FMO DATABASE

FMODB ID: 76QLK

Calculation Name: 1R29-A-Xray372

Preferred Name: B-cell lymphoma 6 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1R29

Chain ID: A

ChEMBL ID: CHEMBL4105786

UniProt ID: P41182

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	OptH
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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1029674.502379
FMO2-HF: Nuclear repulsion	979345.218044
FMO2-HF: Total energy	-50329.284335
FMO2-MP2: Total energy	-50472.389559

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
-5.643	-1.133	0.56	-2.579	-2.492	-0.002

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.022

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

Sort

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	9	ILE	0	0.031	0.011	2.559	-8.556	-4.259	0.561	-2.568	-2.291	-0.002
4	A	10	GLN	0	0.000	-0.001	4.015	2.166	2.379	-0.001	-0.011	-0.201	0.000
5	A	11	PHE	0	0.018	0.009	6.476	-0.030	-0.030	0.000	0.000	0.000	0.000
6	A	12	THR	0	-0.004	-0.014	10.197	0.182	0.182	0.000	0.000	0.000	0.000
7	A	13	ARG	1	1.010	1.003	11.906	0.538	0.538	0.000	0.000	0.000	0.000
8	A	14	HIS	0	0.051	0.038	12.899	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.040	0.016	14.308	0.032	0.032	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.029	0.009	15.990	0.012	0.012	0.000	0.000	0.000	0.000
11	A	17	ASP	-1	-0.919	-0.955	18.034	-0.217	-0.217	0.000	0.000	0.000	0.000
12	A	18	VAL	0	-0.058	-0.033	17.322	0.010	0.010	0.000	0.000	0.000	0.000
13	A	19	LEU	0	0.008	0.014	20.011	0.005	0.005	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.034	0.020	22.185	0.004	0.004	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.014	-0.012	22.176	0.005	0.005	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.036	0.023	22.360	0.003	0.003	0.000	0.000	0.000	0.000
17	A	23	ASN	0	0.045	0.015	25.840	0.010	0.010	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.870	0.930	25.804	0.099	0.099	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.016	-0.002	26.938	0.000	0.000	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.925	0.982	30.131	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.102	-0.053	32.124	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.920	0.951	32.696	0.053	0.053	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.779	-0.844	35.039	0.001	0.001	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.036	-0.012	31.506	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.001	-0.018	29.699	0.002	0.002	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.064	-0.039	32.240	0.008	0.008	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.810	-0.909	31.966	0.047	0.047	0.000	0.000	0.000	0.000
28	A	34	VAL	0	-0.056	-0.035	34.155	0.005	0.005	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.023	-0.001	36.657	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.010	-0.011	35.586	0.004	0.004	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.020	0.001	39.189	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.021	0.006	40.101	0.004	0.004	0.000	0.000	0.000	0.000
33	A	39	SER	0	0.066	0.035	43.359	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.896	0.940	47.090	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.934	-0.953	43.530	0.013	0.013	0.000	0.000	0.000	0.000
36	A	42	GLN	0	-0.013	-0.018	42.413	0.003	0.003	0.000	0.000	0.000	0.000
37	A	43	PHE	0	0.023	0.016	37.207	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.858	0.929	36.886	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	45	ALA	0	-0.003	-0.008	32.073	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.013	0.022	28.698	0.004	0.004	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.861	0.932	29.620	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	48	THR	0	0.004	-0.004	24.951	0.008	0.008	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.014	0.012	24.953	0.017	0.017	0.000	0.000	0.000	0.000
44	A	50	LEU	0	0.023	0.005	26.333	0.010	0.010	0.000	0.000	0.000	0.000
45	A	51	MET	0	-0.077	-0.035	26.630	0.006	0.006	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.035	-0.010	22.293	0.018	0.018	0.000	0.000	0.000	0.000
47	A	53	CYS	0	-0.048	-0.007	23.412	0.013	0.013	0.000	0.000	0.000	0.000
48	A	54	SER	0	-0.037	-0.025	25.950	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.067	0.025	29.081	0.005	0.005	0.000	0.000	0.000	0.000
50	A	56	LEU	0	-0.013	0.005	29.969	0.000	0.000	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.035	-0.008	30.818	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	58	TYR	0	-0.009	-0.001	24.915	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.001	-0.016	29.511	0.004	0.004	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.063	-0.021	32.320	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.026	0.000	30.964	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	62	THR	0	-0.005	0.004	28.993	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.823	-0.892	30.723	0.104	0.104	0.000	0.000	0.000	0.000
