FMO DATABASE

FMODB ID: 6NN5Z

Calculation Name: 4U3Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: A

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-746536.040884
FMO2-HF: Nuclear repulsion	706383.231221
FMO2-HF: Total energy	-40152.809664
FMO2-MP2: Total energy	-40267.913108

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:10:LYS)

Summations of interaction energy for fragment #1(A:10: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.
-147.341	-143.048	28.991	-16.874	-16.408	-0.184

Interaction energy analysis for fragmet #1(A:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.923 / q_NPA : 0.947

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	12	LYS	1	0.941	0.972	3.595	22.002	23.677	-0.006	-0.722	-0.946	0.003
4	A	13	ALA	0	0.057	0.036	2.919	2.128	2.872	0.172	-0.231	-0.685	0.000
5	A	14	GLU	-1	-0.774	-0.882	1.680	-126.523	-127.375	20.208	-10.378	-8.978	-0.124
6	A	15	LYS	1	0.930	0.967	4.631	36.615	36.784	-0.001	-0.020	-0.148	0.000
7	A	16	VAL	0	-0.020	-0.011	7.781	3.638	3.638	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.836	-0.901	5.176	-47.135	-47.061	-0.001	0.000	-0.072	0.000
9	A	18	CYS	0	-0.058	-0.041	6.590	3.567	3.567	0.000	0.000	0.000	0.000
10	A	19	ALA	0	-0.019	0.002	9.394	2.713	2.713	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.012	0.002	11.933	2.389	2.389	0.000	0.000	0.000	0.000
12	A	21	LYS	1	0.874	0.934	8.570	35.187	35.187	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.052	-0.020	13.638	0.078	0.078	0.000	0.000	0.000	0.000
14	A	23	GLY	0	-0.051	-0.019	16.595	1.168	1.168	0.000	0.000	0.000	0.000
15	A	24	ILE	0	-0.018	-0.013	18.376	-0.154	-0.154	0.000	0.000	0.000	0.000
16	A	25	PHE	0	-0.026	-0.020	16.965	0.120	0.120	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.863	0.899	22.580	10.523	10.523	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.023	0.002	26.237	-0.155	-0.155	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.034	-0.008	28.009	0.008	0.008	0.000	0.000	0.000	0.000
20	A	29	LEU	0	-0.009	0.021	25.493	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	30	PRO	0	0.016	-0.007	28.935	0.317	0.317	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.014	0.013	31.740	-0.208	-0.208	0.000	0.000	0.000	0.000
23	A	32	ALA	0	-0.035	-0.028	34.423	0.153	0.153	0.000	0.000	0.000	0.000
24	A	33	ASP	-1	-0.922	-0.952	36.303	-7.439	-7.439	0.000	0.000	0.000	0.000
25	A	34	CYS	0	-0.049	-0.022	37.887	0.246	0.246	0.000	0.000	0.000	0.000
26	A	35	PRO	0	-0.004	0.004	37.684	-0.133	-0.133	0.000	0.000	0.000	0.000
27	A	36	GLY	0	0.023	0.002	34.336	-0.180	-0.180	0.000	0.000	0.000	0.000
28	A	37	ILE	0	-0.005	0.003	31.657	0.221	0.221	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.845	-0.887	31.233	-10.464	-10.464	0.000	0.000	0.000	0.000
