FMO DATABASE

FMODB ID: 52Q3Z

Calculation Name: 4IDL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IDL

Chain ID: A

ChEMBL ID:

UniProt ID:

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-976467.511007
FMO2-HF: Nuclear repulsion	929047.052792
FMO2-HF: Total energy	-47420.458215
FMO2-MP2: Total energy	-47557.978411

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.
-12.898	-2.921	10.912	-9.563	-11.327	-0.085

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 : 0.928 / q_NPA : 0.962

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	3	GLN	0	-0.003	0.010	2.940	-31.953	-26.413	0.375	-2.695	-3.220	-0.016
4	A	4	LEU	0	0.023	0.004	5.383	4.192	4.272	-0.001	-0.004	-0.074	0.000
5	A	5	GLN	0	0.001	0.011	8.127	1.210	1.210	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.010	-0.008	11.493	-1.338	-1.338	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.009	0.012	14.302	0.926	0.926	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.042	0.014	18.102	-0.247	-0.247	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.009	-0.005	21.193	0.239	0.239	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.002	-0.001	22.205	0.384	0.384	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.021	-0.009	25.863	-0.221	-0.221	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.000	0.007	28.734	0.244	0.244	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.036	0.027	31.113	0.095	0.095	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.004	-0.041	33.145	-0.191	-0.191	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.015	-0.005	33.113	0.272	0.272	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.028	0.002	32.209	0.034	0.034	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.023	-0.064	28.687	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.045	-0.017	24.382	0.051	0.051	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.933	0.976	20.827	14.971	14.971	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.027	0.005	17.756	-0.295	-0.295	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.007	-0.007	16.999	0.356	0.356	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.037	-0.012	10.749	-1.135	-1.135	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.023	0.021	13.047	0.342	0.342	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.027	0.008	8.427	-2.635	-2.635	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.008	0.002	7.781	2.507	2.507	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.021	0.007	4.232	-6.107	-6.060	-0.001	-0.052	0.005	0.000
27	A	27	ASN	0	0.005	-0.008	3.692	4.536	5.675	0.012	-0.553	-0.599	0.002
28	A	28	THR	0	0.012	-0.012	5.148	-1.835	-1.756	-0.001	-0.003	-0.075	0.000
29	A	29	ALA	0	0.049	0.034	8.350	0.759	0.759	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.079	-0.037	5.974	-0.767	-0.767	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.033	-0.007	7.199	-1.145	-1.145	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.794	0.876	9.233	28.737	28.737	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.012	-0.001	10.682	2.666	2.666	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.045	-0.002	9.792	-2.973	-2.973	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.077	0.037	11.201	2.447	2.447	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.041	-0.018	12.358	-1.716	-1.716	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.052	0.020	11.783	1.929	1.929	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.808	0.892	15.338	13.778	13.778	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.932	0.985	17.454	16.638	16.638	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.063	0.036	19.308	0.192	0.192	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.010	-0.017	22.926	-0.279	-0.279	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.003	0.002	24.391	0.296	0.296	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.873	0.962	22.774	13.281	13.281	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.010	-0.017	19.133	-0.344	-0.344	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.811	0.922	9.868	26.930	26.930	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.787	-0.877	17.212	-13.901	-13.901	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.022	-0.008	15.205	-0.154	-0.154	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.054	-0.021	17.038	1.121	1.121	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.044	0.018	17.082	1.072	1.072	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.020	0.025	14.712	-1.687	-1.687	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.026	0.031	15.154	1.235	1.235	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.042	0.027	15.038	-1.603	-1.603	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.026	-0.039	13.480	0.365	0.365	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.012	-0.005	16.395	0.241	0.241	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.001	0.008	19.213	0.805	0.805	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.032	-0.010	20.104	0.482	0.482	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.009	-0.007	19.444	-0.957	-0.957	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.891	-0.932	19.699	-14.150	-14.150	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.017	-0.018	20.056	-0.941	-0.941	