FMO DATABASE

FMODB ID: N999Q

Calculation Name: 4FD9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FD9

Chain ID: A

ChEMBL ID:

UniProt ID: Q80W49

Base Structure: X-ray

Registration Date: 2023-06-21

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668478.058535
FMO2-HF: Nuclear repulsion	631999.456757
FMO2-HF: Total energy	-36478.601778
FMO2-MP2: Total energy	-36585.405417

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:1:MET)

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

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.
-11.544	-4.272	6.11	-3.767	-9.615	-0.013

Interaction energy analysis for fragmet #1(A:1:MET)

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 : -0.001

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	3	LEU	0	0.003	0.006	2.262	-1.847	1.313	1.465	-1.450	-3.175	0.001
4	A	4	LYS	1	0.833	0.902	5.127	1.293	1.340	-0.001	-0.005	-0.041	0.000
5	A	5	VAL	0	-0.014	0.012	8.729	0.294	0.294	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.014	-0.005	11.570	-0.071	-0.071	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.019	-0.004	15.257	0.083	0.083	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.040	0.003	18.028	-0.036	-0.036	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.769	-0.878	21.685	-0.179	-0.179	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.811	0.897	25.126	0.202	0.202	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.029	0.015	24.761	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.079	-0.054	24.639	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.042	-0.015	19.432	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.022	0.004	23.208	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.024	-0.023	25.749	0.000	0.000	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.003	0.001	25.218	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.003	-0.006	19.796	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.759	0.882	18.520	0.448	0.448	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.797	-0.892	14.267	-0.859	-0.859	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.048	-0.020	10.127	0.078	0.078	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.036	0.002	7.255	-0.146	-0.146	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.902	-0.939	6.953	-2.042	-2.042	0.000	0.000	0.000	0.000
23	A	23	HIS	0	-0.006	-0.004	5.825	0.291	0.291	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.002	0.024	9.981	0.066	0.066	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.793	-0.901	13.576	-0.197	-0.197	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.008	-0.027	15.479	0.065	0.065	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.023	0.019	17.154	-0.042	-0.042	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.018	-0.003	19.169	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.032	-0.033	20.276	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.022	-0.012	16.086	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.011	0.003	19.614	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.933	0.987	22.624	0.362	0.362	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.051	-0.008	25.355	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.875	-0.947	27.049	-0.223	-0.223	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.878	0.934	25.599	0.351	0.351	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.835	-0.905	23.917	-0.390	-0.390	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.009	0.002	21.216	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.015	-0.024	24.734	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.009	0.015	24.583	0.019	0.019	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.025	-0.035	18.562	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.007	0.014	22.740	0.026	0.026	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.033	-0.016	21.366	0.017	0.017	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.029	-0.025	15.042	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.873	0.939	15.071	0.317	0.317	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.036	-0.002	9.042	-0.154	-0.154	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.014	-0.016	10.390	0.117	0.117	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.020	0.023	6.208	-0.047	-0.047	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.031	0.012	3.964	-0.700	-0.539	0.002	-0.048	-0.115	0.000
49	A	49	VAL	0	-0.008	-0.002	4.684	-0.416	-0.285	-0.001	-0.023	-0.107	0.000
50	A	50	TRP	0	-0.033	-0.034	5.725	-0.309	-0.309	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.033	-0.009	8.308	0.165	0.165	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.028	0.026	11.220	-0.144	-0.144	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.028	-0.023	11.873	0.076	0.076	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.723	-0.838	16.786	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.788	0.868	19.717	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.761	-0.846	18.683	-0.217	-0.217	0.000	0.000	0.000	0.000
57	A	57	HIS	1	0.759	0.845	16.973	0.256	0.256	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.010	0.006	12.608	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.873	0.940	15.579	0.111	0.111	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.022	0.009	18.879	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.010	-0.019	19.916	0.024	0.024	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.014	0.014	14.831	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.027	0.012	15.673	0.029	0.029	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.021	0.001	10.552	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.003	-0.011	11.671	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.911	-0.967	10.152	0.909	0.909	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.867	-0.936	6.347	0.135	0.135	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.006	0.003	10.478	0.076	0.076	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.872	-0.914	14.056	-0.308	-0.308	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.014	-0.022	13.812	0.043	0.043	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.838	-0.926	19.205	-0.072	-0.072	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.744	-0.859	22.694	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.005	-0.009	23.270	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.138	-0.087	24.579	0.022	0.022	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.029	0.035	21.118	0.022	0.022	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.022	-0.019	17.199	0.038	0.038	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.052	0.033	20.473	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.002	0.004	18.249	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.022	-0.009	20.330	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.077	-0.042	22.575	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.014	-0.009	24.032	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.027	-0.019	23.448	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.012	0.020	16.918	0.015	0.015	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.041	-0.021	19.108	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.052	-0.030	15.020	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.041	0.016	11.507	0.054	0.054	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.882	0.945	8.256	-0.197	-0.197	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.053	0.039	2.555	-0.867	0.011	0.791	-0.341	-1.329	-0.002
89	A	89	LEU	0	-0.055	-0.039	4.622	-0.179	-0.030	-0.001	-0.033	-0.114	0.000
90	A	90	GLN	0	0.037	0.002	2.263	-6.353	-3.610	3.815	-2.216	-4.341	-0.013
91	A	91	ALA	0	-0.007	0.006	3.407	-1.644	-1.732	0.041	0.353	-0.306	0.001
92	A	92	ASN	0	0.003	0.003	6.091	0.537	0.628	-0.001	-0.004	-0.087	0.000

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