FMO DATABASE

FMODB ID: KGQ63

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	OptAll
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	-515475.666609
FMO2-HF: Nuclear repulsion	483859.863101
FMO2-HF: Total energy	-31615.803508
FMO2-MP2: Total energy	-31707.842002

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.
43.671	47.81	1.201	-1.913	-3.427	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 : 0.977 / q_NPA : 0.974

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	4	VAL	0	0.058	0.029	2.758	1.685	4.251	1.105	-1.474	-2.197	0.006
4	A	5	ARG	1	0.942	0.965	3.201	32.806	34.187	0.097	-0.392	-1.086	0.001
5	A	6	PHE	0	0.013	0.015	4.605	1.516	1.708	-0.001	-0.047	-0.144	0.000
6	A	7	LEU	0	0.029	0.004	6.624	2.206	2.206	0.000	0.000	0.000	0.000
7	A	8	MET	0	-0.058	-0.031	6.472	1.683	1.683	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.834	0.925	7.613	28.058	28.058	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.006	0.019	10.739	0.949	0.949	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.026	-0.013	13.494	0.835	0.835	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.014	-0.015	16.113	0.453	0.453	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.844	-0.910	15.893	-14.390	-14.390	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.028	-0.013	18.793	0.115	0.115	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.005	0.014	16.553	-0.402	-0.402	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.013	-0.011	19.955	0.905	0.905	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.005	0.016	16.653	-0.535	-0.535	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.818	-0.865	19.057	-11.546	-11.546	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.008	0.002	19.005	-0.640	-0.640	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.877	0.922	15.503	15.405	15.405	0.000	0.000	0.000	0.000
20	A	21	ASN	0	0.004	0.028	21.497	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.046	0.031	23.903	0.423	0.423	0.000	0.000	0.000	0.000
22	A	23	THR	0	-0.053	-0.033	24.797	0.340	0.340	0.000	0.000	0.000	0.000
23	A	24	GLN	0	0.026	0.020	23.643	-0.226	-0.226	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.015	0.004	22.003	0.482	0.482	0.000	0.000	0.000	0.000
25	A	26	HIS	0	-0.021	-0.009	22.302	-0.313	-0.313	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.074	0.033	23.007	0.420	0.420	0.000	0.000	0.000	0.000
27	A	28	THR	0	-0.038	-0.008	21.507	-0.328	-0.328	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.004	-0.004	14.933	0.303	0.303	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.080	-0.055	18.888	0.294	0.294	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.049	0.012	15.600	-0.092	-0.092	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.023	-0.006	10.677	0.280	0.280	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.748	-0.836	11.402	-16.573	-16.573	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.043	0.003	6.477	-0.880	-0.880	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.079	-0.054	7.731	-1.101	-1.101	0.000	0.000	0.000	0.000
35	A	36	MET	0	-0.037	-0.032	8.233	-0.134	-0.134	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.032	-0.026	10.649	0.851	0.851	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.022	-0.007	13.870	-0.699	-0.699	0.000	0.000	0.000	0.000
38	A	39	HIS	0	0.027	0.038	15.812	1.099	1.099	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.004	0.010	18.922	-0.349	-0.349	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.929	0.960	21.536	11.821	11.821	0.000	0.000	0.000	0.000
41	A	42	ALA	0	-0.007	-0.007	24.845	-0.213	-0.213	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.019	0.000	24.575	-0.244	-0.244	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.984	1.002	26.744	9.833	9.833	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.005	-0.003	26.727	-0.450	-0.450	0.000	0.000	0.000	0.000
45	A	46	THR	0	0.002	-0.006	27.510	0.453	0.453	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.028	0.011	28.233	-0.291	-0.291	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.859	0.899	27.197	10.440	10.440	0.000	0.000	0.000	0.000
48	A	49	ASN	0	-0.025	-0.015	30.954	0.026	0.026	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.953	0.984	33.766	8.267	8.267	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.891	-0.934	34.224	-7.602	-7.602	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.087	-0.045	31.869	-0.147	-0.147	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.035	0.014	30.961	0.200	0.200	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.014	0.004	30.550	-0.529	-0.529	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.016	-0.015	27.931	0.159	0.159	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.896	-0.938	29.330	-8.659	-8.659	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.030	-0.029	25.246	-0.292	-0.292	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.013	0.005	23.299	0.231	0.231	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.030	-0.023	19.779	-0.400	-0.400	0.000	0.000	0.000	0.000
59	A	60	ILE	0	0.007	0.007	18.097	0.366	0.366	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.998	0.993	16.935	11.265	11.265	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.094	0.052	13.098	0.100	0.100	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.031	-0.027	14.039	-0.119	-0.119	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.016	-0.014	15.880	0.311	0.311	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.018	0.032	14.095	0.565	0.565	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.806	0.890	15.883	12.513	12.513	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.044	-0.058	14.846	-0.868	-0.868	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.028	0.000	11.801	0.668	0.668	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.007	0.001	15.865	-0.621	-0.621	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.005	-0.014	12.714	0.247	0.247	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.044	0.019	16.840	0.381	0.381	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.909	-0.947	18.560	-13.411	-13.411	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.023	-0.010	20.520	-0.038	-0.038	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.009	-0.002	13.724	-0.282	-0.282	0.000	0.000	0.000	0.000
74	A	75	PRO	0	0.034	0.031	15.422	-0.346	-0.346	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.023	-0.014	11.911	-1.436	-1.436	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.848	-0.925	10.735	-23.266	-23.266	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.009	-0.007	11.264	-1.388	-1.388	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.047	-0.017	9.418	-1.042	-1.042	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.018	-0.001	5.708	-3.262	-3.262	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.088	-0.028	7.193	-2.141	-2.141	0.000	0.000	0.000	0.000

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