FMO DATABASE

FMODB ID: 6YK9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1031513.329018
FMO2-HF: Nuclear repulsion	981183.351261
FMO2-HF: Total energy	-50329.977757
FMO2-MP2: Total energy	-50473.05842

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.
-1.607	0.872	0.002	-1.302	-1.179	0.005

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 : 0.045 / q_NPA : 0.021

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	0.018	0.006	3.650	-2.779	-0.487	0.003	-1.294	-1.001	0.005
4	A	10	GLN	0	0.010	0.006	4.585	0.707	0.894	-0.001	-0.008	-0.178	0.000
5	A	11	PHE	0	0.024	0.009	7.222	-0.083	-0.083	0.000	0.000	0.000	0.000
6	A	12	THR	0	0.004	-0.006	10.789	0.130	0.130	0.000	0.000	0.000	0.000
7	A	13	ARG	1	0.904	0.952	12.323	0.342	0.342	0.000	0.000	0.000	0.000
8	A	14	HIS	0	0.009	0.011	13.294	0.010	0.010	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.039	0.018	14.588	0.035	0.035	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.038	0.018	16.237	0.012	0.012	0.000	0.000	0.000	0.000
11	A	17	ASP	-1	-0.826	-0.909	18.566	-0.196	-0.196	0.000	0.000	0.000	0.000
12	A	18	VAL	0	-0.007	-0.002	17.612	0.015	0.015	0.000	0.000	0.000	0.000
13	A	19	LEU	0	-0.009	0.012	20.228	0.010	0.010	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.028	0.013	22.119	0.008	0.008	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.029	-0.029	22.918	0.011	0.011	0.000	0.000	0.000	0.000
16	A	22	LEU	0	0.039	0.026	21.927	0.006	0.006	0.000	0.000	0.000	0.000
17	A	23	ASN	0	0.055	0.039	25.733	0.011	0.011	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.869	0.927	27.154	0.077	0.077	0.000	0.000	0.000	0.000
19	A	25	LEU	0	-0.026	0.000	26.944	0.002	0.002	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.861	0.908	30.041	0.027	0.027	0.000	0.000	0.000	0.000
21	A	27	SER	0	-0.094	-0.052	31.983	0.000	0.000	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.918	0.951	33.750	0.034	0.034	0.000	0.000	0.000	0.000
23	A	29	ASP	-1	-0.767	-0.832	35.217	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.006	0.008	31.610	0.003	0.003	0.000	0.000	0.000	0.000
25	A	31	LEU	0	0.001	-0.014	29.757	0.001	0.001	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.048	-0.027	31.913	0.006	0.006	0.000	0.000	0.000	0.000
27	A	33	ASP	-1	-0.757	-0.862	31.508	0.033	0.033	0.000	0.000	0.000	0.000
28	A	34	VAL	0	-0.032	-0.010	33.099	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.015	-0.002	35.723	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.001	0.004	34.603	0.003	0.003	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.011	-0.004	38.213	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.022	0.006	39.572	0.002	0.002	0.000	0.000	0.000	0.000
33	A	39	SER	0	0.080	0.035	42.717	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	40	ARG	1	0.788	0.882	46.195	0.006	0.006	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.864	-0.912	43.476	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	42	GLN	0	-0.015	-0.018	41.630	0.003	0.003	0.000	0.000	0.000	0.000
37	A	43	PHE	0	0.018	0.008	36.680	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.788	0.885	36.519	0.000	0.000	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.008	-0.003	31.415	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	46	HIS	0	0.006	0.009	28.119	0.002	0.002	0.000	0.000	0.000	0.000
41	A	47	LYS	1	0.823	0.896	28.893	-0.036	-0.036	0.000	0.000	0.000	0.000
42	A	48	THR	0	0.004	-0.005	24.170	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.008	0.007	24.421	0.005	0.005	0.000	0.000	0.000	0.000
44	A	50	LEU	0	0.023	0.012	25.545	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	51	MET	0	-0.080	-0.035	25.542	0.001	0.001	0.000	0.000	0.000	0.000
46	A	52	ALA	0	-0.041	-0.017	21.436	0.006	0.006	0.000	0.000	0.000	0.000
47	A	53	CYS	0	-0.035	-0.007	22.460	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	54	SER	0	-0.027	-0.031	25.080	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.063	0.034	27.927	0.007	0.007	0.000	0.000	0.000	0.000
50	A	56	LEU	0	-0.007	0.023	28.750	0.006	0.006	0.000	0.000	0.000	0.000
51	A	57	PHE	0	0.052	0.000	29.788	0.003	0.003	0.000	0.000	0.000	0.000
52	A	58	TYR	0	0.017	0.011	24.467	0.008	0.008	0.000	0.000	0.000	0.000
53	A	59	SER	0	-0.011	-0.029	28.285	0.008	0.008	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.057	-0.025	31.174	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.035	-0.005	29.851	0.000	0.000	0.000	0.000	0.000	0.000
56	A	62	THR	0	-0.016	-0.003	27.073	0.007	0.007	0.000	0.000	0.000	0.000
57	A	63	ASP	-1	-0.776	-0.863	29.523	0.066	0.066	0.000	0.000	0.000	0.000
58	A	64	GLN	0	0.011	0.001	33.012	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.040	-0.016	34.340	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.889	0.929	35.813	-0.054	-0.054	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.807	0.911	29.256	-0.091	-0.091	0.000	0.000	0.000	0.000
