FMO DATABASE

FMODB ID: 7NJQK

Calculation Name: 2V1F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | sulfate ion | glycerol | hydroxide ion

Ligand 3-letter code: HEM | SO4 | GOL | OH

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2V1F

Chain ID: A

ChEMBL ID:

UniProt ID: P68082

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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1454473.688358
FMO2-HF: Nuclear repulsion	1396093.90119
FMO2-HF: Total energy	-58379.787168
FMO2-MP2: Total energy	-58554.039705

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:GLY)

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

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.
4.064	5.186	-0.008	-0.367	-0.748	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.924

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	0.011	-0.009	3.824	0.790	1.576	-0.011	-0.268	-0.508	-0.001
133	A	133	LYS	1	0.889	0.927	4.437	55.052	55.174	-0.001	-0.032	-0.089	0.000
137	A	137	LEU	0	-0.036	-0.011	3.670	-0.931	-0.717	0.004	-0.067	-0.151	0.000
4	A	4	ASP	-1	-0.819	-0.917	6.614	-28.519	-28.519	0.000	0.000	0.000	0.000
5	A	5	GLY	0	0.039	0.024	9.640	2.004	2.004	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.758	-0.845	6.520	-47.113	-47.113	0.000	0.000	0.000	0.000
7	A	7	TRP	0	0.064	0.015	4.864	3.823	3.823	0.000	0.000	0.000	0.000
8	A	8	GLN	0	-0.010	0.002	9.679	1.621	1.621	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.030	-0.034	12.606	0.776	0.776	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.012	-0.004	9.383	1.434	1.434	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.008	-0.008	12.745	1.734	1.734	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.020	0.001	15.139	1.743	1.743	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.029	-0.016	15.806	1.098	1.098	0.000	0.000	0.000	0.000
14	A	14	TRP	0	-0.017	-0.004	16.029	0.579	0.579	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.023	0.014	18.041	0.789	0.789	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.784	0.886	20.850	14.782	14.782	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.022	-0.005	19.351	0.616	0.616	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.825	-0.915	20.419	-14.384	-14.384	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.001	0.013	23.589	0.479	0.479	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.846	-0.934	25.965	-10.258	-10.258	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.025	0.040	22.977	-0.180	-0.180	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.007	0.005	25.784	-0.126	-0.126	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.042	0.022	28.762	0.079	0.079	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.018	0.004	23.055	-0.327	-0.327	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.027	0.008	24.343	-0.299	-0.299	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.050	-0.031	25.347	-0.061	-0.061	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.849	-0.928	26.769	-10.839	-10.839	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.028	-0.009	21.103	-0.067	-0.067	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.003	0.000	24.120	-0.121	-0.121	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.013	0.014	26.207	0.200	0.200	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.920	0.998	24.273	12.199	12.199	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.041	-0.020	22.424	-0.102	-0.102	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.006	-0.015	25.342	0.115	0.115	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.059	-0.055	28.942	0.161	0.161	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.016	0.006	27.352	0.210	0.210	0.000	0.000	0.000	0.000
36	A	36	HIS	1	0.835	0.929	23.997	12.054	12.054	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.100	0.068	28.309	-0.112	-0.112	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.829	-0.928	27.281	-10.975	-10.975	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.065	-0.062	24.976	-0.139	-0.139	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.005	0.003	27.746	-0.119	-0.119	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.904	-0.960	30.817	-8.662	-8.662	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.809	0.906	27.132	11.128	11.128	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.049	-0.023	25.558	-0.137	-0.137	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.818	-0.909	31.319	-8.678	-8.678	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.776	0.885	30.471	10.098	10.098	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.001	-0.024	29.330	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.894	0.978	34.391	8.914	8.914	0.000	0.000	0.000	0.000
48	A	48	HIS	0	-0.027	-0.017	36.540	0.116	0.116	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.059	-0.016	33.926	0.136	0.136	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.961	0.984	36.577	7.765	7.765	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.028	-0.019	38.432	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.798	-0.924	33.322	-9.516	-9.516	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.010	-0.009	35.966	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.812	-0.902	38.625	-7.742	-7.742	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.028	-0.018	32.892	-0.213	-0.213	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.864	0.936	32.026	9.347	9.347	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.015	0.015	35.519	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.016	0.012	34.671	0.124	0.124	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.790	-0.895	34.327	-8.797	-8.797	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.835	-0.920	33.594	-9.582	-9.582	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.028	0.025	29.797	-0.337	-0.337	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.898	0.947	29.457	8.584	8.584	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.888	0.956	29.178	8.805	8.805	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.018	0.001	25.561	0.040	0.040	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.051	0.018	25.145	-0.489	-0.489	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.020	-0.021	24.270	-0.542	-0.542	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.023	0.005	24.523	-0.433	-0.433	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.026	-0.012	20.583	-0.549	-0.549	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.018	0.013	19.554	-0.905	-0.905	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.023	-0.022	19.613	-0.654	-0.654	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.026	