FMO DATABASE

FMODB ID: NNK6Q

Calculation Name: 1BKR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q01082

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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-925966.606643
FMO2-HF: Nuclear repulsion	881897.258899
FMO2-HF: Total energy	-44069.347744
FMO2-MP2: Total energy	-44198.16676

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.
-89.129	-90.742	24.626	-12.62	-10.395	-0.138

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 : 0.907 / q_NPA : 0.927

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	ALA	0	0.013	0.014	3.358	1.312	3.510	0.001	-0.971	-1.227	0.000
4	A	5	LYS	1	0.831	0.897	3.494	40.505	41.360	0.013	-0.223	-0.646	0.000
5	A	6	ASP	-1	-0.799	-0.883	1.695	-141.116	-145.902	24.613	-11.412	-8.417	-0.138
6	A	7	ALA	0	0.005	0.005	4.883	6.667	6.787	-0.001	-0.014	-0.105	0.000
7	A	8	LEU	0	0.007	0.013	7.889	3.539	3.539	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.019	0.016	7.327	3.013	3.013	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.056	0.027	8.396	3.066	3.066	0.000	0.000	0.000	0.000
10	A	11	TRP	0	-0.020	-0.009	10.171	2.861	2.861	0.000	0.000	0.000	0.000
11	A	12	CYS	0	-0.026	-0.014	12.701	2.379	2.379	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.028	-0.006	10.649	0.744	0.744	0.000	0.000	0.000	0.000
13	A	14	MET	0	-0.013	-0.011	12.880	1.749	1.749	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.813	0.909	16.085	17.443	17.443	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.009	-0.016	17.147	1.098	1.098	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.001	0.008	18.158	0.679	0.679	0.000	0.000	0.000	0.000
17	A	18	GLY	0	-0.010	-0.014	19.721	0.646	0.646	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.030	-0.030	22.358	0.480	0.480	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.031	0.005	23.226	-0.399	-0.399	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.005	-0.011	24.381	-0.187	-0.187	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.057	0.053	18.758	-0.277	-0.277	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.037	-0.027	17.748	-0.536	-0.536	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.004	0.024	12.611	-0.305	-0.305	0.000	0.000	0.000	0.000
24	A	25	HIS	0	0.010	-0.003	11.120	-2.377	-2.377	0.000	0.000	0.000	0.000
25	A	26	ASN	0	0.002	0.011	9.983	-2.025	-2.025	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.036	0.004	7.915	0.684	0.684	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.061	0.026	12.181	0.633	0.633	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.052	0.021	15.119	0.568	0.568	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.039	-0.031	14.856	0.372	0.372	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.026	-0.035	13.589	0.647	0.647	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.864	0.929	18.558	14.008	14.008	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.830	-0.925	21.207	-13.490	-13.490	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.052	0.016	22.525	0.658	0.658	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.059	-0.011	22.977	0.180	0.180	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.025	0.010	18.252	0.123	0.123	0.000	0.000	0.000	0.000
36	A	37	PHE	0	0.016	0.004	17.938	-0.242	-0.242	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.015	-0.029	21.408	0.619	0.619	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.015	0.012	21.691	0.303	0.303	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.036	-0.014	16.888	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.001	0.024	21.485	0.126	0.126	0.000	0.000	0.000	0.000
41	A	42	HIS	0	0.039	0.043	24.801	-0.123	-0.123	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.840	0.924	21.423	14.910	14.910	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.024	-0.013	20.898	-0.388	-0.388	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.838	0.898	26.344	10.487	10.487	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.027	0.013	29.270	0.048	0.048	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.862	-0.909	30.809	-9.709	-9.709	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.013	0.000	29.332	0.206	0.206	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.050	-0.023	27.529	-0.032	-0.032	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.795	-0.881	31.654	-9.144	-9.144	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.003	-0.011	24.913	-0.044	-0.044	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.850	-0.906	30.381	-9.628	-9.628	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.777	0.855	31.972	9.141	9.141	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.024	0.003	28.282	0.112	0.112	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.901	0.941	29.518	9.676	9.676	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.916	0.956	23.747	13.218	13.218	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.001	-0.006	27.510	-0.225	-0.225	0.000	0.000	0.000	0.000
