FMO DATABASE

FMODB ID: Z7M4N

Calculation Name: 2KHM-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KHM

Chain ID: A

ChEMBL ID:

UniProt ID: Q16987

Base Structure: SolutionNMR

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	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-818676.761934
FMO2-HF: Nuclear repulsion	770715.577976
FMO2-HF: Total energy	-47961.183958
FMO2-MP2: Total energy	-48096.912294

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
24.119	28.231	0.009	-1.838	-2.281	-0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.857 / q_NPA : 0.907

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	3	SER	0	0.002	0.010	3.046	1.411	5.370	0.010	-1.830	-2.138	-0.009
4	A	4	MET	0	0.039	0.024	4.918	5.589	5.742	-0.001	-0.008	-0.143	0.000
5	A	5	THR	0	-0.003	-0.001	7.070	-2.536	-2.536	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.029	0.018	9.192	0.582	0.582	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.005	0.010	10.010	0.115	0.115	0.000	0.000	0.000	0.000
8	A	8	GLN	0	-0.039	-0.011	10.504	2.275	2.275	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.013	0.005	7.477	-3.291	-3.291	0.000	0.000	0.000	0.000
10	A	10	MET	0	-0.021	-0.023	5.429	3.605	3.605	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.061	0.025	7.032	-3.104	-3.104	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.918	0.960	9.596	19.884	19.884	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.083	0.045	10.522	1.401	1.401	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.081	-0.045	10.779	0.839	0.839	0.000	0.000	0.000	0.000
15	A	15	MET	0	0.004	-0.006	10.378	0.300	0.300	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.002	0.025	7.688	-1.542	-1.542	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.014	-0.004	8.160	2.582	2.582	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.024	0.022	8.856	-2.392	-2.392	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.018	-0.025	7.379	-0.122	-0.122	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.027	-0.009	9.179	-1.785	-1.785	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.039	0.030	11.098	-0.996	-0.996	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.027	0.012	12.809	1.408	1.408	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.025	-0.028	16.074	-0.661	-0.661	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.015	0.003	18.274	0.390	0.390	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.006	0.009	21.340	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.056	0.012	19.000	0.104	0.104	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.041	-0.010	13.698	0.178	0.178	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.006	0.016	17.287	-0.516	-0.516	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.025	-0.014	19.246	-0.519	-0.519	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.025	-0.017	20.958	0.560	0.560	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.032	0.023	16.532	0.532	0.532	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.015	-0.005	19.465	0.658	0.658	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.015	-0.001	17.931	0.180	0.180	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.074	0.027	20.355	0.567	0.567	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.022	0.013	22.018	0.512	0.512	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.036	0.027	23.623	0.525	0.525	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.040	0.017	25.284	0.478	0.478	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.010	-0.008	26.216	0.431	0.431	0.000	0.000	0.000	0.000
39	A	39	ALA	0	0.009	0.019	28.686	0.458	0.458	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.004	0.004	30.060	0.386	0.386	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.020	-0.001	31.050	0.353	0.353	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.035	-0.035	32.414	0.346	0.346	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.775	0.865	31.323	10.047	10.047	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.003	0.010	34.715	0.264	0.264	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.011	-0.003	37.206	0.204	0.204	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.035	-0.010	39.123	0.267	0.267	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.063	0.012	41.649	0.019	0.019	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.012	0.025	43.599	0.085	0.085	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.038	0.032	39.966	0.059	0.059	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.010	-0.008	41.982	0.088	0.088	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.016	-0.001	43.923	0.152	0.152	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.803	0.882	40.394	7.792	7.792	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.006	0.002	40.762	0.041	0.041	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.003	-0.013	43.450	0.083	0.083	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.027	-0.025	47.041	0.162	0.162	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.009	0.006	43.540	0.087	0.087	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.006	0.004	45.427	0.021	0.021	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.000	0.007	47.052	0.094	0.094	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.000	0.000	47.251	0.116	0.116	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.008	-0.004	42.959	0.051	0.051	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.021	-0.020	47.579	0.051	0.051	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.038	-0.025	50.296	0.135	0.135	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.049	-0.024	49.741	0.124	0.124	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.013	0.013	50.301	0.023	0.023	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.003	-0.012	46.099	-0.126	-0.126	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.002	0.000	44.280	-0.150	-0.150	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.001	0.004	45.433	-0.112	-0.112	0.000	0.000	0.000	0.000
