FMO DATABASE

FMODB ID: G61M1

Calculation Name: 1B72-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B72

Chain ID: B

ChEMBL ID:

UniProt ID: P14653

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	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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-480215.461016
FMO2-HF: Nuclear repulsion	450307.583665
FMO2-HF: Total energy	-29907.877351
FMO2-MP2: Total energy	-29996.683158

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:235:ARG)

Summations of interaction energy for fragment #1(B:235:ARG)

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.
109.865	114.007	3.575	-3.557	-4.16	-0.019

Interaction energy analysis for fragmet #1(B:235:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.046 / q_NPA : 1.029

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	B	237	ARG	1	0.910	0.933	2.233	8.870	12.835	3.576	-3.542	-3.999	-0.019
4	B	238	ARG	1	0.976	0.989	4.552	40.688	40.865	-0.001	-0.015	-0.161	0.000
5	B	239	ASN	0	0.031	0.029	6.494	-2.348	-2.348	0.000	0.000	0.000	0.000
6	B	240	PHE	0	0.039	0.017	7.840	-1.347	-1.347	0.000	0.000	0.000	0.000
7	B	241	ASN	0	0.044	0.026	11.567	0.641	0.641	0.000	0.000	0.000	0.000
8	B	242	LYS	1	0.948	0.955	14.779	14.407	14.407	0.000	0.000	0.000	0.000
9	B	243	GLN	0	0.074	0.032	17.870	0.325	0.325	0.000	0.000	0.000	0.000
10	B	244	ALA	0	0.039	0.017	14.818	0.297	0.297	0.000	0.000	0.000	0.000
11	B	245	THR	0	-0.025	-0.030	14.819	0.489	0.489	0.000	0.000	0.000	0.000
12	B	246	GLU	-1	-0.829	-0.865	17.276	-12.724	-12.724	0.000	0.000	0.000	0.000
13	B	247	ILE	0	0.034	0.015	19.635	0.451	0.451	0.000	0.000	0.000	0.000
14	B	248	LEU	0	-0.029	-0.021	15.029	0.185	0.185	0.000	0.000	0.000	0.000
15	B	249	ASN	0	-0.004	-0.008	19.471	-0.119	-0.119	0.000	0.000	0.000	0.000
16	B	250	GLU	-1	-0.907	-0.936	21.738	-11.267	-11.267	0.000	0.000	0.000	0.000
17	B	251	TYR	0	0.040	0.020	22.341	0.382	0.382	0.000	0.000	0.000	0.000
18	B	252	PHE	0	-0.051	-0.044	21.572	0.207	0.207	0.000	0.000	0.000	0.000
19	B	253	TYR	0	-0.018	-0.066	23.332	0.254	0.254	0.000	0.000	0.000	0.000
20	B	254	SER	0	0.048	0.055	26.724	0.304	0.304	0.000	0.000	0.000	0.000
21	B	255	HIS	1	0.812	0.885	26.418	11.758	11.758	0.000	0.000	0.000	0.000
22	B	256	LEU	0	0.031	0.030	26.580	-0.194	-0.194	0.000	0.000	0.000	0.000
23	B	257	SER	0	-0.007	0.000	28.401	-0.160	-0.160	0.000	0.000	0.000	0.000
24	B	258	ASN	0	-0.003	-0.017	28.297	-0.087	-0.087	0.000	0.000	0.000	0.000
25	B	259	PRO	0	-0.011	0.038	23.422	-0.212	-0.212	0.000	0.000	0.000	0.000
26	B	260	TYR	0	-0.058	-0.066	22.623	-1.159	-1.159	0.000	0.000	0.000	0.000
27	B	261	PRO	0	-0.014	0.013	20.894	0.348	0.348	0.000	0.000	0.000	0.000
28	B	262	SER	0	0.022	-0.019	22.931	-0.487	-0.487	0.000	0.000	0.000	0.000
29	B	263	GLU	-1	-0.782	-0.895	20.770	-15.349	-15.349	0.000	0.000	0.000	0.000
30	B	264	GLU	-1	-0.755	-0.846	22.084	-12.177	-12.177	0.000	0.000	0.000	0.000
31	B	265	ALA	0	-0.007	0.006	23.481	-0.273	-0.273	0.000	0.000	0.000	0.000
32	B	266	LYS	1	0.755	0.855	18.510	15.390	15.390	0.000	0.000	0.000	0.000
