FMO DATABASE

FMODB ID: 7MZJK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-490057.524833
FMO2-HF: Nuclear repulsion	460409.937755
FMO2-HF: Total energy	-29647.587078
FMO2-MP2: Total energy	-29734.667886

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.
-8.84	-7.145	16.443	-9	-9.138	-0.044

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 : 0.120 / q_NPA : 0.027

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	-0.107	0.071	4.192	0.099	0.657	0.006	-0.205	-0.358	0.000
5	A	775	GLU	0	0.177	-0.123	3.877	-0.247	1.758	-0.029	-1.179	-0.797	0.000
6	A	775	GLU	-1	-0.934	-0.797	7.461	-0.491	-0.491	0.000	0.000	0.000	0.000
7	A	776	LEU	0	0.070	-0.095	7.210	0.064	0.064	0.000	0.000	0.000	0.000
8	A	776	LEU	0	-0.041	0.114	8.025	0.033	0.033	0.000	0.000	0.000	0.000
9	A	777	THR	0	0.033	-0.077	5.010	-0.597	-0.556	-0.002	-0.002	-0.037	0.000
10	A	777	THR	0	-0.093	0.048	4.180	0.998	1.095	-0.001	-0.017	-0.078	0.000
11	A	778	LEU	0	0.103	-0.079	5.936	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	778	LEU	0	-0.069	0.106	5.027	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	779	GLN	0	0.184	-0.065	7.272	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	779	GLN	0	-0.128	0.101	10.475	0.049	0.049	0.000	0.000	0.000	0.000
15	A	780	ARG	0	0.063	-0.099	9.676	-0.151	-0.151	0.000	0.000	0.000	0.000
16	A	780	ARG	1	0.805	1.040	9.354	-0.949	-0.949	0.000	0.000	0.000	0.000
17	A	781	SER	0	0.006	-0.074	9.353	-0.081	-0.081	0.000	0.000	0.000	0.000
18	A	781	SER	0	-0.054	0.037	8.567	0.001	0.001	0.000	0.000	0.000	0.000
19	A	782	LEU	0	0.082	-0.097	10.525	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	782	LEU	0	-0.114	0.118	12.666	0.002	0.002	0.000	0.000	0.000	0.000
21	A	783	PRO	0	0.074	-0.094	13.147	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	784	PHE	0	0.060	0.024	14.107	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	784	PHE	0	-0.090	0.075	13.118	0.025	0.025	0.000	0.000	0.000	0.000
24	A	785	ILE	0	0.095	-0.066	13.960	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	785	ILE	0	-0.077	0.083	10.762	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	786	GLU	0	0.102	-0.111	15.015	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	786	GLU	-1	-0.894	-0.788	17.026	0.179	0.179	0.000	0.000	0.000	0.000
28	A	787	GLY	0	0.033	-0.081	18.216	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	788	MET	0	0.160	0.032	17.740	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	788	MET	0	-0.170	0.069	15.936	0.012	0.012	0.000	0.000	0.000	0.000
31	A	789	LEU	0	0.029	-0.112	18.861	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	789	LEU	0	-0.075	0.091	17.731	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	790	THR	0	0.053	-0.075	20.613	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	790	THR	0	-0.070	0.038	21.985	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	791	ASN	0	0.047	-0.076	22.595	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	791	ASN	0	-0.198	0.015	22.480	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	792	LEU	0	-0.021	-0.108	22.761	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	792	LEU	0	-0.059	0.086	20.412	0.002	0.002	0.000	0.000	0.000	0.000
39	A	793	GLY	0	0.042	-0.078	23.977	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	794	ALA	0	0.154	0.011	22.385	0.012	0.012	0.000	0.000	0.000	0.000
41	A	794	ALA	0	-0.085	0.106	23.658	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	795	MET	0	-0.009	-0.136	19.588	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	795	MET	0	-0.081	0.121	17.991	0.007	0.007	0.000	0.000	0.000	0.000
