FMO DATABASE

FMODB ID: G6661

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

Total energy (hartree)

FMO2-HF: Electronic energy	-667216.711037
FMO2-HF: Nuclear repulsion	630738.658533
FMO2-HF: Total energy	-36478.052504
FMO2-MP2: Total energy	-36584.832584

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.
-7.799	-0.6	4.349	-2.76	-8.789	-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 : -0.026 / q_NPA : -0.024

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

Sort

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	-0.008	0.005	2.601	-1.429	1.446	1.020	-0.852	-3.043	0.001
4	A	4	LYS	1	0.972	0.981	4.920	0.679	0.726	-0.001	-0.007	-0.039	0.000
5	A	5	VAL	0	0.002	0.024	8.541	0.237	0.237	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.027	-0.018	11.292	-0.053	-0.053	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.030	-0.008	14.907	0.052	0.052	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.048	0.012	17.288	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.846	-0.922	21.204	-0.116	-0.116	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.917	0.958	24.644	0.099	0.099	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.028	0.017	24.394	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.037	-0.030	24.163	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.044	-0.026	18.911	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.022	0.007	22.677	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.051	-0.029	25.113	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.016	0.002	24.831	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.015	-0.002	19.248	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.801	0.915	18.067	0.323	0.323	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.930	-0.965	14.138	-0.438	-0.438	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.035	-0.022	10.360	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.033	0.001	7.167	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.951	-0.963	7.254	-1.531	-1.531	0.000	0.000	0.000	0.000
23	A	23	HIS	0	0.010	0.006	5.884	0.368	0.368	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.023	0.026	9.579	0.050	0.050	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.806	-0.901	13.211	-0.279	-0.279	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.025	-0.062	15.280	0.060	0.060	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.026	0.016	17.232	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.019	0.002	19.116	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.028	-0.016	20.377	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.033	-0.022	16.053	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.037	-0.010	19.591	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.966	0.992	22.570	0.282	0.282	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.109	-0.044	24.841	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.824	-0.930	26.641	-0.144	-0.144	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.841	0.936	25.357	0.237	0.237	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.844	-0.920	23.460	-0.268	-0.268	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.006	0.012	21.132	0.015	0.015	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.007	-0.020	25.166	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.010	0.004	24.598	0.014	0.014	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.015	-0.017	18.614	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.022	0.014	22.653	0.015	0.015	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.035	-0.020	20.846	0.016	0.016	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.028	-0.015	14.610	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.892	0.969	14.588	0.113	0.113	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.035	-0.003	8.924	-0.107	-0.107	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.034	-0.018	9.672	0.074	0.074	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.034	0.020	5.939	0.075	0.075	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.006	-0.009	3.756	-0.515	-0.317	0.006	-0.062	-0.142	0.000
49	A	49	VAL	0	0.009	0.012	4.585	-0.468	-0.312	-0.001	-0.034	-0.121	0.000
50	A	50	TRP	0	-0.031	-0.035	6.159	-0.233	-0.233	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.020	0.001	8.696	0.088	0.088	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.010	0.012	11.513	-0.118	-0.118	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.016	0.005	12.082	0.036	0.036	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.779	-0.885	16.969	-0.084	-0.084	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.887	0.941	19.844	0.085	0.085	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.810	-0.869	18.651	-0.239	-0.239	0.000	0.000	0.000	0.000
57	A	57	HIS	1	0.787	0.860	16.644	0.301	0.301	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.027	-0.012	12.105	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.901	0.967	15.715	0.200	0.200	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.010	-0.011	19.128	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.003	-0.017	19.648	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	GLN	0	-0.015	-0.009	15.312	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.015	0.014	16.051	0.024	0.024	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.021	-0.003	10.783	-0.037	-0.037	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.007	-0.011	12.147	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.913	-0.961	9.871	0.671	0.671	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.868	-0.944	6.240	0.340	0.340	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.017	0.010	10.431	0.039	0.039	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.921	-0.960	14.044	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.024	-0.020	13.607	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.837	-0.932	18.929	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.759	-0.871	22.296	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.030	-0.029	22.982	0.010	0.010	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.116	-0.068	24.678	0.012	0.012	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.033	0.038	20.744	0.014	0.014	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.035	-0.021	17.440	0.022	0.022	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.057	0.027	20.615	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.001	-0.002	18.298	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.018	-0.007	20.030	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.105	-0.050	22.603	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.001	-0.007	24.128	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.040	-0.023	23.200	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.047	0.046	16.814	0.004	0.004	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.044	-0.029	19.190	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.044	-0.023	14.836	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.053	0.030	11.162	0.054	0.054	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.881	0.947	8.010	0.145	0.145	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.039	0.029	2.480	-0.683	0.120	0.790	-0.311	-1.282	-0.003
89	A	89	LEU	0	-0.052	-0.040	4.866	-0.551	-0.428	-0.001	-0.023	-0.098	0.000
90	A	90	GLN	0	0.024	-0.005	2.253	-3.690	-0.764	2.525	-1.605	-3.847	-0.011
91	A	91	ALA	0	-0.014	0.007	3.714	-1.093	-1.022	0.011	0.134	-0.217	0.000
92	A	92	ASN	0	0.005	0.004	5.877	-0.164	-0.164	0.000	0.000	0.000	0.000

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