FMO DATABASE

FMODB ID: 8KMYY

Calculation Name: 1LM8-V-Xray549

Preferred Name:

Target Type:

Ligand Name: 4-hydroxyproline

Ligand 3-letter code: HYP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LM8

Chain ID: V

ChEMBL ID:

UniProt ID: Q15370

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-1427523.110516
FMO2-HF: Nuclear repulsion	1367417.676225
FMO2-HF: Total energy	-60105.434291
FMO2-MP2: Total energy	-60284.40178

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(V:60:ARG)

Summations of interaction energy for fragment #1(V:60:ARG)

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.
-159.227	-153.814	23.207	-12.249	-16.369	-0.117

Interaction energy analysis for fragmet #1(V:60:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.816 / q_NPA : 1.903

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	V	62	VAL	0	-0.011	0.006	2.149	8.388	11.290	3.981	-1.848	-5.035	-0.003
4	V	63	LEU	0	-0.023	-0.008	3.129	14.442	15.394	0.021	-0.191	-0.781	-0.001
5	V	64	ARG	1	0.879	0.940	3.285	54.808	55.774	0.009	-0.556	-0.419	-0.004
33	V	92	ASP	-1	-0.836	-0.896	4.417	-65.940	-65.674	-0.001	-0.136	-0.128	-0.001
34	V	93	GLY	0	-0.051	-0.039	2.015	-47.137	-43.080	5.108	-5.401	-3.764	-0.076
35	V	94	GLU	-1	-0.889	-0.920	3.107	-73.331	-72.108	0.099	-0.434	-0.888	-0.008
143	V	202	THR	0	-0.095	-0.070	1.977	-14.370	-19.835	11.528	-2.586	-3.477	-0.012
144	V	203	GLN	0	-0.041	-0.024	4.083	-3.172	-2.912	0.000	-0.094	-0.165	-0.001
147	V	206	ILE	0	-0.039	-0.024	1.901	-6.849	-6.609	2.463	-1.002	-1.701	-0.011
148	V	207	ALA	0	-0.028	-0.007	5.378	4.362	4.374	-0.001	-0.001	-0.011	0.000
6	V	65	SER	0	0.017	0.011	5.573	7.980	7.980	0.000	0.000	0.000	0.000
7	V	66	VAL	0	-0.024	-0.017	8.947	-2.489	-2.489	0.000	0.000	0.000	0.000
8	V	67	ASN	0	0.032	0.007	11.599	3.319	3.319	0.000	0.000	0.000	0.000
9	V	68	SER	0	-0.035	-0.036	13.891	1.850	1.850	0.000	0.000	0.000	0.000
10	V	69	ARG	1	0.879	0.944	17.064	32.580	32.580	0.000	0.000	0.000	0.000
11	V	70	GLU	-1	-0.754	-0.842	19.221	-28.539	-28.539	0.000	0.000	0.000	0.000
12	V	71	PRO	0	-0.001	-0.002	20.223	-1.255	-1.255	0.000	0.000	0.000	0.000
13	V	72	SER	0	-0.033	-0.030	20.164	0.626	0.626	0.000	0.000	0.000	0.000
14	V	73	GLN	0	-0.011	-0.004	21.801	0.198	0.198	0.000	0.000	0.000	0.000
15	V	74	VAL	0	0.044	0.024	19.468	-0.168	-0.168	0.000	0.000	0.000	0.000
