FMO DATABASE

FMODB ID: JLKY9

Calculation Name: 2D7T-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7T

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-951509.494689
FMO2-HF: Nuclear repulsion	905189.938824
FMO2-HF: Total energy	-46319.555865
FMO2-MP2: Total energy	-46451.190628

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(H:1:GLN)

Summations of interaction energy for fragment #1(H:1:GLN)

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.
-0.87	1.906	0.291	-1.138	-1.928	0.004

Interaction energy analysis for fragmet #1(H:1:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.008

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	H	3	GLN	0	0.012	0.002	3.864	-1.690	-0.516	-0.001	-0.430	-0.743	0.002
4	H	4	LEU	0	-0.029	-0.015	6.250	0.289	0.289	0.000	0.000	0.000	0.000
5	H	5	VAL	0	0.032	0.012	9.780	-0.124	-0.124	0.000	0.000	0.000	0.000
6	H	6	GLN	0	-0.014	-0.028	12.389	0.128	0.128	0.000	0.000	0.000	0.000
7	H	7	SER	0	0.003	0.023	16.099	-0.061	-0.061	0.000	0.000	0.000	0.000
8	H	8	GLY	0	0.026	0.015	19.289	0.011	0.011	0.000	0.000	0.000	0.000
9	H	9	ALA	0	-0.029	-0.013	21.226	0.028	0.028	0.000	0.000	0.000	0.000
10	H	10	GLU	-1	-0.758	-0.866	24.270	0.021	0.021	0.000	0.000	0.000	0.000
11	H	11	VAL	0	-0.023	-0.010	27.236	0.008	0.008	0.000	0.000	0.000	0.000
12	H	12	LYS	1	0.815	0.898	29.350	-0.039	-0.039	0.000	0.000	0.000	0.000
13	H	13	LYS	1	0.910	0.954	33.510	-0.027	-0.027	0.000	0.000	0.000	0.000
14	H	14	PRO	0	0.037	-0.003	36.254	0.008	0.008	0.000	0.000	0.000	0.000
15	H	15	GLY	0	-0.021	0.000	37.833	-0.005	-0.005	0.000	0.000	0.000	0.000
16	H	16	ALA	0	-0.023	-0.004	34.784	0.005	0.005	0.000	0.000	0.000	0.000
17	H	17	SER	0	-0.064	-0.058	31.094	0.006	0.006	0.000	0.000	0.000	0.000
18	H	18	VAL	0	0.011	0.004	26.313	-0.016	-0.016	0.000	0.000	0.000	0.000
19	H	19	LYS	1	0.871	0.927	24.239	-0.113	-0.113	0.000	0.000	0.000	0.000
20	H	20	VAL	0	0.011	0.030	20.249	-0.023	-0.023	0.000	0.000	0.000	0.000
21	H	21	SER	0	0.033	-0.002	18.482	0.019	0.019	0.000	0.000	0.000	0.000
22	H	22	CYS	0	-0.017	-0.005	14.330	0.006	0.006	0.000	0.000	0.000	0.000
23	H	23	LYS	1	0.878	0.951	10.675	0.091	0.091	0.000	0.000	0.000	0.000
24	H	24	ALA	0	0.015	0.012	9.597	-0.034	-0.034	0.000	0.000	0.000	0.000
25	H	25	SER	0	-0.047	-0.035	5.642	-0.578	-0.578	0.000	0.000	0.000	0.000
26	H	26	GLY	0	0.077	0.028	2.978	-1.547	-0.831	0.219	-0.524	-0.411	0.003
27	H	27	TYR	0	0.015	0.009	3.502	4.691	5.577	0.073	-0.184	-0.774	-0.001
28	H	28	THR	0	0.016	0.002	6.106	-1.065	-1.065	0.000	0.000	0.000	0.000
29	H	29	PHE	0	0.056	0.032	9.550	-0.103	-0.103	0.000	0.000	0.000	0.000
30	H	30	THR	0	-0.020	-0.019	11.693	0.012	0.012	0.000	0.000	0.000	0.000
31	H	31	GLY	0	-0.044	-0.026	12.851	-0.152	-0.152	0.000	0.000	0.000	0.000
32	H	32	ASN	0	0.021	0.025	9.499	-0.225	-0.225	0.000	0.000	0.000	0.000
33	H	33	TYR	0	0.026	0.009	13.528	-0.156	-0.156	0.000	0.000	0.000	0.000
34	H	34	MET	0	-0.025	0.010	12.476	0.177	0.177	0.000	0.000	0.000	0.000