62	A	68	ASN	0	0.021	-0.001	33.708	0.001	0.001	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.020	0.000	36.188	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	70	SER	0	0.019	0.002	36.635	0.000	0.000	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.022	-0.011	38.432	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	72	ILE	0	-0.023	-0.005	36.158	0.003	0.003	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.012	-0.005	39.486	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	74	LEU	0	-0.030	-0.012	37.089	0.003	0.003	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.882	-0.945	40.969	0.013	0.013	0.000	0.000	0.000	0.000
70	A	76	PRO	0	-0.008	-0.009	43.161	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	77	GLU	-1	-0.911	-0.950	44.841	0.003	0.003	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.085	-0.029	39.216	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	79	ASN	0	0.014	-0.001	41.245	0.000	0.000	0.000	0.000	0.000	0.000
74	A	80	PRO	0	0.011	-0.004	40.826	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	81	GLU	-1	-0.830	-0.911	39.766	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	82	GLY	0	0.073	0.032	38.010	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	83	PHE	0	0.014	0.002	34.712	0.000	0.000	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.020	-0.014	35.000	0.001	0.001	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.052	-0.019	34.059	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	86	LEU	0	-0.013	-0.005	31.501	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	87	LEU	0	-0.001	0.007	30.295	0.000	0.000	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.768	-0.886	30.031	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	89	PHE	0	-0.030	0.014	24.671	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	90	MET	0	-0.041	-0.023	26.034	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	91	TYR	0	-0.002	-0.020	25.213	0.003	0.003	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.080	-0.076	25.614	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.036	-0.009	22.290	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	94	ARG	1	0.898	0.951	24.617	0.087	0.087	0.000	0.000	0.000	0.000
89	A	95	LEU	0	0.057	0.023	28.008	0.006	0.006	0.000	0.000	0.000	0.000
90	A	96	ASN	0	0.011	0.026	30.858	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	97	LEU	0	0.016	0.004	32.379	0.004	0.004	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.923	0.944	35.517	0.028	0.028	0.000	0.000	0.000	0.000
93	A	99	GLU	-1	-0.828	-0.918	39.016	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	100	GLY	0	-0.014	-0.005	42.184	0.002	0.002	0.000	0.000	0.000	0.000
95	A	101	ASN	0	-0.074	-0.048	38.098	0.001	0.001	0.000	0.000	0.000	0.000
96	A	102	ILE	0	0.012	0.016	36.921	0.003	0.003	0.000	0.000	0.000	0.000
97	A	103	MET	0	0.008	-0.001	38.289	0.001	0.001	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.040	0.030	40.291	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	VAL	0	0.023	0.012	34.497	0.002	0.002	0.000	0.000	0.000	0.000
100	A	106	MET	0	0.006	-0.007	35.293	0.002	0.002	0.000	0.000	0.000	0.000
101	A	107	ALA	0	0.020	0.012	36.039	0.003	0.003	0.000	0.000	0.000	0.000
102	A	108	THR	0	0.007	-0.005	35.855	0.004	0.004	0.000	0.000	0.000	0.000
103	A	109	ALA	0	-0.001	-0.004	31.960	0.003	0.003	0.000	0.000	0.000	0.000
104	A	110	MET	0	-0.042	-0.028	32.657	0.003	0.003	0.000	0.000	0.000	0.000
105	A	111	TYR	0	0.041	0.030	34.585	0.004	0.004	0.000	0.000	0.000	0.000
106	A	112	LEU	0	0.005	-0.006	32.026	0.004	0.004	0.000	0.000	0.000	0.000
107	A	113	GLN	0	-0.016	0.015	30.520	0.008	0.008	0.000	0.000	0.000	0.000
108	A	114	MET	0	-0.019	0.005	28.056	0.004	0.004	0.000	0.000	0.000	0.000
109	A	115	GLU	-1	-0.844	-0.929	27.227	0.009	0.009	0.000	0.000	0.000	0.000
110	A	116	HIS	0	0.003	-0.005	21.146	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	117	VAL	0	0.022	0.031	26.468	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	118	VAL	0	0.059	0.042	29.182	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	119	ASP	-1	-0.801	-0.899	28.068	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	120	THR	0	-0.041	-0.025	27.955	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	121	CYS	0	-0.055	-0.015	30.306	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	122	ARG	1	0.939	0.959	31.408	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	123	LYS	1	0.794	0.881	27.951	0.024	0.024	0.000	0.000	0.000	0.000
118	A	124	PHE	0	0.019	0.016	33.402	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	125	ILE	0	0.009	-0.006	35.461	0.000	0.000	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.916	0.960	35.148	0.018	0.018	0.000	0.000	0.000	0.000
121	A	127	ALA	0	-0.006	0.009	35.401	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	128	SER	0	-0.078	-0.027	37.520	0.001	0.001	0.000	0.000	0.000	0.000

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