16	V	75	ILE	0	-0.012	-0.012	22.851	0.862	0.862	0.000	0.000	0.000	0.000
17	V	76	PHE	0	0.028	0.022	17.557	-0.378	-0.378	0.000	0.000	0.000	0.000
18	V	77	CYS	0	-0.022	-0.017	23.044	1.431	1.431	0.000	0.000	0.000	0.000
19	V	78	ASN	0	-0.011	0.011	24.766	-0.886	-0.886	0.000	0.000	0.000	0.000
20	V	79	ARG	1	0.891	0.938	25.687	21.999	21.999	0.000	0.000	0.000	0.000
21	V	80	SER	0	0.041	0.005	25.213	-0.186	-0.186	0.000	0.000	0.000	0.000
22	V	81	PRO	0	-0.004	-0.010	27.281	0.271	0.271	0.000	0.000	0.000	0.000
23	V	82	ARG	1	0.811	0.890	24.231	24.446	24.446	0.000	0.000	0.000	0.000
24	V	83	VAL	0	0.013	0.010	24.062	0.267	0.267	0.000	0.000	0.000	0.000
25	V	84	VAL	0	0.005	0.012	19.977	-0.879	-0.879	0.000	0.000	0.000	0.000
26	V	85	LEU	0	0.035	0.011	16.525	0.943	0.943	0.000	0.000	0.000	0.000
27	V	86	PRO	0	-0.055	-0.020	16.555	-1.364	-1.364	0.000	0.000	0.000	0.000
28	V	87	VAL	0	0.010	0.006	10.448	0.311	0.311	0.000	0.000	0.000	0.000
29	V	88	TRP	0	-0.020	0.003	11.463	-1.297	-1.297	0.000	0.000	0.000	0.000
30	V	89	LEU	0	0.026	0.011	5.743	-1.851	-1.851	0.000	0.000	0.000	0.000
31	V	90	ASN	0	0.031	0.027	6.018	-5.737	-5.737	0.000	0.000	0.000	0.000
32	V	91	PHE	0	-0.017	-0.023	6.486	-5.879	-5.879	0.000	0.000	0.000	0.000
36	V	95	PRO	0	-0.020	-0.013	5.495	5.408	5.408	0.000	0.000	0.000	0.000
37	V	96	GLN	0	0.022	0.003	8.502	1.153	1.153	0.000	0.000	0.000	0.000
38	V	97	PRO	0	0.010	0.011	11.703	0.678	0.678	0.000	0.000	0.000	0.000
39	V	98	TYR	0	0.014	-0.006	14.345	1.817	1.817	0.000	0.000	0.000	0.000
40	V	99	PRO	0	-0.006	-0.011	17.651	0.523	0.523	0.000	0.000	0.000	0.000
41	V	100	THR	0	0.043	0.023	21.240	-0.041	-0.041	0.000	0.000	0.000	0.000
42	V	101	LEU	0	-0.035	-0.005	22.113	0.798	0.798	0.000	0.000	0.000	0.000
43	V	102	PRO	0	0.029	0.019	24.865	-0.336	-0.336	0.000	0.000	0.000	0.000
44	V	103	PRO	0	0.052	0.032	27.894	-0.248	-0.248	0.000	0.000	0.000	0.000
45	V	104	GLY	0	0.011	0.016	29.126	0.609	0.609	0.000	0.000	0.000	0.000
46	V	105	THR	0	-0.060	-0.028	28.025	0.254	0.254	0.000	0.000	0.000	0.000
47	V	106	GLY	0	0.048	0.005	26.880	-0.697	-0.697	0.000	0.000	0.000	0.000
48	V	107	ARG	1	0.813	0.897	23.224	24.008	24.008	0.000	0.000	0.000	0.000
49	V	108	ARG	1	0.909	0.955	24.874	19.959	19.959	0.000	0.000	0.000	0.000
50	V	109	ILE	0	-0.024	-0.010	19.415	0.097	0.097	0.000	0.000	0.000	0.000
51	V	110	HIS	0	0.035	0.030	22.282	0.043	0.043	0.000	0.000	0.000	0.000
