FMO DATABASE

FMODB ID: 1YNNZ

Calculation Name: 3HM4-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3HM4

Chain ID: B

ChEMBL ID:

UniProt ID: Q316R4

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1295423.831712
FMO2-HF: Nuclear repulsion	1239269.89206
FMO2-HF: Total energy	-56153.939652
FMO2-MP2: Total energy	-56314.003365

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:ILE)

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

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.
35.556	44.531	6.003	-4.12	-10.857	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.917

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	8	ILE	0	0.044	0.015	2.321	1.216	3.274	1.667	-1.250	-2.475	-0.008
4	A	9	ALA	0	0.034	0.015	2.555	3.704	5.157	0.483	-0.565	-1.370	-0.005
5	A	10	LYS	1	0.869	0.920	4.115	51.068	51.369	0.002	-0.056	-0.247	0.000
28	A	33	PRO	0	-0.017	-0.015	2.351	-0.970	0.147	1.254	-0.626	-1.745	-0.003
29	A	34	TYR	0	-0.039	-0.013	2.686	-9.825	-7.787	1.043	-1.272	-1.810	-0.012
30	A	35	VAL	0	0.029	0.012	2.892	0.006	0.599	0.227	0.100	-0.921	-0.002
31	A	36	LYS	1	0.776	0.877	4.630	23.750	23.765	-0.001	-0.008	-0.006	0.000
132	A	137	ILE	0	-0.052	-0.025	2.297	-4.405	-3.359	1.329	-0.410	-1.965	-0.004
133	A	138	ALA	0	0.055	0.026	4.661	3.627	3.656	-0.001	-0.005	-0.022	0.000
134	A	139	ILE	0	-0.040	-0.028	4.835	-6.814	-6.677	-0.001	-0.004	-0.131	0.000
147	A	152	PHE	0	0.010	0.006	3.911	0.275	0.463	0.001	-0.024	-0.165	0.000
6	A	11	PRO	0	0.045	0.039	6.670	3.159	3.159	0.000	0.000	0.000	0.000
7	A	12	PHE	0	0.064	0.028	6.543	2.629	2.629	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.021	0.005	6.884	2.143	2.143	0.000	0.000	0.000	0.000
9	A	14	THR	0	-0.001	0.001	9.687	2.341	2.341	0.000	0.000	0.000	0.000
10	A	15	ALA	0	0.007	0.013	12.430	1.729	1.729	0.000	0.000	0.000	0.000
11	A	16	THR	0	-0.008	-0.026	12.189	1.604	1.604	0.000	0.000	0.000	0.000
12	A	17	THR	0	-0.065	-0.052	12.993	1.402	1.402	0.000	0.000	0.000	0.000
13	A	18	ASN	0	-0.006	-0.010	15.443	1.536	1.536	0.000	0.000	0.000	0.000
14	A	19	VAL	0	-0.004	0.021	17.604	1.049	1.049	0.000	0.000	0.000	0.000
15	A	20	LEU	0	0.016	0.007	16.879	0.713	0.713	0.000	0.000	0.000	0.000
16	A	21	SER	0	-0.034	-0.004	19.636	0.946	0.946	0.000	0.000	0.000	0.000
17	A	22	THR	0	-0.068	-0.069	21.476	0.769	0.769	0.000	0.000	0.000	0.000
18	A	23	MET	0	0.002	0.012	23.092	0.528	0.528	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.011	0.003	23.122	0.442	0.442	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.015	0.022	24.765	0.251	0.251	0.000	0.000	0.000	0.000
21	A	26	ILE	0	-0.056	-0.025	20.236	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	27	GLN	0	0.005	-0.005	19.565	-0.634	-0.634	0.000	0.000	0.000	0.000
23	A	28	PRO	0	-0.050	-0.018	15.012	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	29	ILE	0	0.017	0.004	13.983	-0.862	-0.862	0.000	0.000	0.000	0.000
