FMO DATABASE

FMODB ID: LZ6Z9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-715383.652419
FMO2-HF: Nuclear repulsion	675761.773889
FMO2-HF: Total energy	-39621.87853
FMO2-MP2: Total energy	-39735.058522

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.
17.491	19.468	-0.028	-1.043	-0.906	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 : 0.952 / q_NPA : 0.956

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	-0.028	-0.007	3.833	1.556	3.533	-0.028	-1.043	-0.906
4	A	4	THR	0	-0.011	-0.012	6.462	1.057	1.057	0.000	0.000	0.000
5	A	5	PRO	0	-0.001	0.013	10.053	0.433	0.433	0.000	0.000	0.000
6	A	6	LYS	1	0.911	0.955	12.293	18.279	18.279	0.000	0.000	0.000
7	A	7	VAL	0	0.009	-0.003	15.224	0.020	0.020	0.000	0.000	0.000
8	A	8	HIS	0	-0.002	0.007	18.642	0.569	0.569	0.000	0.000	0.000
9	A	9	VAL	0	0.026	0.003	22.090	-0.052	-0.052	0.000	0.000	0.000
10	A	10	TYR	0	-0.002	0.001	23.941	0.067	0.067	0.000	0.000	0.000
11	A	11	SER	0	0.008	-0.011	28.440	-0.071	-0.071	0.000	0.000	0.000
12	A	12	HIS	0	-0.001	0.002	31.591	-0.190	-0.190	0.000	0.000	0.000
13	A	13	PHE	0	-0.018	0.002	32.831	0.119	0.119	0.000	0.000	0.000
14	A	14	PRO	0	0.036	0.028	35.479	-0.138	-0.138	0.000	0.000	0.000
15	A	15	GLY	0	0.011	-0.009	36.542	0.092	0.092	0.000	0.000	0.000
16	A	16	GLU	-1	-0.920	-0.989	37.781	-6.658	-6.658	0.000	0.000	0.000
17	A	17	TYR	0	-0.034	-0.030	40.307	-0.056	-0.056	0.000	0.000	0.000
18	A	18	GLY	0	0.092	0.057	42.908	0.129	0.129	0.000	0.000	0.000
19	A	19	LYS	1	0.867	0.951	39.028	7.532	7.532	0.000	0.000	0.000
20	A	20	PRO	0	-0.012	-0.001	40.654	-0.194	-0.194	0.000	0.000	0.000
21	A	21	ASN	0	-0.030	-0.028	35.738	-0.063	-0.063	0.000	0.000	0.000
22	A	22	THR	0	0.004	-0.007	31.743	-0.002	-0.002	0.000	0.000	0.000
23	A	23	LEU	0	-0.006	-0.006	29.650	-0.050	-0.050	0.000	0.000	0.000
24	A	24	ILE	0	-0.007	-0.014	25.721	-0.115	-0.115	0.000	0.000	0.000
25	A	25	CYS	0	-0.047	-0.002	22.642	-0.316	-0.316	0.000	0.000	0.000
26	A	26	TYR	0	-0.012	0.007	19.112	-0.382	-0.382	0.000	0.000	0.000
27	A	27	VAL	0	0.027	0.000	15.707	-0.297	-0.297	0.000	0.000	0.000
28	A	28	SER	0	0.038	0.008	15.197	-0.464	-0.464	0.000	0.000	0.000
29	A	29	SER	0	-0.049	-0.030	10.973	-0.122	-0.122	0.000	0.000	0.000
30	A	30	PHE	0	0.006	0.029	9.469	-0.730	-0.730	0.000	0.000	0.000
31	A	31	HIS	0	-0.015	0.017	4.956	-2.029	-2.029	0.000	0.000	0.000
32	A	32	PRO	0	0.015	-0.033	4.938	-2.343	-2.343	0.000	0.000	0.000
33	A	33	PRO	0	0.020	-0.016	6.793	0.996	0.996	0.000	0.000	0.000
34	A	34	ASP	-1	-0.865	-0.893	10.008	-21.079	-21.079	0.000	0.000	0.000
35	A	35	ILE	0	-0.073	-0.056	11.720	-0.681	-0.681	0.000	0.000	0.000
36	A	36	SER	0	-0.051	-0.018	14.327	0.588	0.588	0.000	0.000	0.000
37	A	37	ILE	0	0.060	0.024	17.872	-0.179	-0.179	0.000	0.000	0.000
38	A	38	GLU	-1	-0.919	-0.959	20.669	-11.676	-11.676	0.000	0.000	0.000
39	A	39	LEU	0	-0.004	-0.002	24.224	-0.149	-0.149	0.000	0.000	0.000
40	A	40	LEU	0	-0.046	-0.032	25.853	0.107	0.107	0.000	0.000	0.000
41	A	41	LYS	1	1.037	1.004	29.460	8.055	8.055	0.000	0.000	0.000
42	A	42	ASN	0	-0.061	-0.019	33.089	-0.048	-0.048	0.000	0.000	0.000
43	A	43	GLY	0	0.023	0.018	30.987	0.100	0.100	0.000	0.000	0.000
44	A	44	GLN	0	-0.024	-0.012	31.704	-0.163	-0.163	0.000	0.000	0.000
45	A	45	VAL	0	-0.018	-0.019	27.610	-0.049	-0.049	0.000	0.000	0.000
46	A	46	MET	0	-0.036	0.003	30.030	0.239	0.239	0.000	0.000	0.000
