FMO DATABASE

FMODB ID: RLQ78

Calculation Name: 2GMY-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GMY

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D1C9

Base Structure: X-ray

Registration Date: 2025-10-05

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1383155.931509
FMO2-HF: Nuclear repulsion	1325030.502331
FMO2-HF: Total energy	-58125.429178
FMO2-MP2: Total energy	-58295.181913

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:2:LYS)

Summations of interaction energy for fragment #1(A:2: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.
-70.825	-65.536	10.239	-8.328	-7.199	-0.107

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.762 / q_NPA : 1.869

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	4	ARG	1	0.828	0.918	2.540	49.371	52.935	1.222	-2.072	-2.713	-0.023
4	A	5	ILE	0	0.061	0.022	5.209	0.461	0.586	-0.001	-0.005	-0.119	0.000
140	A	141	ARG	1	0.880	0.932	4.024	54.154	54.297	-0.001	-0.032	-0.110	0.000
141	A	142	SER	0	0.020	0.008	4.478	-14.243	-14.257	-0.001	-0.025	0.040	0.000
142	A	143	GLN	0	-0.018	-0.012	1.831	-44.009	-42.538	9.020	-6.194	-4.297	-0.084
5	A	6	ASN	0	0.006	0.004	7.512	3.639	3.639	0.000	0.000	0.000	0.000
6	A	7	TYR	0	0.069	0.023	9.312	4.499	4.499	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.034	0.027	12.527	2.537	2.537	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.906	0.948	11.939	42.218	42.218	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.010	0.000	11.756	1.624	1.624	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.009	-0.001	13.812	2.319	2.319	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.026	0.012	17.119	0.301	0.301	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.846	-0.909	18.988	-24.312	-24.312	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.022	0.008	18.819	0.735	0.735	0.000	0.000	0.000	0.000
14	A	15	PHE	0	-0.005	-0.012	16.957	-0.085	-0.085	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.900	0.939	19.201	26.039	26.039	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.019	0.019	22.776	0.821	0.821	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.000	0.000	19.623	0.695	0.695	0.000	0.000	0.000	0.000
18	A	19	MET	0	0.006	-0.001	20.427	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.023	0.002	22.909	0.854	0.854	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.001	0.008	24.247	0.804	0.804	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.808	-0.885	21.729	-25.912	-25.912	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.004	-0.010	24.511	0.601	0.601	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.013	0.026	27.327	0.673	0.673	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.022	0.003	25.932	0.569	0.569	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.013	0.010	25.547	0.199	0.199	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.044	-0.032	28.463	0.631	0.631	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.046	-0.024	31.076	0.819	0.819	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.012	-0.004	33.380	0.548	0.548	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.031	-0.003	30.865	0.371	0.371	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.811	-0.886	32.960	-17.075	-17.075	0.000	0.000	0.000	0.000
31	A	32	HIS	0	0.064	0.017	29.036	-0.637	-0.637	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.845	0.929	28.496	16.816	16.816	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.043	0.005	28.798	-0.579	-0.579	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.002	0.012	25.560	-0.619	-0.619	0.000	0.000	0.000	0.000
35	A	36	HIS	0	-0.038	-0.043	24.267	-1.583	-1.583	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.008	0.005	23.918	-1.018	-1.018	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.000	-0.002	24.519	-0.747	-0.747	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.811	0.888	20.970	24.647	24.647	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.004	0.009	19.122	-1.871	-1.871	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.822	0.885	20.051	22.051	22.051	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.043	0.017	21.214	-0.560	-0.560	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.014	-0.032	16.075	-1.758	-1.758	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.027	-0.009	16.284	-1.924	-1.924	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.031	0.001	18.062	-0.651	-0.651	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.080	-0.055	16.518	-0.219	-0.219	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.015	0.011	14.468	-2.252	-2.252	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.111	-0.017	11.845	-3.914	-3.914	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.072	0.024	9.392	0.995	0.995	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.031	-0.028	8.736	0.991	0.991	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.009	-0.001	10.544	1.726	1.726	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.033	0.021	13.942	2.136	2.136	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.807	-0.894	12.703	-36.103	-36.103	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.001	0.003	14.268	2.268	2.268	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.833	0.884	16.241	31.739	31.739	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.003	0.023	17.967	1.653	1.653	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.756	0.871	14.396	36.896	36.896	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.833	-0.898	20.163	-26.644	-26.644	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.002	-0.019	22.425	1.244	1.244	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.832	0.874	20.378	25.880	25.880	0.000	0.000	0.000	0.000
60	A	61	HIS	0	-0.066	-0.011	24.493	0.324	0.324	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.853	-0.915	26.225	-20.207	-20.207	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.021	-0.008	28.623	0.623	0.623	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.042	-0.010	27.157	0.558	0.558	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.037	0.008	27.778	-0.627	-0.627	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.733	-0.846	24.288	-23.677	-23.677	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.027	-0.003	26.215	-0.356	-0.356	0.000	0.000	0.000	0.000