25	A	30	PRO	0	-0.020	-0.001	9.145	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	31	GLY	0	0.009	0.005	10.029	0.643	0.643	0.000	0.000	0.000	0.000
27	A	32	GLN	0	-0.027	-0.026	4.875	0.244	0.244	0.000	0.000	0.000	0.000
32	A	37	LYS	1	0.868	0.916	7.165	26.400	26.400	0.000	0.000	0.000	0.000
33	A	38	ASN	0	0.043	0.029	11.265	0.095	0.095	0.000	0.000	0.000	0.000
34	A	39	ASN	0	0.046	0.016	13.006	-1.169	-1.169	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.008	0.022	15.392	0.340	0.340	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.009	0.035	13.409	-0.970	-0.970	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.915	0.948	15.168	13.230	13.230	0.000	0.000	0.000	0.000
38	A	43	GLY	0	0.017	0.011	17.838	-0.680	-0.680	0.000	0.000	0.000	0.000
39	A	44	ASP	-1	-0.828	-0.902	20.140	-11.777	-11.777	0.000	0.000	0.000	0.000
40	A	45	VAL	0	0.008	-0.006	21.882	0.497	0.497	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.017	-0.014	18.513	-1.050	-1.050	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.001	0.019	18.468	0.789	0.789	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.012	-0.011	16.478	-1.077	-1.077	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.024	0.010	16.254	0.833	0.833	0.000	0.000	0.000	0.000
45	A	50	GLY	0	0.029	0.034	16.175	-0.963	-0.963	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.041	-0.031	11.852	0.262	0.262	0.000	0.000	0.000	0.000
47	A	52	THR	0	0.029	0.004	16.525	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.022	0.008	17.475	-0.156	-0.156	0.000	0.000	0.000	0.000
49	A	54	HIS	0	-0.023	0.001	12.179	0.981	0.981	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.857	0.926	10.934	20.131	20.131	0.000	0.000	0.000	0.000
51	A	56	ASN	0	0.019	0.012	14.663	0.651	0.651	0.000	0.000	0.000	0.000
52	A	57	GLY	0	0.027	0.003	12.881	-1.244	-1.244	0.000	0.000	0.000	0.000
53	A	58	SER	0	-0.034	-0.005	12.491	1.344	1.344	0.000	0.000	0.000	0.000
54	A	59	ILE	0	0.018	0.011	11.264	-1.962	-1.962	0.000	0.000	0.000	0.000
55	A	60	SER	0	0.044	0.017	12.580	1.238	1.238	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.027	-0.003	12.998	-1.717	-1.717	0.000	0.000	0.000	0.000
57	A	62	THR	0	0.000	-0.004	14.807	0.843	0.843	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.016	-0.010	15.980	-0.973	-0.973	0.000	0.000	0.000	0.000
59	A	64	THR	0	-0.007	-0.016	18.754	0.724	0.724	0.000	0.000	0.000	0.000
60	A	65	LYS	1	0.861	0.888	21.124	10.296	10.296	0.000	0.000	0.000	0.000
61	A	66	GLN	0	-0.030	-0.010	24.097	0.213	0.213	0.000	0.000	0.000	0.000
62	A	67	CYS	0	0.003	0.015	20.204	-0.038	-0.038	0.000	0.000	0.000	0.000
63	A	68	ALA	0	0.019	0.007	22.470	0.018	0.018	0.000	0.000	0.000	0.000
64	A	69	ILE	0	0.022	0.002	23.395	0.219	0.219	0.000	0.000	0.000	0.000
65	A	70	ALA	0	-0.006	0.010	24.710	0.284	0.284	0.000	0.000	0.000	0.000
66	A	71	VAL	0	0.006	-0.004	21.335	0.101	0.101	0.000	0.000	0.000	0.000
67	A	72	VAL	0	-0.013	0.002	24.784	0.177	0.177	0.000	0.000	0.000	0.000
68	A	73	LYS	1	0.864	0.918	27.628	9.787	9.787	0.000	0.000	0.000	0.000
