FMO DATABASE

FMODB ID: YYQN2

Calculation Name: 4LDD-C-Xray322

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LDD

Chain ID: C

ChEMBL ID:

UniProt ID: Q05128

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1254293.426967
FMO2-HF: Nuclear repulsion	1200087.068892
FMO2-HF: Total energy	-54206.358075
FMO2-MP2: Total energy	-54366.96727

3D Structure Molmil

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(C:44:ACE )

Summations of interaction energy for fragment #1(C:44:ACE )

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.
-2.024	0.851	4.471	-3.726	-3.618	-0.017

Interaction energy analysis for fragmet #1(C:44:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.044

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	C	46	THR	0	-0.016	0.003	3.795	0.493	2.035	-0.004	-0.775	-0.763	-0.003
4	C	47	PRO	0	-0.052	-0.037	4.915	0.324	0.417	0.000	-0.004	-0.088	0.000
5	C	48	SER	0	0.016	0.036	7.473	0.082	0.082	0.000	0.000	0.000	0.000
6	C	49	ASN	0	0.049	0.031	9.082	-0.066	-0.066	0.000	0.000	0.000	0.000
7	C	50	PRO	0	-0.022	-0.019	12.766	0.009	0.009	0.000	0.000	0.000	0.000
8	C	51	LEU	0	0.001	0.005	15.399	0.010	0.010	0.000	0.000	0.000	0.000
9	C	52	ARG	1	0.890	0.946	18.069	-0.003	-0.003	0.000	0.000	0.000	0.000
10	C	53	PRO	0	-0.014	0.010	21.212	0.012	0.012	0.000	0.000	0.000	0.000
11	C	54	ILE	0	0.004	-0.008	22.262	-0.007	-0.007	0.000	0.000	0.000	0.000
12	C	55	ALA	0	-0.018	-0.017	25.195	0.004	0.004	0.000	0.000	0.000	0.000
13	C	56	ASP	-1	-0.825	-0.895	27.014	0.066	0.066	0.000	0.000	0.000	0.000
14	C	57	ASP	-1	-0.916	-0.957	28.447	0.054	0.054	0.000	0.000	0.000	0.000
15	C	58	THR	0	-0.085	-0.064	30.168	-0.005	-0.005	0.000	0.000	0.000	0.000
16	C	59	ILE	0	-0.086	-0.036	28.525	-0.004	-0.004	0.000	0.000	0.000	0.000
17	C	60	ASP	-1	-0.817	-0.900	32.944	0.020	0.020	0.000	0.000	0.000	0.000
18	C	61	HIS	0	-0.053	-0.042	35.641	0.000	0.000	0.000	0.000	0.000	0.000
19	C	62	ALA	0	0.056	0.023	36.601	-0.002	-0.002	0.000	0.000	0.000	0.000
20	C	63	SER	0	-0.049	-0.029	37.049	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	64	HIS	1	0.810	0.896	32.219	-0.020	-0.020	0.000	0.000	0.000	0.000
22	C	65	THR	0	0.016	0.016	36.584	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	66	PRO	0	-0.001	0.003	38.997	-0.002	-0.002	0.000	0.000	0.000	0.000
24	C	67	GLY	0	0.064	0.034	39.545	0.000	0.000	0.000	0.000	0.000	0.000
25	C	68	SER	0	-0.063	-0.032	39.674	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	69	VAL	0	-0.007	0.014	36.419	0.000	0.000	0.000	0.000	0.000	0.000
27	C	70	SER	0	0.006	0.007	33.856	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	71	SER	0	-0.026	-0.024	31.600	0.004	0.004	0.000	0.000	0.000	0.000
29	C	72	ALA	0	-0.015	0.003	27.693	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	73	PHE	0	0.022	-0.011	24.806	0.003	0.003	0.000	0.000	0.000	0.000
