FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VZLN1

Calculation Name: 1JMX-B-Xray549

Preferred Name:

Target Type:

Ligand Name: heme c | 2-amino-3-(6,7-dioxo-6,7-dihydro-1h-indol-3-yl)-propionic acid | nickel (ii) ion

Ligand 3-letter code: HEC | TRQ | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JMX

Chain ID: B

ChEMBL ID:

UniProt ID: P0A182

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 345
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -5654546.780916
FMO2-HF: Nuclear repulsion 5517611.862803
FMO2-HF: Total energy -136934.918112
FMO2-MP2: Total energy -137333.666073


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:4:GLY)


Summations of interaction energy for fragment #1(B:4: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.
35.31241.2052.074-3.91-4.057-0.039
Interaction energy analysis for fragmet #1(B:4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.916
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   
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].
3B6ALA00.0730.0443.860-2.464-1.815-0.004-0.228-0.4170.000
32B35LYS10.7760.8572.56270.73571.4980.460-0.476-0.748-0.003
34B37CYS0-0.114-0.0502.499-40.407-37.3421.495-2.311-2.250-0.028
71B74THR0-0.077-0.0892.736-18.632-17.2720.124-0.889-0.594-0.008
72B76LYS10.9590.9964.66036.20136.257-0.001-0.006-0.0480.000
4B7LEU0-0.0250.0056.3332.0142.0140.0000.0000.0000.000
5B8LYS10.9220.9649.14128.35228.3520.0000.0000.0000.000
6B9ALA00.0750.02312.4690.8360.8360.0000.0000.0000.000
7B10GLY0-0.008-0.00815.2920.5630.5630.0000.0000.0000.000
8B11HIS0-0.047-0.01714.3120.5580.5580.0000.0000.0000.000
9B12GLU-1-0.799-0.90316.092-15.248-15.2480.0000.0000.0000.000
10B13TYR0-0.008-0.00410.778-1.310-1.3100.0000.0000.0000.000
11B14MET00.0190.02314.0541.2361.2360.0000.0000.0000.000
12B15ILE0-0.033-0.00411.461-1.820-1.8200.0000.0000.0000.000
13B16VAL00.0390.00513.4431.8261.8260.0000.0000.0000.000
14B17THR0-0.048-0.02013.551-1.477-1.4770.0000.0000.0000.000
15B18ASN0-0.016-0.03314.7671.0501.0500.0000.0000.0000.000
16B19TYR00.0290.01016.332-0.634-0.6340.0000.0000.0000.000
17B20PRO0-0.055-0.01615.7050.2470.2470.0000.0000.0000.000
18B21ASN00.0330.00814.4461.0211.0210.0000.0000.0000.000
19B22ASN0-0.0210.00111.295-1.834-1.8340.0000.0000.0000.000
20B23LEU00.0410.0199.1851.8321.8320.0000.0000.0000.000
21B24HIS0-0.030-0.0329.052-2.202-2.2020.0000.0000.0000.000
22B25VAL00.0110.0027.8761.4901.4900.0000.0000.0000.000
23B26VAL00.002-0.0119.848-0.871-0.8710.0000.0000.0000.000
24B27ASP-1-0.807-0.88312.172-20.415-20.4150.0000.0000.0000.000
25B28VAL00.0160.00213.5550.9130.9130.0000.0000.0000.000
26B29ALA00.0000.02416.8331.1351.1350.0000.0000.0000.000
27B30SER0-0.034-0.04315.3530.6710.6710.0000.0000.0000.000
28B31ASP-1-0.813-0.87417.346-14.185-14.1850.0000.0000.0000.000
29B32THR0-0.028-0.03213.861-0.021-0.0210.0000.0000.0000.000
30B33VAL00.0170.0009.188-0.465-0.4650.0000.0000.0000.000
