FMO DATABASE

FMODB ID: 5J5NZ

Calculation Name: 2HJD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HJD

Chain ID: A

ChEMBL ID:

UniProt ID: Q20HX4

Base Structure: X-ray

Registration Date: 2023-09-23

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-538029.279962
FMO2-HF: Nuclear repulsion	503961.713335
FMO2-HF: Total energy	-34067.566626
FMO2-MP2: Total energy	-34166.882213

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:12:PHE)

Summations of interaction energy for fragment #1(A:12:PHE)

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.
-31.82	-20.538	13.569	-6.952	-17.901	-0.01

Interaction energy analysis for fragmet #1(A:12:PHE)

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 : -0.013

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	14	LEU	0	0.026	0.022	3.679	0.936	2.242	-0.002	-0.549	-0.755	0.001
4	A	15	ARG	1	0.889	0.914	2.478	-15.882	-14.320	3.894	-1.742	-3.714	0.011
5	A	16	PRO	0	0.044	0.017	4.437	0.253	0.381	-0.001	-0.006	-0.122	0.000
6	A	17	VAL	0	0.048	0.034	4.980	0.049	0.049	0.000	0.000	0.000	0.000
7	A	18	ILE	0	0.005	0.028	2.178	-2.743	-1.141	3.479	-1.073	-4.008	0.010
8	A	19	GLY	0	-0.032	-0.014	5.992	-0.289	-0.289	0.000	0.000	0.000	0.000
9	A	20	LEU	0	-0.013	-0.022	9.496	-0.177	-0.177	0.000	0.000	0.000	0.000
10	A	21	THR	0	0.010	-0.004	7.387	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.845	0.921	6.849	-1.340	-1.340	0.000	0.000	0.000	0.000
12	A	23	GLY	0	0.015	0.006	10.775	0.009	0.009	0.000	0.000	0.000	0.000
13	A	24	LEU	0	-0.032	0.003	10.560	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	25	SER	0	-0.026	-0.037	12.039	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	26	SER	0	0.048	-0.001	10.567	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	27	ALA	0	0.056	0.036	11.630	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.817	-0.863	13.008	-0.392	-0.392	0.000	0.000	0.000	0.000
18	A	29	ILE	0	0.018	0.009	6.897	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.838	-0.907	10.105	-0.812	-0.812	0.000	0.000	0.000	0.000
20	A	31	THR	0	-0.054	-0.036	11.873	0.030	0.030	0.000	0.000	0.000	0.000
21	A	32	LEU	0	-0.025	-0.017	10.662	0.033	0.033	0.000	0.000	0.000	0.000
22	A	33	THR	0	0.013	-0.006	8.963	-0.111	-0.111	0.000	0.000	0.000	0.000
23	A	34	ALA	0	-0.006	-0.012	10.717	0.054	0.054	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.010	-0.010	14.407	0.079	0.079	0.000	0.000	0.000	0.000
25	A	36	ALA	0	0.026	0.027	10.971	0.060	0.060	0.000	0.000	0.000	0.000
26	A	37	ILE	0	0.026	0.009	11.763	0.053	0.053	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.865	0.924	14.353	0.510	0.510	0.000	0.000	0.000	0.000
28	A	39	LEU	0	0.047	0.028	14.932	0.031	0.031	0.000	0.000	0.000	0.000
29	A	40	HIS	0	0.001	0.000	14.213	0.020	0.020	0.000	0.000	0.000	0.000
30	A	41	ARG	1	0.929	0.961	16.304	0.540	0.540	0.000	0.000	0.000	0.000
31	A	42	GLN	0	-0.010	-0.007	19.511	0.014	0.014	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.008	0.007	16.454	0.026	0.026	0.000	0.000	0.000	0.000
33	A	44	LEU	0	-0.016	-0.010	17.778	0.025	0.025	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.872	-0.912	20.889	-0.198	-0.198	0.000	0.000	0.000	0.000
35	A	46	LYS	1	0.830	0.914	23.413	0.208	0.208	0.000	0.000	0.000	0.000
36	A	47	ALA	0	0.020	-0.006	22.163	0.021	0.021	0.000	0.000	0.000	0.000
37	A	48	ASP	-1	-0.899	-0.942	24.175	-0.189	-0.189	0.000	0.000	0.000	0.000
38	A	49	GLN	0	-0.073	-0.066	26.135	0.025	0.025	0.000	0.000	0.000	0.000
39	A	50	LEU	0	-0.041	-0.017	26.306	0.013	0.013	0.000	0.000	0.000	0.000
40	A	51	PHE	0	0.002	0.007	27.118	0.014	0.014	0.000	0.000	0.000	0.000
41	A	52	GLN	0	-0.033	-0.033	29.098	0.024	0.024	0.000	0.000	0.000	0.000
