FMO DATABASE

FMODB ID: RY4R8

Calculation Name: 1HYP-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1HYP

Chain ID: A

ChEMBL ID:

UniProt ID: P24337

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-415786.189396
FMO2-HF: Nuclear repulsion	386766.419606
FMO2-HF: Total energy	-29019.76979
FMO2-MP2: Total energy	-29097.818083

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:6:PRO)

Summations of interaction energy for fragment #1(A:6:PRO)

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.
-5.903	-2.223	0.462	-1.692	-2.45	-0.008

Interaction energy analysis for fragmet #1(A:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.037

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	A	7	SER	0	-0.059	0.055	4.722	0.340	0.593	-0.001	-0.096	-0.156	0.000
4	A	8	CYS	0	0.045	-0.116	3.413	-1.133	0.661	0.015	-0.782	-1.027	0.001
5	A	8	CYS	0	-0.194	0.200	3.333	0.129	0.390	0.022	-0.063	-0.219	0.000
6	A	9	PRO	0	0.060	-0.050	2.766	-3.519	-2.218	0.428	-0.750	-0.979	-0.009
7	A	10	ASP	0	0.130	-0.007	5.301	0.232	0.303	-0.002	-0.001	-0.069	0.000
8	A	10	ASP	-1	-0.878	-0.761	7.640	-1.030	-1.030	0.000	0.000	0.000	0.000
9	A	11	LEU	0	0.037	-0.095	7.420	0.083	0.083	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.078	0.106	8.287	0.055	0.055	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.044	-0.148	10.186	0.168	0.168	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.053	0.051	10.846	0.059	0.059	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.051	-0.108	12.623	0.114	0.114	0.000	0.000	0.000	0.000
14	A	13	ILE	0	-0.064	0.142	12.747	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	14	CYS	0	0.049	-0.143	13.888	0.071	0.071	0.000	0.000	0.000	0.000
16	A	14	CYS	0	-0.233	0.184	13.999	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	15	LEU	0	0.059	-0.093	15.192	0.060	0.060	0.000	0.000	0.000	0.000
18	A	15	LEU	0	-0.067	0.112	13.258	0.009	0.009	0.000	0.000	0.000	0.000
19	A	16	ASN	0	0.113	-0.074	16.824	0.051	0.051	0.000	0.000	0.000	0.000
20	A	16	ASN	0	-0.131	0.054	18.514	0.013	0.013	0.000	0.000	0.000	0.000
21	A	17	ILE	0	0.095	-0.082	19.726	0.034	0.034	0.000	0.000	0.000	0.000
22	A	17	ILE	0	-0.057	0.119	19.707	0.001	0.001	0.000	0.000	0.000	0.000
23	A	18	LEU	0	-0.014	-0.146	20.540	0.030	0.030	0.000	0.000	0.000	0.000
24	A	18	LEU	0	-0.070	0.103	18.787	0.001	0.001	0.000	0.000	0.000	0.000
25	A	19	GLY	0	-0.033	-0.102	22.108	0.025	0.025	0.000	0.000	0.000	0.000
26	A	20	GLY	0	-0.032	-0.023	24.119	0.012	0.012	0.000	0.000	0.000	0.000
27	A	21	SER	0	0.063	0.027	23.762	0.014	0.014	0.000	0.000	0.000	0.000
28	A	21	SER	0	-0.049	0.075	22.775	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	22	LEU	0	0.029	-0.137	22.722	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	22	LEU	0	-0.056	0.116	24.759	0.002	0.002	0.000	0.000	0.000	0.000
31	A	23	GLY	0	-0.028	-0.118	23.747	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	24	THR	0	0.005	0.057	19.447	0.013	0.013	0.000	0.000	0.000	0.000
33	A	24	THR	0	-0.012	0.075	18.361	0.010	0.010	0.000	0.000	0.000	0.000
34	A	25	VAL	0	0.115	-0.090	18.540	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	25	VAL	0	-0.070	0.115	20.842	0.006	0.006	0.000	0.000	0.000	0.000
36	A	26	ASP	0	0.109	-0.106	19.068	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	26	ASP	-1	-0.959	-0.836	21.452	-0.368	-0.368	0.000	0.000	0.000	0.000
38	A	27	ASP	0	0.056	-0.114	17.191	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	27	ASP	-1	-0.939	-0.857	16.368	-0.487	-0.487	0.000	0.000	0.000	0.000
40	A	28	CYS	0	0.104	-0.082	14.481	-0.114	-0.114	0.000	0.000	0.000	0.000