30	A	39	THR	0	0.008	-0.002	26.222	0.004	0.004	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.040	-0.030	25.076	-0.143	-0.143	0.000	0.000	0.000	0.000
32	A	41	VAL	0	0.024	0.007	19.913	0.092	0.092	0.000	0.000	0.000	0.000
33	A	42	THR	0	-0.016	-0.015	20.301	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	43	PHE	0	0.047	0.025	15.005	0.059	0.059	0.000	0.000	0.000	0.000
35	A	44	ASN	0	0.006	0.002	16.280	-0.310	-0.310	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.024	-0.014	13.637	-1.234	-1.234	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.860	-0.901	13.077	-19.556	-19.556	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.017	0.019	13.050	-0.502	-0.502	0.000	0.000	0.000	0.000
39	A	48	THR	0	-0.051	-0.048	13.794	0.753	0.753	0.000	0.000	0.000	0.000
40	A	49	ALA	0	-0.011	-0.026	17.126	-0.640	-0.640	0.000	0.000	0.000	0.000
41	A	50	GLN	0	-0.017	0.005	19.224	1.017	1.017	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.836	0.915	22.810	11.966	11.966	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.024	-0.015	24.902	0.358	0.358	0.000	0.000	0.000	0.000
44	A	53	GLU	-1	-0.792	-0.872	28.444	-11.107	-11.107	0.000	0.000	0.000	0.000
45	A	54	LEU	0	0.000	0.012	31.173	0.364	0.364	0.000	0.000	0.000	0.000
46	A	63	SER	0	-0.023	-0.017	38.212	0.068	0.068	0.000	0.000	0.000	0.000
47	A	64	PRO	0	0.003	-0.007	33.566	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	65	LEU	0	0.019	0.028	32.288	0.053	0.053	0.000	0.000	0.000	0.000
49	A	66	THR	0	-0.036	-0.037	28.124	-0.304	-0.304	0.000	0.000	0.000	0.000
50	A	67	TYR	0	-0.028	-0.025	25.681	0.128	0.128	0.000	0.000	0.000	0.000
51	A	68	ARG	1	0.900	0.940	23.616	11.619	11.619	0.000	0.000	0.000	0.000
52	A	69	GLY	0	0.062	0.029	21.100	0.357	0.357	0.000	0.000	0.000	0.000
53	A	70	THR	0	-0.011	0.010	15.649	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	71	TRP	0	-0.051	-0.022	10.779	-0.168	-0.168	0.000	0.000	0.000	0.000
55	A	72	MET	0	-0.011	-0.009	11.060	-1.506	-1.506	0.000	0.000	0.000	0.000
56	A	73	VAL	0	-0.017	0.002	7.381	1.934	1.934	0.000	0.000	0.000	0.000
57	A	74	ARG	1	0.812	0.912	7.694	18.093	18.093	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.851	-0.948	1.994	-62.883	-60.529	8.619	-5.451	-5.522	-0.063
59	A	76	ASP	-1	-0.851	-0.925	4.006	-24.256	-24.127	0.000	-0.072	-0.057	0.000
60	A	77	GLY	0	-0.038	-0.042	6.735	1.486	1.486	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.056	-0.021	7.893	0.615	0.615	0.000	0.000	0.000	0.000
62	A	79	VAL	0	0.005	-0.005	10.491	-1.795	-1.795	0.000	0.000	0.000	0.000
63	A	80	GLU	-1	-0.820	-0.893	12.754	-17.653	-17.653	0.000	0.000	0.000	0.000
64	A	81	LEU	0	-0.019	-0.003	14.983	-0.931	-0.931	0.000	0.000	0.000	0.000
65	A	82	SER	0	0.004	-0.004	18.101	0.809	0.809	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.019	-0.004	20.259	-0.137	-0.137	0.000	0.000	0.000	0.000
