.000
27	C	56	MET	0	-0.048	-0.026	42.774	-0.014	-0.014	0.000	0.000	0.000	0.000
28	C	57	ILE	0	-0.010	0.000	42.352	0.052	0.052	0.000	0.000	0.000	0.000
29	C	58	LEU	0	-0.007	0.008	37.538	-0.064	-0.064	0.000	0.000	0.000	0.000
30	C	59	PRO	0	0.004	-0.012	36.272	0.093	0.093	0.000	0.000	0.000	0.000
31	C	60	VAL	0	0.015	0.012	36.163	0.029	0.029	0.000	0.000	0.000	0.000
32	C	61	THR	0	0.050	0.019	35.132	-0.151	-0.151	0.000	0.000	0.000	0.000
33	C	62	SER	0	-0.056	-0.006	31.441	-0.354	-0.354	0.000	0.000	0.000	0.000
34	C	63	GLY	0	-0.004	-0.019	32.356	0.079	0.079	0.000	0.000	0.000	0.000
35	C	64	ASP	-1	-0.926	-0.955	27.680	-9.212	-9.212	0.000	0.000	0.000	0.000
36	C	65	TYR	0	-0.047	-0.032	22.638	-0.397	-0.397	0.000	0.000	0.000	0.000
37	C	66	ALA	0	0.014	0.008	27.089	0.171	0.171	0.000	0.000	0.000	0.000
38	C	67	ILE	0	-0.021	-0.009	25.328	-0.091	-0.091	0.000	0.000	0.000	0.000
39	C	68	PRO	0	0.001	0.016	29.189	0.235	0.235	0.000	0.000	0.000	0.000
40	C	69	VAL	0	0.038	0.010	31.299	-0.181	-0.181	0.000	0.000	0.000	0.000
41	C	70	THR	0	-0.048	-0.034	30.474	0.124	0.124	0.000	0.000	0.000	0.000
42	C	71	ASN	0	0.010	0.013	32.758	-0.166	-0.166	0.000	0.000	0.000	0.000
43	C	72	GLY	0	-0.005	-0.001	34.047	-0.100	-0.100	0.000	0.000	0.000	0.000
44	C	73	SER	0	-0.024	-0.017	31.790	-0.224	-0.224	0.000	0.000	0.000	0.000
45	C	74	GLY	0	0.031	0.022	29.315	0.149	0.149	0.000	0.000	0.000	0.000
46	C	75	ALA	0	-0.007	-0.002	26.917	-0.044	-0.044	0.000	0.000	0.000	0.000
47	C	76	VAL	0	0.059	0.013	24.087	-0.222	-0.222	0.000	0.000	0.000	0.000
48	C	77	GLY	0	0.033	0.012	20.601	0.053	0.053	0.000	0.000	0.000	0.000
49	C	78	LYS	1	0.906	0.968	17.865	14.571	14.571	0.000	0.000	0.000	0.000
50	C	79	ALA	0	-0.025	-0.010	21.520	0.150	0.150	0.000	0.000	0.000	0.000
51	C	80	LEU	0	-0.077	-0.033	22.126	0.303	0.303	0.000	0.000	0.000	0.000
52	C	81	ASP	-1	-0.815	-0.917	22.456	-11.844	-11.844	0.000	0.000	0.000	0.000
53	C	82	ILE	0	-0.028	-0.011	16.820	0.214	0.214	0.000	0.000	0.000	0.000
54	C	83	ARG	1	0.867	0.942	20.601	10.765	10.765	0.000	0.000	0.000	0.000
55	C	84	PRO	0	-0.013	-0.004	21.311	0.270	0.270	0.000	0.000	0.000	0.000
56	C	85	PRO	0	-0.011	0.001	23.709	0.350	0.350	0.000	0.000	0.000	0.000

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