FMO DATABASE

FMODB ID: M92MZ

Calculation Name: 1LDD-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LDD

Chain ID: A

ChEMBL ID:

UniProt ID: Q12440

Base Structure: X-ray

Registration Date: 2025-07-08

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-491009.383013
FMO2-HF: Nuclear repulsion	461362.168683
FMO2-HF: Total energy	-29647.214329
FMO2-MP2: Total energy	-29734.376694

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:773:LYS)

Summations of interaction energy for fragment #1(A:773: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.
-5.16	-5.551	19.378	-9.828	-9.164	-0.016

Interaction energy analysis for fragmet #1(A:773:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.156 / 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].
4	A	774	TYR	0	-0.136	0.052	4.171	0.040	0.591	0.006	-0.214	-0.343	0.000
5	A	775	GLU	0	0.229	-0.131	3.788	-1.318	1.319	-0.050	-1.534	-1.054	-0.002
6	A	775	GLU	-1	-0.936	-0.784	7.117	-0.647	-0.647	0.000	0.000	0.000	0.000
7	A	776	LEU	0	0.074	-0.085	6.662	0.130	0.130	0.000	0.000	0.000	0.000
8	A	776	LEU	0	-0.037	0.113	7.821	0.033	0.033	0.000	0.000	0.000	0.000
9	A	777	THR	0	0.043	-0.077	4.650	-0.731	-0.680	-0.001	-0.007	-0.043	0.000
10	A	777	THR	0	-0.072	0.061	3.701	0.988	1.145	0.002	-0.047	-0.112	0.000
11	A	778	LEU	0	0.095	-0.096	5.266	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	778	LEU	0	-0.060	0.107	4.357	-0.109	-0.053	-0.001	-0.007	-0.048	0.000
13	A	779	GLN	0	0.146	-0.084	6.580	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	779	GLN	0	-0.118	0.100	9.953	0.042	0.042	0.000	0.000	0.000	0.000
15	A	780	ARG	0	0.056	-0.119	9.026	-0.141	-0.141	0.000	0.000	0.000	0.000
16	A	780	ARG	1	0.823	1.053	9.018	-0.902	-0.902	0.000	0.000	0.000	0.000
17	A	781	SER	0	-0.020	-0.071	9.029	-0.078	-0.078	0.000	0.000	0.000	0.000
18	A	781	SER	0	-0.037	0.046	8.480	0.021	0.021	0.000	0.000	0.000	0.000
19	A	782	LEU	0	0.082	-0.104	10.310	-0.054	-0.054	0.000	0.000	0.000	0.000
20	A	782	LEU	0	-0.103	0.124	12.199	0.000	0.000	0.000	0.000	0.000	0.000
21	A	783	PRO	0	0.055	-0.091	12.617	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	784	PHE	0	0.070	0.013	13.817	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	784	PHE	0	-0.076	0.081	12.885	0.021	0.021	0.000	0.000	0.000	0.000
24	A	785	ILE	0	0.099	-0.073	13.481	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	785	ILE	0	-0.069	0.087	10.038	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	786	GLU	0	0.078	-0.105	14.418	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	786	GLU	-1	-0.923	-0.822	16.457	0.142	0.142	0.000	0.000	0.000	0.000
28	A	787	GLY	0	0.043	-0.077	17.649	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	788	MET	0	0.138	0.028	17.405	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	788	MET	0	-0.167	0.084	15.059	0.013	0.013	0.000	0.000	0.000	0.000
31	A	789	LEU	0	0.024	-0.128	18.379	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	789	LEU	0	-0.069	0.099	17.179	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	790	THR	0	0.050	-0.066	20.046	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	790	THR	0	-0.079	0.028	21.247	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	791	ASN	0	0.031	-0.079	22.299	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	791	ASN	0	-0.201	0.010	21.808	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	792	LEU	0	-0.012	-0.105	22.582	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	792	LEU	0	-0.061	0.085	20.579	0.002	0.002	0.000	0.000	0.000	0.000
39	A	793	GLY	0	0.060	-0.061	23.539	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	794	ALA	0	0.169	0.007	21.907	0.011	0.011	0.000	0.000	0.000	0.000