35	H	35	HIS	0	0.034	0.031	15.737	-0.248	-0.248	0.000	0.000	0.000	0.000
36	H	36	TRP	0	0.017	-0.015	17.406	-0.013	-0.013	0.000	0.000	0.000	0.000
37	H	37	VAL	0	-0.010	0.000	18.940	-0.009	-0.009	0.000	0.000	0.000	0.000
38	H	38	ARG	1	0.777	0.859	21.254	-0.222	-0.222	0.000	0.000	0.000	0.000
39	H	39	GLN	0	-0.009	0.003	23.293	0.006	0.006	0.000	0.000	0.000	0.000
40	H	40	ALA	0	0.050	0.032	25.114	-0.018	-0.018	0.000	0.000	0.000	0.000
41	H	41	PRO	0	0.032	0.005	28.486	0.004	0.004	0.000	0.000	0.000	0.000
42	H	42	GLY	0	0.017	0.015	30.984	-0.001	-0.001	0.000	0.000	0.000	0.000
43	H	43	GLN	0	-0.066	-0.019	29.740	0.010	0.010	0.000	0.000	0.000	0.000
44	H	44	GLY	0	0.037	0.019	28.278	0.002	0.002	0.000	0.000	0.000	0.000
45	H	45	LEU	0	-0.021	-0.012	20.533	-0.007	-0.007	0.000	0.000	0.000	0.000
46	H	46	GLU	-1	-0.766	-0.857	24.934	0.230	0.230	0.000	0.000	0.000	0.000
47	H	47	TYR	0	-0.015	-0.028	20.200	-0.029	-0.029	0.000	0.000	0.000	0.000
48	H	48	MET	0	-0.047	-0.023	23.230	-0.036	-0.036	0.000	0.000	0.000	0.000
49	H	49	GLY	0	0.007	-0.004	23.129	-0.034	-0.034	0.000	0.000	0.000	0.000
50	H	50	TRP	0	-0.036	0.009	20.305	0.051	0.051	0.000	0.000	0.000	0.000
51	H	51	ILE	0	0.004	-0.005	19.188	-0.068	-0.068	0.000	0.000	0.000	0.000
52	H	52	ASN	0	0.038	0.033	18.928	0.133	0.133	0.000	0.000	0.000	0.000
53	H	53	PRO	0	0.016	-0.003	15.305	-0.101	-0.101	0.000	0.000	0.000	0.000
54	H	54	LYS	1	0.957	0.994	17.335	-0.929	-0.929	0.000	0.000	0.000	0.000
55	H	55	SER	0	0.006	0.005	19.471	-0.053	-0.053	0.000	0.000	0.000	0.000
56	H	56	GLY	0	-0.026	-0.020	22.303	-0.052	-0.052	0.000	0.000	0.000	0.000
57	H	57	ASP	-1	-0.879	-0.942	23.810	0.426	0.426	0.000	0.000	0.000	0.000
58	H	58	THR	0	-0.057	-0.030	23.479	0.034	0.034	0.000	0.000	0.000	0.000
59	H	59	ASN	0	0.040	0.030	25.005	-0.054	-0.054	0.000	0.000	0.000	0.000
60	H	60	TYR	0	0.025	-0.012	25.461	0.023	0.023	0.000	0.000	0.000	0.000
61	H	61	ALA	0	0.040	0.031	27.310	-0.007	-0.007	0.000	0.000	0.000	0.000
62	H	62	GLN	0	0.050	0.005	28.891	-0.023	-0.023	0.000	0.000	0.000	0.000
63	H	63	LYS	1	0.820	0.899	30.895	-0.217	-0.217	0.000	0.000	0.000	0.000
64	H	64	PHE	0	-0.009	-0.019	28.251	-0.018	-0.018	0.000	0.000	0.000	0.000
65	H	65	GLN	0	0.059	0.039	31.000	0.001	0.001	0.000	0.000	0.000	0.000
66	H	66	GLY	0	0.043	0.032	32.473	-0.015	-0.015	0.000	0.000	0.000	0.000
67	H	67	ARG	1	0.728	0.839	31.736	-0.187	-0.187	0.000	0.000	0.000	0.000
68	H	68	VAL	0	0.011	0.012	26.278	-0.013	-0.013	0.000	0.000	0.000	0.000
69	H	69	THR	0	-0.049	-0.024	27.850	-0.006	-0.006	0.000	0.000	0.000	0.000
70	H	70	MET	0	-0.017	0.016	22.535	-0.003	-0.003	0.000	0.000	0.000	0.000
71	H	71	THR	0	-0.006	-0.005	22.642	-0.015	-0.015	0.000	0.000	0.000	0.000
72	H	72	ARG	1	0.849	0.917	18.189	-0.418	-0.418	0.000	0.000	0.000	0.000
73	H	73	ASP	-1	-0.798	-0.871	18.502	0.159	0.159	0.000	0.000	0.000	0.000
74	H	74	THR	0	0.018	-0.014	16.401	0.030	0.030	0.000	0.000	0.000	0.000
75	H	75	SER	0	-0.060	-0.034	15.757	0.016	0.016	0.000	0.000	0.000	0.000