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.050	0.028	21.587	0.286	0.286	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.841	-0.927	22.820	-11.833	-11.833	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.066	-0.038	21.199	0.688	0.688	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.016	0.008	22.701	0.282	0.282	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.877	0.922	25.999	10.971	10.971	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.039	0.012	28.025	0.325	0.325	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.733	0.857	27.346	11.499	11.499	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.033	-0.026	22.345	-0.189	-0.189	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.033	0.023	23.632	0.181	0.181	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.048	-0.013	15.556	-0.352	-0.352	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.005	-0.011	19.230	0.470	0.470	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.844	0.900	13.225	20.902	20.902	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.820	-0.886	17.129	-14.780	-14.780	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.024	-0.013	16.534	-1.149	-1.149	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.003	0.009	16.561	-0.575	-0.575	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.060	-0.040	16.949	0.066	0.066	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.038	-0.002	12.037	-2.117	-2.117	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.029	0.019	12.848	-1.911	-1.911	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.011	0.002	13.496	0.530	0.530	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.036	-0.036	15.259	0.115	0.115	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.003	-0.001	18.202	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.023	-0.016	19.938	-0.221	-0.221	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.034	-0.013	22.169	-0.090	-0.090	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.722	-0.823	25.230	-10.894	-10.894	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.001	-0.003	28.933	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.005	0.015	25.606	-0.058	-0.058	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.890	0.926	29.325	11.074	11.074	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.055	0.026	29.386	-0.410	-0.410	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.877	-0.918	28.273	-11.062	-11.062	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.776	-0.854	25.324	-12.308	-12.308	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.019	0.019	24.421	-0.637	-0.637	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.011	-0.015	20.830	-0.062	-0.062	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.057	-0.009	16.539	0.042	0.042	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.061	0.007	17.118	-0.603	-0.603	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.007	-0.004	11.605	0.088	0.088	0.000	0.000	0.000	0.000
95	A	96	ASN	0	-0.021	-0.036	7.693	-0.906	-0.906	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.009	0.004	5.796	3.206	3.206	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.804	-0.879	5.540	-42.012	-42.012	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.034	-0.005	7.217	3.812	3.812	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.913	0.962	7.966	20.642	20.642	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.980	0.989	2.888	36.338	37.427	0.180	-0.282	-0.987	0.000
101	A	102	PHE	0	0.055	0.035	6.768	0.230	0.230	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.875	-0.935	7.229	-25.321	-25.321	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.031	0.021	8.225	0.610	0.610	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.007	0.003	11.157	1.367	1.367	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.894	0.937	12.008	22.819	22.819	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.025	0.016	9.623	-2.385	-2.385	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.855	0.903	7.927	27.220	27.220	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.812	-0.877	7.973	-27.667	-27.667	0.000	0.000	0.000	0.000
109	A	110	TYR	0	-0.103	-0.067	2.770	-5.924	-4.521	0.124	-0.409	-1.118	-0.003
110	A	111	GLU	-1	-0.706	-0.851	3.720	-32.489	-32.261	0.000	-0.062	-0.166	0.000
111	A	112	SER	0	-0.131	-0.069	1.811	-51.070	-51.038	10.170	-5.429	-4.773	-0.066
112	A	113	TRP	0	0.013	-0.011	3.200	14.114	14.454	0.054	-0.074	-0.320	-0.002
113	A	114	GLY	0	0.003	0.008	6.574	-2.015	-2.015	0.000	0.000	0.000	0.000
114	A	115	GLN	0	-0.003	-0.019	9.417	-1.368	-1.368	0.000	0.000	0.000	0.000
115	A	116	GLY	0	-0.038	-0.010	11.866	1.502	1.502	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.059	-0.021	14.555	0.397	0.397	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.010	-0.007	17.861	0.601	0.601	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.032	0.025	21.183	0.206	0.206	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.009	-0.010	23.692	0.092	0.092	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.003	0.011	26.519	0.131	0.131	0.000	0.000	0.000	0.000
121	A	122	SER	0	0.027	0.019	29.967	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	SER	0	0.012	0.009	33.473	0.020	0.020	0.000	0.000	0.000	0.000

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