58	A	64	GLN	0	0.010	-0.012	34.277	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.057	-0.019	35.530	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.967	0.973	36.710	-0.090	-0.090	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.855	0.945	30.404	-0.122	-0.122	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.007	-0.014	34.685	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.007	0.010	37.136	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	70	SER	0	0.031	0.002	37.409	0.001	0.001	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.014	-0.005	39.376	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	72	ILE	0	-0.032	-0.009	36.961	0.004	0.004	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.018	-0.008	40.349	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.035	-0.014	38.023	0.004	0.004	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.856	-0.932	41.937	0.052	0.052	0.000	0.000	0.000	0.000
70	A	76	PRO	0	-0.027	-0.018	44.222	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.925	-0.962	45.858	0.038	0.038	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.086	-0.027	40.153	0.000	0.000	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.035	0.018	41.688	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	80	PRO	0	0.045	0.003	41.671	0.002	0.002	0.000	0.000	0.000	0.000
75	A	81	GLU	-1	-0.932	-0.957	40.501	0.022	0.022	0.000	0.000	0.000	0.000
76	A	82	GLY	0	0.007	-0.006	38.931	0.000	0.000	0.000	0.000	0.000	0.000
77	A	83	PHE	0	0.023	0.007	35.274	0.004	0.004	0.000	0.000	0.000	0.000
78	A	84	ASN	0	0.012	-0.003	35.796	0.003	0.003	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.011	0.006	34.483	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	86	LEU	0	-0.018	-0.012	32.155	0.002	0.002	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.000	0.006	31.048	0.006	0.006	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.825	-0.927	30.594	0.011	0.011	0.000	0.000	0.000	0.000
83	A	89	PHE	0	-0.048	-0.006	25.395	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	90	MET	0	-0.058	-0.029	26.776	0.003	0.003	0.000	0.000	0.000	0.000
85	A	91	TYR	0	-0.011	-0.032	25.516	0.007	0.007	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.054	-0.051	25.818	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.061	-0.028	22.553	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.908	0.956	24.847	0.035	0.035	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.049	0.029	28.073	0.001	0.001	0.000	0.000	0.000	0.000
90	A	96	ASN	0	-0.023	-0.009	30.885	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.015	0.011	33.546	0.002	0.002	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.952	0.965	35.892	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.823	-0.926	39.340	0.021	0.021	0.000	0.000	0.000	0.000
94	A	100	GLY	0	-0.002	0.010	42.390	0.002	0.002	0.000	0.000	0.000	0.000
95	A	101	ASN	0	-0.004	-0.007	38.217	0.003	0.003	0.000	0.000	0.000	0.000
96	A	102	ILE	0	0.005	0.015	37.816	0.004	0.004	0.000	0.000	0.000	0.000
97	A	103	MET	0	0.019	0.001	39.314	0.006	0.006	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.046	0.029	41.140	0.004	0.004	0.000	0.000	0.000	0.000
99	A	105	VAL	0	0.015	0.015	35.233	0.004	0.004	0.000	0.000	0.000	0.000
100	A	106	MET	0	0.009	-0.002	36.340	0.007	0.007	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.023	0.007	37.136	0.007	0.007	0.000	0.000	0.000	0.000
102	A	108	THR	0	0.004	-0.009	36.841	0.003	0.003	0.000	0.000	0.000	0.000
103	A	109	ALA	0	-0.005	-0.012	32.964	0.005	0.005	0.000	0.000	0.000	0.000
104	A	110	MET	0	-0.049	-0.027	33.861	0.008	0.008	0.000	0.000	0.000	0.000
105	A	111	TYR	0	0.041	0.039	35.743	0.006	0.006	0.000	0.000	0.000	0.000
106	A	112	LEU	0	-0.010	-0.014	32.994	0.004	0.004	0.000	0.000	0.000	0.000
107	A	113	GLN	0	-0.007	0.011	31.689	0.017	0.017	0.000	0.000	0.000	0.000
108	A	114	MET	0	-0.017	0.005	28.760	0.009	0.009	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.831	-0.924	28.085	0.134	0.134	0.000	0.000	0.000	0.000
110	A	116	HIS	0	0.014	0.008	21.717	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	117	VAL	0	0.010	0.009	27.344	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	118	VAL	0	0.054	0.030	29.934	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.888	-0.955	28.703	0.139	0.139	0.000	0.000	0.000	0.000
114	A	120	THR	0	-0.067	-0.036	28.666	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	121	CYS	0	-0.035	-0.004	31.103	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	122	ARG	1	0.956	0.977	32.410	-0.120	-0.120	0.000	0.000	0.000	0.000
117	A	123	LYS	1	0.877	0.938	29.020	-0.114	-0.114	0.000	0.000	0.000	0.000
118	A	124	PHE	0	0.022	0.013	34.266	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	125	ILE	0	0.032	0.007	36.039	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.900	0.958	35.763	-0.082	-0.082	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.048	-0.021	36.049	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	128	SER	0	-0.034	0.001	38.176	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)