FMO DATABASE

FMODB ID: MN92Z

Calculation Name: 4GHJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHJ

Chain ID: A

ChEMBL ID:

UniProt ID: A0A3Q0

Base Structure: X-ray

Registration Date: 2023-09-22

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-416962.079088
FMO2-HF: Nuclear repulsion	389008.848972
FMO2-HF: Total energy	-27953.230116
FMO2-MP2: Total energy	-28035.159903

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:LYS)

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

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.
-38.915	-35.266	3.027	-1.894	-4.783	-0.016

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.968 / q_NPA : 0.965

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	4	VAL	0	0.018	0.010	2.477	2.063	3.646	1.330	-0.863	-2.051	-0.001
4	A	5	THR	0	0.031	0.021	4.844	-0.893	-0.875	-0.001	-0.004	-0.013	0.000
5	A	6	ALA	0	0.066	0.011	7.058	-3.034	-3.034	0.000	0.000	0.000	0.000
6	A	7	ALA	0	-0.004	-0.004	8.307	-1.067	-1.067	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.043	0.023	7.649	0.468	0.468	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.003	0.000	2.232	-8.511	-7.033	1.694	-0.889	-2.283	-0.014
9	A	10	ALA	0	-0.001	-0.006	6.195	-1.413	-1.413	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.949	-0.972	8.812	-21.904	-21.904	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.847	-0.899	4.525	-58.956	-58.776	-0.001	-0.024	-0.155	0.000
12	A	13	ILE	0	-0.069	-0.053	4.636	0.048	0.108	-0.001	-0.002	-0.057	0.000
13	A	14	GLY	0	0.032	0.021	7.990	2.698	2.698	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.883	-0.946	10.351	-21.912	-21.912	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.788	0.888	3.146	57.143	57.473	0.006	-0.112	-0.224	-0.001
16	A	17	LEU	0	0.007	0.014	10.725	1.761	1.761	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.958	0.978	13.456	18.310	18.310	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.055	-0.034	13.542	0.964	0.964	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.004	-0.002	14.347	1.098	1.098	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.796	0.883	16.027	16.372	16.372	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.070	-0.037	18.223	0.941	0.941	0.000	0.000	0.000	0.000
22	A	23	ASN	0	0.006	0.006	16.576	0.924	0.924	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.856	0.925	17.318	17.115	17.115	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.912	-0.934	22.451	-11.828	-11.828	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.022	0.034	22.304	0.357	0.357	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.001	-0.010	23.483	-0.543	-0.543	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.069	-0.073	20.189	0.593	0.593	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.024	-0.030	23.823	-0.184	-0.184	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.793	-0.873	26.522	-11.143	-11.143	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.028	0.014	20.766	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.066	-0.043	24.160	-0.067	-0.067	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.950	-0.962	25.741	-9.802	-9.802	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.015	-0.003	25.493	0.169	0.169	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.026	-0.017	23.680	0.090	0.090	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.015	0.034	25.726	0.077	0.077	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.057	-0.030	22.487	-0.035	-0.035	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.035	0.015	26.731	0.244	0.244	0.000	0.000	0.000	0.000
38	A	39	ARG	1	1.004	0.976	24.833	11.559	11.559	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.859	0.932	23.190	12.804	12.804	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.034	0.012	21.437	-0.372	-0.372	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.091	0.058	19.975	-0.849	-0.849	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.087	-0.037	19.118	-0.809	-0.809	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.032	-0.041	18.934	-0.596	-0.596	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.094	0.053	16.161	-0.925	-0.925	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.760	-0.846	14.490	-18.312	-18.312	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.883	0.944	14.568	15.685	15.685	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.059	0.042	12.427	-0.694	-0.694	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.843	0.923	13.051	16.701	16.701	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.014	-0.013	14.125	1.158	1.158	0.000	0.000	0.000	0.000
50	A	51	GLN	0	0.008	0.026	15.528	-0.750	-0.750	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.044	0.004	13.476	-0.163	-0.163	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.821	-0.916	16.167	-15.088	-15.088	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.004	-0.006	19.322	0.155	0.155	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.010	-0.003	11.839	0.532	0.532	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.017	0.004	16.095	-0.323	-0.323	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.039	0.023	17.558	0.338	0.338	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.031	-0.023	17.669	0.435	0.435	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.013	-0.014	13.088	0.068	0.068	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.026	-0.010	17.496	0.273	0.273	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.011	0.005	20.765	0.484	0.484	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.086	-0.042	17.034	0.280	0.280	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.912	-0.941	20.092	-14.233	-14.233	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.060	-0.027	14.141	-0.590	-0.590	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.019	-0.012	15.511	-1.137	-1.137	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.851	-0.919	16.989	-15.068	-15.068	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.033	-0.031	11.584	0.835	0.835	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.070	-0.039	12.637	-1.530	-1.530	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.851	-0.904	14.200	-16.734	-16.734	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.071	-0.055	12.638	0.220	0.220	0.000	0.000	0.000	0.000
70	A	71	PHE	0	-0.069	-0.028	8.117	-2.578	-2.578	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.075	-0.043	10.325	1.123	1.123	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.058	0.066	12.705	1.357	1.357	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.917	0.947	16.078	17.707	17.707	0.000	0.000	0.000	0.000

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