FMO DATABASE

FMODB ID: N18JQ

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	OptH
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	-470005.105394
FMO2-HF: Nuclear repulsion	440294.589525
FMO2-HF: Total energy	-29710.51587
FMO2-MP2: Total energy	-29799.907419

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.
-1.853	2.02	0.889	-1.695	-3.066	-0.014

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 : 0.004 / q_NPA : -0.004

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	-0.842	-0.935	3.819	-1.648	-0.058	-0.013	-0.583	-0.994	0.002
4	A	61	SER	0	-0.011	-0.006	5.277	0.230	0.347	-0.001	-0.004	-0.112	0.000
5	A	62	LEU	0	0.053	0.021	5.798	0.100	0.100	0.000	0.000	0.000	0.000
6	A	63	LYS	1	0.958	0.985	3.787	0.277	0.642	0.003	-0.051	-0.317	0.000
7	A	64	LYS	1	0.905	0.942	5.913	0.565	0.565	0.000	0.000	0.000	0.000
8	A	65	PHE	0	0.030	0.034	9.271	0.057	0.057	0.000	0.000	0.000	0.000
9	A	66	LEU	0	0.022	0.019	7.054	0.050	0.050	0.000	0.000	0.000	0.000
10	A	67	ASN	0	-0.083	-0.020	9.991	0.038	0.038	0.000	0.000	0.000	0.000
11	A	68	THR	0	-0.046	-0.029	11.676	0.022	0.022	0.000	0.000	0.000	0.000
12	A	69	LYS	1	0.978	0.984	14.904	0.058	0.058	0.000	0.000	0.000	0.000
13	A	70	ASP	-1	-0.852	-0.940	17.875	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	71	GLY	0	0.017	0.004	14.127	0.013	0.013	0.000	0.000	0.000	0.000
15	A	72	ARG	1	0.830	0.915	13.214	0.091	0.091	0.000	0.000	0.000	0.000
16	A	73	LEU	0	0.000	0.003	14.859	0.017	0.017	0.000	0.000	0.000	0.000
17	A	74	VAL	0	0.007	0.007	15.918	0.014	0.014	0.000	0.000	0.000	0.000
18	A	75	ALA	0	0.009	-0.003	12.702	0.019	0.019	0.000	0.000	0.000	0.000
19	A	76	SER	0	-0.001	-0.008	14.611	0.023	0.023	0.000	0.000	0.000	0.000
20	A	77	LEU	0	0.007	0.007	16.916	0.012	0.012	0.000	0.000	0.000	0.000
21	A	78	VAL	0	-0.037	-0.003	15.077	0.009	0.009	0.000	0.000	0.000	0.000
22	A	79	ALA	0	0.030	0.006	15.005	0.015	0.015	0.000	0.000	0.000	0.000
23	A	80	GLU	-1	-0.769	-0.880	16.918	0.046	0.046	0.000	0.000	0.000	0.000
24	A	81	PHE	0	0.008	-0.001	20.311	0.001	0.001	0.000	0.000	0.000	0.000
25	A	82	LEU	0	-0.028	-0.023	15.740	0.005	0.005	0.000	0.000	0.000	0.000
26	A	83	GLN	0	-0.027	-0.013	18.674	0.003	0.003	0.000	0.000	0.000	0.000
27	A	84	PHE	0	-0.029	0.011	21.658	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	85	PHE	0	-0.052	-0.030	23.930	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	86	ASN	0	-0.003	0.008	23.819	0.004	0.004	0.000	0.000	0.000	0.000
30	A	87	LEU	0	-0.017	0.004	20.554	0.008	0.008	0.000	0.000	0.000	0.000
31	A	88	ASP	-1	-0.858	-0.953	19.420	0.131	0.131	0.000	0.000	0.000	0.000
32	A	89	PHE	0	-0.030	-0.022	18.635	0.017	0.017	0.000	0.000	0.000	0.000
33	A	90	THR	0	-0.003	-0.002	16.059	0.038	0.038	0.000	0.000	0.000	0.000
34	A	91	LEU	0	0.025	0.010	14.782	0.048	0.048	0.000	0.000	0.000	0.000
35	A	92	ALA	0	-0.029	-0.008	13.966	0.022	0.022	0.000	0.000	0.000	0.000
36	A	93	VAL	0	-0.013	-0.005	11.481	0.043	0.043	0.000	0.000	0.000	0.000
37	A	94	PHE	0	0.042	0.017	10.254	0.132	0.132	0.000	0.000	0.000	0.000
38	A	95	GLN	0	0.047	0.045	9.385	0.018	0.018	0.000	0.000	0.000	0.000
39	A	96	PRO	0	-0.023	-0.013	7.321	-0.053	-0.053	0.000	0.000	0.000	0.000
