FMO DATABASE

FMODB ID: J3Y79

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	OptHSide
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	-470643.461396
FMO2-HF: Nuclear repulsion	440932.597273
FMO2-HF: Total energy	-29710.864122
FMO2-MP2: Total energy	-29800.238549

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.
-2.102	1.97	0.532	-1.672	-2.932	-0.01

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 : 0.006 / q_NPA : -0.002

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	-0.735	-0.848	3.819	-1.638	0.021	-0.013	-0.619	-1.027	0.003
4	A	61	SER	0	-0.014	-0.008	5.165	0.126	0.248	-0.001	-0.005	-0.116	0.000
5	A	62	LEU	0	0.054	0.018	5.952	0.064	0.064	0.000	0.000	0.000	0.000
6	A	63	LYS	1	0.898	0.933	3.573	0.224	0.655	0.007	-0.063	-0.376	0.000
7	A	64	LYS	1	0.841	0.900	5.963	0.469	0.469	0.000	0.000	0.000	0.000
8	A	65	PHE	0	0.030	0.031	9.340	0.038	0.038	0.000	0.000	0.000	0.000
9	A	66	LEU	0	0.031	0.015	7.058	0.032	0.032	0.000	0.000	0.000	0.000
10	A	67	ASN	0	-0.084	-0.019	9.968	0.006	0.006	0.000	0.000	0.000	0.000
11	A	68	THR	0	-0.046	-0.023	11.702	0.017	0.017	0.000	0.000	0.000	0.000
12	A	69	LYS	1	0.896	0.939	14.939	0.053	0.053	0.000	0.000	0.000	0.000
13	A	70	ASP	-1	-0.855	-0.939	17.888	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	71	GLY	0	0.014	0.003	14.159	0.013	0.013	0.000	0.000	0.000	0.000
15	A	72	ARG	1	0.819	0.892	13.471	0.106	0.106	0.000	0.000	0.000	0.000
16	A	73	LEU	0	-0.010	0.009	14.857	0.014	0.014	0.000	0.000	0.000	0.000
17	A	74	VAL	0	0.006	0.005	15.985	0.013	0.013	0.000	0.000	0.000	0.000
18	A	75	ALA	0	0.012	0.001	12.712	0.018	0.018	0.000	0.000	0.000	0.000
19	A	76	SER	0	-0.016	-0.028	14.629	0.016	0.016	0.000	0.000	0.000	0.000
20	A	77	LEU	0	0.005	0.005	17.155	0.009	0.009	0.000	0.000	0.000	0.000
21	A	78	VAL	0	-0.036	-0.004	15.115	0.008	0.008	0.000	0.000	0.000	0.000
22	A	79	ALA	0	0.020	0.003	15.103	0.012	0.012	0.000	0.000	0.000	0.000
23	A	80	GLU	-1	-0.762	-0.875	16.928	0.040	0.040	0.000	0.000	0.000	0.000
24	A	81	PHE	0	0.018	-0.001	20.361	0.000	0.000	0.000	0.000	0.000	0.000
25	A	82	LEU	0	-0.028	-0.021	15.801	0.004	0.004	0.000	0.000	0.000	0.000
26	A	83	GLN	0	-0.017	-0.010	19.224	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	84	PHE	0	-0.031	0.010	21.728	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	85	PHE	0	-0.050	-0.028	23.935	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	86	ASN	0	-0.018	-0.001	23.776	0.002	0.002	0.000	0.000	0.000	0.000
30	A	87	LEU	0	-0.010	0.009	20.555	0.008	0.008	0.000	0.000	0.000	0.000
31	A	88	ASP	-1	-0.854	-0.948	19.419	0.112	0.112	0.000	0.000	0.000	0.000
32	A	89	PHE	0	-0.028	-0.024	18.630	0.013	0.013	0.000	0.000	0.000	0.000
33	A	90	THR	0	0.003	-0.002	15.943	0.033	0.033	0.000	0.000	0.000	0.000
34	A	91	LEU	0	0.024	0.011	14.780	0.045	0.045	0.000	0.000	0.000	0.000
35	A	92	ALA	0	-0.029	-0.008	13.963	0.014	0.014	0.000	0.000	0.000	0.000
36	A	93	VAL	0	-0.016	-0.005	11.447	0.029	0.029	0.000	0.000	0.000	0.000
37	A	94	PHE	0	0.049	0.018	10.248	0.119	0.119	0.000	0.000	0.000	0.000
38	A	95	GLN	0	0.041	0.045	9.386	0.023	0.023	0.000	0.000	0.000	0.000