44	A	796	LYS	0	0.140	-0.079	19.059	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	796	LYS	1	0.796	1.023	19.711	0.000	0.000	0.000	0.000	0.000	0.000
46	A	797	LEU	0	0.149	-0.081	15.011	0.032	0.032	0.000	0.000	0.000	0.000
47	A	797	LEU	0	-0.084	0.131	12.215	0.005	0.005	0.000	0.000	0.000	0.000
48	A	798	HIS	0	0.104	-0.075	13.986	0.029	0.029	0.000	0.000	0.000	0.000
49	A	798	HIS	0	-0.026	0.101	15.717	0.008	0.008	0.000	0.000	0.000	0.000
50	A	799	LYS	0	-0.002	-0.122	14.962	0.024	0.024	0.000	0.000	0.000	0.000
51	A	799	LYS	1	0.890	1.061	18.277	-0.063	-0.063	0.000	0.000	0.000	0.000
52	A	800	ILE	0	0.183	-0.057	14.347	0.034	0.034	0.000	0.000	0.000	0.000
53	A	800	ILE	0	-0.074	0.125	12.476	0.000	0.000	0.000	0.000	0.000	0.000
54	A	801	HIS	0	0.103	-0.083	10.665	0.070	0.070	0.000	0.000	0.000	0.000
55	A	801	HIS	0	-0.090	0.091	6.729	0.043	0.043	0.000	0.000	0.000	0.000
56	A	802	SER	0	-0.007	-0.109	11.191	0.075	0.075	0.000	0.000	0.000	0.000
57	A	802	SER	0	-0.089	0.038	15.140	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	803	PHE	0	0.104	-0.069	13.963	0.037	0.037	0.000	0.000	0.000	0.000
59	A	803	PHE	0	-0.030	0.114	15.262	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	804	LEU	0	0.070	-0.083	10.799	0.002	0.002	0.000	0.000	0.000	0.000
61	A	804	LEU	0	-0.057	0.104	9.525	0.015	0.015	0.000	0.000	0.000	0.000
62	A	805	LYS	0	0.039	-0.113	10.281	0.131	0.131	0.000	0.000	0.000	0.000
63	A	805	LYS	1	0.866	1.051	8.696	-0.257	-0.257	0.000	0.000	0.000	0.000
64	A	806	ILE	0	-0.031	-0.115	11.164	0.059	0.059	0.000	0.000	0.000	0.000
65	A	806	ILE	0	-0.080	0.096	14.869	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	807	THR	0	0.018	-0.096	13.582	-0.037	-0.037	0.000	0.000	0.000	0.000
67	A	807	THR	0	-0.047	0.057	14.728	0.003	0.003	0.000	0.000	0.000	0.000
68	A	808	VAL	0	0.052	-0.072	10.725	-0.072	-0.072	0.000	0.000	0.000	0.000
69	A	808	VAL	0	-0.063	0.091	9.112	0.034	0.034	0.000	0.000	0.000	0.000
70	A	809	PRO	0	-0.007	-0.089	12.131	0.020	0.020	0.000	0.000	0.000	0.000
71	A	810	LYS	0	0.162	0.036	10.544	0.211	0.211	0.000	0.000	0.000	0.000
72	A	810	LYS	1	0.903	1.061	11.614	-0.548	-0.548	0.000	0.000	0.000	0.000
73	A	811	ASP	0	0.019	-0.130	10.182	0.320	0.320	0.000	0.000	0.000	0.000
74	A	811	ASP	-1	-0.918	-0.805	13.801	0.649	0.649	0.000	0.000	0.000	0.000
75	A	812	TRP	0	-0.033	-0.123	9.822	0.032	0.032	0.000	0.000	0.000	0.000
76	A	812	TRP	0	-0.034	0.108	9.838	0.010	0.010	0.000	0.000	0.000	0.000
77	A	813	GLY	0	-0.006	-0.114	6.170	0.743	0.743	0.000	0.000	0.000	0.000
78	A	814	TYR	0	0.113	0.008	4.851	-0.336	-0.336	0.000	0.000	0.000	0.000
79	A	814	TYR	0	-0.034	0.116	6.589	-0.071	-0.071	0.000	0.000	0.000	0.000
80	A	815	ASN	0	0.027	-0.145	5.434	-0.323	-0.323	0.000	0.000	0.000	0.000
81	A	815	ASN	0	-0.055	0.090	7.454	0.049	0.049	0.000	0.000	0.000	0.000
82	A	816	ARG	0	0.037	-0.074	2.977	-0.746	-0.840	0.013	0.405	-0.325	-0.002
83	A	816	ARG	1	0.884	1.045	2.489	-2.540	-1.923	1.129	-0.922	-0.825	0.006
84	A	817	ILE	0	0.132	-0.077	2.089	-5.607	-5.348	5.588	-2.915	-2.933	-0.034
85	A	817	ILE	0	-0.092	0.131	1.847	0.928	-2.128	7.222	-2.309	-1.856	-0.002
86	A	818	THR	0	0.046	-0.075	3.445	0.110	0.128	0.048	0.055	-0.121	0.000
87	A	818	THR	0	-0.054	0.056	4.592	0.009	0.023	-0.001	-0.007	-0.006	0.000
88	A	819	LEU	0	0.115	-0.067	6.139	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	819	LEU	0	-0.049	0.097	10.530	0.014	0.014	0.000	0.000	0.000	0.000
90	A	820	GLN	0	0.153	-0.079	8.933	0.063	0.063	0.000	0.000	0.000	0.000
91	A	820	GLN	0	-0.057	0.099	7.861	0.057	0.057	0.000	0.000	0.000	0.000
92	A	821	GLN	0	0.035	-0.096	5.293	0.012	0.017	-0.002	-0.003	0.000	0.000
93	A	821	GLN	0	-0.100	0.049	2.420	-0.284	0.947	2.472	-1.901	-1.802	-0.012