76	H	76	ILE	0	0.051	0.032	15.010	-0.047	-0.047	0.000	0.000	0.000	0.000
77	H	77	SER	0	-0.054	-0.015	11.665	0.030	0.030	0.000	0.000	0.000	0.000
78	H	78	THR	0	0.004	0.007	12.642	-0.005	-0.005	0.000	0.000	0.000	0.000
79	H	79	VAL	0	0.003	-0.002	15.309	0.018	0.018	0.000	0.000	0.000	0.000
80	H	80	TYR	0	-0.009	-0.016	17.586	-0.065	-0.065	0.000	0.000	0.000	0.000
81	H	81	MET	0	0.001	0.009	20.788	0.046	0.046	0.000	0.000	0.000	0.000
82	H	82	GLU	-1	-0.846	-0.892	23.349	0.106	0.106	0.000	0.000	0.000	0.000
83	H	83	VAL	0	0.011	0.006	26.405	0.018	0.018	0.000	0.000	0.000	0.000
84	H	84	ARG	1	1.000	0.981	29.110	-0.162	-0.162	0.000	0.000	0.000	0.000
85	H	85	ARG	1	0.875	0.929	32.897	-0.139	-0.139	0.000	0.000	0.000	0.000
86	H	86	LEU	0	0.005	0.025	30.551	0.003	0.003	0.000	0.000	0.000	0.000
87	H	87	ARG	1	0.799	0.872	33.688	-0.139	-0.139	0.000	0.000	0.000	0.000
88	H	88	SER	0	0.085	0.039	34.476	0.001	0.001	0.000	0.000	0.000	0.000
89	H	89	ASP	-1	-0.821	-0.896	33.904	0.123	0.123	0.000	0.000	0.000	0.000
90	H	90	ASP	-1	-0.741	-0.833	30.697	0.169	0.169	0.000	0.000	0.000	0.000
91	H	91	THR	0	0.004	0.026	29.518	0.000	0.000	0.000	0.000	0.000	0.000
92	H	92	ALA	0	-0.015	-0.011	26.409	0.006	0.006	0.000	0.000	0.000	0.000
93	H	93	VAL	0	0.008	0.014	20.843	-0.019	-0.019	0.000	0.000	0.000	0.000
94	H	94	TYR	0	-0.014	-0.039	21.800	0.041	0.041	0.000	0.000	0.000	0.000
95	H	95	TYR	0	0.019	0.016	16.029	-0.033	-0.033	0.000	0.000	0.000	0.000
96	H	97	ALA	0	0.051	0.012	12.913	-0.009	-0.009	0.000	0.000	0.000	0.000
97	H	98	THR	0	-0.044	-0.043	9.758	0.015	0.015	0.000	0.000	0.000	0.000
98	H	99	GLY	0	0.045	0.015	10.679	0.178	0.178	0.000	0.000	0.000	0.000
99	H	100	TRP	0	-0.034	-0.009	8.547	-0.240	-0.240	0.000	0.000	0.000	0.000
100	H	101	TRP	0	-0.020	-0.010	13.211	-0.226	-0.226	0.000	0.000	0.000	0.000
101	H	102	GLY	0	0.039	0.031	15.279	-0.134	-0.134	0.000	0.000	0.000	0.000
102	H	103	MET	0	-0.062	-0.028	14.331	0.046	0.046	0.000	0.000	0.000	0.000
103	H	104	ASP	-1	-0.831	-0.915	10.426	1.870	1.870	0.000	0.000	0.000	0.000
104	H	105	VAL	0	-0.033	-0.014	6.187	0.067	0.067	0.000	0.000	0.000	0.000
105	H	106	TRP	0	0.002	-0.019	9.420	-0.195	-0.195	0.000	0.000	0.000	0.000
106	H	107	GLY	0	0.019	0.016	10.401	-0.072	-0.072	0.000	0.000	0.000	0.000
107	H	108	GLN	0	0.009	0.000	12.625	0.039	0.039	0.000	0.000	0.000	0.000
108	H	109	GLY	0	0.004	0.006	14.446	0.002	0.002	0.000	0.000	0.000	0.000
109	H	110	THR	0	-0.049	-0.043	17.766	-0.039	-0.039	0.000	0.000	0.000	0.000
110	H	111	LEU	0	-0.009	0.009	20.933	0.027	0.027	0.000	0.000	0.000	0.000
111	H	112	VAL	0	-0.004	0.000	24.300	-0.017	-0.017	0.000	0.000	0.000	0.000
112	H	113	THR	0	0.000	-0.008	27.276	0.008	0.008	0.000	0.000	0.000	0.000
113	H	114	VAL	0	-0.037	-0.014	30.852	-0.008	-0.008	0.000	0.000	0.000	0.000
114	H	115	SER	0	-0.005	-0.001	33.749	-0.003	-0.003	0.000	0.000	0.000	0.000
115	H	116	SER	0	0.060	0.027	36.678	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:1:GLN)