31B34TYR0-0.032-0.0186.8620.4590.4590.0000.0000.0000.000
33B36SER00.0100.0075.4585.7585.7580.0000.0000.0000.000
35B38VAL00.0130.0096.8994.2164.2160.0000.0000.0000.000
36B39MET0-0.039-0.0029.291-1.637-1.6370.0000.0000.0000.000
37B40PRO00.0180.01111.9310.4620.4620.0000.0000.0000.000
38B41ASP-1-0.838-0.89214.250-16.140-16.1400.0000.0000.0000.000
39B42LYS10.8950.93717.82714.63014.6300.0000.0000.0000.000
40B43PHE00.0590.03717.3310.0580.0580.0000.0000.0000.000
41B44GLY00.0100.02619.4460.8040.8040.0000.0000.0000.000
42B45PRO0-0.050-0.02822.5470.1100.1100.0000.0000.0000.000
43B46GLY00.0810.04518.653-0.154-0.1540.0000.0000.0000.000
44B47THR0-0.0070.00818.356-0.692-0.6920.0000.0000.0000.000
45B48ALA00.0210.01716.070-0.179-0.1790.0000.0000.0000.000
46B49MET0-0.064-0.02917.7710.9970.9970.0000.0000.0000.000
47B50MET0-0.0150.01912.508-1.060-1.0600.0000.0000.0000.000
48B51ALA00.0540.02716.0051.4071.4070.0000.0000.0000.000
49B52PRO0-0.016-0.02117.484-0.559-0.5590.0000.0000.0000.000
50B53ASP-1-0.767-0.84114.163-21.426-21.4260.0000.0000.0000.000
51B54ASN0-0.068-0.02114.978-0.568-0.5680.0000.0000.0000.000
52B55ARG10.7920.8638.18931.44431.4440.0000.0000.0000.000
53B56THR0-0.027-0.04710.394-3.195-3.1950.0000.0000.0000.000
54B57ALA00.001-0.00211.7381.9481.9480.0000.0000.0000.000
55B58TYR00.0090.00113.576-0.699-0.6990.0000.0000.0000.000
56B59VAL0-0.032-0.03314.4010.4320.4320.0000.0000.0000.000
57B60LEU0-0.0080.02317.4180.1690.1690.0000.0000.0000.000
58B61ASN0-0.013-0.03116.7710.4140.4140.0000.0000.0000.000
59B62ASN00.005-0.00820.1810.5590.5590.0000.0000.0000.000
60B63HIS0-0.0090.00121.7300.9610.9610.0000.0000.0000.000
61B64TYR0-0.028-0.03324.2450.5650.5650.0000.0000.0000.000
62B65GLY00.0200.01924.7650.4760.4760.0000.0000.0000.000
63B66ASP-1-0.777-0.83920.928-13.547-13.5470.0000.0000.0000.000
64B67ILE0-0.016-0.01219.486-0.156-0.1560.0000.0000.0000.000
65B68TYR00.013-0.02814.9860.0780.0780.0000.0000.0000.000
66B69GLY00.0190.01514.2450.5520.5520.0000.0000.0000.000
67B70ILE0-0.020-0.0128.079-1.242-1.2420.0000.0000.0000.000
68B71ASP-1-0.735-0.8197.572-38.450-38.4500.0000.0000.0000.000
69B72LEU00.0580.0136.241-7.344-7.3440.0000.0000.0000.000
70B73ASP-1-0.770-0.8485.397-41.709-41.7090.0000.0000.0000.000
73B77ASN00.0660.0237.3541.9411.9410.0000.0000.0000.000
74B78THR0-0.045-0.03210.3930.4770.4770.0000.0000.0000.000
75B79PHE00.0110.00512.8191.3061.3060.0000.0000.0000.000
76B80HIS0-0.059-0.05315.892-1.295-1.2950.0000.0000.0000.000
77B81ALA00.0440.04718.4660.5690.5690.0000.0000.0000.000
78B82ASN0-0.015-0.02222.1500.4010.4010.0000.0000.0000.000
79B83LEU0-0.017-0.01824.6440.4270.4270.0000.0000.0000.000
80B84SER0-0.050-0.02327.6000.6240.6240.0000.0000.0000.000
81B85SER0-0.0160.00429.0240.2270.2270.0000.0000.0000.000
82B86VAL0-0.0130.00630.6040.1960.1960.0000.0000.0000.000
83B87PRO00.0380.00334.450-0.043-0.0430.0000.0000.0000.000
84B88GLY00.0240.01435.7100.2280.2280.0000.0000.0000.000