31	C	74	ILE	0	0.002	0.002	21.359	-0.004	-0.004	0.000	0.000	0.000	0.000
32	C	75	LEU	0	-0.013	-0.005	18.183	-0.003	-0.003	0.000	0.000	0.000	0.000
33	C	76	GLU	-1	-0.880	-0.934	18.653	0.131	0.131	0.000	0.000	0.000	0.000
34	C	77	ALA	0	-0.011	-0.013	14.766	-0.006	-0.006	0.000	0.000	0.000	0.000
35	C	78	MET	0	0.051	0.049	15.852	0.042	0.042	0.000	0.000	0.000	0.000
36	C	79	VAL	0	-0.027	0.026	11.292	0.001	0.001	0.000	0.000	0.000	0.000
37	C	80	ASN	0	0.067	0.034	12.864	-0.015	-0.015	0.000	0.000	0.000	0.000
38	C	81	VAL	0	0.021	0.025	8.136	0.053	0.053	0.000	0.000	0.000	0.000
39	C	82	ILE	0	0.049	0.021	8.739	-0.119	-0.119	0.000	0.000	0.000	0.000
40	C	83	SER	0	0.013	-0.001	7.342	0.363	0.363	0.000	0.000	0.000	0.000
41	C	84	GLY	0	0.014	0.011	8.091	-0.182	-0.182	0.000	0.000	0.000	0.000
42	C	85	PRO	0	-0.006	0.008	9.875	-0.015	-0.015	0.000	0.000	0.000	0.000
43	C	86	LYS	1	0.968	0.986	13.348	-0.352	-0.352	0.000	0.000	0.000	0.000
44	C	87	VAL	0	0.022	0.002	12.461	0.089	0.089	0.000	0.000	0.000	0.000
45	C	88	LEU	0	-0.080	-0.051	9.733	-0.039	-0.039	0.000	0.000	0.000	0.000
46	C	89	MET	0	0.008	0.006	12.973	-0.087	-0.087	0.000	0.000	0.000	0.000
47	C	90	LYS	1	0.953	0.963	14.077	-0.205	-0.205	0.000	0.000	0.000	0.000
48	C	91	GLN	0	-0.078	-0.059	16.466	-0.045	-0.045	0.000	0.000	0.000	0.000
49	C	92	ILE	0	0.001	0.002	13.176	-0.013	-0.013	0.000	0.000	0.000	0.000
50	C	93	PRO	0	0.043	0.020	15.442	0.012	0.012	0.000	0.000	0.000	0.000
51	C	94	ILE	0	-0.031	-0.019	11.402	0.023	0.023	0.000	0.000	0.000	0.000
52	C	95	TRP	0	0.057	0.026	15.543	-0.028	-0.028	0.000	0.000	0.000	0.000
53	C	96	LEU	0	-0.012	-0.019	13.557	-0.008	-0.008	0.000	0.000	0.000	0.000
54	C	97	PRO	0	0.014	0.016	17.608	-0.014	-0.014	0.000	0.000	0.000	0.000
55	C	98	LEU	0	-0.006	-0.010	19.052	-0.013	-0.013	0.000	0.000	0.000	0.000
56	C	99	GLY	0	-0.002	-0.003	21.328	-0.013	-0.013	0.000	0.000	0.000	0.000
57	C	100	VAL	0	-0.006	-0.011	24.532	0.006	0.006	0.000	0.000	0.000	0.000
58	C	101	ALA	0	-0.009	-0.014	28.256	-0.006	-0.006	0.000	0.000	0.000	0.000
59	C	102	ASP	-1	-0.875	-0.929	30.292	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	103	GLN	0	-0.011	-0.017	33.584	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	104	LYS	1	0.902	0.959	36.018	0.014	0.014	0.000	0.000	0.000	0.000
62	C	105	THR	0	0.001	0.009	32.975	0.000	0.000	0.000	0.000	0.000	0.000
63	C	106	TYR	0	-0.023	-0.053	31.237	0.001	0.001	0.000	0.000	0.000	0.000
64	C	107	SER	0	0.087	0.067	34.120	0.002	0.002	0.000	0.000	0.000	0.000
65	C	108	PHE	0	0.087	0.034	31.329	-0.002	-0.002	0.000	0.000	0.000	0.000
66	C	109	ASP	-1	-0.838	-0.890	32.312	0.003	0.003	0.000	0.000	0.000	0.000
67	C	110	SER	0	-0.016	-0.031	32.626	0.000	0.000	0.000	0.000	0.000	0.000
68	C	111	THR	0	-0.040	-0.021	27.846	-0.005	-0.005	0.000	0.000	0.000	0.000
69	C	112	THR	0	-0.002	-0.031	27.901	0.001	0.001	0.000	0.000	0.000	0.000