40	A	97	GLU	-1	-0.973	-0.972	5.756	1.331	1.331	0.000	0.000	0.000	0.000
41	A	98	THR	0	-0.068	-0.043	5.025	0.189	0.230	-0.001	-0.003	-0.037	0.000
42	A	99	SER	0	-0.069	-0.035	2.553	-3.553	-1.829	0.902	-1.044	-1.582	-0.016
43	A	100	THR	0	-0.020	-0.018	4.848	-0.145	-0.109	-0.001	-0.010	-0.024	0.000
44	A	101	LEU	0	0.000	-0.002	7.011	0.061	0.061	0.000	0.000	0.000	0.000
45	A	102	GLN	0	0.003	-0.016	10.044	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	103	GLY	0	-0.002	0.019	12.444	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	104	LEU	0	-0.075	-0.049	11.895	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	105	GLU	-1	-0.868	-0.934	14.666	-0.032	-0.032	0.000	0.000	0.000	0.000
49	A	106	GLY	0	0.044	0.022	18.366	0.009	0.009	0.000	0.000	0.000	0.000
50	A	107	ARG	1	0.754	0.823	20.926	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	108	GLU	-1	-0.912	-0.945	23.999	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	109	ASN	0	0.033	0.008	22.273	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	110	LEU	0	0.022	0.028	20.452	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	111	ALA	0	0.021	0.003	23.343	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	112	ARG	1	0.894	0.944	24.823	0.015	0.015	0.000	0.000	0.000	0.000
56	A	113	ASP	-1	-0.979	-0.991	22.487	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	114	LEU	0	-0.069	-0.036	23.163	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	115	GLY	0	-0.020	0.005	26.676	0.001	0.001	0.000	0.000	0.000	0.000
59	A	116	ILE	0	-0.071	-0.035	27.551	0.002	0.002	0.000	0.000	0.000	0.000
60	A	117	ILE	0	-0.026	-0.020	31.024	0.000	0.000	0.000	0.000	0.000	0.000
61	A	118	GLU	-1	-0.794	-0.866	29.674	0.019	0.019	0.000	0.000	0.000	0.000
62	A	119	ALA	0	0.022	0.005	33.390	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	120	GLU	-1	-0.868	-0.940	35.803	0.014	0.014	0.000	0.000	0.000	0.000
64	A	121	GLY	0	-0.062	-0.024	37.301	0.002	0.002	0.000	0.000	0.000	0.000
65	A	122	THR	0	-0.030	-0.031	31.930	0.001	0.001	0.000	0.000	0.000	0.000
66	A	123	VAL	0	-0.007	-0.006	31.752	0.003	0.003	0.000	0.000	0.000	0.000
67	A	124	GLY	0	-0.025	-0.005	31.818	0.003	0.003	0.000	0.000	0.000	0.000
68	A	125	GLY	0	-0.030	-0.014	30.124	0.003	0.003	0.000	0.000	0.000	0.000
69	A	126	PRO	0	0.012	0.032	24.819	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	127	LEU	0	0.061	0.009	24.150	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	128	LEU	0	-0.004	-0.010	21.444	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	129	LEU	0	-0.032	-0.012	25.214	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	130	GLU	-1	-0.845	-0.927	28.637	0.009	0.009	0.000	0.000	0.000	0.000
74	A	131	VAL	0	-0.019	-0.014	25.732	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	132	ILE	0	-0.017	-0.014	26.467	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	133	ARG	1	0.902	0.951	29.548	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	134	ARG	1	0.869	0.941	32.217	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	135	TRP	0	-0.040	0.012	27.893	-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)