57	A	58	ASN	0	-0.025	0.010	30.321	0.123	0.123	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.041	0.027	26.116	0.041	0.041	0.000	0.000	0.000	0.000
59	A	60	HIS	0	-0.017	-0.012	27.200	-0.339	-0.339	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.047	0.021	29.194	0.009	0.009	0.000	0.000	0.000	0.000
61	A	62	ASN	0	-0.037	-0.044	26.793	0.332	0.332	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.005	0.011	22.386	-0.227	-0.227	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.006	0.005	25.919	0.127	0.127	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.033	-0.014	28.836	0.444	0.444	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.033	0.007	24.527	0.078	0.078	0.000	0.000	0.000	0.000
66	A	67	PHE	0	-0.014	-0.018	21.853	-0.161	-0.161	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.043	0.018	26.016	0.042	0.042	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.007	0.001	28.637	0.170	0.170	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.009	-0.008	24.326	0.064	0.064	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.798	-0.902	26.433	-10.205	-10.205	0.000	0.000	0.000	0.000
71	A	72	GLN	0	-0.068	-0.045	28.052	0.388	0.388	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.003	0.006	30.202	0.258	0.258	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.069	-0.029	25.108	-0.063	-0.063	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.008	0.023	26.903	-0.146	-0.146	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.091	-0.051	21.589	-0.237	-0.237	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.016	-0.005	23.481	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.878	0.929	23.375	9.591	9.591	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.056	-0.023	18.597	0.075	0.075	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.056	-0.019	18.203	-0.417	-0.417	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.789	-0.886	22.353	-10.405	-10.405	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.029	-0.037	24.345	-0.483	-0.483	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.854	-0.893	25.868	-10.129	-10.129	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.891	-0.944	22.458	-12.174	-12.174	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.094	-0.060	19.108	-0.871	-0.871	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.033	-0.035	21.931	-0.333	-0.333	0.000	0.000	0.000	0.000
86	A	87	VAL	0	0.051	0.045	21.895	0.264	0.264	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.935	-0.962	22.638	-12.942	-12.942	0.000	0.000	0.000	0.000
88	A	89	HIS	0	-0.041	-0.038	18.297	-1.360	-1.360	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.004	0.032	17.653	0.018	0.018	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.753	-0.868	14.628	-19.076	-19.076	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.773	-0.870	8.747	-31.348	-31.348	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.929	0.970	11.290	18.052	18.052	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.000	-0.016	12.284	0.158	0.158	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.019	0.023	14.143	0.260	0.260	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.026	-0.015	7.775	-0.337	-0.337	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.049	-0.040	11.898	0.036	0.036	0.000	0.000	0.000	0.000
97	A	98	TYR	0	0.024	0.023	13.977	0.539	0.539	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.029	0.008	13.566	0.399	0.399	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.025	-0.021	10.755	-0.117	-0.117	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.029	-0.016	13.839	0.741	0.741	0.000	0.000	0.000	0.000
101	A	102	TYR	0	0.025	0.001	17.436	0.436	0.436	0.000	0.000	0.000	0.000
102	A	103	TYR	0	-0.040	-0.015	13.248	0.444	0.444	0.000	0.000	0.000	0.000
103	A	104	HIS	0	0.025	0.004	13.312	0.807	0.807	0.000	0.000	0.000	0.000
104	A	105	TYR	0	0.038	0.030	17.496	0.557	0.557	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.014	-0.003	20.182	0.363	0.363	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.049	-0.043	17.650	-0.476	-0.476	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.841	0.929	16.980	15.081	15.081	0.000	0.000	0.000	0.000
108	A	109	MET	0	0.014	0.030	22.265	0.234	0.234	0.000	0.000	0.000	0.000

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