FMO DATABASE

FMODB ID: 3QZ8L

Calculation Name: 2D68-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D68

Chain ID: A

ChEMBL ID:

UniProt ID: O95684

Base Structure: X-ray

Registration Date: 2023-03-13

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-473909.207421
FMO2-HF: Nuclear repulsion	444198.282883
FMO2-HF: Total energy	-29710.924537
FMO2-MP2: Total energy	-29800.263206

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:58:VAL)

Summations of interaction energy for fragment #1(A:58:VAL)

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.
-2.011	2.065	0.375	-1.516	-2.936	-0.007

Interaction energy analysis for fragmet #1(A:58:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.007

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	60	GLU	-1	-0.748	-0.853	3.650	-2.171	-0.332	0.007	-0.658	-1.188	0.002
4	A	61	SER	0	-0.025	-0.013	4.308	0.234	0.408	0.000	-0.017	-0.157	0.000
5	A	62	LEU	0	0.055	0.025	6.202	0.106	0.106	0.000	0.000	0.000	0.000
6	A	63	LYS	1	0.891	0.934	3.342	0.596	1.108	0.020	-0.084	-0.449	0.000
7	A	64	LYS	1	0.850	0.904	5.850	0.764	0.764	0.000	0.000	0.000	0.000
8	A	65	PHE	0	0.019	0.032	9.270	0.071	0.071	0.000	0.000	0.000	0.000
9	A	66	LEU	0	0.036	0.017	6.907	0.065	0.065	0.000	0.000	0.000	0.000
10	A	67	ASN	0	-0.106	-0.035	9.947	0.006	0.006	0.000	0.000	0.000	0.000
11	A	68	THR	0	-0.030	-0.019	11.657	0.047	0.047	0.000	0.000	0.000	0.000
12	A	69	LYS	1	0.894	0.938	14.938	0.121	0.121	0.000	0.000	0.000	0.000
13	A	70	ASP	-1	-0.847	-0.931	17.718	-0.120	-0.120	0.000	0.000	0.000	0.000
14	A	71	GLY	0	0.037	0.010	14.107	0.014	0.014	0.000	0.000	0.000	0.000
15	A	72	ARG	1	0.810	0.886	13.233	0.220	0.220	0.000	0.000	0.000	0.000
16	A	73	LEU	0	-0.011	0.009	14.605	0.016	0.016	0.000	0.000	0.000	0.000
17	A	74	VAL	0	0.010	0.003	16.051	0.015	0.015	0.000	0.000	0.000	0.000
18	A	75	ALA	0	0.010	-0.002	12.510	0.019	0.019	0.000	0.000	0.000	0.000
19	A	76	SER	0	-0.009	-0.023	14.418	0.018	0.018	0.000	0.000	0.000	0.000
20	A	77	LEU	0	-0.001	0.006	16.965	0.017	0.017	0.000	0.000	0.000	0.000
21	A	78	VAL	0	-0.035	-0.006	15.184	0.015	0.015	0.000	0.000	0.000	0.000
22	A	79	ALA	0	0.017	0.007	15.417	0.018	0.018	0.000	0.000	0.000	0.000
23	A	80	GLU	-1	-0.757	-0.876	17.284	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	81	PHE	0	0.024	-0.001	20.607	0.008	0.008	0.000	0.000	0.000	0.000
25	A	82	LEU	0	-0.026	-0.021	16.097	0.011	0.011	0.000	0.000	0.000	0.000
26	A	83	GLN	0	-0.022	-0.012	19.330	0.000	0.000	0.000	0.000	0.000	0.000
27	A	84	PHE	0	-0.030	0.007	21.829	0.004	0.004	0.000	0.000	0.000	0.000
28	A	85	PHE	0	-0.035	-0.020	24.184	0.000	0.000	0.000	0.000	0.000	0.000
29	A	86	ASN	0	-0.015	-0.005	23.946	0.004	0.004	0.000	0.000	0.000	0.000
30	A	87	LEU	0	0.000	0.013	20.648	0.010	0.010	0.000	0.000	0.000	0.000
31	A	88	ASP	-1	-0.866	-0.947	19.398	0.061	0.061	0.000	0.000	0.000	0.000
32	A	89	PHE	0	-0.033	-0.027	18.358	0.011	0.011	0.000	0.000	0.000	0.000
33	A	90	THR	0	0.005	0.005	15.860	0.033	0.033	0.000	0.000	0.000	0.000
34	A	91	LEU	0	0.004	0.005	14.730	0.024	0.024	0.000	0.000	0.000	0.000
35	A	92	ALA	0	-0.029	-0.016	13.753	0.001	0.001	0.000	0.000	0.000	0.000
36	A	93	VAL	0	-0.012	0.007	11.234	0.031	0.031	0.000	0.000	0.000	0.000
