FMO DATABASE

FMODB ID: 94242

Calculation Name: 4M9O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M9O

Chain ID: A

ChEMBL ID:

UniProt ID: Q04475

Base Structure: X-ray

Registration Date: 2023-06-26

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-715408.847783
FMO2-HF: Nuclear repulsion	675785.670871
FMO2-HF: Total energy	-39623.176912
FMO2-MP2: Total energy	-39736.585014

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:1:LYS)

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

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.
18.209	20.201	-0.029	-1.032	-0.931	0

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.948 / q_NPA : 0.954

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].
3	A	3	SER	0	-0.016	-0.007	3.833	1.949	3.891	-0.028	-1.027	-0.887
4	A	4	THR	0	-0.013	-0.015	6.552	0.928	0.928	0.000	0.000	0.000
5	A	5	PRO	0	-0.003	0.008	10.156	0.513	0.513	0.000	0.000	0.000
6	A	6	LYS	1	0.920	0.966	11.492	18.903	18.903	0.000	0.000	0.000
7	A	7	VAL	0	-0.001	-0.007	15.297	0.017	0.017	0.000	0.000	0.000
8	A	8	HIS	0	0.007	0.014	18.717	0.597	0.597	0.000	0.000	0.000
9	A	9	VAL	0	0.025	-0.002	22.159	-0.049	-0.049	0.000	0.000	0.000
10	A	10	TYR	0	-0.015	-0.009	24.094	0.065	0.065	0.000	0.000	0.000
11	A	11	SER	0	0.015	0.000	28.504	-0.075	-0.075	0.000	0.000	0.000
12	A	12	HIS	0	-0.008	-0.001	31.643	-0.235	-0.235	0.000	0.000	0.000
13	A	13	PHE	0	-0.016	0.004	32.874	0.103	0.103	0.000	0.000	0.000
14	A	14	PRO	0	0.044	0.027	35.535	-0.150	-0.150	0.000	0.000	0.000
15	A	15	GLY	0	-0.004	-0.005	36.604	0.088	0.088	0.000	0.000	0.000
16	A	16	GLU	-1	-0.903	-0.964	37.847	-6.690	-6.690	0.000	0.000	0.000
17	A	17	TYR	0	-0.026	-0.036	39.867	0.021	0.021	0.000	0.000	0.000
18	A	18	GLY	0	0.084	0.054	42.983	0.133	0.133	0.000	0.000	0.000
19	A	19	LYS	1	0.862	0.943	39.431	7.499	7.499	0.000	0.000	0.000
20	A	20	PRO	0	-0.015	-0.005	40.625	-0.199	-0.199	0.000	0.000	0.000
21	A	21	ASN	0	-0.047	-0.033	35.881	-0.059	-0.059	0.000	0.000	0.000
22	A	22	THR	0	0.006	0.000	31.850	0.011	0.011	0.000	0.000	0.000
23	A	23	LEU	0	0.014	0.015	29.451	-0.055	-0.055	0.000	0.000	0.000
24	A	24	ILE	0	-0.012	-0.019	25.770	-0.127	-0.127	0.000	0.000	0.000
25	A	25	CYS	0	-0.056	0.001	22.627	-0.328	-0.328	0.000	0.000	0.000
26	A	26	TYR	0	-0.010	0.008	19.000	-0.384	-0.384	0.000	0.000	0.000
27	A	27	VAL	0	0.016	-0.002	15.705	-0.301	-0.301	0.000	0.000	0.000
28	A	28	SER	0	0.048	0.013	15.232	-0.464	-0.464	0.000	0.000	0.000
29	A	29	SER	0	-0.055	-0.031	11.056	-0.126	-0.126	0.000	0.000	0.000
30	A	30	PHE	0	0.013	0.030	9.536	-0.674	-0.674	0.000	0.000	0.000
31	A	31	HIS	0	-0.017	0.011	5.045	-2.130	-2.130	0.000	0.000	0.000
32	A	32	PRO	0	0.027	-0.023	4.778	-2.522	-2.472	-0.001	-0.005	-0.044
33	A	33	PRO	0	0.026	-0.004	6.808	1.052	1.052	0.000	0.000	0.000
34	A	34	ASP	-1	-0.882	-0.906	9.854	-22.477	-22.477	0.000	0.000	0.000
35	A	35	ILE	0	-0.059	-0.048	11.525	-0.700	-0.700	0.000	0.000	0.000
36	A	36	SER	0	-0.004	0.001	14.131	0.608	0.608	0.000	0.000	0.000
37	A	37	ILE	0	0.007	0.004	17.712	-0.202	-0.202	0.000	0.000	0.000
38	A	38	GLU	-1	-0.848	-0.907	20.531	-11.662	-11.662	0.000	0.000	0.000
39	A	39	LEU	0	0.007	0.013	24.113	-0.157	-0.157	0.000	0.000	0.000
40	A	40	LEU	0	-0.038	-0.035	25.699	0.083	0.083	0.000	0.000	0.000
41	A	41	LYS	1	0.936	0.956	29.411	8.051	8.051	0.000	0.000	0.000
42	A	42	ASN	0	-0.046	-0.033	33.051	-0.057	-0.057	0.000	0.000	0.000
43	A	43	GLY	0	0.027	0.023	31.012	0.103	0.103	0.000	0.000	0.000
44	A	44	GLN	0	-0.031	-0.014	31.718	-0.089	-0.089	0.000	0.000	0.000
