FMO DATABASE

FMODB ID: 76K4K

Calculation Name: 3B33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B33

Chain ID: A

ChEMBL ID:

UniProt ID: Q87TF0

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-823389.613128
FMO2-HF: Nuclear repulsion	781334.830372
FMO2-HF: Total energy	-42054.782756
FMO2-MP2: Total energy	-42177.041137

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-1.232	0.729	0.002	-1.009	-0.954	0.005

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.007

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	5	LEU	0	0.070	0.023	3.814	0.315	1.865	-0.017	-0.829	-0.704	0.004
4	A	6	PRO	0	0.053	0.016	6.710	0.268	0.268	0.000	0.000	0.000	0.000
5	A	7	SER	0	0.039	0.024	3.811	-0.363	0.048	0.019	-0.180	-0.250	0.001
6	A	8	ALA	0	-0.007	0.002	4.922	-0.576	-0.576	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.005	0.006	5.909	-0.473	-0.473	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.019	-0.002	8.833	-0.206	-0.206	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.017	-0.026	5.078	-0.419	-0.419	0.000	0.000	0.000	0.000
10	A	12	ASN	0	-0.068	-0.043	7.963	-0.344	-0.344	0.000	0.000	0.000	0.000
11	A	13	MET	0	-0.064	0.006	11.131	-0.169	-0.169	0.000	0.000	0.000	0.000
12	A	14	VAL	0	-0.001	-0.015	14.002	0.015	0.015	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.001	-0.004	17.340	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.028	0.036	16.458	0.089	0.089	0.000	0.000	0.000	0.000
15	A	17	THR	0	0.005	-0.022	14.921	0.012	0.012	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.001	-0.001	16.497	0.080	0.080	0.000	0.000	0.000	0.000
17	A	19	ILE	0	-0.015	0.005	16.301	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.000	0.003	19.052	0.007	0.007	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.783	-0.908	22.512	0.346	0.346	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.910	-0.960	24.150	0.247	0.247	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.016	0.005	27.423	-0.024	-0.024	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.074	-0.045	26.469	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.014	0.014	24.148	0.003	0.003	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.005	-0.009	19.051	0.028	0.028	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.883	0.942	18.437	-0.458	-0.458	0.000	0.000	0.000	0.000
26	A	28	TYR	0	-0.040	-0.019	10.518	0.214	0.214	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.035	0.011	14.309	-0.124	-0.124	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.024	0.009	11.830	0.062	0.062	0.000	0.000	0.000	0.000
29	A	31	PRO	0	0.080	0.035	10.127	-0.130	-0.130	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.005	0.017	13.231	-0.115	-0.115	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.004	-0.007	15.953	-0.088	-0.088	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.831	-0.907	13.363	0.777	0.777	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.031	-0.025	16.577	-0.074	-0.074	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.073	-0.020	19.137	-0.053	-0.053	0.000	0.000	0.000	0.000
35	A	37	PHE	0	0.016	-0.015	20.836	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.060	-0.012	21.836	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.012	-0.009	20.677	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.004	0.006	17.215	0.036	0.036	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.097	0.038	13.893	-0.032	-0.032	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.891	0.944	15.902	-0.438	-0.438	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.907	0.957	17.165	-0.348	-0.348	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.014	0.017	18.232	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.016	-0.011	15.635	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.968	-0.995	19.000	0.437	0.437	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.122	-0.046	21.877	-0.068	-0.068	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.042	0.021	24.189	0.018	0.018	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.054	0.008	24.877	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.053	-0.028	26.837	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	51	GLN	0	-0.030	-0.013	27.295	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.026	0.005	22.904	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.034	-0.015	26.212	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	54	GLN	0	0.012	-0.001	29.458	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	55	HIS	0	-0.015	-0.012	33.007	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.006	0.011	31.958	0.012	0.012	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.033	-0.004	33.775	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.016	-0.004	31.148	0.010	0.010	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.822	-0.907	34.021	0.158	0.158	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.001	-0.016	33.532	0.012	0.012	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.026	-0.007	33.945	0.008	0.008	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.016	-0.003	28.684	0.009	0.009	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.022	-0.020	29.183	0.020	0.020	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.031	-0.008	30.784	0.003	0.003	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.041	0.013	32.271	0.001	0.001	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.031	0.043	27.382	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.021	-0.026	26.911	0.001	0.001	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.074	-0.028	29.901	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.019	-0.017	33.013	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.014	-0.003	29.288	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	71	GLN	0	-0.065	-0.032	28.883	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.003	-0.024	25.503	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.048	-0.015	28.163	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	74	THR	0	0.013	-0.022	27.847	0.018	0.018	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.803	-0.907	29.836	0.168	0.168	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.003	-0.019	30.402	0.013	0.013	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-1.010	-1.004	31.993	0.151	0.151	0.000	0.000	0.000	0.000
76	A	78	VAL	0	0.010	0.035	29.593	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	79	THR	0	-0.031	-0.028	31.724	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.024	0.001	26.095	0.002	0.002	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.021	-0.018	30.652	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.022	0.004	26.350	0.007	0.007	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.923	-0.960	29.016	0.222	0.222	0.000	0.000	0.000	0.000
82	A	84	GLY	0	-0.052	-0.017	31.003	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.906	0.939	30.592	-0.179	-0.179	0.000	0.000	0.000	0.000
84	A	86	PRO	0	-0.001	0.017	31.473	0.012	0.012	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.013	-0.010	25.802	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	MET	0	-0.007	0.012	29.755	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.042	-0.042	25.368	0.012	0.012	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.895	-0.923	27.277	0.204	0.204	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.048	-0.042	25.338	0.031	0.031	0.000	0.000	0.000	0.000
90	A	92	THR	0	0.046	0.037	24.427	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.040	-0.006	24.209	0.041	0.041	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.073	0.051	22.710	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.009	0.025	23.659	0.032	0.032	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.011	-0.013	16.930	0.020	0.020	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.035	-0.005	21.596	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	TRP	0	0.015	-0.006	13.766	0.043	0.043	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.004	-0.014	16.826	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.891	0.927	20.112	-0.201	-0.201	0.000	0.000	0.000	0.000
99	A	101	GLN	0	0.060	0.051	22.513	-0.022	-0.022	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.016	0.012	22.941	0.033	0.033	0.000	0.000	0.000	0.000
101	A	103	MET	0	-0.013	-0.002	18.937	0.001	0.001	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.039	0.013	23.271	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	105	LEU	0	0.002	-0.006	17.667	0.055	0.055	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.002	-0.001	20.541	-0.047	-0.047	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.931	-0.966	19.212	0.499	0.499	0.000	0.000	0.000	0.000
106	A	108	MET	0	-0.019	-0.017	20.788	-0.056	-0.056	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.929	0.966	20.984	-0.273	-0.273	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.950	0.976	23.831	-0.273	-0.273	0.000	0.000	0.000	0.000
109	A	111	ILE	0	-0.021	0.017	26.438	-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:3:THR)