FMO DATABASE

FMODB ID: 14ZGZ

Calculation Name: 4LDD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LDD

Chain ID: C

ChEMBL ID:

UniProt ID: Q05128

Base Structure: X-ray

Registration Date: 2023-06-20

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	143
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1247761.269237
FMO2-HF: Nuclear repulsion	1193725.851458
FMO2-HF: Total energy	-54035.417779
FMO2-MP2: Total energy	-54195.505075

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(C:45:ASP)

Summations of interaction energy for fragment #1(C:45:ASP)

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.
-91.834	-88.374	0.324	-1.606	-2.177	-0.005

Interaction energy analysis for fragmet #1(C:45:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.981

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	47	PRO	0	-0.056	-0.041	3.807	-4.006	-2.098	-0.027	-0.899	-0.982	0.003
4	C	48	SER	0	0.018	0.036	6.504	-0.211	-0.211	0.000	0.000	0.000	0.000
5	C	49	ASN	0	0.049	0.031	8.997	0.979	0.979	0.000	0.000	0.000	0.000
6	C	50	PRO	0	-0.021	-0.019	12.613	-0.212	-0.212	0.000	0.000	0.000	0.000
7	C	51	LEU	0	0.000	0.005	14.972	-0.682	-0.682	0.000	0.000	0.000	0.000
8	C	52	ARG	1	0.892	0.947	17.910	-13.140	-13.140	0.000	0.000	0.000	0.000
9	C	53	PRO	0	-0.016	0.009	20.889	-0.036	-0.036	0.000	0.000	0.000	0.000
10	C	54	ILE	0	0.007	-0.007	22.237	-0.385	-0.385	0.000	0.000	0.000	0.000
11	C	55	ALA	0	-0.015	-0.015	25.420	0.196	0.196	0.000	0.000	0.000	0.000
12	C	56	ASP	-1	-0.829	-0.896	27.468	9.843	9.843	0.000	0.000	0.000	0.000
13	C	57	ASP	-1	-0.915	-0.957	28.887	8.998	8.998	0.000	0.000	0.000	0.000
14	C	58	THR	0	-0.085	-0.064	30.769	-0.291	-0.291	0.000	0.000	0.000	0.000
15	C	59	ILE	0	-0.084	-0.036	28.749	-0.076	-0.076	0.000	0.000	0.000	0.000
16	C	60	ASP	-1	-0.820	-0.900	33.249	7.531	7.531	0.000	0.000	0.000	0.000
17	C	61	HIS	0	-0.054	-0.042	35.600	-0.026	-0.026	0.000	0.000	0.000	0.000
18	C	62	ALA	0	0.056	0.023	36.582	0.048	0.048	0.000	0.000	0.000	0.000
19	C	63	SER	0	-0.048	-0.028	37.152	-0.116	-0.116	0.000	0.000	0.000	0.000
20	C	64	HIS	1	0.809	0.896	32.278	-8.910	-8.910	0.000	0.000	0.000	0.000
21	C	65	THR	0	0.018	0.016	36.424	0.077	0.077	0.000	0.000	0.000	0.000
22	C	66	PRO	0	0.003	0.005	38.689	-0.029	-0.029	0.000	0.000	0.000	0.000
23	C	67	GLY	0	0.061	0.033	39.063	0.147	0.147	0.000	0.000	0.000	0.000
24	C	68	SER	0	-0.036	-0.022	39.137	0.091	0.091	0.000	0.000	0.000	0.000
25	C	69	VAL	0	-0.038	0.001	36.227	0.036	0.036	0.000	0.000	0.000	0.000
26	C	70	SER	0	0.006	0.008	33.466	0.193	0.193	0.000	0.000	0.000	0.000
27	C	71	SER	0	-0.028	-0.025	31.340	-0.169	-0.169	0.000	0.000	0.000	0.000
28	C	72	ALA	0	-0.020	0.001	27.701	0.242	0.242	0.000	0.000	0.000	0.000
29	C	73	PHE	0	0.026	-0.009	24.583	-0.108	-0.108	0.000	0.000	0.000	0.000