41	A	29	CYS	0	0.113	-0.107	14.646	-0.094	-0.094	0.000	0.000	0.000	0.000
42	A	29	CYS	0	-0.231	0.204	18.826	0.007	0.007	0.000	0.000	0.000	0.000
43	A	30	ALA	0	0.124	-0.084	16.414	0.002	0.002	0.000	0.000	0.000	0.000
44	A	30	ALA	0	-0.079	0.108	16.392	0.004	0.004	0.000	0.000	0.000	0.000
45	A	31	LEU	0	0.020	-0.114	11.825	0.002	0.002	0.000	0.000	0.000	0.000
46	A	31	LEU	0	-0.087	0.086	10.312	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	32	ILE	0	0.022	-0.097	11.783	-0.144	-0.144	0.000	0.000	0.000	0.000
48	A	32	ILE	0	-0.088	0.070	11.625	0.011	0.011	0.000	0.000	0.000	0.000
49	A	33	GLY	0	-0.012	-0.112	12.989	0.041	0.041	0.000	0.000	0.000	0.000
50	A	34	GLY	0	-0.005	-0.002	12.923	0.083	0.083	0.000	0.000	0.000	0.000
51	A	35	LEU	0	0.008	0.002	10.832	-0.096	-0.096	0.000	0.000	0.000	0.000
52	A	35	LEU	0	-0.089	0.083	7.624	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	36	GLY	0	0.012	-0.100	11.646	0.155	0.155	0.000	0.000	0.000	0.000
54	A	37	ASP	0	0.147	0.028	13.057	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	37	ASP	-1	-1.012	-0.878	17.135	-0.252	-0.252	0.000	0.000	0.000	0.000
56	A	38	ILE	0	0.104	-0.111	14.428	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	38	ILE	0	-0.078	0.097	13.736	0.010	0.010	0.000	0.000	0.000	0.000
58	A	39	GLU	0	0.075	-0.115	10.266	0.092	0.092	0.000	0.000	0.000	0.000
59	A	39	GLU	-1	-0.897	-0.777	7.673	-1.075	-1.075	0.000	0.000	0.000	0.000
60	A	40	ALA	0	0.130	-0.102	9.685	-0.111	-0.111	0.000	0.000	0.000	0.000
61	A	40	ALA	0	-0.039	0.136	12.432	0.010	0.010	0.000	0.000	0.000	0.000
62	A	41	ILE	0	0.054	-0.093	11.447	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	41	ILE	0	-0.109	0.084	14.288	0.017	0.017	0.000	0.000	0.000	0.000
64	A	42	VAL	0	0.062	-0.117	10.137	0.010	0.010	0.000	0.000	0.000	0.000
65	A	42	VAL	0	-0.082	0.095	8.209	0.028	0.028	0.000	0.000	0.000	0.000
66	A	43	CYS	0	0.047	-0.135	7.572	0.158	0.158	0.000	0.000	0.000	0.000
67	A	44	LEU	0	0.096	-0.094	8.379	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	44	LEU	0	-0.026	0.113	11.994	0.012	0.012	0.000	0.000	0.000	0.000
69	A	45	CYS	0	0.077	-0.084	11.740	0.032	0.032	0.000	0.000	0.000	0.000
70	A	45	CYS	0	-0.281	0.223	12.329	0.013	0.013	0.000	0.000	0.000	0.000
71	A	46	ILE	0	0.009	-0.101	8.668	0.111	0.111	0.000	0.000	0.000	0.000
72	A	46	ILE	0	-0.059	0.104	6.386	0.042	0.042	0.000	0.000	0.000	0.000
73	A	47	GLN	0	0.133	-0.097	10.053	0.078	0.078	0.000	0.000	0.000	0.000
74	A	47	GLN	0	-0.044	0.106	8.552	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	48	LEU	0	0.101	-0.074	11.301	0.044	0.044	0.000	0.000	0.000	0.000
76	A	48	LEU	0	-0.118	0.076	14.665	0.013	0.013	0.000	0.000	0.000	0.000
77	A	49	ARG	0	0.106	-0.077	13.468	0.023	0.023	0.000	0.000	0.000	0.000
78	A	49	ARG	1	0.707	0.958	12.654	0.068	0.068	0.000	0.000	0.000	0.000
79	A	50	ALA	0	0.089	-0.101	12.194	0.069	0.069	0.000	0.000	0.000	0.000
80	A	50	ALA	0	-0.086	0.113	11.379	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	51	LEU	0	-0.024	-0.129	13.542	0.018	0.018	0.000	0.000	0.000	0.000
82	A	51	LEU	0	-0.058	0.098	15.498	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	52	GLY	0	-0.006	-0.090	16.717	0.019	0.019	0.000	0.000	0.000	0.000
84	A	53	ILE	0	0.049	-0.026	18.116	0.022	0.022	0.000	0.000	0.000	0.000
85	A	53	ILE	0	-0.080	0.111	18.273	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	54	LEU	0	0.105	-0.086	19.395	0.004	0.004	0.000	0.000	0.000	0.000
87	A	54	LEU	0	-0.078	0.103	22.137	0.001	0.001	0.000	0.000	0.000	0.000
88	A	55	ASN	0	0.107	-0.055	21.792	0.008	0.008	0.000	0.000	0.000	0.000