37	A	94	PHE	0	0.060	0.016	10.160	0.062	0.062	0.000	0.000	0.000	0.000
38	A	95	GLN	0	0.029	0.051	9.489	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	96	PRO	0	-0.019	-0.009	7.198	-0.108	-0.108	0.000	0.000	0.000	0.000
40	A	97	GLU	-1	-0.966	-0.971	5.649	0.637	0.637	0.000	0.000	0.000	0.000
41	A	98	THR	0	-0.072	-0.061	4.877	-0.028	0.033	-0.001	-0.003	-0.057	0.000
42	A	99	SER	0	-0.060	-0.034	2.810	-2.636	-1.169	0.350	-0.751	-1.067	-0.009
43	A	100	THR	0	-0.027	-0.021	5.179	-0.069	-0.046	-0.001	-0.003	-0.018	0.000
44	A	101	LEU	0	0.019	0.012	7.313	0.089	0.089	0.000	0.000	0.000	0.000
45	A	102	GLN	0	-0.013	-0.031	10.089	0.002	0.002	0.000	0.000	0.000	0.000
46	A	103	GLY	0	-0.005	0.019	12.581	0.014	0.014	0.000	0.000	0.000	0.000
47	A	104	LEU	0	-0.063	-0.034	12.290	-0.037	-0.037	0.000	0.000	0.000	0.000
48	A	105	GLU	-1	-0.815	-0.892	15.346	-0.123	-0.123	0.000	0.000	0.000	0.000
49	A	106	GLY	0	0.068	0.030	19.024	0.011	0.011	0.000	0.000	0.000	0.000
50	A	107	ARG	1	0.743	0.811	21.251	0.017	0.017	0.000	0.000	0.000	0.000
51	A	108	GLU	-1	-0.906	-0.943	24.343	-0.046	-0.046	0.000	0.000	0.000	0.000
52	A	109	ASN	0	-0.026	-0.025	21.644	0.007	0.007	0.000	0.000	0.000	0.000
53	A	110	LEU	0	-0.027	-0.010	20.360	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	111	ALA	0	0.027	0.011	23.362	0.001	0.001	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.848	0.913	24.134	0.077	0.077	0.000	0.000	0.000	0.000
56	A	113	ASP	-1	-0.842	-0.909	22.985	-0.094	-0.094	0.000	0.000	0.000	0.000
57	A	114	LEU	0	-0.030	-0.006	22.713	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	115	GLY	0	-0.010	0.006	26.502	0.005	0.005	0.000	0.000	0.000	0.000
59	A	116	ILE	0	-0.069	-0.039	27.244	0.005	0.005	0.000	0.000	0.000	0.000
60	A	117	ILE	0	-0.012	-0.014	30.857	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	118	GLU	-1	-0.808	-0.853	30.383	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	119	ALA	0	0.035	0.020	33.527	0.000	0.000	0.000	0.000	0.000	0.000
63	A	120	GLU	-1	-0.878	-0.940	35.857	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	121	GLY	0	-0.027	-0.008	37.278	0.002	0.002	0.000	0.000	0.000	0.000
65	A	122	THR	0	-0.047	-0.052	31.875	0.002	0.002	0.000	0.000	0.000	0.000
66	A	123	VAL	0	0.017	0.011	31.800	0.001	0.001	0.000	0.000	0.000	0.000
67	A	124	GLY	0	-0.008	0.003	32.311	0.002	0.002	0.000	0.000	0.000	0.000
68	A	125	GLY	0	-0.018	-0.012	30.281	0.004	0.004	0.000	0.000	0.000	0.000
69	A	126	PRO	0	0.005	0.037	24.992	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	127	LEU	0	0.020	-0.004	24.279	0.000	0.000	0.000	0.000	0.000	0.000
71	A	128	LEU	0	-0.002	-0.003	21.728	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	129	LEU	0	-0.011	-0.003	25.200	0.001	0.001	0.000	0.000	0.000	0.000
73	A	130	GLU	-1	-0.750	-0.857	28.667	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	131	VAL	0	-0.026	-0.017	25.356	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	132	ILE	0	-0.026	-0.014	26.102	0.000	0.000	0.000	0.000	0.000	0.000
76	A	133	ARG	1	0.771	0.861	29.415	0.011	0.011	0.000	0.000	0.000	0.000
77	A	134	ARG	1	0.831	0.913	31.908	0.029	0.029	0.000	0.000	0.000	0.000
78	A	135	TRP	0	-0.041	0.003	27.258	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:58:VAL)