30	C	74	ILE	0	-0.004	0.001	21.716	0.441	0.441	0.000	0.000	0.000	0.000
31	C	75	LEU	0	-0.009	-0.004	17.996	-0.229	-0.229	0.000	0.000	0.000	0.000
32	C	76	GLU	-1	-0.877	-0.933	19.079	12.259	12.259	0.000	0.000	0.000	0.000
33	C	77	ALA	0	-0.013	-0.013	15.441	-0.160	-0.160	0.000	0.000	0.000	0.000
34	C	78	MET	0	0.053	0.050	16.846	0.350	0.350	0.000	0.000	0.000	0.000
35	C	79	VAL	0	-0.031	0.024	12.592	0.443	0.443	0.000	0.000	0.000	0.000
36	C	80	ASN	0	0.067	0.035	14.171	-1.094	-1.094	0.000	0.000	0.000	0.000
37	C	81	VAL	0	0.021	0.024	10.207	1.165	1.165	0.000	0.000	0.000	0.000
38	C	82	ILE	0	0.045	0.019	10.327	-1.547	-1.547	0.000	0.000	0.000	0.000
39	C	83	SER	0	0.010	-0.002	9.555	2.682	2.682	0.000	0.000	0.000	0.000
40	C	84	GLY	0	0.017	0.012	10.073	-1.266	-1.266	0.000	0.000	0.000	0.000
41	C	85	PRO	0	-0.003	0.010	11.808	-0.289	-0.289	0.000	0.000	0.000	0.000
42	C	86	LYS	1	0.968	0.986	15.372	-15.565	-15.565	0.000	0.000	0.000	0.000
43	C	87	VAL	0	0.021	0.002	14.659	1.045	1.045	0.000	0.000	0.000	0.000
44	C	88	LEU	0	-0.078	-0.051	11.990	-0.648	-0.648	0.000	0.000	0.000	0.000
45	C	89	MET	0	0.003	0.003	15.016	-1.144	-1.144	0.000	0.000	0.000	0.000
46	C	90	LYS	1	0.957	0.965	15.969	-11.641	-11.641	0.000	0.000	0.000	0.000
47	C	91	GLN	0	-0.075	-0.058	18.106	-1.030	-1.030	0.000	0.000	0.000	0.000
48	C	92	ILE	0	-0.004	0.000	15.001	-0.477	-0.477	0.000	0.000	0.000	0.000
49	C	93	PRO	0	0.046	0.022	16.799	0.619	0.619	0.000	0.000	0.000	0.000
50	C	94	ILE	0	-0.033	-0.021	12.384	0.352	0.352	0.000	0.000	0.000	0.000
51	C	95	TRP	0	0.054	0.026	16.540	-0.089	-0.089	0.000	0.000	0.000	0.000
52	C	96	LEU	0	-0.012	-0.019	13.896	0.534	0.534	0.000	0.000	0.000	0.000
53	C	97	PRO	0	0.018	0.017	17.909	-0.360	-0.360	0.000	0.000	0.000	0.000
54	C	98	LEU	0	-0.005	-0.010	18.816	0.385	0.385	0.000	0.000	0.000	0.000
55	C	99	GLY	0	-0.004	-0.004	21.043	0.187	0.187	0.000	0.000	0.000	0.000
56	C	100	VAL	0	-0.006	-0.010	24.220	-0.276	-0.276	0.000	0.000	0.000	0.000
57	C	101	ALA	0	-0.006	-0.012	27.874	0.217	0.217	0.000	0.000	0.000	0.000
58	C	102	ASP	-1	-0.875	-0.929	29.728	9.133	9.133	0.000	0.000	0.000	0.000
59	C	103	GLN	0	-0.013	-0.018	32.894	0.133	0.133	0.000	0.000	0.000	0.000
60	C	104	LYS	1	0.902	0.959	35.218	-8.674	-8.674	0.000	0.000	0.000	0.000
61	C	105	THR	0	0.004	0.010	31.697	-0.127	-0.127	0.000	0.000	0.000	0.000
62	C	106	TYR	0	-0.023	-0.053	29.463	-0.086	-0.086	0.000	0.000	0.000	0.000
63	C	107	SER	0	0.088	0.068	33.155	0.080	0.080	0.000	0.000	0.000	0.000
64	C	108	PHE	0	0.089	0.035	31.118	0.347	0.347	0.000	0.000	0.000	0.000
65	C	109	ASP	-1	-0.840	-0.891	31.790	8.785	8.785	0.000	0.000	0.000	0.000
66	C	110	SER	0	-0.018	-0.032	31.993	0.200	0.200	0.000	0.000	0.000	0.000
67	C	111	THR	0	-0.039	-0.020	27.143	0.469	0.469	0.000	0.000	0.000	0.000
68	C	112	THR	0	0.000	-0.030	27.242	0.502	0.502	0.000	0.000	0.000	0.000
