FMO DATABASE

FMODB ID: 76YKK

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	OptAll
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	-603195.921036
FMO2-HF: Nuclear repulsion	566985.780112
FMO2-HF: Total energy	-36210.140924
FMO2-MP2: Total energy	-36312.492006

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.
-11.115	-4.225	6.591	-5.022	-8.459	-0.015

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 : -0.011 / q_NPA : -0.014

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	3	LEU	0	0.010	0.020	3.879	-0.555	1.782	-0.015	-1.251	-1.071	0.003
4	A	4	ALA	0	0.024	0.009	6.310	-0.081	-0.081	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.013	0.017	9.328	0.186	0.186	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.005	0.005	12.617	-0.021	-0.021	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.021	-0.003	14.444	0.023	0.023	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.024	0.011	17.590	0.008	0.008	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.054	-0.027	18.152	0.037	0.037	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.007	0.006	17.905	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.009	-0.002	21.409	0.032	0.032	0.000	0.000	0.000	0.000
12	A	12	CYS	0	0.004	0.004	22.399	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.024	0.001	24.321	0.022	0.022	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.009	0.006	27.261	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.808	0.895	20.018	-0.266	-0.266	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.071	0.036	21.462	0.005	0.005	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.070	0.021	22.074	0.028	0.028	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.003	0.007	20.109	0.019	0.019	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.023	-0.017	16.835	0.056	0.056	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.014	0.010	18.909	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	HIS	0	0.000	0.003	21.036	-0.044	-0.044	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.808	-0.876	16.291	0.533	0.533	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.894	0.944	17.240	-0.322	-0.322	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.034	0.022	16.000	0.046	0.046	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.003	-0.006	12.529	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.009	0.008	14.461	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.020	-0.011	10.378	0.031	0.031	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.845	-0.916	12.915	-0.503	-0.503	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.051	-0.017	8.011	-0.085	-0.085	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.012	0.014	9.913	0.215	0.215	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.685	-0.819	9.806	-1.223	-1.223	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.034	-0.039	10.069	0.107	0.107	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.128	-0.083	11.574	0.209	0.209	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.011	0.013	14.113	0.108	0.108	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.106	-0.057	15.345	0.128	0.128	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.023	0.019	14.513	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.895	-0.954	11.521	-1.379	-1.379	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.025	-0.017	14.710	0.049	0.049	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.078	-0.039	12.178	0.110	0.110	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.033	-0.025	12.810	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.031	-0.013	11.585	0.009	0.009	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.001	-0.010	13.542	0.040	0.040	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.008	0.007	10.058	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.040	-0.015	11.455	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.716	-0.876	11.443	0.730	0.730	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.047	-0.030	12.379	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.062	-0.020	9.685	0.043	0.043	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.047	-0.027	14.289	-0.062	-0.062	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.005	0.000	13.025	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.017	-0.008	15.156	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.041	-0.045	16.497	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.019	-0.009	17.278	0.009	0.009	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.858	-0.927	14.181	0.169	0.169	0.000	0.000	0.000	0.000
54	A	54	TRP	0	0.041	0.022	10.911	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.002	-0.012	8.714	0.206	0.206	0.000	0.000	0.000	0.000
56	A	56	LEU	0	0.015	0.015	2.772	-1.408	-0.539	0.169	-0.236	-0.802	0.001
57	A	57	LEU	0	0.016	0.006	4.000	0.654	1.039	0.000	-0.070	-0.315	0.000
58	A	58	VAL	0	0.004	-0.001	2.406	-6.108	-2.975	4.132	-3.075	-4.191	-0.021
59	A	59	SER	0	0.043	0.005	3.484	-1.089	-0.992	0.023	0.093	-0.212	0.000
60	A	60	GLY	0	0.003	0.013	6.168	0.447	0.447	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.006	-0.032	9.193	0.043	0.043	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.001	-0.003	5.773	-0.377	-0.377	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.005	0.022	7.426	0.300	0.300	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.859	0.921	8.208	-0.669	-0.669	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.059	-0.050	9.561	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.011	0.000	6.926	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	67	HIS	0	-0.023	-0.011	9.019	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.821	0.890	11.660	-0.874	-0.874	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.026	0.039	14.296	-0.068	-0.068	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.710	-0.835	13.999	0.829	0.829	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.081	-0.032	16.236	-0.065	-0.065	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.024	-0.011	14.361	-0.064	-0.064	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.062	-0.024	15.696	0.022	0.022	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.006	-0.014	11.904	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.903	-0.952	11.151	0.161	0.161	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.002	-0.014	6.692	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.045	-0.014	7.360	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.005	0.014	6.448	0.103	0.103	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.039	-0.031	2.911	-0.499	-0.430	2.282	-0.483	-1.868	0.002
80	A	80	GLY	0	0.018	0.007	6.628	0.166	0.166	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.010	0.000	8.104	-0.189	-0.189	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.030	-0.010	8.771	0.053	0.053	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.841	-0.903	11.046	0.296	0.296	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.934	-0.974	13.071	-0.132	-0.132	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.034	-0.010	11.389	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.032	0.019	13.688	0.025	0.025	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.008	-0.009	15.016	-0.071	-0.071	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.000	-0.004	17.644	0.034	0.034	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.017	-0.005	19.485	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.056	-0.018	20.995	0.039	0.039	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.026	0.005	18.181	-0.032	-0.032	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.044	-0.012	15.693	0.012	0.012	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.004	-0.006	14.136	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	HIS	0	-0.024	-0.025	16.594	0.015	0.015	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.854	0.934	14.807	-0.327	-0.327	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.013	0.002	17.515	0.011	0.011	0.000	0.000	0.000	0.000

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