-0.014	19.562	-0.499	-0.499	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.001	0.008	13.379	-0.857	-0.857	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.057	0.014	15.082	-1.320	-1.320	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.030	-0.014	15.934	-0.575	-0.575	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.013	-0.009	11.568	-0.700	-0.700	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.012	-0.010	10.894	-2.176	-2.176	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.784	0.867	11.346	14.279	14.279	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.868	0.942	11.770	18.775	18.775	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.838	0.912	8.116	26.823	26.823	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.031	0.010	5.914	-4.066	-4.066	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.068	-0.016	6.963	1.488	1.488	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.012	-0.028	7.955	3.345	3.345	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.835	-0.924	11.797	-19.179	-19.179	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.020	-0.014	13.614	1.108	1.108	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.819	-0.915	14.977	-17.816	-17.816	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.013	0.000	11.148	0.917	0.917	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.961	1.000	15.260	15.935	15.935	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.015	0.010	17.383	0.683	0.683	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.011	0.025	16.530	0.745	0.745	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.049	0.019	16.250	0.592	0.592	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.050	0.011	18.343	0.867	0.867	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.046	-0.019	21.464	0.730	0.730	0.000	0.000	0.000	0.000
93	A	93	HIS	0	-0.035	-0.033	20.500	0.752	0.752	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.041	0.043	21.230	0.382	0.382	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.016	-0.021	23.036	0.600	0.600	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.903	0.956	26.128	10.661	10.661	0.000	0.000	0.000	0.000
97	A	97	HIS	0	-0.013	-0.017	24.450	0.670	0.670	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.891	0.969	25.970	10.839	10.839	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.062	0.028	21.573	0.176	0.176	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.071	0.047	21.934	-0.621	-0.621	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.035	0.020	14.790	-0.119	-0.119	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.850	0.917	17.923	14.391	14.391	0.000	0.000	0.000	0.000
103	A	103	TYR	0	0.018	-0.009	20.165	0.077	0.077	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.021	0.012	16.289	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.847	-0.901	16.023	-17.300	-17.300	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.032	0.004	17.046	-0.100	-0.100	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.001	0.008	17.906	0.304	0.304	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.019	-0.020	14.310	-0.750	-0.750	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.866	-0.936	16.226	-17.135	-17.135	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.064	-0.027	18.534	0.484	0.484	0.000	0.000	0.000	0.000
111	A	111	ILE	0	0.008	0.003	16.536	0.464	0.464	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.009	0.005	14.153	0.324	0.324	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.001	-0.003	18.231	0.279	0.279	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.012	-0.014	21.964	0.473	0.473	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.040	-0.007	17.311	0.400	0.400	0.000	0.000	0.000	0.000
116	A	116	HIS	0	0.016	-0.010	19.878	0.887	0.887	0.000	0.000	0.000	0.000
117	A	117	SER	0	-0.051	-0.031	23.296	0.563	0.563	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.809	0.910	25.409	11.554	11.554	0.000	0.000	0.000	0.000
119	A	119	HIS	1	0.802	0.898	23.233	12.882	12.882	0.000	0.000	0.000	0.000
120	A	120	PRO	0	0.063	0.054	24.883	-0.453	-0.453	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.009	-0.012	25.516	0.353	0.353	0.000	0.000	0.000	0.000
122	A	122	ASP	-1	-0.863	-0.916	24.638	-13.082	-13.082	0.000	0.000	0.000	0.000
123	A	123	PHE	0	-0.020	-0.025	16.333	-0.720	-0.720	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.044	0.034	19.938	0.171	0.171	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.040	0.005	17.954	-0.745	-0.745	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.830	-0.884	14.817	-19.462	-19.462	0.000	0.000	0.000	0.000
127	A	127	ALA	0	0.008	-0.009	13.624	-1.928	-1.928	0.000	0.000	0.000	0.000
128	A	128	GLN	0	0.056	0.031	14.126	-0.294	-0.294	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.012	0.021	12.230	-0.892	-0.892	0.000	0.000	0.000	0.000
130	A	130	ALA	0	-0.029	-0.015	9.338	-2.845	-2.845	0.000	0.000	0.000	0.000
131	A	131	MET	0	-0.001	-0.004	9.213	-2.700	-2.700	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.026	-0.024	10.940	0.306	0.306	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.031	-0.006	6.192	-3.788	-3.788	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.014	-0.011	7.902	0.664	0.664	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.935	-0.974	7.668	-28.973	-28.973	0.000	0.000	0.000	0.000
138	A	138	PHE	0	0.011	0.003	6.497	2.484	2.484	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.943	0.975	10.014	23.869	23.869	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.026	-0.013	7.883	2.924	2.924	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.801	-0.902	7.991	-33.348	-33.348	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.018	-0.012	10.586	2.191	2.191	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.007	0.002	13.042	1.450	1.450	0.000	0.000	0.000	0.000
144	A	144	ALA	0	-0.013	0.004	12.120	1.226	1.226	0.000	0.000	0.000	0.000
145	A	145	LYS	1	0.806	0.898	14.139	21.079	21.079	0.000	0.000	0.000	0.000
146	A	146	TYR	0	-0.052	-0.051	16.800	0.958	0.958	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.953	0.980	16.975	17.443	17.443	0.000	0.000	0.000	0.000
148	A	148	GLU	-1	-0.933	-0.963	16.912	-16.894	-16.894	0.000	0.000	0.000	0.000
149	A	149	LEU	0	-0.047	-0.022	20.108	0.704	0.704	0.000	0.000	0.000	0.000
150	A	150	GLY	0	-0.020	0.006	22.108	0.606	0.606	0.000	0.000	0.000	0.000
151	A	151	PHE	0	-0.066	-0.027	21.666	0.436	0.436	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.019	-0.021	21.669	-0.681	-0.681	0.000	0.000	0.000	0.000
153	A	153	GLY	-1	-0.881	-0.943	23.287	-11.578	-11.578	0.000	0.000	0.000	0.000

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