FMO DATABASE

FMODB ID: 2N4VR

Calculation Name: 1KBA-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1KBA

Chain ID: A

ChEMBL ID:
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UniProt ID: P01398

Base Structure: X-ray

Registration Date: 2023-09-22

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361966.346135
FMO2-HF: Nuclear repulsion	334022.59178
FMO2-HF: Total energy	-27943.754355
FMO2-MP2: Total energy	-28016.774247

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:1:ARG)

Summations of interaction energy for fragment #1(A:1: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.
-140.221	-125.574	32.574	-18.545	-28.677	-0.166

Interaction energy analysis for fragmet #1(A:1:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.926

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	3	CYS	0	-0.029	0.023	2.818	-11.249	-7.175	4.183	-3.079	-5.177	-0.003
4	A	4	LEU	0	0.028	0.021	4.773	3.285	3.332	-0.001	-0.008	-0.037	0.000
5	A	5	ILE	0	-0.046	-0.025	8.532	-0.464	-0.464	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.010	0.009	10.999	0.872	0.872	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.007	0.027	14.250	0.188	0.188	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.002	-0.019	15.741	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.025	0.021	12.759	-0.166	-0.166	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.030	-0.013	12.379	0.045	0.045	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.050	0.008	8.513	-1.161	-1.161	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.014	0.007	7.389	1.764	1.764	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.006	-0.014	4.180	-3.407	-3.251	-0.001	-0.039	-0.116	0.000
14	A	14	CYS	0	-0.096	-0.026	2.272	-1.052	0.781	1.454	-1.072	-2.215	0.005
15	A	15	PRO	0	0.064	0.039	4.117	0.396	0.569	-0.001	-0.041	-0.130	0.000
16	A	16	ASN	0	0.006	0.000	4.965	-2.381	-2.331	-0.001	-0.001	-0.048	0.000
17	A	17	GLY	0	0.018	0.002	6.507	1.825	1.825	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.102	-0.063	5.309	0.963	0.963	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.838	-0.930	2.923	-54.844	-51.865	0.259	-1.434	-1.805	-0.011
20	A	20	ILE	0	-0.012	0.007	1.779	-37.755	-38.834	11.178	-5.319	-4.781	-0.070
21	A	22	PHE	0	-0.048	-0.034	4.513	2.881	2.963	-0.001	-0.012	-0.069	0.000
22	A	23	LEU	0	0.049	0.028	8.209	0.433	0.433	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.770	0.883	11.386	18.579	18.579	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.034	0.016	14.498	0.541	0.541	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.034	0.004	17.996	0.701	0.701	0.000	0.000	0.000	0.000
26	A	27	CYS	0	-0.051	-0.003	20.693	0.037	0.037	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.738	-0.854	24.536	-10.793	-10.793	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.926	0.952	27.152	8.868	8.868	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.013	-0.012	29.553	0.335	0.335	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.008	-0.022	27.994	-0.147	-0.147	0.000	0.000	0.000	0.000
31	A	33	ILE	0	0.001	0.015	30.662	0.137	0.137	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.861	0.951	27.911	10.574	10.574	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.055	0.027	25.692	-0.128	-0.128	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.063	-0.051	21.192	0.123	0.123	0.000	0.000	0.000	0.000
35	A	37	VAL	0	0.004	-0.011	20.026	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.011	0.000	15.388	-0.352	-0.352	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.839	-0.913	13.878	-17.762	-17.762	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.003	-0.015	10.111	0.502	0.502	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.072	0.035	8.086	1.410	1.410	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.022	0.008	6.455	4.225	4.225	0.000	0.000	0.000	0.000
41	A	44	ALA	0	0.044	0.010	6.395	-3.482	-3.482	0.000	0.000	0.000	0.000
42	A	45	THR	0	-0.017	0.000	8.554	0.761	0.761	0.000	0.000	0.000	0.000
43	A	46	CYS	0	-0.006	-0.007	8.143	-0.931	-0.931	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.016	-0.018	11.148	1.743	1.743	0.000	0.000	0.000	0.000
45	A	48	GLN	0	0.041	0.016	14.232	0.852	0.852	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.001	-0.015	17.026	0.105	0.105	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.908	0.973	18.683	14.732	14.732	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.065	0.013	21.503	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.042	-0.018	22.601	-0.125	-0.125	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.015	0.005	17.132	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	54	ARG	1	0.954	0.976	20.765	12.395	12.395	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.019	-0.015	16.831	0.267	0.267	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.028	-0.009	12.148	0.020	0.020	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.044	0.037	9.690	0.683	0.683	0.000	0.000	0.000	0.000
55	A	59	CYS	0	-0.002	0.019	4.649	5.919	6.142	-0.002	-0.014	-0.207	0.000
56	A	60	THR	0	0.058	0.038	2.750	-4.429	-2.497	0.636	-0.767	-1.802	0.004
57	A	61	THR	0	0.008	-0.029	2.757	2.277	4.429	1.788	-0.816	-3.124	0.000
58	A	62	ASP	-1	-0.795	-0.871	1.860	-101.481	-99.391	13.053	-6.317	-8.827	-0.090
59	A	63	ASN	0	-0.021	-0.037	3.206	9.244	9.179	0.030	0.374	-0.339	-0.001
60	A	65	ASN	0	-0.037	-0.008	6.210	1.321	1.321	0.000	0.000	0.000	0.000
61	A	66	HIS	0	-0.012	-0.012	8.034	2.962	2.962	0.000	0.000	0.000	0.000

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