33	B	267	GLU	-1	-0.920	-0.961	18.873	-15.684	-15.684	0.000	0.000	0.000	0.000
34	B	268	GLU	-1	-0.884	-0.919	19.872	-12.534	-12.534	0.000	0.000	0.000	0.000
35	B	269	LEU	0	-0.017	-0.022	18.801	-0.233	-0.233	0.000	0.000	0.000	0.000
36	B	270	ALA	0	-0.011	-0.002	15.962	-0.520	-0.520	0.000	0.000	0.000	0.000
37	B	271	LYS	1	0.975	0.988	16.553	13.142	13.142	0.000	0.000	0.000	0.000
38	B	272	LYS	1	0.843	0.911	19.058	12.532	12.532	0.000	0.000	0.000	0.000
39	B	273	CYS	0	-0.081	-0.024	15.469	0.103	0.103	0.000	0.000	0.000	0.000
40	B	274	GLY	0	-0.008	0.009	15.222	-0.570	-0.570	0.000	0.000	0.000	0.000
41	B	275	ILE	0	-0.107	-0.053	10.897	-2.079	-2.079	0.000	0.000	0.000	0.000
42	B	276	THR	0	0.037	-0.008	9.901	1.263	1.263	0.000	0.000	0.000	0.000
43	B	277	VAL	0	0.156	0.063	12.448	-0.284	-0.284	0.000	0.000	0.000	0.000
44	B	278	SER	0	0.016	0.007	10.560	0.998	0.998	0.000	0.000	0.000	0.000
45	B	279	GLN	0	0.007	0.021	6.948	1.133	1.133	0.000	0.000	0.000	0.000
46	B	280	VAL	0	0.053	0.040	10.714	0.323	0.323	0.000	0.000	0.000	0.000
47	B	281	SER	0	0.004	-0.007	14.292	1.287	1.287	0.000	0.000	0.000	0.000
48	B	282	ASN	0	-0.019	-0.017	8.691	2.137	2.137	0.000	0.000	0.000	0.000
49	B	283	TRP	0	-0.009	0.018	12.434	0.333	0.333	0.000	0.000	0.000	0.000
50	B	284	PHE	0	0.083	0.033	14.216	0.838	0.838	0.000	0.000	0.000	0.000
51	B	285	GLY	0	-0.024	0.006	15.723	0.930	0.930	0.000	0.000	0.000	0.000
52	B	286	ASN	0	-0.070	-0.064	11.284	0.882	0.882	0.000	0.000	0.000	0.000
53	B	287	LYS	1	0.760	0.877	15.262	15.909	15.909	0.000	0.000	0.000	0.000
54	B	288	ARG	1	0.942	0.970	18.284	15.706	15.706	0.000	0.000	0.000	0.000
55	B	289	ILE	0	-0.042	-0.017	17.846	0.768	0.768	0.000	0.000	0.000	0.000
56	B	290	ARG	1	0.906	0.932	12.094	21.508	21.508	0.000	0.000	0.000	0.000
57	B	291	TYR	0	0.054	0.040	19.821	0.447	0.447	0.000	0.000	0.000	0.000
58	B	292	LYS	1	0.975	0.975	22.558	13.235	13.235	0.000	0.000	0.000	0.000
59	B	293	LYS	1	0.914	0.961	21.374	13.181	13.181	0.000	0.000	0.000	0.000
60	B	294	ASN	0	-0.077	-0.049	24.097	0.388	0.388	0.000	0.000	0.000	0.000
61	B	295	ILE	0	0.088	0.057	25.788	-0.164	-0.164	0.000	0.000	0.000	0.000
62	B	296	GLY	0	0.035	0.022	27.716	-0.038	-0.038	0.000	0.000	0.000	0.000
63	B	297	LYS	1	0.927	0.969	22.248	13.435	13.435	0.000	0.000	0.000	0.000
64	B	298	PHE	0	-0.042	-0.024	20.540	-0.540	-0.540	0.000	0.000	0.000	0.000
65	B	299	GLN	0	0.051	0.036	25.919	-0.287	-0.287	0.000	0.000	0.000	0.000
66	B	300	GLU	-1	-0.899	-0.936	28.195	-10.734	-10.734	0.000	0.000	0.000	0.000
67	B	301	GLU	-1	-0.755	-0.835	21.745	-14.354	-14.354	0.000	0.000	0.000	0.000
68	B	302	ALA	0	-0.010	-0.024	26.630	0.007	0.007	0.000	0.000	0.000	0.000
69	B	303	ASN	0	-0.029	-0.025	28.406	0.260	0.260	0.000	0.000	0.000	0.000
70	B	304	ILE	0	-0.034	-0.002	27.450	0.210	0.210	0.000	0.000	0.000	0.000
71	B	305	TYR	0	-0.081	-0.073	23.154	-0.200	-0.200	0.000	0.000	0.000	0.000
72	B	306	ALA	0	-0.028	0.011	28.441	0.016	0.016	0.000	0.000	0.000	0.000
73	B	307	ALA	0	0.015	0.012	30.769	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:235:ARG)