FMO DATABASE

FMODB ID: R9GV8

Calculation Name: 3B4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q86U42

Base Structure: X-ray

Registration Date: 2023-09-19

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-513695.95393
FMO2-HF: Nuclear repulsion	482653.298954
FMO2-HF: Total energy	-31042.654977
FMO2-MP2: Total energy	-31133.710077

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:169:ALA)

Summations of interaction energy for fragment #1(A:169:ALA)

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.
-7.94	-1.26	3.348	-4.318	-5.71	-0.01

Interaction energy analysis for fragmet #1(A:169:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.005

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	171	ALA	0	-0.029	-0.017	3.164	-2.318	0.048	0.046	-1.144	-1.268	0.005
4	A	172	ARG	1	0.779	0.863	2.614	-1.766	-0.088	2.939	-1.801	-2.816	-0.006
5	A	173	SER	0	0.000	-0.008	3.909	-0.900	-0.335	-0.001	-0.260	-0.304	0.001
6	A	174	ILE	0	-0.004	0.022	6.168	0.435	0.435	0.000	0.000	0.000	0.000
7	A	175	TYR	0	-0.013	-0.020	9.923	-0.171	-0.171	0.000	0.000	0.000	0.000
8	A	176	VAL	0	0.058	0.025	12.184	0.085	0.085	0.000	0.000	0.000	0.000
9	A	177	GLY	0	-0.020	-0.025	15.039	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	178	ASN	0	-0.024	-0.026	18.105	0.013	0.013	0.000	0.000	0.000	0.000
11	A	179	VAL	0	0.055	0.041	16.682	0.012	0.012	0.000	0.000	0.000	0.000
12	A	180	ASP	-1	-0.830	-0.893	19.964	-0.175	-0.175	0.000	0.000	0.000	0.000
13	A	181	TYR	0	-0.042	-0.046	21.401	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	182	GLY	0	-0.024	-0.013	23.184	0.000	0.000	0.000	0.000	0.000	0.000
15	A	183	ALA	0	-0.047	-0.012	19.583	0.006	0.006	0.000	0.000	0.000	0.000
16	A	184	THR	0	-0.016	-0.026	19.299	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	185	ALA	0	0.007	-0.022	14.567	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	186	GLU	-1	-0.939	-0.960	16.116	-0.187	-0.187	0.000	0.000	0.000	0.000
19	A	187	GLU	-1	-0.693	-0.816	18.505	-0.174	-0.174	0.000	0.000	0.000	0.000
20	A	188	LEU	0	-0.048	-0.031	14.603	0.005	0.005	0.000	0.000	0.000	0.000
21	A	189	GLU	-1	-0.885	-0.936	13.984	-0.210	-0.210	0.000	0.000	0.000	0.000
22	A	190	ALA	0	0.052	0.025	15.653	0.031	0.031	0.000	0.000	0.000	0.000
23	A	191	HIS	0	-0.094	-0.045	18.155	0.023	0.023	0.000	0.000	0.000	0.000
24	A	192	PHE	0	-0.017	-0.040	13.966	0.015	0.015	0.000	0.000	0.000	0.000
25	A	193	HIS	0	-0.032	-0.008	15.303	0.055	0.055	0.000	0.000	0.000	0.000
26	A	194	GLY	0	-0.006	-0.005	16.698	0.023	0.023	0.000	0.000	0.000	0.000
27	A	195	CYS	0	-0.097	-0.035	14.086	0.029	0.029	0.000	0.000	0.000	0.000
28	A	196	GLY	0	0.004	-0.003	12.899	0.070	0.070	0.000	0.000	0.000	0.000
29	A	197	SER	0	0.016	0.014	11.198	-0.066	-0.066	0.000	0.000	0.000	0.000
30	A	198	VAL	0	0.013	0.009	9.716	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	199	ASN	0	-0.020	-0.004	6.381	0.236	0.236	0.000	0.000	0.000	0.000
32	A	200	ARG	1	0.945	0.968	5.811	1.294	1.294	0.000	0.000	0.000	0.000
33	A	201	VAL	0	0.039	0.036	8.173	-0.085	-0.085	0.000	0.000	0.000	0.000
34	A	202	THR	0	-0.069	-0.034	8.283	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	203	ILE	0	0.063	0.025	10.811	0.008	0.008	0.000	0.000	0.000	0.000
36	A	204	LEU	0	-0.051	-0.020	11.564	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	205	CYS	0	-0.023	-0.004	15.841	0.025	0.025	0.000	0.000	0.000	0.000