94	A	822	LEU	0	0.171	-0.061	6.816	0.010	0.010	0.000	0.000	0.000	0.000
95	A	822	LEU	0	-0.127	0.097	8.053	0.012	0.012	0.000	0.000	0.000	0.000
96	A	823	GLU	0	0.074	-0.121	8.743	0.049	0.049	0.000	0.000	0.000	0.000
97	A	823	GLU	-1	-1.029	-0.854	11.705	-0.185	-0.185	0.000	0.000	0.000	0.000
98	A	824	GLY	0	-0.006	-0.103	10.524	0.026	0.026	0.000	0.000	0.000	0.000
99	A	825	TYR	0	0.141	0.059	9.848	0.003	0.003	0.000	0.000	0.000	0.000
100	A	825	TYR	0	-0.097	0.073	9.013	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	826	LEU	0	0.071	-0.109	11.114	0.031	0.031	0.000	0.000	0.000	0.000
102	A	826	LEU	0	-0.092	0.072	12.103	0.009	0.009	0.000	0.000	0.000	0.000
103	A	827	ASN	0	0.125	-0.043	13.825	0.028	0.028	0.000	0.000	0.000	0.000
104	A	827	ASN	0	-0.105	0.080	14.913	0.026	0.026	0.000	0.000	0.000	0.000
105	A	828	THR	0	0.106	-0.037	14.439	0.019	0.019	0.000	0.000	0.000	0.000
106	A	828	THR	0	-0.062	0.040	13.505	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	829	LEU	0	0.059	-0.073	15.023	0.003	0.003	0.000	0.000	0.000	0.000
108	A	829	LEU	0	-0.104	0.055	13.141	0.014	0.014	0.000	0.000	0.000	0.000
109	A	830	ALA	0	0.091	-0.072	16.589	0.026	0.026	0.000	0.000	0.000	0.000
110	A	830	ALA	0	-0.101	0.054	19.011	0.000	0.000	0.000	0.000	0.000	0.000
111	A	831	ASP	0	0.062	-0.086	18.966	0.009	0.009	0.000	0.000	0.000	0.000
112	A	831	ASP	-1	-1.034	-0.881	18.958	-0.114	-0.114	0.000	0.000	0.000	0.000
113	A	832	GLU	0	0.021	-0.130	19.342	0.000	0.000	0.000	0.000	0.000	0.000
114	A	832	GLU	-1	-0.883	-0.798	17.370	0.047	0.047	0.000	0.000	0.000	0.000
115	A	833	GLY	0	-0.020	-0.088	20.884	0.002	0.002	0.000	0.000	0.000	0.000
116	A	834	ARG	0	0.116	0.006	20.119	0.005	0.005	0.000	0.000	0.000	0.000
117	A	834	ARG	1	0.642	0.945	17.476	-0.105	-0.105	0.000	0.000	0.000	0.000
118	A	835	LEU	0	-0.003	-0.105	19.051	0.017	0.017	0.000	0.000	0.000	0.000
119	A	835	LEU	0	-0.081	0.072	15.974	0.004	0.004	0.000	0.000	0.000	0.000
120	A	836	LYS	0	0.228	-0.072	20.476	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	836	LYS	1	0.652	1.001	23.838	-0.024	-0.024	0.000	0.000	0.000	0.000
122	A	837	TYR	0	0.154	-0.084	21.284	0.013	0.013	0.000	0.000	0.000	0.000
123	A	837	TYR	0	-0.068	0.105	19.696	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	838	ILE	0	0.012	-0.118	21.950	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	838	ILE	0	-0.111	0.097	24.493	0.001	0.001	0.000	0.000	0.000	0.000
126	A	839	ALA	0	0.147	-0.094	24.028	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	839	ALA	0	-0.052	0.120	27.706	0.000	0.000	0.000	0.000	0.000	0.000
128	A	840	ASN	0	0.011	-0.099	25.702	0.006	0.006	0.000	0.000	0.000	0.000
129	A	840	ASN	0	-0.108	0.080	26.711	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	841	GLY	0	0.042	-0.089	21.397	0.003	0.003	0.000	0.000	0.000	0.000
131	A	842	SER	0	-0.036	0.010	20.429	0.003	0.003	0.000	0.000	0.000	0.000
132	A	842	SER	0	-0.012	0.055	22.365	0.002	0.002	0.000	0.000	0.000	0.000
133	A	843	TYR	0	0.045	-0.097	18.712	-0.015	-0.015	0.000	0.000	0.000	0.000
134	A	843	TYR	0	-0.065	0.065	16.150	0.006	0.006	0.000	0.000	0.000	0.000
135	A	844	GLU	0	0.134	-0.072	20.170	0.016	0.016	0.000	0.000	0.000	0.000
136	A	844	GLU	-1	-0.864	-0.791	23.863	0.034	0.034	0.000	0.000	0.000	0.000
137	A	845	ILE	0	0.059	-0.103	21.392	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	845	ILE	0	-0.067	0.111	20.639	0.003	0.003	0.000	0.000	0.000	0.000
139	A	846	VAL	0	-0.116	-0.165	22.206	0.001	0.001	0.000	0.000	0.000	0.000
140	A	846	VAL	0	0.043	0.054	23.531	-0.002	-0.002	0.000	0.000	0.000	0.000

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