41	A	794	ALA	0	-0.088	0.110	22.956	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	795	MET	0	0.005	-0.130	19.210	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	795	MET	0	-0.101	0.116	17.558	0.007	0.007	0.000	0.000	0.000	0.000
44	A	796	LYS	0	0.176	-0.057	18.867	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	796	LYS	1	0.789	1.027	19.360	0.011	0.011	0.000	0.000	0.000	0.000
46	A	797	LEU	0	0.174	-0.082	14.848	0.032	0.032	0.000	0.000	0.000	0.000
47	A	797	LEU	0	-0.076	0.131	12.159	0.006	0.006	0.000	0.000	0.000	0.000
48	A	798	HIS	0	0.090	-0.075	13.998	0.024	0.024	0.000	0.000	0.000	0.000
49	A	798	HIS	0	-0.039	0.096	15.902	0.009	0.009	0.000	0.000	0.000	0.000
50	A	799	LYS	0	0.013	-0.131	15.015	0.024	0.024	0.000	0.000	0.000	0.000
51	A	799	LYS	1	0.899	1.063	18.152	-0.059	-0.059	0.000	0.000	0.000	0.000
52	A	800	ILE	0	0.169	-0.062	14.164	0.037	0.037	0.000	0.000	0.000	0.000
53	A	800	ILE	0	-0.068	0.121	12.106	0.000	0.000	0.000	0.000	0.000	0.000
54	A	801	HIS	0	0.124	-0.069	10.674	0.063	0.063	0.000	0.000	0.000	0.000
55	A	801	HIS	0	-0.097	0.088	6.967	0.031	0.031	0.000	0.000	0.000	0.000
56	A	802	SER	0	-0.015	-0.107	11.310	0.086	0.086	0.000	0.000	0.000	0.000
57	A	802	SER	0	-0.082	0.042	15.081	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	803	PHE	0	0.097	-0.072	13.829	0.041	0.041	0.000	0.000	0.000	0.000
59	A	803	PHE	0	-0.018	0.118	15.178	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	804	LEU	0	0.075	-0.083	10.560	0.007	0.007	0.000	0.000	0.000	0.000
61	A	804	LEU	0	-0.061	0.103	9.218	0.012	0.012	0.000	0.000	0.000	0.000
62	A	805	LYS	0	0.051	-0.093	10.281	0.119	0.119	0.000	0.000	0.000	0.000
63	A	805	LYS	1	0.849	1.034	8.997	-0.255	-0.255	0.000	0.000	0.000	0.000
64	A	806	ILE	0	0.011	-0.115	11.215	0.071	0.071	0.000	0.000	0.000	0.000
65	A	806	ILE	0	-0.123	0.083	15.145	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	807	THR	0	0.008	-0.095	14.081	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	807	THR	0	-0.074	0.049	14.495	0.003	0.003	0.000	0.000	0.000	0.000
68	A	808	VAL	0	0.057	-0.069	10.679	-0.068	-0.068	0.000	0.000	0.000	0.000
69	A	808	VAL	0	-0.072	0.089	9.044	0.030	0.030	0.000	0.000	0.000	0.000
70	A	809	PRO	0	0.021	-0.077	12.166	0.028	0.028	0.000	0.000	0.000	0.000
71	A	810	LYS	0	0.174	0.025	11.060	0.189	0.189	0.000	0.000	0.000	0.000
72	A	810	LYS	1	0.894	1.064	12.306	-0.495	-0.495	0.000	0.000	0.000	0.000
73	A	811	ASP	0	0.020	-0.127	10.507	0.245	0.245	0.000	0.000	0.000	0.000
74	A	811	ASP	-1	-0.931	-0.810	13.760	0.604	0.604	0.000	0.000	0.000	0.000
75	A	812	TRP	0	-0.034	-0.131	9.833	0.078	0.078	0.000	0.000	0.000	0.000
76	A	812	TRP	0	-0.042	0.109	9.621	0.012	0.012	0.000	0.000	0.000	0.000
77	A	813	GLY	0	-0.039	-0.123	6.582	0.767	0.767	0.000	0.000	0.000	0.000
78	A	814	TYR	0	0.134	-0.014	4.788	-0.273	-0.250	-0.002	-0.003	-0.019	0.000
79	A	814	TYR	0	-0.014	0.127	6.450	-0.079	-0.079	0.000	0.000	0.000	0.000
80	A	815	ASN	0	0.028	-0.104	5.121	-0.398	-0.342	-0.002	-0.001	-0.054	0.000
81	A	815	ASN	0	-0.063	0.081	7.341	0.116	0.116	0.000	0.000	0.000	0.000
82	A	816	ARG	0	0.090	-0.074	3.204	-0.761	-0.763	0.003	0.188	-0.189	0.000
83	A	816	ARG	1	0.844	1.033	2.501	-2.451	-1.650	0.628	-0.702	-0.727	0.005
84	A	817	ILE	0	0.028	-0.097	2.437	-3.122	-1.767	1.630	-1.222	-1.763	-0.005
85	A	817	ILE	0	-0.083	0.122	1.790	2.120	-2.966	10.568	-3.316	-2.167	-0.001
86	A	818	THR	0	0.095	-0.040	3.061	0.824	0.234	0.142	0.618	-0.170	0.000
87	A	818	THR	0	-0.087	0.038	4.485	-0.009	0.012	-0.001	-0.015	-0.005	0.000
88	A	819	LEU	0	0.117	-0.091	6.013	-0.050	-0.050	0.000	0.000	0.000	0.000
89	A	819	LEU	0	-0.054	0.106	10.413	0.015	0.015	0.000	0.000	0.000	0.000
90	A	820	GLN	0	0.146	-0.072	8.195	0.035	0.035	0.000	0.000	0.000	0.000
91	A	820	GLN	0	-0.055	0.099	7.504	0.073	0.073	0.000	0.000	0.000	0.000
