FMO DATABASE

FMODB ID: 2N96R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1029253.808366
FMO2-HF: Nuclear repulsion	978924.029552
FMO2-HF: Total energy	-50329.778814
FMO2-MP2: Total energy	-50472.858383

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.
-1.505	1.224	-0.016	-1.529	-1.184	0.008

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 : 0.039 / q_NPA : 0.017

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	9	ILE	0	0.030	0.013	3.786	-2.846	-0.117	-0.016	-1.529	-1.184	0.008
4	A	10	GLN	0	-0.010	-0.004	5.139	0.924	0.924	0.000	0.000	0.000	0.000
5	A	11	PHE	0	0.022	0.010	7.831	-0.127	-0.127	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.004	-0.010	11.348	0.107	0.107	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.994	1.000	12.898	0.364	0.364	0.000	0.000	0.000	0.000
8	A	14	HIS	0	0.049	0.036	13.686	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.035	0.014	14.651	0.030	0.030	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.030	0.011	16.394	0.009	0.009	0.000	0.000	0.000	0.000
11	A	17	ASP	-1	-0.900	-0.954	18.862	-0.166	-0.166	0.000	0.000	0.000	0.000
12	A	18	VAL	0	-0.029	-0.012	17.875	0.013	0.013	0.000	0.000	0.000	0.000
13	A	19	LEU	0	0.000	0.012	20.566	0.008	0.008	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.030	0.018	22.516	0.005	0.005	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.037	-0.032	22.908	0.006	0.006	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.031	0.018	22.530	0.005	0.005	0.000	0.000	0.000	0.000
17	A	23	ASN	0	0.054	0.037	26.201	0.010	0.010	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.880	0.936	27.259	0.068	0.068	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.014	0.002	27.295	0.001	0.001	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.864	0.924	30.474	0.013	0.013	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.097	-0.053	32.408	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.918	0.950	33.726	0.029	0.029	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.783	-0.832	35.409	0.006	0.006	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.026	-0.007	31.955	0.002	0.002	0.000	0.000	0.000	0.000
25	A	31	LEU	0	0.005	-0.012	29.919	0.001	0.001	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.063	-0.035	32.284	0.006	0.006	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.783	-0.888	32.226	0.046	0.046	0.000	0.000	0.000	0.000
28	A	34	VAL	0	-0.051	-0.020	33.816	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.011	0.003	36.448	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.009	-0.006	35.219	0.004	0.004	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.016	-0.001	38.854	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.020	0.006	39.665	0.002	0.002	0.000	0.000	0.000	0.000
33	A	39	SER	0	0.074	0.037	42.947	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.900	0.944	46.667	0.000	0.000	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.917	-0.955	43.362	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	42	GLN	0	-0.011	-0.013	42.178	0.003	0.003	0.000	0.000	0.000	0.000
37	A	43	PHE	0	0.013	0.010	37.147	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.852	0.915	36.822	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	45	ALA	0	-0.001	-0.005	31.951	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.008	0.011	28.629	0.002	0.002	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.852	0.915	29.386	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	48	THR	0	-0.003	-0.007	24.737	0.001	0.001	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.012	0.011	24.882	0.008	0.008	0.000	0.000	0.000	0.000
44	A	50	LEU	0	0.030	0.010	26.059	0.001	0.001	0.000	0.000	0.000	0.000
45	A	51	MET	0	-0.077	-0.033	26.231	0.001	0.001	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.042	-0.013	21.864	0.009	0.009	0.000	0.000	0.000	0.000
47	A	53	CYS	0	-0.047	-0.017	22.848	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	54	SER	0	-0.037	-0.029	25.401	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.064	0.026	28.380	0.008	0.008	0.000	0.000	0.000	0.000
50	A	56	LEU	0	-0.012	0.016	29.203	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.041	-0.004	30.288	0.002	0.002	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.001	0.003	24.577	0.008	0.008	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.009	-0.027	28.864	0.008	0.008	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.064	-0.023	31.593	0.001	0.001	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.038	0.002	30.478	0.001	0.001	0.000	0.000	0.000	0.000
56	A	62	THR	0	0.010	0.008	27.621	0.005	0.005	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.796	-0.867	30.126	0.081	0.081	0.000	0.000	0.000	0.000
58	A	64	GLN	0	0.021	-0.007	33.647	0.000	0.000	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.052	-0.019	35.003	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.890	0.922	36.154	-0.069	-0.069	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.823	0.931	29.792	-0.109	-0.109	0.000	0.000	0.000	0.000
