FMO DATABASE

FMODB ID: VKZ31

Calculation Name: 1H3O-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H3O

Chain ID: A

ChEMBL ID:

UniProt ID: Q16514

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-225718.528628
FMO2-HF: Nuclear repulsion	206140.792186
FMO2-HF: Total energy	-19577.736442
FMO2-MP2: Total energy	-19635.43381

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(A:869:MET)

Summations of interaction energy for fragment #1(A:869:MET)

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.
0.781	2.635	-0.006	-0.642	-1.207	0.003

Interaction energy analysis for fragmet #1(A:869:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.159 / q_NPA : 0.034

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	870	PHE	0	-0.093	0.087	4.508	0.046	0.358	0.000	-0.151	-0.161	0.000
5	A	871	LEU	0	0.025	-0.105	3.867	-0.927	0.514	-0.001	-0.802	-0.638	0.004
6	A	871	LEU	0	-0.056	0.084	5.242	0.145	0.192	-0.001	-0.002	-0.043	0.000
7	A	872	LEU	0	0.125	-0.088	3.558	-2.885	-3.245	0.005	0.400	-0.045	-0.001
8	A	872	LEU	0	-0.098	0.105	6.844	0.165	0.165	0.000	0.000	0.000	0.000
9	A	873	GLN	0	0.144	-0.085	4.516	0.727	0.768	-0.002	-0.007	-0.033	0.000
10	A	873	GLN	0	-0.034	0.123	3.945	0.023	0.204	0.003	-0.046	-0.138	0.000
11	A	874	ALA	0	0.150	-0.076	5.440	0.522	0.556	-0.002	-0.002	-0.031	0.000
12	A	874	ALA	0	-0.098	0.096	9.791	0.050	0.050	0.000	0.000	0.000	0.000
13	A	875	PRO	0	-0.045	-0.132	8.564	0.244	0.244	0.000	0.000	0.000	0.000
14	A	876	LEU	0	0.122	0.024	7.844	0.397	0.397	0.000	0.000	0.000	0.000
15	A	876	LEU	0	-0.070	0.118	6.116	-0.086	-0.086	0.000	0.000	0.000	0.000
16	A	877	GLN	0	0.160	-0.077	8.783	0.249	0.249	0.000	0.000	0.000	0.000
17	A	877	GLN	0	-0.106	0.098	9.047	-0.099	-0.099	0.000	0.000	0.000	0.000
18	A	878	ARG	0	0.085	-0.082	10.383	0.165	0.165	0.000	0.000	0.000	0.000
19	A	878	ARG	1	0.852	1.041	12.797	0.721	0.721	0.000	0.000	0.000	0.000
20	A	879	ARG	0	0.107	-0.064	12.622	0.131	0.131	0.000	0.000	0.000	0.000
21	A	879	ARG	1	0.877	1.075	12.870	0.744	0.744	0.000	0.000	0.000	0.000
22	A	880	ILE	0	0.073	-0.109	12.660	0.084	0.084	0.000	0.000	0.000	0.000
23	A	880	ILE	0	-0.044	0.109	9.948	0.001	0.001	0.000	0.000	0.000	0.000
24	A	881	LEU	0	0.094	-0.109	13.939	0.081	0.081	0.000	0.000	0.000	0.000
25	A	881	LEU	0	-0.090	0.096	14.323	0.000	0.000	0.000	0.000	0.000	0.000
26	A	882	GLU	0	0.067	-0.081	16.162	0.071	0.071	0.000	0.000	0.000	0.000
27	A	882	GLU	-1	-0.981	-0.834	17.134	-0.413	-0.413	0.000	0.000	0.000	0.000
28	A	883	ILE	0	0.069	-0.132	17.243	0.049	0.049	0.000	0.000	0.000	0.000
29	A	883	ILE	0	-0.079	0.114	15.778	0.002	0.002	0.000	0.000	0.000	0.000
30	A	884	GLY	0	0.041	-0.082	18.209	0.040	0.040	0.000	0.000	0.000	0.000
31	A	885	LYS	0	0.158	0.074	19.880	0.032	0.032	0.000	0.000	0.000	0.000
32	A	885	LYS	1	0.885	1.062	20.620	0.196	0.196	0.000	0.000	0.000	0.000
33	A	886	LYS	0	-0.001	-0.121	22.398	0.023	0.023	0.000	0.000	0.000	0.000
34	A	886	LYS	1	0.764	0.994	21.318	0.284	0.284	0.000	0.000	0.000	0.000
35	A	887	HIS	0	-0.065	-0.102	23.191	0.013	0.013	0.000	0.000	0.000	0.000
36	A	887	HIS	1	0.731	0.970	21.734	0.193	0.193	0.000	0.000	0.000	0.000
37	A	888	GLY	0	0.155	-0.069	23.879	0.006	0.006	0.000	0.000	0.000	0.000
38	A	889	ILE	0	0.067	0.022	21.196	0.022	0.022	0.000	0.000	0.000	0.000
39	A	889	ILE	0	-0.123	0.098	19.124	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	890	THR	0	0.009	-0.098	22.002	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	890	THR	0	-0.008	0.068	23.248	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	891	GLU	0	0.050	-0.132	19.028	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	891	GLU	-1	-0.982	-0.829	19.347	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	892	LEU	0	0.062	-0.098	15.536	0.007	0.007	0.000	0.000	0.000	0.000