85B89GLU-1-0.832-0.90935.227-8.363-8.3630.0000.0000.0000.000
86B90VAL0-0.006-0.00330.914-0.273-0.2730.0000.0000.0000.000
87B91GLY00.003-0.00331.1310.2870.2870.0000.0000.0000.000
88B92ARG10.8590.91927.23610.77010.7700.0000.0000.0000.000
89B93SER00.0210.03026.6030.3390.3390.0000.0000.0000.000
90B94MET0-0.005-0.01127.985-0.316-0.3160.0000.0000.0000.000
91B95TYR00.023-0.02125.3250.3530.3530.0000.0000.0000.000
92B96SER0-0.0190.01126.926-0.096-0.0960.0000.0000.0000.000
93B97PHE00.015-0.01619.9240.1180.1180.0000.0000.0000.000
94B98ALA0-0.016-0.00624.1710.0530.0530.0000.0000.0000.000
95B99ILE00.0240.02118.727-0.107-0.1070.0000.0000.0000.000
96B100SER0-0.024-0.03022.9510.2270.2270.0000.0000.0000.000
97B101PRO00.0290.00123.417-0.603-0.6030.0000.0000.0000.000
98B102ASP-1-0.798-0.86924.027-12.395-12.3950.0000.0000.0000.000
99B103GLY0-0.010-0.00120.407-0.397-0.3970.0000.0000.0000.000
100B104LYS10.8700.94020.47711.40611.4060.0000.0000.0000.000
101B105GLU-1-0.764-0.83723.050-10.654-10.6540.0000.0000.0000.000
102B106VAL00.0060.01220.418-0.323-0.3230.0000.0000.0000.000
103B107TYR0-0.046-0.05423.7250.4550.4550.0000.0000.0000.000
104B108ALA00.0490.00825.638-0.351-0.3510.0000.0000.0000.000
105B109THR0-0.060-0.03327.6430.4270.4270.0000.0000.0000.000
106B110VAL00.0020.01529.370-0.264-0.2640.0000.0000.0000.000
107B111ASN00.000-0.01331.7380.5770.5770.0000.0000.0000.000
108B112PRO00.0120.01433.850-0.199-0.1990.0000.0000.0000.000
109B113THR0-0.041-0.02335.2830.3770.3770.0000.0000.0000.000
110B114GLN00.0290.01736.612-0.079-0.0790.0000.0000.0000.000
111B115ARG10.9050.95334.5359.1819.1810.0000.0000.0000.000
112B116LEU00.0040.00439.328-0.041-0.0410.0000.0000.0000.000
113B117ASN0-0.005-0.00442.342-0.122-0.1220.0000.0000.0000.000
114B118ASP-1-0.804-0.87944.072-6.766-6.7660.0000.0000.0000.000
115B119HIS10.8450.91344.7106.9816.9810.0000.0000.0000.000
116B120TYR00.016-0.00638.172-0.237-0.2370.0000.0000.0000.000
117B121VAL00.0100.00141.5730.2140.2140.0000.0000.0000.000
118B122VAL0-0.022-0.00739.036-0.205-0.2050.0000.0000.0000.000
119B123LYS10.8430.92238.7528.1078.1070.0000.0000.0000.000
120B124PRO00.014-0.00839.626-0.112-0.1120.0000.0000.0000.000
121B125PRO0-0.013-0.00136.051-0.120-0.1200.0000.0000.0000.000
122B126ARG10.8080.89232.9049.6209.6200.0000.0000.0000.000
123B127LEU0-0.016-0.01030.407-0.274-0.2740.0000.0000.0000.000
124B128GLU-1-0.788-0.89529.285-10.228-10.2280.0000.0000.0000.000
125B129VAL0-0.021-0.01827.945-0.293-0.2930.0000.0000.0000.000
126B130PHE00.0210.01223.9020.1810.1810.0000.0000.0000.000
127B131SER0-0.008-0.01124.351-0.250-0.2500.0000.0000.0000.000
128B132THR0-0.018-0.04218.836-0.132-0.1320.0000.0000.0000.000
129B133ALA0-0.023-0.01419.044-0.884-0.8840.0000.0000.0000.000
130B134ASP-1-0.862-0.91320.820-12.995-12.9950.0000.0000.0000.000
131B135GLY0-0.016-0.00117.630-0.024-0.0240.0000.0000.0000.000
132B136LEU0-0.063-0.04514.527-0.091-0.0910.0000.0000.0000.000