62	A	68	ASN	0	0.002	-0.009	34.333	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.012	0.008	36.817	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	70	SER	0	0.013	-0.009	37.099	0.001	0.001	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.018	-0.010	39.120	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	72	ILE	0	-0.025	-0.005	36.508	0.003	0.003	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.016	-0.007	39.922	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.031	-0.011	37.481	0.003	0.003	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.866	-0.938	41.396	0.022	0.022	0.000	0.000	0.000	0.000
70	A	76	PRO	0	-0.020	-0.015	43.602	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.928	-0.960	45.104	0.011	0.011	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.090	-0.030	39.564	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.022	0.008	41.546	0.000	0.000	0.000	0.000	0.000	0.000
74	A	80	PRO	0	0.024	0.003	41.240	0.000	0.000	0.000	0.000	0.000	0.000
75	A	81	GLU	-1	-0.877	-0.947	40.238	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	82	GLY	0	0.060	0.025	38.577	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	83	PHE	0	0.012	0.000	35.061	0.001	0.001	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.016	-0.012	35.474	0.002	0.002	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.044	-0.010	34.221	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	86	LEU	0	-0.017	-0.012	31.758	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	87	LEU	0	0.001	0.009	30.734	0.002	0.002	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.766	-0.891	30.466	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	89	PHE	0	-0.018	0.008	25.090	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	90	MET	0	-0.060	-0.024	26.468	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	91	TYR	0	0.001	-0.020	25.369	0.003	0.003	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.062	-0.060	26.055	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.060	-0.026	22.543	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.910	0.961	24.826	0.074	0.074	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.045	0.025	28.115	0.006	0.006	0.000	0.000	0.000	0.000
90	A	96	ASN	0	-0.009	-0.008	30.739	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.009	0.009	32.742	0.004	0.004	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.933	0.956	35.654	0.021	0.021	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.809	-0.909	39.138	-0.018	-0.018	0.000	0.000	0.000	0.000
94	A	100	GLY	0	-0.020	-0.005	42.088	0.003	0.003	0.000	0.000	0.000	0.000
95	A	101	ASN	0	-0.029	-0.016	38.104	0.001	0.001	0.000	0.000	0.000	0.000
96	A	102	ILE	0	0.003	0.017	37.207	0.003	0.003	0.000	0.000	0.000	0.000
97	A	103	MET	0	0.005	-0.002	38.725	0.002	0.002	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.037	0.025	40.461	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	VAL	0	0.026	0.013	34.827	0.003	0.003	0.000	0.000	0.000	0.000
100	A	106	MET	0	0.001	-0.003	35.638	0.003	0.003	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.022	0.008	36.395	0.004	0.004	0.000	0.000	0.000	0.000
102	A	108	THR	0	0.009	-0.002	36.289	0.004	0.004	0.000	0.000	0.000	0.000
103	A	109	ALA	0	-0.007	-0.011	32.270	0.004	0.004	0.000	0.000	0.000	0.000
104	A	110	MET	0	-0.050	-0.031	33.113	0.004	0.004	0.000	0.000	0.000	0.000
105	A	111	TYR	0	0.052	0.042	34.934	0.005	0.005	0.000	0.000	0.000	0.000
106	A	112	LEU	0	-0.003	-0.009	32.331	0.004	0.004	0.000	0.000	0.000	0.000
107	A	113	GLN	0	-0.016	0.009	30.933	0.011	0.011	0.000	0.000	0.000	0.000
108	A	114	MET	0	-0.009	0.011	28.174	0.005	0.005	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.837	-0.924	27.150	0.032	0.032	0.000	0.000	0.000	0.000
110	A	116	HIS	0	-0.003	-0.010	20.971	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	117	VAL	0	0.026	0.024	26.532	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	118	VAL	0	0.061	0.039	29.230	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.808	-0.899	28.193	0.004	0.004	0.000	0.000	0.000	0.000
114	A	120	THR	0	-0.048	-0.029	28.068	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	121	CYS	0	-0.044	-0.011	30.407	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	122	ARG	1	0.947	0.968	31.758	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	123	LYS	1	0.800	0.885	27.861	0.005	0.005	0.000	0.000	0.000	0.000
118	A	124	PHE	0	0.013	0.009	33.543	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	125	ILE	0	0.018	0.000	35.493	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.910	0.960	35.164	0.009	0.009	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.047	-0.017	35.496	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	128	SER	0	-0.037	0.001	37.639	-0.002	-0.002	0.000	0.000	0.000	0.000

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