69	C	113	ALA	0	-0.005	0.002	27.572	0.323	0.323	0.000	0.000	0.000	0.000
70	C	114	ALA	0	-0.005	-0.004	25.714	0.333	0.333	0.000	0.000	0.000	0.000
71	C	115	ILE	0	-0.016	-0.003	22.203	0.642	0.642	0.000	0.000	0.000	0.000
72	C	116	MET	0	0.025	0.031	22.834	0.676	0.676	0.000	0.000	0.000	0.000
73	C	117	LEU	0	-0.034	-0.002	24.826	0.142	0.142	0.000	0.000	0.000	0.000
74	C	118	ALA	0	-0.021	-0.019	20.576	0.128	0.128	0.000	0.000	0.000	0.000
75	C	119	SER	0	-0.023	-0.005	17.652	-0.447	-0.447	0.000	0.000	0.000	0.000
76	C	120	TYR	0	-0.019	-0.042	15.245	0.562	0.562	0.000	0.000	0.000	0.000
77	C	121	THR	0	-0.012	0.001	10.153	0.665	0.665	0.000	0.000	0.000	0.000
78	C	122	ILE	0	0.034	0.009	8.514	-0.383	-0.383	0.000	0.000	0.000	0.000
79	C	123	THR	0	-0.030	-0.025	5.153	2.657	2.657	0.000	0.000	0.000	0.000
80	C	124	HIS	1	0.903	0.965	3.756	-34.799	-34.540	0.000	-0.035	-0.225	0.000
81	C	125	PHE	0	0.075	0.073	2.711	3.038	4.320	0.353	-0.668	-0.966	-0.008
82	C	126	GLY	0	0.008	0.006	5.079	-2.601	-2.619	-0.001	0.000	0.019	0.000
83	C	127	DLY	2	1.041	1.097	7.877	-42.588	-42.588	0.000	0.000	0.000	0.000
84	C	128	ALA	-1	-0.050	-0.194	14.799	19.368	19.368	0.000	0.000	0.000	0.000
85	C	129	THR	0	-0.074	-0.047	10.795	2.150	2.150	0.000	0.000	0.000	0.000
86	C	130	ASN	0	0.020	0.018	12.208	0.604	0.604	0.000	0.000	0.000	0.000
87	C	131	PRO	0	-0.038	0.050	9.198	1.267	1.267	0.000	0.000	0.000	0.000
88	C	132	LEU	0	0.002	-0.007	8.326	-1.734	-1.734	0.000	0.000	0.000	0.000
89	C	133	VAL	0	0.013	0.006	7.642	2.548	2.548	0.000	0.000	0.000	0.000
90	C	134	ARG	1	0.914	0.965	7.298	-32.939	-32.939	0.000	0.000	0.000	0.000
91	C	135	VAL	0	0.045	0.047	9.346	1.572	1.572	0.000	0.000	0.000	0.000
92	C	136	ASN	0	0.005	-0.024	8.631	-1.012	-1.012	0.000	0.000	0.000	0.000
93	C	137	ARG	1	0.837	0.910	12.730	-14.531	-14.531	0.000	0.000	0.000	0.000
94	C	138	LEU	0	-0.031	-0.012	13.751	0.238	0.238	0.000	0.000	0.000	0.000
95	C	139	GLY	0	0.002	0.003	17.118	-0.907	-0.907	0.000	0.000	0.000	0.000
96	C	140	PRO	0	0.007	0.009	19.558	0.563	0.563	0.000	0.000	0.000	0.000
97	C	141	GLY	0	0.029	0.024	21.535	-0.090	-0.090	0.000	0.000	0.000	0.000
98	C	142	ILE	0	-0.029	-0.034	22.023	-0.473	-0.473	0.000	0.000	0.000	0.000
99	C	143	PRO	0	0.038	0.007	25.307	0.190	0.190	0.000	0.000	0.000	0.000
100	C	144	ASP	-1	-0.884	-0.912	26.479	10.574	10.574	0.000	0.000	0.000	0.000
101	C	145	HIS	0	0.045	0.032	25.126	-0.119	-0.119	0.000	0.000	0.000	0.000
102	C	146	PRO	0	0.003	-0.011	25.550	0.492	0.492	0.000	0.000	0.000	0.000
103	C	147	LEU	0	-0.002	0.017	22.857	0.304	0.304	0.000	0.000	0.000	0.000
104	C	148	ARG	1	0.966	0.964	16.445	-16.440	-16.440	0.000	0.000	0.000	0.000
105	C	149	LEU	0	0.007	0.015	15.980	0.422	0.422	0.000	0.000	0.000	0.000
106	C	150	LEU	0	0.016	0.005	18.896	0.460	0.460	0.000	0.000	0.000	0.000