89	A	55	ASN	0	-0.127	0.054	23.811	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	56	LEU	0	0.099	-0.106	18.306	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	56	LEU	0	-0.065	0.105	16.114	0.001	0.001	0.000	0.000	0.000	0.000
92	A	57	ASN	0	0.170	-0.044	19.066	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	57	ASN	0	-0.109	0.075	20.378	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	58	ARG	0	0.177	-0.036	20.873	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	58	ARG	1	0.865	1.050	24.039	0.124	0.124	0.000	0.000	0.000	0.000
96	A	59	ASN	0	0.042	-0.078	20.048	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	59	ASN	0	-0.102	0.044	19.385	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	60	LEU	0	0.175	-0.062	17.351	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	60	LEU	0	-0.076	0.089	15.195	0.003	0.003	0.000	0.000	0.000	0.000
100	A	61	GLN	0	0.061	-0.114	18.195	-0.033	-0.033	0.000	0.000	0.000	0.000
101	A	61	GLN	0	-0.162	0.066	21.516	0.009	0.009	0.000	0.000	0.000	0.000
102	A	62	LEU	0	0.112	-0.096	21.532	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	62	LEU	0	-0.114	0.096	21.772	0.005	0.005	0.000	0.000	0.000	0.000
104	A	63	ILE	0	0.082	-0.086	17.851	0.015	0.015	0.000	0.000	0.000	0.000
105	A	63	ILE	0	-0.065	0.101	15.769	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	64	LEU	0	0.053	-0.064	19.172	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	64	LEU	0	-0.077	0.078	16.210	0.008	0.008	0.000	0.000	0.000	0.000
108	A	65	ASN	0	0.105	-0.070	19.850	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	65	ASN	0	-0.095	0.056	24.075	0.005	0.005	0.000	0.000	0.000	0.000
110	A	66	SER	0	-0.006	-0.084	22.084	0.020	0.020	0.000	0.000	0.000	0.000
111	A	66	SER	0	-0.061	0.043	20.321	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	67	CYS	0	0.061	-0.115	20.710	0.010	0.010	0.000	0.000	0.000	0.000
113	A	68	GLY	0	0.055	-0.078	21.968	0.003	0.003	0.000	0.000	0.000	0.000
114	A	69	ARG	0	0.095	0.002	25.029	0.010	0.010	0.000	0.000	0.000	0.000
115	A	69	ARG	1	0.845	1.070	24.163	0.181	0.181	0.000	0.000	0.000	0.000
116	A	70	SER	0	-0.006	-0.090	26.422	0.003	0.003	0.000	0.000	0.000	0.000
117	A	70	SER	0	-0.009	0.077	30.807	0.000	0.000	0.000	0.000	0.000	0.000
118	A	71	TYR	0	0.083	-0.122	28.535	0.015	0.015	0.000	0.000	0.000	0.000
119	A	71	TYR	0	-0.136	0.069	25.643	0.004	0.004	0.000	0.000	0.000	0.000
120	A	72	PRO	0	-0.029	-0.085	27.002	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	73	SER	0	0.067	0.015	22.790	0.012	0.012	0.000	0.000	0.000	0.000
122	A	73	SER	0	-0.006	0.077	20.893	0.003	0.003	0.000	0.000	0.000	0.000
123	A	74	ASN	0	0.039	-0.055	24.097	0.002	0.002	0.000	0.000	0.000	0.000
124	A	74	ASN	0	-0.058	0.084	25.356	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	75	ALA	0	0.116	-0.095	19.748	0.027	0.027	0.000	0.000	0.000	0.000
126	A	75	ALA	0	-0.023	0.124	18.786	-0.008	-0.008	0.000	0.000	0.000	0.000
127	A	76	THR	0	-0.034	-0.118	19.387	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	76	THR	0	-0.040	0.078	19.950	0.008	0.008	0.000	0.000	0.000	0.000
129	A	77	CYS	0	0.105	-0.128	16.055	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	78	PRO	0	0.036	-0.074	13.515	0.027	0.027	0.000	0.000	0.000	0.000
131	A	79	ARG	0	0.115	0.031	15.651	0.008	0.008	0.000	0.000	0.000	0.000
132	A	79	ARG	1	0.891	1.059	18.008	-0.037	-0.037	0.000	0.000	0.000	0.000
133	A	80	THR	0	-0.081	-0.121	18.256	0.025	0.025	0.000	0.000	0.000	0.000
134	A	80	THR	0	0.105	0.053	20.850	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:6:PRO)