FMO DATABASE

FMODB ID: Z669N

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-747093.74742
FMO2-HF: Nuclear repulsion	706940.70761
FMO2-HF: Total energy	-40153.03981
FMO2-MP2: Total energy	-40268.168988

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.
-142.063	-139.247	36.741	-20.727	-18.827	-0.202

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 : 0.901 / q_NPA : 0.932

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	0.904	0.973	2.918	27.616	30.366	0.020	-1.355	-1.414	0.005
4	A	13	ALA	0	0.074	0.031	2.648	1.025	1.932	0.405	-0.427	-0.885	0.001
5	A	14	GLU	-1	-0.769	-0.880	1.674	-126.181	-127.683	22.462	-11.115	-9.845	-0.128
6	A	15	LYS	1	0.895	0.950	4.453	39.938	40.155	-0.001	-0.034	-0.182	0.000
7	A	16	VAL	0	-0.023	-0.005	7.541	4.092	4.092	0.000	0.000	0.000	0.000
8	A	17	GLU	-1	-0.839	-0.907	4.741	-50.434	-50.345	-0.001	-0.002	-0.085	0.000
9	A	18	CYS	0	-0.038	-0.038	6.295	3.735	3.735	0.000	0.000	0.000	0.000
10	A	19	ALA	0	-0.018	0.006	9.221	2.897	2.897	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.021	-0.001	11.785	2.558	2.558	0.000	0.000	0.000	0.000
12	A	21	LYS	1	0.867	0.922	8.016	36.939	36.939	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.037	-0.012	13.056	0.172	0.172	0.000	0.000	0.000	0.000
14	A	23	GLY	0	-0.027	0.003	16.393	1.121	1.121	0.000	0.000	0.000	0.000
15	A	24	ILE	0	-0.028	-0.021	18.116	-0.051	-0.051	0.000	0.000	0.000	0.000
16	A	25	PHE	0	-0.009	-0.012	16.661	0.029	0.029	0.000	0.000	0.000	0.000
17	A	26	ARG	1	0.848	0.889	22.330	10.616	10.616	0.000	0.000	0.000	0.000
18	A	27	GLY	0	0.031	0.011	25.880	-0.165	-0.165	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.023	-0.008	27.596	0.026	0.026	0.000	0.000	0.000	0.000
20	A	29	LEU	0	0.016	0.027	24.790	0.046	0.046	0.000	0.000	0.000	0.000
21	A	30	PRO	0	0.006	-0.003	28.296	0.314	0.314	0.000	0.000	0.000	0.000
22	A	31	ALA	0	0.007	0.008	30.843	-0.233	-0.233	0.000	0.000	0.000	0.000
23	A	32	ALA	0	-0.032	-0.029	33.565	0.158	0.158	0.000	0.000	0.000	0.000
24	A	33	ASP	-1	-0.922	-0.951	35.670	-7.475	-7.475	0.000	0.000	0.000	0.000
25	A	34	CYS	0	-0.048	-0.020	37.126	0.247	0.247	0.000	0.000	0.000	0.000
26	A	35	PRO	0	-0.002	0.005	36.800	-0.144	-0.144	0.000	0.000	0.000	0.000
27	A	36	GLY	0	0.025	0.003	33.353	-0.177	-0.177	0.000	0.000	0.000	0.000
28	A	37	ILE	0	-0.009	0.001	31.574	0.228	0.228	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.840	-0.877	30.823	-10.562	-10.562	0.000	0.000	0.000	0.000
30	A	39	THR	0	0.009	0.000	26.041	0.059	0.059	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.031	-0.030	24.874	-0.193	-0.193	0.000	0.000	0.000	0.000
32	A	41	VAL	0	0.017	0.011	19.564	0.153	0.153	0.000	0.000	0.000	0.000