69	A	74	ALA	0	-0.034	-0.001	26.955	0.302	0.302	0.000	0.000	0.000	0.000
70	A	75	MET	0	-0.052	-0.021	25.406	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	76	LEU	0	-0.015	0.004	29.079	0.148	0.148	0.000	0.000	0.000	0.000
72	A	77	GLY	0	-0.012	0.007	32.052	0.319	0.319	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.942	-0.979	33.059	-8.924	-8.924	0.000	0.000	0.000	0.000
74	A	79	ASP	-1	-0.901	-0.920	34.558	-7.870	-7.870	0.000	0.000	0.000	0.000
75	A	80	ILE	0	-0.073	-0.037	31.003	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	81	GLN	0	-0.092	-0.060	35.294	0.323	0.323	0.000	0.000	0.000	0.000
77	A	82	ASP	-1	-0.884	-0.944	35.290	-8.444	-8.444	0.000	0.000	0.000	0.000
78	A	83	ILE	0	0.016	0.009	30.045	-0.253	-0.253	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.030	-0.005	30.805	-0.441	-0.441	0.000	0.000	0.000	0.000
80	A	85	GLN	0	-0.055	-0.045	30.651	-0.263	-0.263	0.000	0.000	0.000	0.000
81	A	86	ASP	-1	-0.718	-0.871	31.210	-9.351	-9.351	0.000	0.000	0.000	0.000
82	A	87	THR	0	-0.043	-0.055	25.855	-0.503	-0.503	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.890	0.940	26.484	9.144	9.144	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.830	-0.897	26.982	-10.122	-10.122	0.000	0.000	0.000	0.000
85	A	90	ALA	0	0.044	0.029	26.806	-0.358	-0.358	0.000	0.000	0.000	0.000
86	A	91	VAL	0	0.020	-0.007	21.172	-0.598	-0.598	0.000	0.000	0.000	0.000
87	A	92	GLY	0	0.029	0.025	22.216	-0.717	-0.717	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.931	-0.961	23.328	-11.756	-11.756	0.000	0.000	0.000	0.000
89	A	94	VAL	0	0.046	0.013	19.267	-0.566	-0.566	0.000	0.000	0.000	0.000
90	A	95	THR	0	-0.038	-0.039	17.738	-1.055	-1.055	0.000	0.000	0.000	0.000
91	A	96	ASN	0	-0.030	-0.030	18.617	-0.690	-0.690	0.000	0.000	0.000	0.000
92	A	97	MET	0	-0.020	0.000	19.951	-0.338	-0.338	0.000	0.000	0.000	0.000
93	A	98	ILE	0	-0.009	0.001	13.976	-0.671	-0.671	0.000	0.000	0.000	0.000
94	A	99	SER	0	0.018	0.010	15.110	-1.081	-1.081	0.000	0.000	0.000	0.000
95	A	100	GLY	0	-0.016	-0.012	16.188	-0.345	-0.345	0.000	0.000	0.000	0.000
96	A	101	GLN	0	0.046	0.020	16.344	-0.905	-0.905	0.000	0.000	0.000	0.000
97	A	102	ALA	0	-0.002	0.006	11.308	-0.768	-0.768	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.842	0.906	12.389	14.924	14.924	0.000	0.000	0.000	0.000
99	A	104	ALA	0	-0.003	0.015	14.552	0.195	0.195	0.000	0.000	0.000	0.000
100	A	105	ALA	0	0.065	0.028	12.188	-0.072	-0.072	0.000	0.000	0.000	0.000
101	A	106	LEU	0	-0.042	-0.037	8.351	-1.101	-1.101	0.000	0.000	0.000	0.000
102	A	107	SER	0	-0.033	0.000	11.889	0.082	0.082	0.000	0.000	0.000	0.000
103	A	108	GLU	-1	-0.942	-0.962	14.899	-17.401	-17.401	0.000	0.000	0.000	0.000
104	A	109	MET	0	-0.106	-0.044	7.341	-0.902	-0.902	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.010	0.003	12.642	-0.731	-0.731	0.000	0.000	0.000	0.000
106	A	111	MET	0	-0.091	-0.041	8.514	0.158	0.158	0.000	0.000	0.000	0.000
107	A	112	THR	0	0.025	0.011	14.095	0.124	0.124	0.000	0.000	0.000	0.000