107	C	151	ARG	1	0.893	1.002	21.617	-13.078	-13.078	0.000	0.000	0.000	0.000
108	C	152	ILE	0	-0.093	-0.053	16.117	0.011	0.011	0.000	0.000	0.000	0.000
109	C	153	GLY	0	0.082	0.049	16.915	0.618	0.618	0.000	0.000	0.000	0.000
110	C	154	ASN	0	-0.052	-0.024	12.426	1.692	1.692	0.000	0.000	0.000	0.000
111	C	155	GLN	0	-0.009	-0.014	13.729	-1.077	-1.077	0.000	0.000	0.000	0.000
112	C	156	ALA	0	-0.022	-0.004	11.534	0.825	0.825	0.000	0.000	0.000	0.000
113	C	157	PHE	0	0.043	0.023	12.337	-1.340	-1.340	0.000	0.000	0.000	0.000
114	C	158	LEU	0	0.068	0.025	12.261	1.600	1.600	0.000	0.000	0.000	0.000
115	C	159	GLN	0	0.051	0.011	9.632	1.274	1.274	0.000	0.000	0.000	0.000
116	C	160	GLU	-1	-0.955	-0.980	12.716	14.468	14.468	0.000	0.000	0.000	0.000
117	C	161	PHE	0	-0.044	-0.017	15.806	-0.786	-0.786	0.000	0.000	0.000	0.000
118	C	162	VAL	0	-0.024	0.001	13.517	-0.421	-0.421	0.000	0.000	0.000	0.000
119	C	163	LEU	0	-0.025	-0.019	11.632	0.115	0.115	0.000	0.000	0.000	0.000
120	C	164	PRO	0	0.027	0.013	16.219	-0.308	-0.308	0.000	0.000	0.000	0.000
121	C	165	PRO	0	0.047	0.034	17.614	0.654	0.654	0.000	0.000	0.000	0.000
122	C	166	VAL	0	-0.030	-0.015	17.509	-0.616	-0.616	0.000	0.000	0.000	0.000
123	C	167	GLN	0	-0.018	-0.019	15.201	1.418	1.418	0.000	0.000	0.000	0.000
124	C	168	LEU	0	0.019	0.028	11.734	-0.250	-0.250	0.000	0.000	0.000	0.000
125	C	169	PRO	0	-0.016	-0.015	10.557	0.399	0.399	0.000	0.000	0.000	0.000
126	C	170	GLN	0	0.011	-0.009	8.108	-1.844	-1.844	0.000	0.000	0.000	0.000
127	C	171	TYR	0	-0.016	-0.015	5.101	3.272	3.272	0.000	0.000	0.000	0.000
128	C	172	PHE	0	-0.039	-0.022	5.533	-2.451	-2.451	0.000	0.000	0.000	0.000
129	C	173	THR	0	0.029	0.017	5.008	4.750	4.779	-0.001	-0.004	-0.023	0.000
130	C	174	PHE	0	0.014	-0.012	6.499	-2.906	-2.906	0.000	0.000	0.000	0.000
131	C	175	ASP	-1	-0.900	-0.941	9.163	18.741	18.741	0.000	0.000	0.000	0.000
132	C	176	LEU	0	-0.048	-0.030	12.537	-1.051	-1.051	0.000	0.000	0.000	0.000
133	C	177	THR	0	-0.054	-0.053	14.463	-0.708	-0.708	0.000	0.000	0.000	0.000
134	C	178	ALA	0	0.039	0.006	18.089	-0.669	-0.669	0.000	0.000	0.000	0.000
135	C	179	LEU	0	-0.014	0.000	17.340	0.597	0.597	0.000	0.000	0.000	0.000
136	C	180	LYS	1	0.963	1.008	19.875	-11.308	-11.308	0.000	0.000	0.000	0.000
137	C	181	LEU	0	-0.020	-0.013	22.133	0.427	0.427	0.000	0.000	0.000	0.000
138	C	182	ILE	0	0.030	0.014	24.273	-0.429	-0.429	0.000	0.000	0.000	0.000
139	C	183	THR	0	-0.027	-0.023	26.102	0.101	0.101	0.000	0.000	0.000	0.000
140	C	184	GLN	0	0.035	0.011	28.818	-0.151	-0.151	0.000	0.000	0.000	0.000
141	C	185	PRO	0	-0.002	0.002	31.345	0.162	0.162	0.000	0.000	0.000	0.000
142	C	186	LEU	0	-0.033	-0.014	31.201	0.009	0.009	0.000	0.000	0.000	0.000
143	C	187	PRO	0	0.032	0.021	35.522	-0.039	-0.039	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:45:ASP)