FMO DATABASE

FMODB ID: 2NMGR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-824269.124848
FMO2-HF: Nuclear repulsion	782213.816731
FMO2-HF: Total energy	-42055.308117
FMO2-MP2: Total energy	-42177.518154

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.
-0.262	1.701	0.007	-0.931	-1.038	0.004

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 : 0.007 / 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	0.075	0.026	3.814	1.443	2.972	-0.017	-0.757	-0.755	0.003
4	A	6	PRO	0	0.069	0.020	6.710	0.445	0.445	0.000	0.000	0.000	0.000
5	A	7	SER	0	0.024	0.014	3.590	-0.975	-0.541	0.024	-0.174	-0.283	0.001
6	A	8	ALA	0	0.010	0.014	5.163	0.198	0.198	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.013	0.009	6.346	-0.375	-0.375	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.019	-0.001	8.818	-0.060	-0.060	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.023	-0.024	5.726	-0.481	-0.481	0.000	0.000	0.000	0.000
10	A	12	ASN	0	-0.065	-0.039	8.832	-0.215	-0.215	0.000	0.000	0.000	0.000
11	A	13	MET	0	-0.061	0.009	11.828	-0.125	-0.125	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.009	-0.015	14.535	0.002	0.002	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.001	-0.011	17.723	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.022	0.034	16.866	0.035	0.035	0.000	0.000	0.000	0.000
15	A	17	THR	0	0.001	-0.019	14.855	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.008	0.002	16.415	0.024	0.024	0.000	0.000	0.000	0.000
17	A	19	ILE	0	-0.018	-0.003	15.576	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.011	0.000	18.470	0.005	0.005	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.740	-0.877	21.887	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.869	-0.941	23.503	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.043	-0.008	26.810	0.003	0.003	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.064	-0.039	25.861	0.006	0.006	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.010	0.015	23.785	0.010	0.010	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.002	-0.005	18.623	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.779	0.856	18.051	0.031	0.031	0.000	0.000	0.000	0.000
26	A	28	TYR	0	-0.037	-0.018	9.982	0.004	0.004	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.021	0.007	13.981	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.011	0.011	12.098	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	31	PRO	0	0.077	0.032	10.679	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.015	0.013	13.715	-0.048	-0.048	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.005	-0.007	16.397	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.834	-0.913	13.571	0.290	0.290	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.042	-0.028	16.803	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.077	-0.024	19.603	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	37	PHE	0	0.022	-0.012	20.932	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.060	-0.016	22.220	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.005	-0.005	20.958	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	40	SER	0	0.023	0.017	17.130	0.005	0.005	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.082	0.037	13.920	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	42	LYS	1	0.885	0.938	15.961	-0.088	-0.088	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.869	0.934	17.134	-0.109	-0.109	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.023	0.021	17.823	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.016	-0.011	15.290	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.889	-0.938	18.753	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.094	-0.027	21.595	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	48	SER	0	0.051	0.026	23.824	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.041	0.001	24.534	0.007	0.007	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.044	-0.024	26.507	0.005	0.005	0.000	0.000	0.000	0.000
49	A	51	GLN	0	-0.027	-0.009	27.283	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.037	0.000	22.703	0.004	0.004	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.033	-0.016	26.240	0.006	0.006	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.004	-0.010	29.499	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	HIS	0	-0.020	-0.014	33.104	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.007	0.011	31.957	0.005	0.005	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.029	0.001	33.790	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.017	-0.007	30.874	0.004	0.004	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.817	-0.900	33.844	0.006	0.006	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.009	-0.015	33.229	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.023	-0.008	33.465	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.005	-0.008	28.617	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.023	-0.022	28.588	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	THR	0	-0.032	-0.007	30.196	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	65	GLN	0	0.011	0.003	31.664	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	66	PRO	0	0.043	0.055	26.854	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.018	-0.018	26.697	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.063	-0.019	29.236	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.036	-0.041	32.283	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.008	-0.003	28.684	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	GLN	0	-0.065	-0.031	28.349	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.006	-0.020	25.111	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.055	-0.020	27.756	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	THR	0	0.018	-0.015	27.754	0.002	0.002	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.801	-0.905	29.781	0.023	0.023	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.004	-0.016	30.495	0.004	0.004	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-1.005	-1.003	32.192	0.038	0.038	0.000	0.000	0.000	0.000
76	A	78	VAL	0	0.006	0.031	29.670	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	79	THR	0	-0.021	-0.025	32.029	0.004	0.004	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.019	-0.001	25.941	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.020	-0.016	30.908	0.005	0.005	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.022	0.006	26.660	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.887	-0.946	28.619	0.074	0.074	0.000	0.000	0.000	0.000
82	A	84	GLY	0	-0.044	-0.016	31.287	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.908	0.941	31.723	-0.072	-0.072	0.000	0.000	0.000	0.000
84	A	86	PRO	0	0.011	0.023	31.919	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.026	-0.012	26.352	0.005	0.005	0.000	0.000	0.000	0.000
86	A	88	MET	0	-0.008	0.011	30.280	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.041	-0.042	25.597	0.010	0.010	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.897	-0.924	27.484	0.037	0.037	0.000	0.000	0.000	0.000
89	A	91	VAL	0	-0.053	-0.052	25.137	0.010	0.010	0.000	0.000	0.000	0.000
90	A	92	THR	0	0.045	0.036	24.285	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.038	-0.003	23.963	0.007	0.007	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.068	0.038	22.302	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	95	PRO	0	-0.003	0.031	23.114	0.001	0.001	0.000	0.000	0.000	0.000
94	A	96	ILE	0	-0.016	-0.014	16.347	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.029	-0.003	20.888	0.000	0.000	0.000	0.000	0.000	0.000
96	A	98	TRP	0	0.013	-0.007	12.679	-0.028	-0.028	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.010	-0.013	16.140	0.013	0.013	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.893	0.928	19.346	0.142	0.142	0.000	0.000	0.000	0.000
99	A	101	GLN	0	0.031	0.038	21.721	0.008	0.008	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.023	0.001	22.129	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	103	MET	0	0.009	0.012	18.086	0.008	0.008	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.020	0.007	22.587	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	105	LEU	0	0.005	-0.004	17.102	0.005	0.005	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.002	-0.003	20.089	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.933	-0.968	19.129	0.074	0.074	0.000	0.000	0.000	0.000
106	A	108	MET	0	-0.020	-0.013	20.895	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.918	0.964	21.449	-0.099	-0.099	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.955	0.979	24.275	-0.119	-0.119	0.000	0.000	0.000	0.000
109	A	111	ILE	0	-0.014	0.019	26.972	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)