70	C	113	ALA	0	-0.003	0.002	28.082	0.002	0.002	0.000	0.000	0.000	0.000
71	C	114	ALA	0	-0.005	-0.004	26.678	-0.001	-0.001	0.000	0.000	0.000	0.000
72	C	115	ILE	0	-0.017	-0.003	22.662	-0.005	-0.005	0.000	0.000	0.000	0.000
73	C	116	MET	0	0.027	0.032	23.373	0.003	0.003	0.000	0.000	0.000	0.000
74	C	117	LEU	0	-0.035	-0.002	25.304	0.003	0.003	0.000	0.000	0.000	0.000
75	C	118	ALA	0	-0.021	-0.019	21.525	-0.009	-0.009	0.000	0.000	0.000	0.000
76	C	119	SER	0	-0.023	-0.006	18.343	0.015	0.015	0.000	0.000	0.000	0.000
77	C	120	TYR	0	-0.022	-0.043	15.732	-0.026	-0.026	0.000	0.000	0.000	0.000
78	C	121	THR	0	-0.011	0.001	10.887	-0.007	-0.007	0.000	0.000	0.000	0.000
79	C	122	ILE	0	0.038	0.009	8.073	-0.038	-0.038	0.000	0.000	0.000	0.000
80	C	123	THR	0	-0.037	-0.028	5.929	-0.007	-0.007	0.000	0.000	0.000	0.000
81	C	124	HIS	1	0.904	0.964	2.209	-3.593	-4.367	3.603	-1.674	-1.155	-0.006
82	C	125	PHE	0	0.058	0.066	3.129	-1.800	-1.416	0.267	-0.523	-0.128	-0.004
83	C	126	GLY	0	0.062	-0.010	4.758	0.581	0.784	0.000	-0.010	-0.193	0.000
84	C	127	LYS	1	0.918	0.945	6.331	0.235	0.235	0.000	0.000	0.000	0.000
85	C	128	ALA	0	-0.018	-0.055	9.813	-0.004	-0.004	0.000	0.000	0.000	0.000
86	C	129	THR	0	-0.082	-0.009	9.236	0.041	0.041	0.000	0.000	0.000	0.000
87	C	130	ASN	0	0.029	0.025	11.130	-0.039	-0.039	0.000	0.000	0.000	0.000
88	C	131	PRO	0	0.036	0.051	7.427	-0.090	-0.090	0.000	0.000	0.000	0.000
89	C	132	LEU	0	-0.020	-0.016	7.758	0.010	0.010	0.000	0.000	0.000	0.000
90	C	133	VAL	0	0.018	0.009	7.293	0.113	0.113	0.000	0.000	0.000	0.000
91	C	134	ARG	1	0.908	0.961	8.491	0.427	0.427	0.000	0.000	0.000	0.000
92	C	135	VAL	0	0.045	0.047	9.945	-0.010	-0.010	0.000	0.000	0.000	0.000
93	C	136	ASN	0	0.006	-0.023	10.504	-0.013	-0.013	0.000	0.000	0.000	0.000
94	C	137	ARG	1	0.838	0.909	13.831	0.083	0.083	0.000	0.000	0.000	0.000
95	C	138	LEU	0	-0.031	-0.012	15.009	-0.018	-0.018	0.000	0.000	0.000	0.000
96	C	139	GLY	0	0.000	0.003	18.498	0.016	0.016	0.000	0.000	0.000	0.000
97	C	140	PRO	0	0.004	0.008	21.559	-0.011	-0.011	0.000	0.000	0.000	0.000
98	C	141	GLY	0	0.034	0.027	23.438	0.008	0.008	0.000	0.000	0.000	0.000
99	C	142	ILE	0	-0.030	-0.035	23.999	0.005	0.005	0.000	0.000	0.000	0.000
100	C	143	PRO	0	0.036	0.006	27.070	-0.002	-0.002	0.000	0.000	0.000	0.000
101	C	144	ASP	-1	-0.884	-0.912	28.618	-0.052	-0.052	0.000	0.000	0.000	0.000
102	C	145	HIS	0	0.044	0.032	26.480	0.004	0.004	0.000	0.000	0.000	0.000
103	C	146	PRO	0	0.007	-0.009	26.929	-0.006	-0.006	0.000	0.000	0.000	0.000
104	C	147	LEU	0	-0.006	0.016	23.576	0.000	0.000	0.000	0.000	0.000	0.000
105	C	148	ARG	1	0.968	0.964	18.140	0.110	0.110	0.000	0.000	0.000	0.000
106	C	149	LEU	0	0.012	0.017	16.828	-0.016	-0.016	0.000	0.000	0.000	0.000
107	C	150	LEU	0	0.011	0.003	19.855	-0.010	-0.010	0.000	0.000	0.000	0.000
