FMO DATABASE

FMODB ID: 98LR2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-602646.31853
FMO2-HF: Nuclear repulsion	566436.874414
FMO2-HF: Total energy	-36209.444116
FMO2-MP2: Total energy	-36311.865477

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.
-11.135	-3.986	7.146	-5.202	-9.093	-0.021

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 : -0.009

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	0.018	0.026	3.866	-0.706	1.765	-0.018	-1.325	-1.128	0.003
4	A	4	ALA	0	0.015	0.003	6.238	-0.049	-0.049	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.034	0.025	9.162	0.179	0.179	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.000	0.005	12.529	0.001	0.001	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.019	0.015	14.372	0.036	0.036	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.023	0.001	17.247	0.010	0.010	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.068	-0.040	18.010	0.051	0.051	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.022	0.023	18.203	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.006	-0.002	21.206	0.033	0.033	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.011	-0.014	21.909	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.022	0.014	24.504	0.020	0.020	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.004	0.007	27.448	0.012	0.012	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.860	0.933	20.015	-0.270	-0.270	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.052	0.017	21.008	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.081	0.032	22.065	0.028	0.028	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.023	0.016	20.201	0.018	0.018	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.041	-0.028	16.713	0.049	0.049	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.057	-0.021	18.827	0.020	0.020	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.023	-0.026	20.493	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.843	-0.909	15.997	0.566	0.566	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.958	0.981	17.755	-0.277	-0.277	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.021	0.014	16.280	0.051	0.051	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.026	0.014	12.287	-0.051	-0.051	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.004	0.005	14.627	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.033	-0.024	10.188	0.017	0.017	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.890	-0.961	12.963	-0.486	-0.486	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.047	-0.029	7.897	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.025	0.030	9.889	0.195	0.195	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.620	-0.805	9.679	-1.374	-1.374	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.045	-0.034	9.580	0.148	0.148	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.172	-0.105	11.400	0.203	0.203	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.027	-0.008	13.633	0.121	0.121	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.103	-0.049	15.088	0.132	0.132	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.006	0.015	14.386	-0.141	-0.141	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.916	-0.974	11.738	-1.330	-1.330	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.060	-0.016	14.504	0.062	0.062	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.056	-0.027	12.236	0.105	0.105	0.000	0.000	0.000	0.000
40	A	40	CYS	0	0.014	0.017	13.120	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.034	-0.022	11.438	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.024	0.010	13.583	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.018	-0.002	9.695	0.011	0.011	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.076	-0.029	11.128	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.743	-0.917	11.292	0.740	0.740	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.022	-0.004	12.120	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.071	-0.021	9.242	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.032	-0.028	13.844	-0.077	-0.077	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.039	0.003	12.801	-0.040	-0.040	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.008	-0.004	14.933	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.075	-0.056	16.408	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.005	-0.006	17.087	0.011	0.011	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.881	-0.935	14.137	0.109	0.109	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.050	0.030	10.527	-0.082	-0.082	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.002	-0.010	7.887	0.184	0.184	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.000	-0.006	2.517	-1.723	-0.687	0.514	-0.353	-1.197	0.002
57	A	57	LEU	0	0.005	0.007	4.023	0.816	1.356	0.002	-0.112	-0.430	0.000
58	A	58	VAL	0	0.021	0.010	2.431	-5.635	-2.694	3.770	-2.883	-3.828	-0.027
59	A	59	SER	0	0.035	0.004	3.519	-0.978	-0.851	0.020	0.084	-0.232	0.000
60	A	60	GLY	0	-0.013	-0.001	6.069	0.563	0.563	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.025	-0.022	9.108	0.022	0.022	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.006	-0.003	6.022	-0.379	-0.379	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.004	0.022	7.340	0.231	0.231	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.849	0.941	8.101	-0.806	-0.806	0.000	0.000	0.000	0.000
65	A	65	GLN	0	0.001	-0.002	9.817	-0.100	-0.100	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.037	-0.019	6.960	-0.059	-0.059	0.000	0.000	0.000	0.000
67	A	67	HIS	0	-0.027	0.002	9.055	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.883	0.930	11.865	-0.764	-0.764	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.004	0.016	15.017	-0.047	-0.047	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.760	-0.903	14.332	0.858	0.858	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.118	-0.043	16.495	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.016	0.011	14.704	-0.071	-0.071	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.059	-0.029	15.609	0.035	0.035	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.017	0.007	11.540	-0.052	-0.052	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.916	-0.956	10.847	0.278	0.278	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.019	-0.013	6.413	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.041	-0.015	7.067	-0.101	-0.101	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.003	0.020	6.071	0.358	0.358	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.030	-0.029	2.929	-0.714	-0.708	2.859	-0.611	-2.253	0.001
80	A	80	GLY	0	0.009	-0.003	6.299	-0.159	-0.131	-0.001	-0.002	-0.025	0.000
81	A	81	ILE	0	-0.002	0.006	7.768	-0.179	-0.179	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.016	0.001	8.404	0.004	0.004	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.892	-0.960	10.752	0.205	0.205	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.943	-0.982	12.735	-0.174	-0.174	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.036	0.000	11.158	-0.055	-0.055	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.019	0.015	13.478	0.029	0.029	0.000	0.000	0.000	0.000
87	A	87	SER	0	0.026	-0.004	14.883	-0.103	-0.103	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.036	-0.012	17.307	0.034	0.034	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.010	-0.005	19.148	0.031	0.031	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.051	-0.022	20.339	0.053	0.053	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.021	0.001	17.834	-0.045	-0.045	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.020	0.001	15.900	0.024	0.024	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.015	-0.012	13.933	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	HIS	0	0.004	-0.001	16.403	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.923	0.986	15.068	-0.198	-0.198	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.013	-0.005	17.252	0.026	0.026	0.000	0.000	0.000	0.000

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