FMO DATABASE

FMODB ID: MNRLZ

Calculation Name: 2HD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HD3

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEJ8

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	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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-602540.270003
FMO2-HF: Nuclear repulsion	566330.374885
FMO2-HF: Total energy	-36209.895118
FMO2-MP2: Total energy	-36312.267446

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:1:MET)

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

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.
-11.004	-4.22	7.835	-5.231	-9.39	-0.019

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.011

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

Sort

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	3	LEU	0	0.015	0.032	3.866	-0.678	1.793	-0.018	-1.324	-1.128	0.003
4	A	4	ALA	0	0.015	0.005	6.248	-0.057	-0.057	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.040	0.026	9.180	0.187	0.187	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.001	0.005	12.549	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.026	0.016	14.397	0.038	0.038	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.027	0.006	17.282	0.010	0.010	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.069	-0.040	18.038	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.004	0.011	17.960	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.006	0.003	21.196	0.033	0.033	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.012	-0.012	22.451	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.024	0.005	24.489	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.004	0.003	27.469	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.832	0.933	19.864	-0.275	-0.275	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.059	0.021	21.252	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.075	0.028	22.088	0.027	0.027	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.027	0.014	20.221	0.019	0.019	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.057	-0.029	16.821	0.049	0.049	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.008	-0.002	18.824	0.015	0.015	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.016	-0.017	20.519	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.827	-0.892	16.191	0.554	0.554	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.974	0.986	17.786	-0.284	-0.284	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.021	0.015	15.994	0.049	0.049	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.017	0.009	12.356	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.003	0.010	14.621	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.039	-0.027	10.242	0.021	0.021	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.856	-0.936	12.965	-0.488	-0.488	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.043	-0.021	7.913	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.024	0.030	9.894	0.211	0.211	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.656	-0.815	9.682	-1.375	-1.375	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.042	-0.035	9.557	0.151	0.151	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.155	-0.102	11.397	0.222	0.222	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.020	-0.001	13.627	0.121	0.121	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.087	-0.044	15.092	0.129	0.129	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.013	0.012	14.389	-0.141	-0.141	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.905	-0.966	11.314	-1.421	-1.421	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.063	-0.024	14.499	0.062	0.062	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.055	-0.027	12.183	0.116	0.116	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.019	-0.008	13.124	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.034	-0.015	11.406	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.018	0.002	13.577	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.019	0.005	9.948	0.011	0.011	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.057	-0.028	11.147	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.724	-0.897	11.306	0.756	0.756	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.047	-0.025	12.146	-0.066	-0.066	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.075	-0.023	9.321	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.032	-0.025	13.935	-0.074	-0.074	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.034	0.005	12.819	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.014	-0.008	14.961	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.035	-0.044	16.434	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.043	-0.021	17.077	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.858	-0.926	14.022	0.122	0.122	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.042	0.021	10.565	-0.085	-0.085	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.002	-0.010	8.330	0.193	0.193	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.007	-0.003	2.421	-1.697	-0.762	0.703	-0.376	-1.262	0.001
57	A	57	LEU	0	0.000	0.004	4.048	0.775	1.296	0.001	-0.106	-0.417	0.000
58	A	58	VAL	0	0.023	0.009	2.411	-5.646	-2.828	4.318	-2.943	-4.194	-0.025
59	A	59	SER	0	0.036	0.010	3.552	-1.028	-0.897	0.020	0.075	-0.227	0.000
60	A	60	GLY	0	0.000	0.009	6.045	0.563	0.563	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.029	-0.011	9.083	0.022	0.022	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.004	-0.004	6.080	-0.376	-0.376	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.003	0.019	7.375	0.235	0.235	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.846	0.913	8.127	-0.753	-0.753	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.064	-0.045	9.890	-0.060	-0.060	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.026	-0.013	6.970	-0.052	-0.052	0.000	0.000	0.000	0.000
67	A	67	HIS	0	-0.037	-0.007	9.061	-0.126	-0.126	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.841	0.905	11.876	-0.836	-0.836	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.020	0.021	15.026	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.707	-0.830	14.477	0.849	0.849	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.108	-0.039	16.515	-0.045	-0.045	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.005	-0.013	14.541	-0.066	-0.066	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.059	-0.027	15.636	0.036	0.036	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.018	-0.002	11.700	-0.051	-0.051	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.905	-0.950	10.828	0.247	0.247	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.005	-0.019	6.410	-0.069	-0.069	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.031	-0.006	7.094	-0.098	-0.098	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.012	0.023	6.085	0.315	0.315	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.043	-0.037	2.934	-0.526	-0.646	2.812	-0.555	-2.137	0.002
80	A	80	GLY	0	0.011	0.002	6.393	-0.106	-0.078	-0.001	-0.002	-0.025	0.000
81	A	81	ILE	0	-0.004	0.003	7.837	-0.189	-0.189	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.020	0.001	8.511	0.017	0.017	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.817	-0.911	10.766	0.232	0.232	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.937	-0.979	12.807	-0.173	-0.173	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.040	-0.002	11.221	-0.046	-0.046	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.010	0.014	13.507	0.022	0.022	0.000	0.000	0.000	0.000
87	A	87	SER	0	0.017	-0.006	14.873	-0.082	-0.082	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.003	0.001	17.285	0.033	0.033	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.016	-0.008	19.135	0.030	0.030	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.059	-0.024	20.311	0.046	0.046	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.019	-0.001	17.829	-0.043	-0.043	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.022	-0.001	15.904	0.020	0.020	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.008	-0.007	13.964	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	94	HIS	0	-0.008	-0.010	16.454	0.009	0.009	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.844	0.933	14.786	-0.244	-0.244	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.016	0.001	17.267	0.023	0.023	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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