52	V	111	SER	0	0.028	0.005	16.553	-1.613	-1.613	0.000	0.000	0.000	0.000
53	V	112	TYR	0	0.046	0.016	16.446	1.530	1.530	0.000	0.000	0.000	0.000
54	V	113	ARG	1	0.841	0.898	16.518	31.214	31.214	0.000	0.000	0.000	0.000
55	V	114	GLY	0	0.002	0.009	14.274	-0.881	-0.881	0.000	0.000	0.000	0.000
56	V	115	HIS	0	-0.034	-0.019	11.863	-2.976	-2.976	0.000	0.000	0.000	0.000
57	V	116	LEU	0	0.011	-0.004	7.764	1.929	1.929	0.000	0.000	0.000	0.000
58	V	117	TRP	0	-0.040	-0.010	10.547	-0.504	-0.504	0.000	0.000	0.000	0.000
59	V	118	LEU	0	0.056	0.036	9.348	-0.227	-0.227	0.000	0.000	0.000	0.000
60	V	119	PHE	0	0.022	-0.003	12.928	1.278	1.278	0.000	0.000	0.000	0.000
61	V	120	ARG	1	0.764	0.872	14.041	38.001	38.001	0.000	0.000	0.000	0.000
62	V	121	ASP	-1	-0.784	-0.870	17.538	-23.828	-23.828	0.000	0.000	0.000	0.000
63	V	122	ALA	0	-0.011	-0.031	19.706	-1.157	-1.157	0.000	0.000	0.000	0.000
64	V	123	GLY	0	-0.029	-0.001	21.237	-0.155	-0.155	0.000	0.000	0.000	0.000
65	V	124	THR	0	-0.008	-0.035	22.382	-0.134	-0.134	0.000	0.000	0.000	0.000
66	V	125	HIS	0	-0.053	-0.028	16.141	-1.767	-1.767	0.000	0.000	0.000	0.000
67	V	126	ASP	-1	-0.747	-0.851	17.842	-27.371	-27.371	0.000	0.000	0.000	0.000
68	V	127	GLY	0	0.042	0.019	17.462	-0.638	-0.638	0.000	0.000	0.000	0.000
69	V	128	LEU	0	-0.059	-0.030	17.861	2.176	2.176	0.000	0.000	0.000	0.000
70	V	129	LEU	0	0.041	0.037	17.748	-1.862	-1.862	0.000	0.000	0.000	0.000
71	V	130	VAL	0	-0.017	-0.018	16.485	1.670	1.670	0.000	0.000	0.000	0.000
72	V	131	ASN	0	-0.020	-0.022	19.372	0.100	0.100	0.000	0.000	0.000	0.000
73	V	132	GLN	0	0.008	0.001	21.659	-0.376	-0.376	0.000	0.000	0.000	0.000
74	V	133	THR	0	0.002	0.017	16.639	-0.925	-0.925	0.000	0.000	0.000	0.000
75	V	134	GLU	-1	-0.799	-0.890	12.725	-38.510	-38.510	0.000	0.000	0.000	0.000
76	V	135	LEU	0	-0.035	-0.017	9.401	-1.175	-1.175	0.000	0.000	0.000	0.000
77	V	136	PHE	0	-0.026	-0.020	13.543	2.208	2.208	0.000	0.000	0.000	0.000
78	V	137	VAL	0	0.014	-0.004	12.676	-2.582	-2.582	0.000	0.000	0.000	0.000
79	V	138	PRO	0	-0.048	0.004	15.174	1.893	1.893	0.000	0.000	0.000	0.000
80	V	139	SER	0	0.058	0.027	17.778	-1.218	-1.218	0.000	0.000	0.000	0.000
81	V	140	LEU	0	0.037	0.012	20.503	0.005	0.005	0.000	0.000	0.000	0.000
82	V	141	ASN	0	-0.044	-0.019	23.451	-0.002	-0.002	0.000	0.000	0.000	0.000
83	V	142	VAL	0	0.047	0.031	26.364	0.352	0.352	0.000	0.000	0.000	0.000
