FMO DATABASE

FMODB ID: 7274K

Calculation Name: 5G4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5G4D

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTB8

Base Structure: X-ray

Registration Date: 2023-09-19

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-536417.839855
FMO2-HF: Nuclear repulsion	503583.039529
FMO2-HF: Total energy	-32834.800325
FMO2-MP2: Total energy	-32929.599854

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:-2:ALA)

Summations of interaction energy for fragment #1(A:-2:ALA)

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.
-11.401	-8.289	11.524	-5.257	-9.378	-0.029

Interaction energy analysis for fragmet #1(A:-2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.000

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	0	ASP	-1	-0.800	-0.879	3.813	-2.273	-0.640	-0.009	-0.741	-0.883	0.004
4	A	1	MET	0	-0.039	-0.026	2.347	0.155	0.254	1.091	-0.202	-0.989	-0.001
5	A	2	TYR	0	-0.033	-0.069	2.103	0.443	-0.137	4.069	-0.741	-2.748	-0.010
6	A	3	VAL	0	-0.023	-0.006	3.772	-0.722	-0.697	0.024	0.044	-0.094	0.000
7	A	4	VAL	0	0.015	0.000	7.517	0.220	0.220	0.000	0.000	0.000	0.000
8	A	5	ILE	0	-0.049	-0.022	10.459	-0.124	-0.124	0.000	0.000	0.000	0.000
9	A	6	VAL	0	0.024	0.009	13.635	0.026	0.026	0.000	0.000	0.000	0.000
10	A	7	TYR	0	-0.042	-0.028	17.107	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	8	ASP	-1	-0.903	-0.936	20.289	0.161	0.161	0.000	0.000	0.000	0.000
12	A	9	VAL	0	-0.031	-0.019	23.036	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.096	0.055	25.849	0.006	0.006	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.008	-0.012	28.899	0.002	0.002	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.914	-0.963	30.671	0.057	0.057	0.000	0.000	0.000	0.000
16	A	13	ARG	1	0.784	0.874	27.054	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	14	VAL	0	0.020	0.033	24.481	0.002	0.002	0.000	0.000	0.000	0.000
18	A	15	ASN	0	-0.023	-0.038	24.109	0.021	0.021	0.000	0.000	0.000	0.000
19	A	16	ARG	1	0.950	0.972	24.498	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	17	VAL	0	0.109	0.076	19.888	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.956	0.994	19.806	-0.133	-0.133	0.000	0.000	0.000	0.000
22	A	19	LYS	1	0.845	0.905	19.567	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	20	PHE	0	-0.015	0.000	16.590	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	21	LEU	0	0.087	0.041	14.347	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.944	0.972	14.755	-0.135	-0.135	0.000	0.000	0.000	0.000
26	A	23	ARG	1	0.832	0.929	15.943	0.006	0.006	0.000	0.000	0.000	0.000
27	A	24	HIS	1	0.796	0.882	12.005	0.057	0.057	0.000	0.000	0.000	0.000
28	A	25	LEU	0	-0.010	0.018	8.733	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	26	HIS	0	0.028	0.018	8.929	-0.151	-0.151	0.000	0.000	0.000	0.000
30	A	27	TRP	0	-0.052	-0.022	12.506	0.033	0.033	0.000	0.000	0.000	0.000
31	A	28	VAL	0	-0.021	-0.002	13.142	0.010	0.010	0.000	0.000	0.000	0.000
32	A	29	GLN	0	0.020	-0.009	16.026	-0.045	-0.045	0.000	0.000	0.000	0.000
33	A	30	ASN	0	-0.042	-0.029	19.296	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	31	SER	0	0.021	0.019	20.228	0.005	0.005	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.025	0.019	14.544	0.013	0.013	0.000	0.000	0.000	0.000
36	A	33	PHE	0	-0.018	-0.016	13.042	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.765	-0.813	8.808	1.662	1.662	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.045	0.013	6.861	-0.215	-0.215	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.947	-0.959	2.302	-4.534	-2.499	2.568	-2.532	-2.071	-0.015
40	A	37	VAL	0	-0.018	-0.010	3.607	-0.601	-0.475	0.001	0.032	-0.159	0.000
41	A	38	THR	0	0.044	0.016	4.907	-0.751	-0.747	-0.001	-0.004	0.002	0.000
42	A	39	LEU	0	0.047	-0.004	7.315	0.383	0.383	0.000	0.000	0.000	0.000
43	A	40	ALA	0	0.012	0.010	9.477	0.201	0.201	0.000	0.000	0.000	0.000
44	A	41	GLU	-1	-0.828	-0.901	9.133	-0.214	-0.214	0.000	0.000	0.000	0.000
45	A	42	PHE	0	0.002	-0.007	8.916	0.188	0.188	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.908	-0.960	10.816	-0.194	-0.194	0.000	0.000	0.000	0.000
47	A	44	ARG	1	0.878	0.940	12.628	0.524	0.524	0.000	0.000	0.000	0.000
48	A	45	ILE	0	-0.047	-0.019	10.591	0.061	0.061	0.000	0.000	0.000	0.000
49	A	46	LYS	1	0.971	0.985	14.491	0.153	0.153	0.000	0.000	0.000	0.000
50	A	47	ALA	0	0.026	0.008	16.161	0.022	0.022	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.022	0.008	18.146	0.014	0.014	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.072	-0.057	16.023	0.025	0.025	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.004	-0.004	19.912	0.009	0.009	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.899	-0.926	22.179	-0.062	-0.062	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.179	-0.093	21.371	0.009	0.009	0.000	0.000	0.000	0.000
56	A	53	ILE	0	-0.076	-0.036	21.872	0.014	0.014	0.000	0.000	0.000	0.000
57	A	54	ASP	-1	-0.845	-0.923	25.327	0.018	0.018	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.982	-1.013	24.396	0.000	0.000	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.933	-0.950	26.884	0.024	0.024	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.982	-0.979	29.073	0.059	0.059	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.762	-0.863	24.826	0.082	0.082	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.007	0.000	22.877	0.002	0.002	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.010	-0.021	16.782	0.023	0.023	0.000	0.000	0.000	0.000
64	A	61	VAL	0	0.000	0.009	15.646	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	62	ILE	0	-0.012	-0.015	10.964	0.043	0.043	0.000	0.000	0.000	0.000
66	A	63	TYR	0	0.004	0.002	11.171	-0.058	-0.058	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.923	0.964	7.835	0.158	0.158	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.015	-0.009	5.782	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	66	ARG	1	0.983	0.977	4.375	-0.438	-0.237	0.000	-0.037	-0.163	0.000
70	A	67	SER	0	0.028	0.010	2.165	-1.938	-1.463	3.778	-2.202	-2.051	-0.007
71	A	68	MET	0	0.026	0.023	3.227	-0.791	-1.698	0.004	1.128	-0.224	0.000
72	A	69	PRO	0	-0.024	0.017	5.146	-0.628	-0.627	-0.001	-0.002	0.002	0.000
73	A	70	LYS	1	1.002	0.983	8.437	-0.811	-0.811	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.767	0.845	9.299	-1.532	-1.532	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.931	-0.957	14.288	0.425	0.425	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.028	-0.016	17.456	0.004	0.004	0.000	0.000	0.000	0.000
77	A	74	LEU	0	0.030	0.019	19.759	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	75	GLY	0	-0.006	0.004	23.423	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	76	MET	0	-0.012	-0.008	21.286	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ALA)