FMO DATABASE

FMODB ID: QY3JY

Calculation Name: 3GHD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZN4

Base Structure: X-ray

Registration Date: 2023-09-20

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-401533.361502
FMO2-HF: Nuclear repulsion	374916.834732
FMO2-HF: Total energy	-26616.52677
FMO2-MP2: Total energy	-26694.426034

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:14:LYS)

Summations of interaction energy for fragment #1(A:14: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.
-18.627	-12.249	15.387	-10.333	-11.434	-0.091

Interaction energy analysis for fragmet #1(A:14:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.943 / 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	16	ILE	0	-0.012	-0.013	3.103	-8.260	-4.358	0.010	-1.941	-1.972	0.004
4	A	17	VAL	0	0.021	0.020	5.762	2.448	2.448	0.000	0.000	0.000	0.000
5	A	18	VAL	0	-0.054	-0.027	9.396	-0.466	-0.466	0.000	0.000	0.000	0.000
6	A	19	GLN	0	0.023	-0.001	12.287	1.384	1.384	0.000	0.000	0.000	0.000
7	A	20	PRO	0	-0.034	-0.013	16.033	-0.196	-0.196	0.000	0.000	0.000	0.000
8	A	21	LYS	1	0.856	0.924	18.252	13.756	13.756	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.843	-0.892	15.459	-19.103	-19.103	0.000	0.000	0.000	0.000
10	A	23	THR	0	0.015	-0.007	17.720	-0.145	-0.145	0.000	0.000	0.000	0.000
11	A	24	VAL	0	0.050	0.017	15.537	-1.336	-1.336	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.813	-0.899	15.567	-17.953	-17.953	0.000	0.000	0.000	0.000
13	A	26	ARG	1	0.918	0.961	14.887	18.765	18.765	0.000	0.000	0.000	0.000
14	A	27	VAL	0	0.065	0.026	11.067	-1.749	-1.749	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.034	0.021	10.956	-2.834	-2.834	0.000	0.000	0.000	0.000
16	A	29	LYS	1	0.841	0.922	10.858	16.547	16.547	0.000	0.000	0.000	0.000
17	A	30	ILE	0	-0.039	-0.013	8.169	-2.387	-2.387	0.000	0.000	0.000	0.000
18	A	31	LEU	0	0.048	0.041	6.462	-5.433	-5.433	0.000	0.000	0.000	0.000
19	A	32	SER	0	0.043	0.018	5.762	-7.353	-7.353	0.000	0.000	0.000	0.000
20	A	33	ARG	1	0.913	0.963	6.689	29.232	29.232	0.000	0.000	0.000	0.000
21	A	34	ASN	0	-0.075	-0.048	3.593	-1.442	-0.419	0.004	-0.493	-0.533	-0.002
22	A	35	LYS	1	0.941	0.983	1.723	-6.146	-8.548	12.620	-5.852	-4.366	-0.073
23	A	36	ALA	0	-0.038	-0.013	2.390	-15.065	-11.918	2.632	-2.386	-3.394	-0.019
24	A	37	GLY	0	0.076	0.045	2.757	7.710	8.078	0.122	0.400	-0.891	-0.001
25	A	38	SER	0	-0.062	-0.045	3.875	6.532	6.872	-0.001	-0.061	-0.278	0.000
26	A	39	ALA	0	0.016	0.006	5.622	-3.989	-3.989	0.000	0.000	0.000	0.000
27	A	40	VAL	0	-0.003	-0.006	7.257	2.278	2.278	0.000	0.000	0.000	0.000
28	A	41	VAL	0	0.009	0.011	9.857	-0.206	-0.206	0.000	0.000	0.000	0.000
29	A	42	MET	0	-0.015	-0.015	12.902	0.068	0.068	0.000	0.000	0.000	0.000
30	A	43	GLU	-1	-0.851	-0.945	15.393	-14.161	-14.161	0.000	0.000	0.000	0.000
31	A	44	GLY	0	-0.012	-0.006	19.055	0.480	0.480	0.000	0.000	0.000	0.000