108	C	151	ARG	1	0.887	1.001	22.966	0.061	0.061	0.000	0.000	0.000	0.000
109	C	152	ILE	0	-0.086	-0.051	18.014	-0.006	-0.006	0.000	0.000	0.000	0.000
110	C	153	GLY	0	0.080	0.049	18.898	-0.017	-0.017	0.000	0.000	0.000	0.000
111	C	154	ASN	0	-0.050	-0.024	13.995	-0.025	-0.025	0.000	0.000	0.000	0.000
112	C	155	GLN	0	-0.013	-0.016	14.674	0.000	0.000	0.000	0.000	0.000	0.000
113	C	156	ALA	0	-0.020	-0.003	12.149	0.005	0.005	0.000	0.000	0.000	0.000
114	C	157	PHE	0	0.040	0.020	12.505	0.000	0.000	0.000	0.000	0.000	0.000
115	C	158	LEU	0	0.064	0.022	12.113	0.006	0.006	0.000	0.000	0.000	0.000
116	C	159	GLN	0	0.059	0.018	7.931	0.152	0.152	0.000	0.000	0.000	0.000
117	C	160	GLU	-1	-0.963	-0.985	11.752	0.171	0.171	0.000	0.000	0.000	0.000
118	C	161	PHE	0	-0.048	-0.017	14.914	-0.023	-0.023	0.000	0.000	0.000	0.000
119	C	162	VAL	0	-0.023	0.002	12.865	-0.015	-0.015	0.000	0.000	0.000	0.000
120	C	163	LEU	0	-0.020	-0.016	10.260	0.035	0.035	0.000	0.000	0.000	0.000
121	C	164	PRO	0	0.027	0.012	14.853	-0.024	-0.024	0.000	0.000	0.000	0.000
122	C	165	PRO	0	0.045	0.034	15.849	0.051	0.051	0.000	0.000	0.000	0.000
123	C	166	VAL	0	-0.030	-0.015	15.477	-0.029	-0.029	0.000	0.000	0.000	0.000
124	C	167	GLN	0	-0.029	-0.026	13.183	0.115	0.115	0.000	0.000	0.000	0.000
125	C	168	LEU	0	0.010	0.001	11.731	-0.043	-0.043	0.000	0.000	0.000	0.000
126	C	169	PRO	0	0.025	0.018	8.078	0.057	0.057	0.000	0.000	0.000	0.000
127	C	170	GLN	0	0.002	-0.006	5.975	-0.008	-0.008	0.000	0.000	0.000	0.000
128	C	171	TYR	0	-0.007	-0.005	3.067	0.025	0.323	0.056	-0.145	-0.208	0.000
129	C	172	PHE	0	-0.032	-0.020	3.273	-1.361	-1.220	0.029	-0.094	-0.077	0.000
130	C	173	THR	0	0.027	0.010	2.905	2.649	3.631	0.520	-0.494	-1.007	-0.004
131	C	174	PHE	0	0.014	-0.010	4.974	-0.234	-0.228	0.000	-0.007	0.001	0.000
132	C	175	ASP	-1	-0.902	-0.943	8.009	0.192	0.192	0.000	0.000	0.000	0.000
133	C	176	LEU	0	-0.045	-0.029	11.564	-0.007	-0.007	0.000	0.000	0.000	0.000
134	C	177	THR	0	-0.056	-0.053	13.793	-0.036	-0.036	0.000	0.000	0.000	0.000
135	C	178	ALA	0	0.039	0.005	17.240	-0.028	-0.028	0.000	0.000	0.000	0.000
136	C	179	LEU	0	-0.015	0.000	17.068	0.016	0.016	0.000	0.000	0.000	0.000
137	C	180	LYS	1	0.968	1.010	19.476	-0.105	-0.105	0.000	0.000	0.000	0.000
138	C	181	LEU	0	-0.025	-0.016	21.808	0.000	0.000	0.000	0.000	0.000	0.000
139	C	182	ILE	0	0.036	0.016	23.999	-0.002	-0.002	0.000	0.000	0.000	0.000
140	C	183	THR	0	-0.031	-0.023	25.948	-0.006	-0.006	0.000	0.000	0.000	0.000
141	C	184	GLN	0	0.032	0.009	28.690	0.004	0.004	0.000	0.000	0.000	0.000
142	C	185	PRO	0	-0.004	0.001	31.165	-0.004	-0.004	0.000	0.000	0.000	0.000
143	C	186	LEU	0	-0.031	-0.017	31.286	0.002	0.002	0.000	0.000	0.000	0.000
144	C	187	PRO	0	0.010	0.003	35.537	-0.002	-0.002	0.000	0.000	0.000	0.000
145	C	188	NME	0	0.020	0.021	38.742	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:44:ACE )