42	A	53	VAL	0	-0.066	-0.032	32.213	0.011	0.011	0.000	0.000	0.000	0.000
43	A	54	LEU	0	-0.018	0.021	29.208	0.008	0.008	0.000	0.000	0.000	0.000
44	A	55	PRO	0	0.019	0.012	33.738	0.001	0.001	0.000	0.000	0.000	0.000
45	A	56	ASP	-1	-0.845	-0.931	35.339	-0.091	-0.091	0.000	0.000	0.000	0.000
46	A	57	ASP	-1	-0.894	-0.955	36.342	-0.067	-0.067	0.000	0.000	0.000	0.000
47	A	58	ILE	0	0.009	0.005	31.783	0.002	0.002	0.000	0.000	0.000	0.000
48	A	59	LYS	1	0.768	0.901	31.600	0.101	0.101	0.000	0.000	0.000	0.000
49	A	60	ILE	0	-0.066	-0.031	31.878	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	61	GLY	0	-0.007	0.010	32.547	0.002	0.002	0.000	0.000	0.000	0.000
51	A	62	THR	0	-0.126	-0.078	33.155	0.006	0.006	0.000	0.000	0.000	0.000
52	A	63	ALA	0	-0.021	-0.001	35.482	0.006	0.006	0.000	0.000	0.000	0.000
53	A	64	ALA	0	0.004	-0.011	31.272	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	65	GLY	0	-0.018	0.001	32.369	0.008	0.008	0.000	0.000	0.000	0.000
55	A	66	GLY	0	0.037	0.015	33.417	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	67	GLU	-1	-0.913	-0.970	32.758	-0.067	-0.067	0.000	0.000	0.000	0.000
57	A	68	GLN	0	0.029	0.005	31.517	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	69	HIS	0	0.061	0.037	28.778	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	70	LEU	0	-0.019	-0.008	28.201	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.766	-0.878	26.818	-0.158	-0.158	0.000	0.000	0.000	0.000
61	A	72	TYR	0	0.005	-0.003	24.543	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	73	ILE	0	-0.020	-0.011	23.580	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	74	GLU	-1	-0.953	-0.980	22.340	-0.133	-0.133	0.000	0.000	0.000	0.000
64	A	75	ALA	0	0.035	0.019	21.193	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	76	MET	0	-0.041	-0.014	20.182	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	77	ILE	0	-0.040	-0.020	17.744	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	78	GLU	-1	-0.935	-0.968	16.580	-0.310	-0.310	0.000	0.000	0.000	0.000
68	A	79	MET	0	-0.016	-0.001	15.773	-0.096	-0.096	0.000	0.000	0.000	0.000
69	A	80	HIS	0	0.028	-0.010	14.194	-0.125	-0.125	0.000	0.000	0.000	0.000
70	A	81	ALA	0	-0.009	0.001	12.253	-0.110	-0.110	0.000	0.000	0.000	0.000
71	A	82	GLN	0	-0.021	-0.002	10.872	-0.161	-0.161	0.000	0.000	0.000	0.000
72	A	83	MET	0	0.033	0.018	10.672	-0.163	-0.163	0.000	0.000	0.000	0.000
73	A	84	SER	0	0.004	0.008	7.037	-0.268	-0.268	0.000	0.000	0.000	0.000
74	A	85	ALA	0	-0.009	-0.007	5.767	-0.754	-0.754	0.000	0.000	0.000	0.000
75	A	86	VAL	0	-0.020	-0.001	6.947	-0.369	-0.369	0.000	0.000	0.000	0.000
76	A	87	ASN	0	-0.020	-0.021	5.253	-0.118	-0.118	0.000	0.000	0.000	0.000
77	A	88	THR	0	-0.071	-0.043	2.200	-3.338	-1.728	2.066	-1.172	-2.504	-0.006
78	A	89	LEU	0	-0.025	-0.020	2.743	-4.475	-2.321	0.438	-1.053	-1.539	-0.017
79	A	90	VAL	0	0.038	0.012	5.544	-0.099	-0.099	0.000	0.000	0.000	0.000
80	A	91	GLY	0	-0.023	-0.004	2.962	0.000	0.681	0.257	-0.277	-0.662	0.000
81	A	92	LEU	0	-0.082	-0.051	2.488	-4.381	-1.911	3.370	-1.425	-4.415	-0.009
82	A	93	LEU	0	-0.055	-0.007	3.157	1.585	1.354	0.068	0.345	-0.182	0.000
83	A	94	GLY	0	-0.003	0.007	5.600	0.413	0.413	0.000	0.000	0.000	0.000
84	A	95	PHE	0	-0.053	-0.034	6.970	0.375	0.375	0.000	0.000	0.000	0.000
85	A	96	ILE	0	0.047	0.023	9.484	-0.165	-0.165	0.000	0.000	0.000	0.000
86	A	97	PRO	0	-0.001	0.019	11.026	0.124	0.124	0.000	0.000	0.000	0.000
87	A	98	LYS	1	0.881	0.934	13.929	0.587	0.587	0.000	0.000	0.000	0.000
88	A	99	VAL	0	-0.019	-0.007	15.555	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	100	SER	0	-0.001	0.001	18.716	0.044	0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PHE)