33	A	42	THR	0	-0.019	-0.018	19.986	0.180	0.180	0.000	0.000	0.000	0.000
34	A	43	PHE	0	0.050	0.029	14.630	0.110	0.110	0.000	0.000	0.000	0.000
35	A	44	ASN	0	0.003	-0.001	15.670	-0.491	-0.491	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.019	-0.017	13.630	-1.244	-1.244	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.839	-0.893	12.900	-20.057	-20.057	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.024	0.026	13.024	-0.795	-0.795	0.000	0.000	0.000	0.000
39	A	48	THR	0	-0.043	-0.044	13.718	0.862	0.862	0.000	0.000	0.000	0.000
40	A	49	ALA	0	-0.025	-0.027	16.919	-0.739	-0.739	0.000	0.000	0.000	0.000
41	A	50	GLN	0	-0.027	-0.007	19.073	1.157	1.157	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.840	0.916	22.237	11.934	11.934	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.010	-0.011	24.682	0.343	0.343	0.000	0.000	0.000	0.000
44	A	53	GLU	-1	-0.809	-0.875	28.115	-11.275	-11.275	0.000	0.000	0.000	0.000
45	A	54	LEU	0	-0.034	-0.013	30.865	0.438	0.438	0.000	0.000	0.000	0.000
46	A	63	SER	0	0.006	-0.011	37.922	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	64	PRO	0	0.012	0.014	33.188	-0.137	-0.137	0.000	0.000	0.000	0.000
48	A	65	LEU	0	0.037	0.031	32.365	-0.021	-0.021	0.000	0.000	0.000	0.000
49	A	66	THR	0	-0.039	-0.030	28.212	-0.347	-0.347	0.000	0.000	0.000	0.000
50	A	67	TYR	0	-0.046	-0.037	25.698	0.177	0.177	0.000	0.000	0.000	0.000
51	A	68	ARG	1	0.884	0.922	23.527	11.808	11.808	0.000	0.000	0.000	0.000
52	A	69	GLY	0	0.040	0.024	21.237	0.400	0.400	0.000	0.000	0.000	0.000
53	A	70	THR	0	0.008	0.014	15.856	0.008	0.008	0.000	0.000	0.000	0.000
54	A	71	TRP	0	-0.097	-0.037	10.707	-0.143	-0.143	0.000	0.000	0.000	0.000
55	A	72	MET	0	0.007	0.011	10.840	-1.378	-1.378	0.000	0.000	0.000	0.000
56	A	73	VAL	0	-0.006	-0.002	6.968	1.897	1.897	0.000	0.000	0.000	0.000
57	A	74	ARG	1	0.826	0.900	7.203	18.243	18.243	0.000	0.000	0.000	0.000
58	A	75	GLU	-1	-0.837	-0.926	1.857	-63.428	-64.328	13.795	-6.988	-5.906	-0.073
59	A	76	ASP	-1	-0.808	-0.899	3.134	-27.288	-26.033	0.061	-0.806	-0.510	-0.007
60	A	77	GLY	0	-0.046	-0.037	5.819	1.404	1.404	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.051	-0.024	7.006	1.813	1.813	0.000	0.000	0.000	0.000
62	A	79	VAL	0	-0.021	-0.015	9.918	-2.009	-2.009	0.000	0.000	0.000	0.000
63	A	80	GLU	-1	-0.797	-0.881	12.439	-17.569	-17.569	0.000	0.000	0.000	0.000
64	A	81	LEU	0	-0.012	0.002	14.795	-0.866	-0.866	0.000	0.000	0.000	0.000
65	A	82	SER	0	-0.004	-0.016	17.673	0.681	0.681	0.000	0.000	0.000	0.000
66	A	83	LEU	0	-0.026	-0.010	20.027	-0.288	-0.288	0.000	0.000	0.000	0.000
67	A	84	VAL	0	0.053	0.032	23.127	0.309	0.309	0.000	0.000	0.000	0.000
68	A	94	GLU	-1	-0.902	-0.954	24.121	-11.737	-11.737	0.000	0.000	0.000	0.000
