FMO DATABASE

FMODB ID: V5M71

Calculation Name: 3B5N-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: B

ChEMBL ID:

UniProt ID: P40357

Base Structure: X-ray

Registration Date: 2023-09-20

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	69
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-288619.541521
FMO2-HF: Nuclear repulsion	261098.055774
FMO2-HF: Total energy	-27521.485747
FMO2-MP2: Total energy	-27601.230753

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(B:189:ALA)

Summations of interaction energy for fragment #1(B:189: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.
-7.459	-3.565	4.484	-3.685	-4.694	-0.017

Interaction energy analysis for fragmet #1(B:189:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.015

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	B	191	ALA	0	0.059	0.017	3.710	-2.256	-0.384	-0.005	-0.883	-0.984	0.004
4	B	192	GLU	-1	-0.891	-0.947	2.175	-7.602	-6.109	4.484	-2.660	-3.317	-0.021
5	B	193	VAL	0	-0.048	-0.020	3.873	0.590	1.119	0.005	-0.142	-0.393	0.000
6	B	194	GLN	0	-0.013	-0.016	5.845	0.617	0.617	0.000	0.000	0.000	0.000
7	B	195	ALA	0	0.025	0.018	6.946	0.238	0.238	0.000	0.000	0.000	0.000
8	B	196	ARG	1	1.019	1.009	7.902	1.287	1.287	0.000	0.000	0.000	0.000
9	B	197	HIS	0	-0.006	-0.004	9.659	0.151	0.151	0.000	0.000	0.000	0.000
10	B	198	GLN	0	-0.006	-0.010	11.536	0.105	0.105	0.000	0.000	0.000	0.000
11	B	199	GLU	-1	-0.971	-0.983	11.309	-0.808	-0.808	0.000	0.000	0.000	0.000
12	B	200	LEU	0	-0.019	-0.019	12.899	0.063	0.063	0.000	0.000	0.000	0.000
13	B	201	LEU	0	0.038	0.024	15.700	0.058	0.058	0.000	0.000	0.000	0.000
14	B	202	LYS	1	0.915	0.970	17.393	0.399	0.399	0.000	0.000	0.000	0.000
15	B	203	LEU	0	-0.022	-0.017	18.190	0.027	0.027	0.000	0.000	0.000	0.000
16	B	204	GLU	-1	-0.920	-0.955	19.827	-0.146	-0.146	0.000	0.000	0.000	0.000
17	B	205	LYS	1	0.946	0.969	21.694	0.170	0.170	0.000	0.000	0.000	0.000
18	B	206	SER	0	-0.015	-0.012	23.198	0.017	0.017	0.000	0.000	0.000	0.000
19	B	207	MET	0	0.012	0.013	24.256	0.014	0.014	0.000	0.000	0.000	0.000
20	B	208	ALA	0	-0.007	0.007	25.853	0.014	0.014	0.000	0.000	0.000	0.000
21	B	209	GLU	-1	-0.937	-0.964	27.823	-0.114	-0.114	0.000	0.000	0.000	0.000
22	B	210	LEU	0	-0.032	-0.016	28.777	0.007	0.007	0.000	0.000	0.000	0.000
23	B	211	THR	0	-0.025	-0.040	29.244	0.007	0.007	0.000	0.000	0.000	0.000
24	B	212	GLN	0	-0.076	-0.034	31.778	0.006	0.006	0.000	0.000	0.000	0.000
25	B	213	LEU	0	0.009	0.007	32.769	0.005	0.005	0.000	0.000	0.000	0.000
26	B	214	PHE	0	-0.061	-0.036	32.734	0.003	0.003	0.000	0.000	0.000	0.000
27	B	215	ASN	0	0.033	0.013	34.917	0.005	0.005	0.000	0.000	0.000	0.000
28	B	216	ASP	-1	-0.826	-0.900	37.776	-0.064	-0.064	0.000	0.000	0.000	0.000
29	B	217	MET	0	-0.089	-0.043	39.291	0.005	0.005	0.000	0.000	0.000	0.000
30	B	218	GLU	-1	-0.959	-0.980	40.474	-0.059	-0.059	0.000	0.000	0.000	0.000