108	A	113	PHE	0	0.023	-0.003	11.361	-0.134	-0.134	0.000	0.000	0.000	0.000
109	A	114	GLN	0	0.018	0.017	16.621	0.239	0.239	0.000	0.000	0.000	0.000
110	A	115	GLY	0	0.003	-0.014	17.699	-0.924	-0.924	0.000	0.000	0.000	0.000
111	A	116	ALA	0	-0.026	-0.001	19.355	0.657	0.657	0.000	0.000	0.000	0.000
112	A	117	THR	0	0.032	0.007	21.632	-0.186	-0.186	0.000	0.000	0.000	0.000
113	A	118	PRO	0	-0.025	-0.016	20.670	-0.093	-0.093	0.000	0.000	0.000	0.000
114	A	119	SER	0	-0.051	-0.016	21.675	0.798	0.798	0.000	0.000	0.000	0.000
115	A	120	VAL	0	0.003	0.003	21.980	-0.651	-0.651	0.000	0.000	0.000	0.000
116	A	121	ILE	0	-0.037	-0.012	20.773	0.441	0.441	0.000	0.000	0.000	0.000
117	A	122	MET	0	-0.010	-0.005	23.733	-0.248	-0.248	0.000	0.000	0.000	0.000
118	A	123	GLY	0	0.037	0.020	26.058	0.324	0.324	0.000	0.000	0.000	0.000
119	A	124	ASP	-1	-0.834	-0.887	25.309	-10.761	-10.761	0.000	0.000	0.000	0.000
120	A	125	GLY	0	-0.052	-0.027	23.176	0.181	0.181	0.000	0.000	0.000	0.000
121	A	126	HIS	0	0.002	0.019	21.465	-0.422	-0.422	0.000	0.000	0.000	0.000
122	A	127	THR	0	-0.012	-0.030	19.670	-0.381	-0.381	0.000	0.000	0.000	0.000
123	A	128	ILE	0	0.027	0.022	15.981	0.437	0.437	0.000	0.000	0.000	0.000
124	A	129	SER	0	0.009	-0.025	15.971	-0.447	-0.447	0.000	0.000	0.000	0.000
125	A	130	HIS	0	-0.012	-0.008	12.562	0.679	0.679	0.000	0.000	0.000	0.000
126	A	131	VAL	0	-0.007	-0.005	14.844	-0.082	-0.082	0.000	0.000	0.000	0.000
127	A	132	THR	0	-0.003	-0.026	11.788	-0.508	-0.508	0.000	0.000	0.000	0.000
128	A	133	LYS	1	0.856	0.926	14.489	16.797	16.797	0.000	0.000	0.000	0.000
129	A	134	SER	0	-0.040	-0.029	9.811	0.239	0.239	0.000	0.000	0.000	0.000
130	A	135	PRO	0	-0.037	-0.028	6.279	0.206	0.206	0.000	0.000	0.000	0.000
131	A	136	VAL	0	0.011	0.022	7.584	-1.028	-1.028	0.000	0.000	0.000	0.000
135	A	140	PRO	0	0.004	0.027	7.084	2.871	2.871	0.000	0.000	0.000	0.000
136	A	141	PHE	0	0.041	-0.001	10.329	-1.904	-1.904	0.000	0.000	0.000	0.000
137	A	142	LYS	1	0.954	0.983	13.284	19.754	19.754	0.000	0.000	0.000	0.000
138	A	143	THR	0	0.036	0.003	16.659	-0.049	-0.049	0.000	0.000	0.000	0.000
139	A	144	ASN	0	-0.018	-0.020	19.951	-0.173	-0.173	0.000	0.000	0.000	0.000
140	A	145	HIS	0	0.049	0.039	22.641	0.626	0.626	0.000	0.000	0.000	0.000
141	A	146	GLY	0	0.021	0.016	21.300	0.125	0.125	0.000	0.000	0.000	0.000
142	A	147	GLU	-1	-0.932	-0.962	16.170	-17.830	-17.830	0.000	0.000	0.000	0.000
143	A	148	PHE	0	0.042	0.019	14.292	0.779	0.779	0.000	0.000	0.000	0.000
144	A	149	THR	0	-0.043	-0.024	9.831	-1.563	-1.563	0.000	0.000	0.000	0.000
145	A	150	VAL	0	0.010	0.025	10.037	1.354	1.354	0.000	0.000	0.000	0.000
146	A	151	GLU	-1	-0.831	-0.916	8.595	-24.491	-24.491	0.000	0.000	0.000	0.000
148	A	153	CYS	0	-0.058	-0.016	7.951	-1.461	-1.461	0.000	0.000	0.000	0.000
149	A	154	LEU	0	0.045	0.011	7.336	0.587	0.587	0.000	0.000	0.000	0.000
150	A	155	GLU	-2	-1.658	-1.778	10.401	-35.383	-35.383	0.000	0.000	0.000	0.000

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