32	A	45	ASP	-1	-0.851	-0.927	17.684	-15.247	-15.247	0.000	0.000	0.000	0.000
33	A	46	GLU	-1	-0.875	-0.917	17.766	-13.470	-13.470	0.000	0.000	0.000	0.000
34	A	47	ILE	0	-0.014	-0.014	11.884	-0.445	-0.445	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.004	0.006	15.357	0.781	0.781	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.030	-0.011	13.802	1.036	1.036	0.000	0.000	0.000	0.000
37	A	50	VAL	0	-0.021	0.005	7.526	-1.285	-1.285	0.000	0.000	0.000	0.000
38	A	51	VAL	0	0.012	0.025	10.059	1.648	1.648	0.000	0.000	0.000	0.000
39	A	52	THR	0	-0.021	-0.033	7.636	-2.665	-2.665	0.000	0.000	0.000	0.000
40	A	53	GLU	-1	-0.871	-0.958	7.933	-29.183	-29.183	0.000	0.000	0.000	0.000
41	A	54	ARG	1	0.832	0.879	10.206	18.857	18.857	0.000	0.000	0.000	0.000
42	A	55	ASP	-1	-0.758	-0.834	11.907	-17.638	-17.638	0.000	0.000	0.000	0.000
43	A	56	ILE	0	0.007	0.007	11.524	1.247	1.247	0.000	0.000	0.000	0.000
44	A	57	LEU	0	-0.022	-0.016	13.795	1.208	1.208	0.000	0.000	0.000	0.000
45	A	58	ASP	-1	-0.778	-0.860	16.005	-14.867	-14.867	0.000	0.000	0.000	0.000
46	A	59	LYS	1	0.798	0.872	15.349	16.770	16.770	0.000	0.000	0.000	0.000
47	A	60	VAL	0	-0.052	-0.020	17.716	0.545	0.545	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.009	0.003	18.129	0.607	0.607	0.000	0.000	0.000	0.000
49	A	62	ALA	0	-0.003	0.006	20.319	0.627	0.627	0.000	0.000	0.000	0.000
50	A	63	LYS	1	0.859	0.945	21.816	12.553	12.553	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.021	0.019	23.842	0.415	0.415	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.943	0.980	22.766	12.689	12.689	0.000	0.000	0.000	0.000
53	A	66	ASN	0	0.005	-0.015	23.457	-0.982	-0.982	0.000	0.000	0.000	0.000
54	A	67	PRO	0	0.012	-0.011	18.937	-0.110	-0.110	0.000	0.000	0.000	0.000
55	A	68	LYS	1	0.910	0.948	20.778	13.449	13.449	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.878	-0.915	22.634	-11.311	-11.311	0.000	0.000	0.000	0.000
57	A	70	VAL	0	-0.042	-0.001	19.679	0.340	0.340	0.000	0.000	0.000	0.000
58	A	71	LYS	1	0.821	0.895	19.953	12.148	12.148	0.000	0.000	0.000	0.000
59	A	72	VAL	0	0.018	-0.001	14.173	0.152	0.152	0.000	0.000	0.000	0.000
60	A	73	GLU	-1	-0.770	-0.893	16.699	-13.616	-13.616	0.000	0.000	0.000	0.000
61	A	74	GLU	-1	-0.854	-0.932	18.628	-12.626	-12.626	0.000	0.000	0.000	0.000
62	A	75	ILE	0	-0.039	-0.020	15.262	0.386	0.386	0.000	0.000	0.000	0.000
63	A	76	MET	0	-0.054	-0.003	14.287	-0.697	-0.697	0.000	0.000	0.000	0.000
64	A	77	THR	0	-0.022	0.002	13.103	1.371	1.371	0.000	0.000	0.000	0.000
65	A	78	LYS	1	0.889	0.934	14.321	13.418	13.418	0.000	0.000	0.000	0.000
66	A	79	ASN	0	0.009	-0.018	13.823	-0.381	-0.381	0.000	0.000	0.000	0.000
67	A	80	PRO	0	0.004	0.007	12.873	0.707	0.707	0.000	0.000	0.000	0.000
68	A	81	VAL	0	-0.007	-0.003	13.049	0.452	0.452	0.000	0.000	0.000	0.000
69	A	82	LYS	1	0.806	0.909	15.897	13.077	13.077	0.000	0.000	0.000	0.000
70	A	83	ILE	0	0.013	0.015	18.438	0.437	0.437	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:LYS)