45	A	892	LEU	0	-0.101	0.082	12.595	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	893	HIS	0	0.156	-0.066	15.432	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	893	HIS	0	-0.119	0.062	14.314	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	894	PRO	0	0.022	-0.107	11.966	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	895	ASP	0	0.015	-0.021	9.248	-0.176	-0.176	0.000	0.000	0.000	0.000
50	A	895	ASP	-1	-0.867	-0.791	10.472	0.494	0.494	0.000	0.000	0.000	0.000
51	A	896	VAL	0	0.142	-0.104	9.599	0.109	0.109	0.000	0.000	0.000	0.000
52	A	896	VAL	0	-0.078	0.123	12.191	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	897	VAL	0	0.040	-0.118	7.866	0.011	0.011	0.000	0.000	0.000	0.000
54	A	897	VAL	0	-0.078	0.102	6.001	-0.054	-0.054	0.000	0.000	0.000	0.000
55	A	898	SER	0	0.087	-0.074	4.977	-0.779	-0.766	-0.002	-0.005	-0.007	0.000
56	A	898	SER	0	0.007	0.097	5.049	0.621	0.677	-0.001	-0.004	-0.050	0.000
57	A	899	TYR	0	0.058	-0.096	5.977	0.198	0.207	-0.002	0.000	-0.007	0.000
58	A	899	TYR	0	-0.067	0.116	10.224	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	900	VAL	0	0.087	-0.102	8.799	0.065	0.065	0.000	0.000	0.000	0.000
60	A	900	VAL	0	-0.076	0.106	9.333	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	901	SER	0	0.056	-0.078	5.055	0.109	0.120	-0.002	-0.002	-0.007	0.000
62	A	901	SER	0	0.001	0.070	4.310	-0.957	-0.888	-0.001	-0.021	-0.047	0.000
63	A	902	HIS	0	0.053	-0.077	6.384	-0.205	-0.205	0.000	0.000	0.000	0.000
64	A	902	HIS	0	-0.069	0.105	6.324	0.118	0.118	0.000	0.000	0.000	0.000
65	A	903	ALA	0	0.122	-0.095	6.939	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	903	ALA	0	-0.078	0.109	11.126	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	904	THR	0	-0.051	-0.114	9.448	0.085	0.085	0.000	0.000	0.000	0.000
68	A	904	THR	0	-0.033	0.044	8.946	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	905	GLN	0	0.076	-0.080	7.775	-0.093	-0.093	0.000	0.000	0.000	0.000
70	A	905	GLN	0	-0.059	0.105	6.970	0.163	0.163	0.000	0.000	0.000	0.000
71	A	906	GLN	0	0.096	-0.087	9.093	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	906	GLN	0	-0.111	0.087	10.383	0.016	0.016	0.000	0.000	0.000	0.000
73	A	907	ARG	0	0.130	-0.078	12.009	0.024	0.024	0.000	0.000	0.000	0.000
74	A	907	ARG	1	0.782	1.039	13.222	0.228	0.228	0.000	0.000	0.000	0.000
75	A	908	LEU	0	0.058	-0.128	12.751	0.066	0.066	0.000	0.000	0.000	0.000
76	A	908	LEU	0	-0.079	0.099	11.207	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	909	GLN	0	0.081	-0.100	12.772	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	909	GLN	0	-0.084	0.087	12.163	0.029	0.029	0.000	0.000	0.000	0.000
79	A	910	ASN	0	0.168	-0.009	14.005	0.018	0.018	0.000	0.000	0.000	0.000
80	A	910	ASN	0	-0.139	0.039	17.136	0.024	0.024	0.000	0.000	0.000	0.000
81	A	911	LEU	0	0.024	-0.093	17.064	0.029	0.029	0.000	0.000	0.000	0.000
82	A	911	LEU	0	-0.096	0.060	17.195	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	912	VAL	0	0.126	-0.071	17.152	0.024	0.024	0.000	0.000	0.000	0.000
84	A	912	VAL	0	-0.084	0.099	15.761	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	913	GLU	0	0.113	-0.101	18.018	0.001	0.001	0.000	0.000	0.000	0.000
86	A	913	GLU	-1	-0.921	-0.803	16.946	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	914	LYS	0	0.080	-0.082	19.767	0.015	0.015	0.000	0.000	0.000	0.000
88	A	914	LYS	1	0.692	0.955	21.374	0.045	0.045	0.000	0.000	0.000	0.000
89	A	915	ILE	0	0.048	-0.091	21.596	0.019	0.019	0.000	0.000	0.000	0.000
90	A	915	ILE	0	-0.131	0.054	20.392	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	916	SER	0	-0.027	-0.117	22.149	0.003	0.003	0.000	0.000	0.000	0.000
92	A	916	SER	0	-0.069	0.044	20.991	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	917	GLU	0	-0.130	-0.122	23.642	0.015	0.015	0.000	0.000	0.000	0.000
94	A	917	GLU	-1	-0.785	-0.863	23.600	-0.044	-0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:869:MET)