FMO DATABASE

FMODB ID: QV53Y

Calculation Name: 1B34-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: A

ChEMBL ID:

UniProt ID: P62314

Base Structure: X-ray

Registration Date: 2023-09-23

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-515713.762891
FMO2-HF: Nuclear repulsion	484098.491635
FMO2-HF: Total energy	-31615.271256
FMO2-MP2: Total energy	-31707.367023

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
44.938	49.73	1.074	-2.189	-3.677	0.007

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.953 / q_NPA : 0.959

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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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	4	VAL	0	0.062	0.023	2.512	2.344	5.234	0.937	-1.544	-2.284	0.002
4	A	5	ARG	1	0.955	0.963	3.192	31.860	33.591	0.138	-0.610	-1.259	0.005
5	A	6	PHE	0	0.021	0.024	4.617	1.373	1.544	-0.001	-0.035	-0.134	0.000
6	A	7	LEU	0	0.045	0.017	6.545	2.048	2.048	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.064	-0.024	6.261	1.543	1.543	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.814	0.916	6.842	27.998	27.998	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.002	0.011	10.792	0.701	0.701	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.043	-0.021	13.413	0.758	0.758	0.000	0.000	0.000	0.000
11	A	12	HIS	0	-0.029	-0.036	16.075	0.351	0.351	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.888	-0.923	15.704	-14.309	-14.309	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.021	-0.002	18.708	0.442	0.442	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.017	0.016	16.359	-0.467	-0.467	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.013	-0.007	19.793	0.847	0.847	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.016	-0.007	16.813	-0.626	-0.626	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.829	-0.863	19.111	-11.442	-11.442	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.033	0.013	19.187	-0.652	-0.652	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.892	0.946	16.227	15.153	15.153	0.000	0.000	0.000	0.000
20	A	21	ASN	0	0.002	0.014	21.811	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.014	0.006	24.060	0.407	0.407	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.029	-0.021	25.177	0.426	0.426	0.000	0.000	0.000	0.000
23	A	24	GLN	0	0.011	0.011	23.909	-0.321	-0.321	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.005	-0.003	21.905	0.448	0.448	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.021	0.000	22.279	-0.345	-0.345	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.087	0.049	22.732	0.460	0.460	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.021	-0.001	21.447	-0.260	-0.260	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.008	-0.002	14.803	0.266	0.266	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.067	-0.038	18.582	0.230	0.230	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.047	0.015	15.469	-0.099	-0.099	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.020	-0.010	10.692	0.268	0.268	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.781	-0.876	11.613	-16.701	-16.701	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.054	0.010	6.977	-0.641	-0.641	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.072	-0.031	8.186	-1.206	-1.206	0.000	0.000	0.000	0.000
35	A	36	MET	0	-0.055	-0.049	8.585	-0.235	-0.235	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.045	-0.025	11.043	0.945	0.945	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.007	0.001	14.135	-0.685	-0.685	0.000	0.000	0.000	0.000
38	A	39	HIS	0	0.026	0.036	15.978	1.046	1.046	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.001	0.012	18.752	-0.394	-0.394	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.995	0.988	21.378	11.274	11.274	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.040	-0.020	24.754	-0.192	-0.192	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.003	-0.012	24.433	-0.235	-0.235	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.984	0.999	26.693	9.713	9.713	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.021	-0.009	26.866	-0.487	-0.487	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.007	-0.019	27.729	0.425	0.425	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.018	0.004	28.520	-0.287	-0.287	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.892	0.922	27.283	10.478	10.478	0.000	0.000	0.000	0.000
48	A	49	ASN	0	-0.032	-0.011	31.367	0.077	0.077	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.952	0.975	34.120	8.206	8.206	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.902	-0.929	34.213	-7.574	-7.574	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.084	-0.050	31.976	-0.120	-0.120	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.024	0.012	31.369	0.234	0.234	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.015	0.008	30.823	-0.501	-0.501	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.003	-0.010	28.200	0.141	0.141	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.889	-0.926	28.986	-8.711	-8.711	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.021	-0.022	25.139	-0.293	-0.293	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.018	0.003	23.274	0.235	0.235	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.010	-0.004	20.004	-0.405	-0.405	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.015	-0.015	18.332	0.369	0.369	0.000	0.000	0.000	0.000
60	A	61	ARG	1	1.001	0.998	17.394	11.156	11.156	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.131	0.082	13.655	0.085	0.085	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.012	-0.013	14.544	-0.209	-0.209	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.035	-0.029	16.088	0.385	0.385	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.003	0.009	14.725	0.588	0.588	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.810	0.893	16.039	12.447	12.447	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.041	-0.052	14.988	-0.970	-0.970	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.032	0.007	12.230	0.746	0.746	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.019	-0.017	16.015	-0.620	-0.620	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.011	-0.009	12.572	0.237	0.237	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.050	0.022	16.574	0.456	0.456	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.896	-0.943	18.472	-13.225	-13.225	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.020	-0.013	20.473	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.037	-0.017	13.383	-0.273	-0.273	0.000	0.000	0.000	0.000
74	A	75	PRO	0	0.004	0.018	14.990	-0.273	-0.273	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.036	0.005	11.895	-1.381	-1.381	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.870	-0.948	10.974	-22.246	-22.246	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.003	-0.010	11.102	-1.397	-1.397	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.041	0.006	9.050	-1.162	-1.162	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.064	-0.024	5.502	-3.452	-3.452	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.023	-0.002	7.598	0.252	0.252	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)