67	A	68	TRP	0	0.009	-0.010	25.449	-0.575	-0.575	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.015	0.023	22.192	-0.522	-0.522	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.065	-0.049	22.084	-1.574	-1.574	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.022	-0.008	23.718	-0.455	-0.455	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.048	0.056	22.970	0.407	0.407	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.031	-0.015	21.486	0.104	0.104	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.014	-0.015	23.208	0.026	0.026	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.012	0.001	26.741	1.036	1.036	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.874	0.942	28.954	19.661	19.661	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.860	-0.925	31.447	-16.556	-16.556	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.043	-0.012	30.513	0.417	0.417	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.006	-0.007	32.635	0.050	0.050	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.067	-0.025	30.393	0.254	0.254	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.063	-0.040	27.166	-0.048	-0.048	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.024	-0.016	33.624	0.458	0.458	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.867	-0.951	35.757	-15.921	-15.921	0.000	0.000	0.000	0.000
83	A	84	GLN	0	0.019	0.021	36.100	-0.193	-0.193	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.801	-0.884	31.927	-18.443	-18.443	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.848	0.918	32.141	16.273	16.273	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.020	0.016	33.394	-0.328	-0.328	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.006	0.005	30.045	-0.324	-0.324	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.006	-0.018	27.225	-0.698	-0.698	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.000	0.005	29.254	-0.514	-0.514	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.019	0.004	31.256	-0.195	-0.195	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.007	-0.008	24.980	-0.510	-0.510	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.761	-0.854	26.327	-22.501	-22.501	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.001	0.017	27.296	-0.474	-0.474	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.042	0.013	27.535	-0.358	-0.358	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.084	-0.059	21.914	-0.822	-0.822	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.837	0.923	23.653	21.615	21.615	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.045	0.030	25.808	0.630	0.630	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.046	-0.030	26.364	0.660	0.660	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.952	-0.970	25.285	-22.806	-22.806	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.047	-0.032	29.155	0.821	0.821	0.000	0.000	0.000	0.000
101	A	102	GLY	0	-0.005	0.003	31.512	0.592	0.592	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.069	-0.034	32.517	0.284	0.284	0.000	0.000	0.000	0.000
103	A	104	PRO	0	0.018	0.008	33.843	0.365	0.365	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.857	-0.926	36.998	-15.058	-15.058	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.858	-0.922	38.773	-15.041	-15.041	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.067	-0.026	34.523	-0.029	-0.029	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.007	-0.001	36.672	-0.083	-0.083	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.964	-0.982	38.087	-13.711	-13.711	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.007	-0.025	37.790	0.186	0.186	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.036	-0.016	34.121	-0.031	-0.031	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.963	0.972	37.704	14.287	14.287	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.053	-0.002	41.006	0.312	0.312	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.074	-0.044	38.615	0.351	0.351	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.034	-0.009	34.733	-0.277	-0.277	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.002	-0.024	39.518	0.208	0.208	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.859	-0.950	39.302	-15.078	-15.078	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.910	-0.949	38.578	-15.946	-15.946	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.824	-0.889	36.316	-16.147	-16.147	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.046	0.021	34.701	-0.715	-0.715	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.013	0.010	33.964	-0.686	-0.686	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.833	0.923	32.595	15.927	15.927	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.036	0.016	30.459	-0.920	-0.920	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.013	-0.015	29.129	-0.886	-0.886	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.027	-0.010	28.594	-0.856	-0.856	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.015	0.007	26.380	-1.030	-1.030	0.000	0.000	0.000	0.000
126	A	127	ILE	0	0.023	0.011	24.649	-1.339	-1.339	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.027	0.021	23.755	-1.204	-1.204	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.012	0.013	23.074	-1.309	-1.309	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.038	-0.009	18.175	-1.859	-1.859	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.039	0.024	18.803	-2.710	-2.710	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.035	-0.009	19.073	-1.394	-1.394	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.019	-0.036	16.357	-3.502	-3.502	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.023	-0.022	14.500	-1.785	-1.785	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.874	0.931	13.609	26.920	26.920	0.000	0.000	0.000	0.000
135	A	136	ILE	0	-0.002	0.009	13.313	-3.113	-3.113	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.001	0.003	10.681	-4.609	-4.609	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.047	0.018	9.012	-7.817	-7.817	0.000	0.000	0.000	0.000
138	A	139	GLY	0	0.019	0.026	9.001	-5.260	-5.260	0.000	0.000	0.000	0.000
139	A	140	PHE	0	-0.003	-0.014	8.754	-4.206	-4.206	0.000	0.000	0.000	0.000
143	A	144	HIS	0	-0.002	0.006	5.759	0.616	0.616	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.010	0.002	8.717	-3.574	-3.574	0.000	0.000	0.000	0.000
145	A	146	VAL	0	-0.009	-0.005	9.314	0.238	0.238	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.867	-0.937	12.137	-34.618	-34.618	0.000	0.000	0.000	0.000
147	A	148	ALA	-1	-0.938	-0.957	15.787	-29.341	-29.341	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:2:LYS)