69	A	95	LYS	1	0.815	0.884	16.318	16.880	16.880	0.000	0.000	0.000	0.000
70	A	96	GLU	-1	-0.757	-0.837	19.753	-12.725	-12.725	0.000	0.000	0.000	0.000
71	A	97	LEU	0	-0.030	-0.012	14.775	-1.087	-1.087	0.000	0.000	0.000	0.000
72	A	98	TYR	0	-0.033	-0.043	15.292	1.012	1.012	0.000	0.000	0.000	0.000
73	A	99	GLU	-1	-0.761	-0.864	12.947	-17.699	-17.699	0.000	0.000	0.000	0.000
74	A	100	LEU	0	-0.034	-0.009	12.023	0.751	0.751	0.000	0.000	0.000	0.000
75	A	101	ILE	0	-0.040	-0.015	13.264	-0.296	-0.296	0.000	0.000	0.000	0.000
76	A	102	ASP	-1	-0.801	-0.889	15.875	-15.314	-15.314	0.000	0.000	0.000	0.000
77	A	103	SER	0	0.010	-0.006	15.430	-0.786	-0.786	0.000	0.000	0.000	0.000
78	A	104	ASN	0	-0.040	-0.025	16.482	-0.869	-0.869	0.000	0.000	0.000	0.000
79	A	105	SER	0	0.007	-0.010	18.248	1.267	1.267	0.000	0.000	0.000	0.000
80	A	106	VAL	0	0.011	0.016	16.119	-1.077	-1.077	0.000	0.000	0.000	0.000
81	A	107	ARG	1	0.805	0.874	17.036	15.662	15.662	0.000	0.000	0.000	0.000
82	A	108	TYR	0	-0.029	-0.025	18.090	-0.723	-0.723	0.000	0.000	0.000	0.000
83	A	109	MET	0	-0.070	-0.033	14.740	0.156	0.156	0.000	0.000	0.000	0.000
84	A	110	GLY	0	0.019	0.018	19.735	0.588	0.588	0.000	0.000	0.000	0.000
85	A	111	ALA	0	0.056	0.033	20.428	-0.632	-0.632	0.000	0.000	0.000	0.000
86	A	112	PRO	0	-0.018	-0.024	17.861	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	113	GLY	0	0.058	0.028	19.419	0.376	0.376	0.000	0.000	0.000	0.000
88	A	114	ALA	0	-0.021	0.004	21.133	0.435	0.435	0.000	0.000	0.000	0.000
89	A	115	GLY	0	-0.015	-0.017	19.959	0.087	0.087	0.000	0.000	0.000	0.000
90	A	116	LYS	1	0.854	0.939	20.692	9.845	9.845	0.000	0.000	0.000	0.000
91	A	117	PRO	0	0.077	0.049	22.208	-0.101	-0.101	0.000	0.000	0.000	0.000
92	A	118	SER	0	-0.005	-0.016	23.795	0.240	0.240	0.000	0.000	0.000	0.000
93	A	119	LYS	1	0.944	0.956	22.339	11.944	11.944	0.000	0.000	0.000	0.000
94	A	120	GLU	-1	-0.871	-0.932	26.072	-9.736	-9.736	0.000	0.000	0.000	0.000
95	A	121	MET	0	-0.004	0.012	27.750	-0.046	-0.046	0.000	0.000	0.000	0.000
96	A	122	ALA	0	0.019	-0.001	22.732	-0.157	-0.157	0.000	0.000	0.000	0.000
97	A	123	PRO	0	0.011	-0.008	24.099	-0.412	-0.412	0.000	0.000	0.000	0.000
98	A	124	PHE	0	0.007	0.008	25.775	-0.161	-0.161	0.000	0.000	0.000	0.000
99	A	125	TYR	0	0.022	0.012	23.174	0.101	0.101	0.000	0.000	0.000	0.000
100	A	126	VAL	0	-0.064	-0.024	21.640	-0.732	-0.732	0.000	0.000	0.000	0.000
101	A	127	LEU	0	-0.009	0.012	21.384	0.429	0.429	0.000	0.000	0.000	0.000
102	A	128	LYS	1	0.894	0.917	21.541	12.567	12.567	0.000	0.000	0.000	0.000
103	A	129	LYS	1	0.840	0.937	15.859	19.351	19.351	0.000	0.000	0.000	0.000
104	A	130	THR	0	-0.037	-0.014	21.997	0.560	0.560	0.000	0.000	0.000	0.000

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