92	A	821	GLN	0	0.086	-0.084	4.639	0.001	0.036	-0.001	-0.026	-0.008	0.000
93	A	821	GLN	0	-0.067	0.093	2.114	0.192	-0.264	6.457	-3.540	-2.462	-0.013
94	A	822	LEU	0	0.110	-0.087	6.147	-0.042	-0.042	0.000	0.000	0.000	0.000
95	A	822	LEU	0	-0.132	0.091	7.633	0.017	0.017	0.000	0.000	0.000	0.000
96	A	823	GLU	0	0.072	-0.131	8.087	0.044	0.044	0.000	0.000	0.000	0.000
97	A	823	GLU	-1	-1.018	-0.841	11.359	-0.199	-0.199	0.000	0.000	0.000	0.000
98	A	824	GLY	0	-0.022	-0.107	9.812	0.034	0.034	0.000	0.000	0.000	0.000
99	A	825	TYR	0	0.168	0.048	9.018	0.018	0.018	0.000	0.000	0.000	0.000
100	A	825	TYR	0	-0.083	0.092	8.152	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	826	LEU	0	0.060	-0.106	10.256	0.046	0.046	0.000	0.000	0.000	0.000
102	A	826	LEU	0	-0.092	0.081	11.426	0.010	0.010	0.000	0.000	0.000	0.000
103	A	827	ASN	0	0.147	-0.040	13.044	0.037	0.037	0.000	0.000	0.000	0.000
104	A	827	ASN	0	-0.081	0.091	14.469	0.030	0.030	0.000	0.000	0.000	0.000
105	A	828	THR	0	0.071	-0.052	13.754	0.022	0.022	0.000	0.000	0.000	0.000
106	A	828	THR	0	-0.053	0.054	12.975	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	829	LEU	0	0.097	-0.055	14.405	0.010	0.010	0.000	0.000	0.000	0.000
108	A	829	LEU	0	-0.112	0.047	12.819	0.016	0.016	0.000	0.000	0.000	0.000
109	A	830	ALA	0	0.060	-0.092	16.002	0.024	0.024	0.000	0.000	0.000	0.000
110	A	830	ALA	0	-0.117	0.054	18.072	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	831	ASP	0	0.040	-0.086	18.107	0.018	0.018	0.000	0.000	0.000	0.000
112	A	831	ASP	-1	-1.047	-0.889	18.133	-0.142	-0.142	0.000	0.000	0.000	0.000
113	A	832	GLU	0	-0.110	-0.101	18.788	0.001	0.001	0.000	0.000	0.000	0.000
114	A	832	GLU	-1	-0.893	-0.883	16.615	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	833	GLY	0	0.121	-0.052	20.448	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	834	ARG	0	0.126	0.001	18.998	0.009	0.009	0.000	0.000	0.000	0.000
117	A	834	ARG	1	0.677	1.004	16.436	-0.052	-0.052	0.000	0.000	0.000	0.000
118	A	835	LEU	0	-0.020	-0.124	18.460	0.019	0.019	0.000	0.000	0.000	0.000
119	A	835	LEU	0	-0.076	0.077	15.430	0.002	0.002	0.000	0.000	0.000	0.000
120	A	836	LYS	0	0.233	-0.068	19.849	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	836	LYS	1	0.681	1.013	23.448	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	837	TYR	0	0.159	-0.049	20.477	0.010	0.010	0.000	0.000	0.000	0.000
123	A	837	TYR	0	-0.119	0.061	19.368	0.000	0.000	0.000	0.000	0.000	0.000
124	A	838	ILE	0	0.046	-0.106	21.469	0.006	0.006	0.000	0.000	0.000	0.000
125	A	838	ILE	0	-0.065	0.109	24.119	0.000	0.000	0.000	0.000	0.000	0.000
126	A	839	ALA	0	0.149	-0.086	23.989	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	839	ALA	0	-0.066	0.106	27.512	0.000	0.000	0.000	0.000	0.000	0.000
128	A	840	ASN	0	0.005	-0.109	25.398	0.006	0.006	0.000	0.000	0.000	0.000
129	A	840	ASN	0	-0.117	0.076	26.198	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	841	GLY	0	0.040	-0.099	21.126	0.001	0.001	0.000	0.000	0.000	0.000
131	A	842	SER	0	-0.038	0.010	19.995	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	842	SER	0	-0.028	0.047	21.870	0.003	0.003	0.000	0.000	0.000	0.000
133	A	843	TYR	0	0.073	-0.060	18.098	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	843	TYR	0	-0.095	0.043	16.015	0.004	0.004	0.000	0.000	0.000	0.000
135	A	844	GLU	0	0.145	-0.100	19.585	0.019	0.019	0.000	0.000	0.000	0.000
136	A	844	GLU	-1	-0.889	-0.792	23.347	0.017	0.017	0.000	0.000	0.000	0.000
137	A	845	ILE	0	0.068	-0.084	20.797	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	845	ILE	0	-0.071	0.103	19.913	0.002	0.002	0.000	0.000	0.000	0.000
139	A	846	VAL	0	-0.109	-0.147	21.595	0.002	0.002	0.000	0.000	0.000	0.000
140	A	846	VAL	0	0.036	0.043	22.803	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:773:LYS)