84	V	143	ASP	-1	-0.880	-0.943	29.301	-18.437	-18.437	0.000	0.000	0.000	0.000
85	V	144	GLY	0	-0.022	-0.006	30.098	0.424	0.424	0.000	0.000	0.000	0.000
86	V	145	GLN	0	-0.011	-0.004	29.727	-0.199	-0.199	0.000	0.000	0.000	0.000
87	V	146	PRO	0	-0.052	-0.018	26.247	-0.890	-0.890	0.000	0.000	0.000	0.000
88	V	147	ILE	0	-0.008	-0.007	21.196	0.198	0.198	0.000	0.000	0.000	0.000
89	V	148	PHE	0	0.016	-0.004	23.177	-0.365	-0.365	0.000	0.000	0.000	0.000
90	V	149	ALA	0	0.010	0.020	19.712	-0.759	-0.759	0.000	0.000	0.000	0.000
91	V	150	ASN	0	-0.017	-0.022	21.603	1.376	1.376	0.000	0.000	0.000	0.000
92	V	151	ILE	0	0.006	0.005	20.134	-0.562	-0.562	0.000	0.000	0.000	0.000
93	V	152	THR	0	-0.032	-0.017	22.258	1.371	1.371	0.000	0.000	0.000	0.000
94	V	153	LEU	0	0.018	0.000	22.615	-0.946	-0.946	0.000	0.000	0.000	0.000
95	V	154	PRO	0	0.018	0.031	21.180	0.402	0.402	0.000	0.000	0.000	0.000
96	V	155	VAL	0	-0.006	-0.010	23.651	0.833	0.833	0.000	0.000	0.000	0.000
97	V	156	TYR	0	-0.015	-0.016	21.942	-0.053	-0.053	0.000	0.000	0.000	0.000
98	V	157	THR	0	0.055	0.026	24.074	1.175	1.175	0.000	0.000	0.000	0.000
99	V	158	LEU	0	0.052	0.018	26.750	-0.038	-0.038	0.000	0.000	0.000	0.000
100	V	159	LYS	1	0.859	0.929	25.905	23.325	23.325	0.000	0.000	0.000	0.000
101	V	160	GLU	-1	-0.768	-0.873	23.183	-26.047	-26.047	0.000	0.000	0.000	0.000
102	V	161	ARG	1	0.891	0.939	26.392	21.119	21.119	0.000	0.000	0.000	0.000
103	V	162	CYS	0	-0.022	-0.020	28.817	0.642	0.642	0.000	0.000	0.000	0.000
104	V	163	LEU	0	-0.011	0.001	25.668	0.415	0.415	0.000	0.000	0.000	0.000
105	V	164	GLN	0	-0.005	0.003	23.628	1.201	1.201	0.000	0.000	0.000	0.000
106	V	165	VAL	0	-0.016	0.004	27.437	0.238	0.238	0.000	0.000	0.000	0.000
107	V	166	VAL	0	0.021	0.017	30.889	0.366	0.366	0.000	0.000	0.000	0.000
108	V	167	ARG	1	0.812	0.876	23.632	25.912	25.912	0.000	0.000	0.000	0.000
109	V	168	SER	0	-0.085	-0.040	28.378	0.107	0.107	0.000	0.000	0.000	0.000
110	V	169	LEU	0	-0.047	-0.015	29.704	0.505	0.505	0.000	0.000	0.000	0.000
111	V	170	VAL	0	-0.069	-0.031	31.983	0.548	0.548	0.000	0.000	0.000	0.000
112	V	171	LYS	1	0.961	0.987	30.313	17.775	17.775	0.000	0.000	0.000	0.000
113	V	172	PRO	0	0.097	0.036	26.367	0.386	0.386	0.000	0.000	0.000	0.000
114	V	173	GLU	-1	-0.870	-0.936	28.801	-19.379	-19.379	0.000	0.000	0.000	0.000
115	V	174	ASN	0	-0.048	-0.028	31.557	0.872	0.872	0.000	0.000	0.000	0.000