39	A	96	PRO	0	-0.024	-0.015	7.328	-0.065	-0.065	0.000	0.000	0.000	0.000
40	A	97	GLU	-1	-0.979	-0.972	5.745	1.187	1.187	0.000	0.000	0.000	0.000
41	A	98	THR	0	-0.061	-0.048	5.027	0.233	0.271	-0.001	-0.003	-0.034	0.000
42	A	99	SER	0	-0.071	-0.034	2.691	-3.267	-1.471	0.541	-0.976	-1.360	-0.013
43	A	100	THR	0	-0.015	-0.013	5.013	-0.140	-0.114	-0.001	-0.006	-0.019	0.000
44	A	101	LEU	0	0.002	0.003	7.077	0.057	0.057	0.000	0.000	0.000	0.000
45	A	102	GLN	0	0.002	-0.018	10.209	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	103	GLY	0	0.000	0.018	12.821	0.007	0.007	0.000	0.000	0.000	0.000
47	A	104	LEU	0	-0.060	-0.033	12.321	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	105	GLU	-1	-0.830	-0.897	14.892	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	106	GLY	0	0.058	0.025	18.601	0.010	0.010	0.000	0.000	0.000	0.000
50	A	107	ARG	1	0.767	0.821	21.140	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	108	GLU	-1	-0.905	-0.942	24.223	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	109	ASN	0	-0.005	-0.012	21.810	0.001	0.001	0.000	0.000	0.000	0.000
53	A	110	LEU	0	-0.017	0.002	20.588	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	111	ALA	0	0.027	0.009	23.598	0.000	0.000	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.861	0.924	24.331	0.024	0.024	0.000	0.000	0.000	0.000
56	A	113	ASP	-1	-0.865	-0.929	22.798	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	114	LEU	0	-0.043	-0.020	23.009	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	115	GLY	0	-0.015	0.009	26.670	0.002	0.002	0.000	0.000	0.000	0.000
59	A	116	ILE	0	-0.071	-0.035	27.540	0.002	0.002	0.000	0.000	0.000	0.000
60	A	117	ILE	0	-0.025	-0.019	31.100	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	118	GLU	-1	-0.818	-0.860	30.108	0.016	0.016	0.000	0.000	0.000	0.000
62	A	119	ALA	0	0.028	0.007	33.632	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	120	GLU	-1	-0.862	-0.937	36.024	0.012	0.012	0.000	0.000	0.000	0.000
64	A	121	GLY	0	-0.049	-0.015	37.314	0.002	0.002	0.000	0.000	0.000	0.000
65	A	122	THR	0	-0.023	-0.041	32.010	0.001	0.001	0.000	0.000	0.000	0.000
66	A	123	VAL	0	0.007	0.003	31.775	0.003	0.003	0.000	0.000	0.000	0.000
67	A	124	GLY	0	-0.022	-0.004	31.934	0.002	0.002	0.000	0.000	0.000	0.000
68	A	125	GLY	0	-0.024	-0.008	30.133	0.003	0.003	0.000	0.000	0.000	0.000
69	A	126	PRO	0	0.014	0.040	24.784	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	127	LEU	0	0.046	0.002	24.378	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	128	LEU	0	-0.015	-0.013	21.677	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	129	LEU	0	-0.015	-0.005	25.230	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	130	GLU	-1	-0.770	-0.867	28.651	0.012	0.012	0.000	0.000	0.000	0.000
74	A	131	VAL	0	-0.027	-0.018	25.687	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	132	ILE	0	-0.018	-0.015	26.106	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	133	ARG	1	0.804	0.890	29.566	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	134	ARG	1	0.847	0.914	32.223	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	135	TRP	0	-0.042	0.009	27.770	-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)