38	A	206	ASP	-1	-0.818	-0.898	19.690	-0.247	-0.247	0.000	0.000	0.000	0.000
39	A	207	LYS	1	0.767	0.878	22.266	0.154	0.154	0.000	0.000	0.000	0.000
40	A	208	PHE	0	0.044	0.006	21.794	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	209	SER	0	0.045	0.033	26.320	0.006	0.006	0.000	0.000	0.000	0.000
42	A	210	GLY	0	0.034	0.023	29.404	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	211	HIS	0	0.051	0.027	29.380	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	212	PRO	0	0.014	0.018	24.218	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	213	LYS	1	0.875	0.911	22.110	0.199	0.199	0.000	0.000	0.000	0.000
46	A	214	GLY	0	0.062	0.027	19.238	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	215	PHE	0	-0.058	-0.019	13.021	0.034	0.034	0.000	0.000	0.000	0.000
48	A	216	ALA	0	0.063	0.033	13.085	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	217	TYR	0	-0.049	-0.032	7.669	0.020	0.020	0.000	0.000	0.000	0.000
50	A	218	ILE	0	0.028	0.022	9.158	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	219	GLU	-1	-0.858	-0.906	3.015	-5.156	-3.085	0.364	-1.113	-1.322	-0.010
52	A	220	PHE	0	0.054	0.020	6.071	0.217	0.217	0.000	0.000	0.000	0.000
53	A	221	SER	0	0.007	-0.007	5.360	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	222	ASP	-1	-0.871	-0.923	6.981	0.780	0.780	0.000	0.000	0.000	0.000
55	A	223	LYS	1	0.914	0.933	7.178	-2.010	-2.010	0.000	0.000	0.000	0.000
56	A	224	GLU	-1	-0.964	-0.981	7.933	0.271	0.271	0.000	0.000	0.000	0.000
57	A	225	SER	0	0.059	0.031	9.861	-0.068	-0.068	0.000	0.000	0.000	0.000
58	A	226	VAL	0	-0.015	0.010	7.591	-0.103	-0.103	0.000	0.000	0.000	0.000
59	A	227	ARG	1	0.921	0.958	10.607	-0.490	-0.490	0.000	0.000	0.000	0.000
60	A	228	THR	0	0.057	0.031	14.007	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	229	SER	0	0.004	-0.016	12.787	-0.060	-0.060	0.000	0.000	0.000	0.000
62	A	230	LEU	0	-0.027	-0.026	13.632	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	231	ALA	0	-0.013	0.008	16.568	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	232	LEU	0	-0.001	0.003	17.142	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	233	ASP	-1	-0.851	-0.903	18.907	-0.085	-0.085	0.000	0.000	0.000	0.000
66	A	234	GLU	-1	-0.962	-0.975	20.099	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	235	SER	0	-0.021	-0.022	20.870	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	236	LEU	0	-0.018	-0.019	23.549	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	237	PHE	0	0.035	0.011	19.664	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	238	ARG	1	0.771	0.839	22.009	0.167	0.167	0.000	0.000	0.000	0.000
71	A	239	GLY	0	-0.012	0.001	25.339	0.002	0.002	0.000	0.000	0.000	0.000
72	A	240	ARG	1	0.826	0.914	23.839	0.142	0.142	0.000	0.000	0.000	0.000
73	A	241	GLN	0	0.013	0.011	24.648	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	242	ILE	0	-0.017	0.014	18.137	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	243	LYS	1	0.946	0.986	18.574	0.096	0.096	0.000	0.000	0.000	0.000
76	A	244	VAL	0	-0.005	0.000	14.364	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	245	ILE	0	-0.034	-0.016	14.012	0.048	0.048	0.000	0.000	0.000	0.000
78	A	246	PRO	0	0.035	0.012	10.631	-0.085	-0.085	0.000	0.000	0.000	0.000
79	A	247	LYS	1	0.806	0.902	5.302	1.962	1.962	0.000	0.000	0.000	0.000
80	A	248	ARG	1	0.907	0.973	9.535	0.379	0.379	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:169:ALA)