116	V	175	TYR	0	0.063	0.041	25.663	0.640	0.640	0.000	0.000	0.000	0.000
117	V	176	ARG	1	0.733	0.820	28.554	21.244	21.244	0.000	0.000	0.000	0.000
118	V	177	ARG	1	0.858	0.918	33.870	17.322	17.322	0.000	0.000	0.000	0.000
119	V	178	LEU	0	-0.016	0.009	33.525	0.423	0.423	0.000	0.000	0.000	0.000
120	V	179	ASP	-1	-0.907	-0.934	37.210	-15.367	-15.367	0.000	0.000	0.000	0.000
121	V	180	ILE	0	-0.022	-0.013	32.979	-0.043	-0.043	0.000	0.000	0.000	0.000
122	V	181	VAL	0	0.015	0.009	33.174	0.029	0.029	0.000	0.000	0.000	0.000
123	V	182	ARG	1	0.907	0.923	30.490	18.965	18.965	0.000	0.000	0.000	0.000
124	V	183	SER	0	0.033	0.022	28.759	-0.124	-0.124	0.000	0.000	0.000	0.000
125	V	184	LEU	0	-0.007	-0.008	28.500	-0.754	-0.754	0.000	0.000	0.000	0.000
126	V	185	TYR	0	-0.042	-0.031	29.289	-0.425	-0.425	0.000	0.000	0.000	0.000
127	V	186	GLU	-1	-0.704	-0.834	25.534	-21.972	-21.972	0.000	0.000	0.000	0.000
128	V	187	ASP	-1	-0.820	-0.896	24.575	-24.505	-24.505	0.000	0.000	0.000	0.000
129	V	188	LEU	0	-0.037	-0.016	24.776	-0.639	-0.639	0.000	0.000	0.000	0.000
130	V	189	GLU	-1	-0.864	-0.916	24.176	-22.958	-22.958	0.000	0.000	0.000	0.000
131	V	190	ASP	-1	-0.891	-0.923	18.763	-33.790	-33.790	0.000	0.000	0.000	0.000
132	V	191	HIS	0	-0.073	-0.036	17.598	0.334	0.334	0.000	0.000	0.000	0.000
133	V	192	PRO	0	0.011	0.010	17.521	-1.628	-1.628	0.000	0.000	0.000	0.000
134	V	193	ASN	0	0.026	-0.001	12.425	-2.238	-2.238	0.000	0.000	0.000	0.000
135	V	194	VAL	0	0.058	0.019	9.363	-1.747	-1.747	0.000	0.000	0.000	0.000
136	V	195	GLN	0	0.043	0.021	6.569	-9.623	-9.623	0.000	0.000	0.000	0.000
137	V	196	LYS	1	0.926	0.963	8.503	32.461	32.461	0.000	0.000	0.000	0.000
138	V	197	ASP	-1	-0.870	-0.923	10.694	-43.598	-43.598	0.000	0.000	0.000	0.000
139	V	198	LEU	0	-0.016	-0.010	5.198	-1.963	-1.963	0.000	0.000	0.000	0.000
140	V	199	GLU	-1	-0.943	-0.957	5.830	-70.686	-70.686	0.000	0.000	0.000	0.000
141	V	200	ARG	1	0.855	0.918	6.327	41.080	41.080	0.000	0.000	0.000	0.000
142	V	201	LEU	0	0.020	0.010	8.103	-0.542	-0.542	0.000	0.000	0.000	0.000
145	V	204	GLU	-1	-0.807	-0.895	6.065	-44.353	-44.353	0.000	0.000	0.000	0.000
146	V	205	ARG	1	0.879	0.952	5.600	67.186	67.186	0.000	0.000	0.000	0.000
149	V	208	HIS	0	-0.041	-0.030	8.255	3.908	3.908	0.000	0.000	0.000	0.000
150	V	209	GLN	-1	-0.960	-0.954	8.579	-43.235	-43.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(V:60:ARG)