31	B	219	GLU	-1	-0.934	-0.969	41.564	-0.048	-0.048	0.000	0.000	0.000	0.000
32	B	220	LEU	0	-0.016	-0.006	43.065	0.003	0.003	0.000	0.000	0.000	0.000
33	B	221	VAL	0	-0.044	-0.025	45.007	0.002	0.002	0.000	0.000	0.000	0.000
34	B	222	ILE	0	-0.035	-0.017	45.008	0.003	0.003	0.000	0.000	0.000	0.000
35	B	223	GLU	-1	-0.942	-0.966	48.223	-0.040	-0.040	0.000	0.000	0.000	0.000
36	B	224	GLN	0	-0.043	-0.033	48.278	0.001	0.001	0.000	0.000	0.000	0.000
37	B	225	GLN	0	-0.055	-0.025	51.198	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	226	GLU	-1	-0.920	-0.953	52.903	-0.032	-0.032	0.000	0.000	0.000	0.000
39	B	227	ASN	0	-0.064	-0.042	54.534	0.000	0.000	0.000	0.000	0.000	0.000
40	B	228	VAL	0	-0.012	-0.011	53.948	0.001	0.001	0.000	0.000	0.000	0.000
41	B	229	ASP	-1	-0.836	-0.901	56.947	-0.034	-0.034	0.000	0.000	0.000	0.000
42	B	230	VAL	0	-0.060	-0.029	58.958	0.001	0.001	0.000	0.000	0.000	0.000
43	B	231	ILE	0	-0.071	-0.035	58.223	0.001	0.001	0.000	0.000	0.000	0.000
44	B	232	ASP	-1	-0.912	-0.955	60.452	-0.033	-0.033	0.000	0.000	0.000	0.000
45	B	233	LYS	1	0.926	0.967	62.421	0.026	0.026	0.000	0.000	0.000	0.000
46	B	234	ASN	0	-0.020	-0.020	64.897	0.002	0.002	0.000	0.000	0.000	0.000
47	B	235	VAL	0	-0.045	-0.021	64.497	0.001	0.001	0.000	0.000	0.000	0.000
48	B	236	GLU	-1	-0.937	-0.955	66.632	-0.027	-0.027	0.000	0.000	0.000	0.000
49	B	237	ASP	-1	-0.866	-0.942	68.301	-0.023	-0.023	0.000	0.000	0.000	0.000
50	B	238	ALA	0	-0.041	-0.024	70.194	0.001	0.001	0.000	0.000	0.000	0.000
51	B	239	GLN	0	-0.051	-0.025	70.533	0.001	0.001	0.000	0.000	0.000	0.000
52	B	240	LEU	0	0.056	0.026	72.093	0.001	0.001	0.000	0.000	0.000	0.000
53	B	241	ASP	-1	-0.898	-0.941	74.765	-0.020	-0.020	0.000	0.000	0.000	0.000
54	B	242	VAL	0	-0.074	-0.035	74.441	0.001	0.001	0.000	0.000	0.000	0.000
55	B	243	GLU	-1	-0.946	-0.963	76.420	-0.022	-0.022	0.000	0.000	0.000	0.000
56	B	244	GLN	0	-0.034	-0.025	77.813	0.001	0.001	0.000	0.000	0.000	0.000
57	B	245	GLY	0	-0.011	-0.009	80.186	0.001	0.001	0.000	0.000	0.000	0.000
58	B	246	VAL	0	0.007	-0.003	79.814	0.001	0.001	0.000	0.000	0.000	0.000
59	B	247	GLY	0	0.048	0.038	82.600	0.000	0.000	0.000	0.000	0.000	0.000
60	B	248	HIS	0	-0.026	-0.021	84.020	0.001	0.001	0.000	0.000	0.000	0.000
61	B	249	THR	0	-0.087	-0.051	84.942	0.000	0.000	0.000	0.000	0.000	0.000
62	B	250	ASP	-1	-0.912	-0.947	86.659	-0.018	-0.018	0.000	0.000	0.000	0.000
63	B	251	LYS	1	0.939	0.955	88.033	0.017	0.017	0.000	0.000	0.000	0.000
64	B	252	ALA	0	0.005	0.004	90.303	0.001	0.001	0.000	0.000	0.000	0.000
65	B	253	VAL	0	0.007	0.003	90.105	0.000	0.000	0.000	0.000	0.000	0.000
66	B	254	LYS	1	0.883	0.937	92.701	0.016	0.016	0.000	0.000	0.000	0.000
67	B	255	SER	0	-0.048	-0.028	94.631	0.000	0.000	0.000	0.000	0.000	0.000
68	B	256	ALA	0	-0.025	0.000	95.566	0.000	0.000	0.000	0.000	0.000	0.000
69	B	257	ARG	1	0.909	0.978	91.909	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:189:ALA)