67	A	84	VAL	0	0.038	0.025	23.184	0.249	0.249	0.000	0.000	0.000	0.000
68	A	94	GLU	-1	-0.920	-0.968	24.449	-11.918	-11.918	0.000	0.000	0.000	0.000
69	A	95	LYS	1	0.830	0.903	16.462	16.922	16.922	0.000	0.000	0.000	0.000
70	A	96	GLU	-1	-0.791	-0.883	20.099	-12.798	-12.798	0.000	0.000	0.000	0.000
71	A	97	LEU	0	-0.013	-0.006	15.472	-1.087	-1.087	0.000	0.000	0.000	0.000
72	A	98	TYR	0	-0.035	-0.040	15.613	1.017	1.017	0.000	0.000	0.000	0.000
73	A	99	GLU	-1	-0.780	-0.871	13.732	-17.427	-17.427	0.000	0.000	0.000	0.000
74	A	100	LEU	0	-0.021	-0.003	12.341	0.532	0.532	0.000	0.000	0.000	0.000
75	A	101	ILE	0	-0.049	-0.019	14.061	-0.127	-0.127	0.000	0.000	0.000	0.000
76	A	102	ASP	-1	-0.812	-0.905	16.113	-15.236	-15.236	0.000	0.000	0.000	0.000
77	A	103	SER	0	0.001	-0.012	15.805	-0.958	-0.958	0.000	0.000	0.000	0.000
78	A	104	ASN	0	-0.047	-0.028	16.860	-0.774	-0.774	0.000	0.000	0.000	0.000
79	A	105	SER	0	-0.007	-0.001	19.007	1.198	1.198	0.000	0.000	0.000	0.000
80	A	106	VAL	0	0.023	0.019	16.584	-0.983	-0.983	0.000	0.000	0.000	0.000
81	A	107	ARG	1	0.825	0.886	17.765	15.435	15.435	0.000	0.000	0.000	0.000
82	A	108	TYR	0	-0.001	0.011	18.774	-0.646	-0.646	0.000	0.000	0.000	0.000
83	A	109	MET	0	-0.075	-0.034	15.534	0.250	0.250	0.000	0.000	0.000	0.000
84	A	110	GLY	0	0.027	0.028	20.367	0.474	0.474	0.000	0.000	0.000	0.000
85	A	111	ALA	0	0.036	0.018	20.895	-0.661	-0.661	0.000	0.000	0.000	0.000
86	A	112	PRO	0	-0.021	-0.020	18.374	-0.080	-0.080	0.000	0.000	0.000	0.000
87	A	113	GLY	0	0.000	0.007	19.694	0.445	0.445	0.000	0.000	0.000	0.000
88	A	114	ALA	0	0.088	0.040	21.127	0.580	0.580	0.000	0.000	0.000	0.000
89	A	115	GLY	0	-0.041	-0.026	20.266	0.297	0.297	0.000	0.000	0.000	0.000
90	A	116	LYS	1	0.861	0.942	20.996	9.800	9.800	0.000	0.000	0.000	0.000
91	A	117	PRO	0	0.061	0.041	22.574	-0.054	-0.054	0.000	0.000	0.000	0.000
92	A	118	SER	0	-0.003	-0.016	24.257	0.220	0.220	0.000	0.000	0.000	0.000
93	A	119	LYS	1	0.971	0.963	23.400	11.690	11.690	0.000	0.000	0.000	0.000
94	A	120	GLU	-1	-0.929	-0.937	26.860	-9.580	-9.580	0.000	0.000	0.000	0.000
95	A	121	MET	0	0.020	0.005	28.171	0.133	0.133	0.000	0.000	0.000	0.000
96	A	122	ALA	0	0.024	0.000	23.086	-0.168	-0.168	0.000	0.000	0.000	0.000
97	A	123	PRO	0	0.013	-0.013	24.767	-0.364	-0.364	0.000	0.000	0.000	0.000
98	A	124	PHE	0	0.015	0.015	26.260	-0.096	-0.096	0.000	0.000	0.000	0.000
99	A	125	TYR	0	0.021	0.005	23.802	0.123	0.123	0.000	0.000	0.000	0.000
100	A	126	VAL	0	-0.072	-0.026	22.213	-0.714	-0.714	0.000	0.000	0.000	0.000
101	A	127	LEU	0	-0.006	0.010	21.555	0.402	0.402	0.000	0.000	0.000	0.000
102	A	128	LYS	1	0.921	0.944	22.001	12.117	12.117	0.000	0.000	0.000	0.000
103	A	129	LYS	1	0.884	0.952	16.322	18.761	18.761	0.000	0.000	0.000	0.000
104	A	130	THR	0	-0.034	-0.010	22.307	0.604	0.604	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LYS)