47	A	47	SER	0	-0.005	-0.009	30.679	-0.249	-0.249	0.000	0.000	0.000
48	A	48	ASP	-1	-0.893	-0.945	33.104	-8.428	-8.428	0.000	0.000	0.000
49	A	49	THR	0	-0.055	-0.014	28.413	-0.126	-0.126	0.000	0.000	0.000
50	A	50	LYS	1	0.940	0.963	28.819	9.227	9.227	0.000	0.000	0.000
51	A	51	GLN	0	0.006	-0.016	21.201	-0.071	-0.071	0.000	0.000	0.000
52	A	52	THR	0	-0.002	0.010	21.972	0.200	0.200	0.000	0.000	0.000
53	A	53	ASP	-1	-0.883	-0.938	21.760	-12.557	-12.557	0.000	0.000	0.000
54	A	54	LEU	0	-0.068	-0.042	13.844	-0.167	-0.167	0.000	0.000	0.000
55	A	55	ALA	0	0.032	0.032	18.078	0.112	0.112	0.000	0.000	0.000
56	A	56	PHE	0	-0.019	-0.022	11.169	-0.937	-0.937	0.000	0.000	0.000
57	A	57	GLU	-1	-0.864	-0.945	15.047	-13.066	-13.066	0.000	0.000	0.000
58	A	58	LYS	1	0.892	0.929	14.566	14.283	14.283	0.000	0.000	0.000
59	A	59	GLY	0	0.037	0.021	13.147	-0.257	-0.257	0.000	0.000	0.000
60	A	60	TRP	0	-0.025	-0.010	9.214	-1.508	-1.508	0.000	0.000	0.000
61	A	61	GLN	0	-0.028	-0.009	9.990	-0.762	-0.762	0.000	0.000	0.000
62	A	62	PHE	0	0.058	0.037	9.003	0.635	0.635	0.000	0.000	0.000
63	A	63	HIS	0	-0.089	-0.047	13.419	-0.048	-0.048	0.000	0.000	0.000
64	A	64	LEU	0	0.036	0.024	16.617	0.174	0.174	0.000	0.000	0.000
65	A	65	THR	0	0.031	0.016	19.241	0.111	0.111	0.000	0.000	0.000
66	A	66	LYS	1	0.909	0.978	22.718	12.082	12.082	0.000	0.000	0.000
67	A	67	SER	0	-0.022	-0.017	24.952	0.224	0.224	0.000	0.000	0.000
68	A	68	VAL	0	0.029	-0.001	28.672	-0.021	-0.021	0.000	0.000	0.000
69	A	69	ALA	0	0.027	0.028	31.982	0.055	0.055	0.000	0.000	0.000
70	A	70	PHE	0	-0.047	-0.017	33.565	-0.088	-0.088	0.000	0.000	0.000
71	A	71	THR	0	0.047	0.016	36.876	0.020	0.020	0.000	0.000	0.000
72	A	72	PRO	0	-0.056	-0.002	37.526	-0.010	-0.010	0.000	0.000	0.000
73	A	73	GLU	-1	-0.820	-0.927	39.229	-6.778	-6.778	0.000	0.000	0.000
74	A	74	LYS	1	0.920	0.945	40.475	6.450	6.450	0.000	0.000	0.000
75	A	75	GLY	0	-0.007	-0.001	40.384	0.094	0.094	0.000	0.000	0.000
76	A	76	ASP	-1	-0.870	-0.909	37.237	-7.841	-7.841	0.000	0.000	0.000
77	A	77	GLU	-1	-0.955	-0.978	31.767	-9.520	-9.520	0.000	0.000	0.000
78	A	78	TYR	0	-0.026	-0.025	31.311	-0.069	-0.069	0.000	0.000	0.000
79	A	79	THR	0	0.021	0.009	26.676	-0.255	-0.255	0.000	0.000	0.000
80	A	81	SER	0	-0.014	-0.017	21.685	-0.158	-0.158	0.000	0.000	0.000
81	A	82	VAL	0	0.034	0.007	16.029	-0.070	-0.070	0.000	0.000	0.000
82	A	83	ARG	1	0.885	0.941	15.612	16.517	16.517	0.000	0.000	0.000
83	A	84	HIS	0	0.054	0.018	8.183	0.668	0.668	0.000	0.000	0.000
84	A	85	MET	0	-0.014	-0.001	5.656	-0.450	-0.450	0.000	0.000	0.000
85	A	86	LYS	1	0.908	0.947	10.100	25.829	25.829	0.000	0.000	0.000
86	A	87	GLU	-1	-0.892	-0.942	13.443	-17.194	-17.194	0.000	0.000	0.000
87	A	88	THR	0	-0.019	-0.005	15.157	-0.353	-0.353	0.000	0.000	0.000
88	A	89	LYS	1	0.969	0.998	15.266	17.682	17.682	0.000	0.000	0.000
89	A	90	LYS	1	0.944	0.966	19.399	12.179	12.179	0.000	0.000	0.000
90	A	91	PHE	0	0.005	-0.002	18.246	-0.170	-0.170	0.000	0.000	0.000
91	A	92	SER	0	0.073	0.023	24.170	0.021	0.021	0.000	0.000	0.000
92	A	93	TRP	0	-0.013	0.002	27.573	-0.013	-0.013	0.000	0.000	0.000
93	A	94	GLU	-1	-0.932	-0.965	28.860	-9.864	-9.864	0.000	0.000	0.000
94	A	95	PRO	0	-0.041	0.001	31.375	0.008	0.008	0.000	0.000	0.000
95	A	96	ASN	0	0.002	-0.014	33.973	0.200	0.200	0.000	0.000	0.000
96	A	97	MET	0	-0.038	0.032	36.846	0.108	0.108	0.000	0.000	0.000

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