45	A	45	VAL	0	-0.022	-0.022	27.432	-0.061	-0.061	0.000	0.000	0.000
46	A	46	MET	0	-0.025	0.010	29.934	0.224	0.224	0.000	0.000	0.000
47	A	47	SER	0	-0.010	-0.021	30.534	-0.269	-0.269	0.000	0.000	0.000
48	A	48	ASP	-1	-0.900	-0.944	32.939	-8.507	-8.507	0.000	0.000	0.000
49	A	49	THR	0	-0.038	-0.007	28.237	-0.086	-0.086	0.000	0.000	0.000
50	A	50	LYS	1	0.928	0.961	28.762	9.234	9.234	0.000	0.000	0.000
51	A	51	GLN	0	0.009	-0.017	20.858	-0.142	-0.142	0.000	0.000	0.000
52	A	52	THR	0	0.020	0.021	21.879	0.178	0.178	0.000	0.000	0.000
53	A	53	ASP	-1	-0.879	-0.939	21.954	-12.580	-12.580	0.000	0.000	0.000
54	A	54	LEU	0	-0.087	-0.041	13.908	-0.152	-0.152	0.000	0.000	0.000
55	A	55	ALA	0	0.029	0.029	18.093	0.124	0.124	0.000	0.000	0.000
56	A	56	PHE	0	-0.016	-0.023	10.848	-0.858	-0.858	0.000	0.000	0.000
57	A	57	GLU	-1	-0.787	-0.881	15.029	-13.048	-13.048	0.000	0.000	0.000
58	A	58	LYS	1	0.804	0.866	14.574	13.990	13.990	0.000	0.000	0.000
59	A	59	GLY	0	0.030	0.018	13.152	-0.255	-0.255	0.000	0.000	0.000
60	A	60	TRP	0	0.003	0.001	9.313	-1.630	-1.630	0.000	0.000	0.000
61	A	61	GLN	0	-0.002	0.021	10.002	-0.742	-0.742	0.000	0.000	0.000
62	A	62	PHE	0	0.057	0.035	8.901	0.662	0.662	0.000	0.000	0.000
63	A	63	HIS	0	-0.105	-0.068	13.438	0.027	0.027	0.000	0.000	0.000
64	A	64	LEU	0	0.013	0.015	16.638	0.165	0.165	0.000	0.000	0.000
65	A	65	THR	0	0.035	0.014	19.264	0.054	0.054	0.000	0.000	0.000
66	A	66	LYS	1	0.833	0.916	22.741	12.255	12.255	0.000	0.000	0.000
67	A	67	SER	0	-0.024	-0.017	24.834	0.224	0.224	0.000	0.000	0.000
68	A	68	VAL	0	0.035	0.000	28.551	-0.022	-0.022	0.000	0.000	0.000
69	A	69	ALA	0	0.009	0.028	31.789	0.058	0.058	0.000	0.000	0.000
70	A	70	PHE	0	-0.036	-0.025	34.383	-0.078	-0.078	0.000	0.000	0.000
71	A	71	THR	0	0.048	0.016	36.735	0.036	0.036	0.000	0.000	0.000
72	A	72	PRO	0	-0.047	0.008	37.515	-0.011	-0.011	0.000	0.000	0.000
73	A	73	GLU	-1	-0.811	-0.923	39.254	-6.783	-6.783	0.000	0.000	0.000
74	A	74	LYS	1	0.912	0.942	40.461	6.473	6.473	0.000	0.000	0.000
75	A	75	GLY	0	0.001	0.002	40.435	0.089	0.089	0.000	0.000	0.000
76	A	76	ASP	-1	-0.779	-0.849	37.049	-7.958	-7.958	0.000	0.000	0.000
77	A	77	GLU	-1	-0.959	-0.976	31.539	-9.659	-9.659	0.000	0.000	0.000
78	A	78	TYR	0	-0.035	-0.033	31.364	-0.049	-0.049	0.000	0.000	0.000
79	A	79	THR	0	0.023	0.008	26.742	-0.285	-0.285	0.000	0.000	0.000
80	A	81	SER	0	0.000	0.001	21.633	-0.185	-0.185	0.000	0.000	0.000
81	A	82	VAL	0	0.024	0.003	15.957	-0.071	-0.071	0.000	0.000	0.000
82	A	83	ARG	1	0.850	0.927	15.475	16.928	16.928	0.000	0.000	0.000
83	A	84	HIS	0	0.053	0.012	7.930	0.506	0.506	0.000	0.000	0.000
84	A	85	MET	0	-0.004	0.004	5.661	-0.454	-0.454	0.000	0.000	0.000
85	A	86	LYS	1	0.930	0.959	10.081	26.732	26.732	0.000	0.000	0.000
86	A	87	GLU	-1	-0.841	-0.916	13.562	-17.706	-17.706	0.000	0.000	0.000
87	A	88	THR	0	-0.016	-0.011	15.302	-0.381	-0.381	0.000	0.000	0.000
88	A	89	LYS	1	0.900	0.965	14.693	18.660	18.660	0.000	0.000	0.000
89	A	90	LYS	1	0.914	0.949	19.500	12.375	12.375	0.000	0.000	0.000
90	A	91	PHE	0	0.013	-0.003	18.122	-0.151	-0.151	0.000	0.000	0.000
91	A	92	SER	0	0.064	0.024	24.231	0.021	0.021	0.000	0.000	0.000
92	A	93	TRP	0	-0.017	-0.003	27.666	0.017	0.017	0.000	0.000	0.000
93	A	94	GLU	-1	-0.912	-0.960	28.903	-9.921	-9.921	0.000	0.000	0.000
94	A	95	PRO	0	-0.042	0.002	31.467	0.021	0.021	0.000	0.000	0.000
95	A	96	ASN	0	0.021	-0.003	34.056	0.183	0.183	0.000	0.000	0.000
96	A	97	MET	0	-0.047	-0.005	36.930	0.205	0.205	0.000	0.000	0.000

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