68	A	68	GLN	0	0.015	-0.008	41.149	-0.151	-0.151	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.044	0.026	44.626	-0.109	-0.109	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.045	0.037	46.863	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.014	0.021	40.821	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.020	-0.020	42.766	-0.067	-0.067	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.023	0.008	43.790	-0.078	-0.078	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.009	-0.008	42.934	0.051	0.051	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.002	-0.005	38.366	-0.061	-0.061	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.044	0.024	41.390	-0.082	-0.082	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.000	-0.003	43.523	0.054	0.054	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.026	-0.003	40.069	0.046	0.046	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.057	0.016	37.983	-0.055	-0.055	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.007	0.022	40.510	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.035	-0.033	43.678	0.063	0.063	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.029	-0.008	37.934	0.023	0.023	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.010	-0.026	40.080	-0.161	-0.161	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.038	-0.013	41.035	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.049	-0.026	42.070	0.130	0.130	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.094	-0.043	38.185	-0.055	-0.055	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.039	0.019	39.024	-0.218	-0.218	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.011	-0.002	39.153	-0.049	-0.049	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.049	-0.010	34.194	-0.223	-0.223	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.033	0.014	31.444	0.021	0.021	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.056	0.016	33.485	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	92	CYS	0	0.000	-0.007	28.224	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.793	-0.873	30.520	-10.400	-10.400	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.013	0.010	31.796	0.090	0.090	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.012	0.014	30.808	0.130	0.130	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.027	-0.025	28.633	0.044	0.044	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.012	-0.022	31.501	-0.199	-0.199	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.030	0.010	34.730	0.200	0.200	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.007	-0.001	31.314	0.134	0.134	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.036	-0.012	31.602	0.068	0.068	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.696	-0.809	34.085	-7.954	-7.954	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.034	0.025	37.152	0.229	0.229	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.015	0.001	32.862	0.127	0.127	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.002	-0.013	36.257	0.085	0.085	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.020	0.022	38.465	0.195	0.195	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.007	-0.002	37.389	0.170	0.170	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.019	-0.012	36.574	0.100	0.100	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.030	-0.024	39.725	0.162	0.162	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.006	0.007	43.274	0.167	0.167	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.033	0.004	38.893	0.129	0.129	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.006	0.005	42.989	0.078	0.078	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.084	-0.041	44.385	0.174	0.174	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.043	-0.033	45.775	0.138	0.138	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.004	-0.007	46.851	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.009	-0.001	42.136	-0.028	-0.028	0.000	0.000	0.000	0.000
116	A	116	GLY	0	0.032	0.021	45.229	0.113	0.113	0.000	0.000	0.000	0.000
117	A	117	GLN	0	-0.026	-0.022	44.578	-0.150	-0.150	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.024	0.010	38.290	0.013	0.013	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.016	0.007	41.048	-0.231	-0.231	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.057	0.016	31.340	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.007	0.023	36.167	-0.251	-0.251	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.023	0.009	37.033	-0.129	-0.129	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.014	-0.015	34.496	-0.070	-0.070	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.029	0.026	33.787	-0.114	-0.114	0.000	0.000	0.000	0.000
125	A	125	GLN	0	0.034	0.022	34.731	-0.064	-0.064	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.031	-0.007	37.556	0.113	0.113	0.000	0.000	0.000	0.000
127	A	127	THR	0	-0.031	-0.023	31.208	-0.103	-0.103	0.000	0.000	0.000	0.000
128	A	128	GLN	0	-0.033	-0.016	34.608	0.055	0.055	0.000	0.000	0.000	0.000
129	A	129	MET	0	-0.018	0.006	36.065	0.049	0.049	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.018	0.027	34.623	0.126	0.126	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.019	0.018	34.407	0.016	0.016	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.019	-0.020	35.032	-0.064	-0.064	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.036	-0.025	38.292	0.124	0.124	0.000	0.000	0.000	0.000
134	A	134	VAL	0	0.001	-0.005	34.126	0.111	0.111	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.020	-0.014	36.155	0.056	0.056	0.000	0.000	0.000	0.000
136	A	136	GLN	0	-0.016	-0.019	37.586	0.091	0.091	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.021	-0.006	40.275	0.131	0.131	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.066	-0.039	35.995	0.054	0.054	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.066	-0.011	39.788	-0.085	-0.085	0.000	0.000	0.000	0.000
140	A	140	GLY	-1	-0.947	-0.957	41.098	-6.987	-6.987	0.000	0.000	0.000	0.000

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