133B137GLU-1-0.888-0.92718.599-13.828-13.8280.0000.0000.0000.000
134B138ALA0-0.0340.00421.6260.8490.8490.0000.0000.0000.000
135B139LYS10.9540.95023.36811.58311.5830.0000.0000.0000.000
136B140PRO0-0.043-0.02527.024-0.108-0.1080.0000.0000.0000.000
137B141VAL00.0220.02027.7850.3040.3040.0000.0000.0000.000
138B142ARG10.7830.86430.38010.46910.4690.0000.0000.0000.000
139B143THR0-0.023-0.01331.840-0.211-0.2110.0000.0000.0000.000
140B144PHE00.0360.03334.0590.2370.2370.0000.0000.0000.000
141B145PRO00.0130.01836.495-0.190-0.1900.0000.0000.0000.000
142B146MET0-0.003-0.00534.112-0.007-0.0070.0000.0000.0000.000
143B147PRO00.0160.02038.0340.1390.1390.0000.0000.0000.000
144B148ARG10.9220.93738.2827.7987.7980.0000.0000.0000.000
145B149GLN00.0230.00437.5610.1830.1830.0000.0000.0000.000
146B150VAL00.0270.02633.1140.0160.0160.0000.0000.0000.000
147B151TYR00.0170.00531.705-0.107-0.1070.0000.0000.0000.000
148B152LEU0-0.0290.01627.335-0.225-0.2250.0000.0000.0000.000
149B153MET0-0.038-0.00228.2180.5420.5420.0000.0000.0000.000
150B154ARG10.8950.94825.40411.71411.7140.0000.0000.0000.000
151B155ALA00.0380.02926.7090.4520.4520.0000.0000.0000.000
152B156ALA0-0.046-0.02028.111-0.222-0.2220.0000.0000.0000.000
153B157ASP-1-0.787-0.90028.513-11.182-11.1820.0000.0000.0000.000
154B158ASP-1-0.840-0.89730.317-9.174-9.1740.0000.0000.0000.000
155B159GLY0-0.0050.00230.4210.1460.1460.0000.0000.0000.000
156B160SER0-0.091-0.04631.5050.1370.1370.0000.0000.0000.000
157B161LEU0-0.023-0.01429.010-0.350-0.3500.0000.0000.0000.000
158B162TYR00.0250.00831.6780.3980.3980.0000.0000.0000.000
159B163VAL0-0.012-0.01531.701-0.387-0.3870.0000.0000.0000.000
160B164ALA00.0300.02133.1140.3400.3400.0000.0000.0000.000
161B165GLY00.0420.00634.775-0.190-0.1900.0000.0000.0000.000
162B166PRO0-0.051-0.01037.5530.0760.0760.0000.0000.0000.000
163B167ASP-1-0.754-0.85140.755-7.091-7.0910.0000.0000.0000.000
164B168ILE00.0070.01235.977-0.242-0.2420.0000.0000.0000.000
165B169TYR00.0260.00137.3550.2380.2380.0000.0000.0000.000
166B170LYS10.8440.92236.3478.3888.3880.0000.0000.0000.000
167B171MET0-0.013-0.01734.7520.1900.1900.0000.0000.0000.000
168B172ASP-1-0.759-0.83635.076-8.791-8.7910.0000.0000.0000.000
169B173VAL00.0130.00030.8480.1020.1020.0000.0000.0000.000
170B174LYS10.8590.93030.47710.02510.0250.0000.0000.0000.000
171B175THR0-0.007-0.04135.7550.1240.1240.0000.0000.0000.000
172B176GLY00.0100.01337.2300.1470.1470.0000.0000.0000.000
173B177LYS10.9110.96138.2377.6067.6060.0000.0000.0000.000
174B178TYR0-0.004-0.00638.484-0.103-0.1030.0000.0000.0000.000
175B179THR00.003-0.00740.2660.2350.2350.0000.0000.0000.000
176B180VAL0-0.017-0.00940.930-0.213-0.2130.0000.0000.0000.000
177B181ALA0-0.035-0.01439.0860.1030.1030.0000.0000.0000.000
178B182LEU00.018-0.00739.0490.0360.0360.0000.0000.0000.000
179B183PRO0-0.0270.00441.510-0.124-0.1240.0000.0000.0000.000
180B184LEU0-0.015-0.02539.009-0.045-0.0450.0000.0000.0000.000
181B185ARG10.9170.94842.4297.5537.5530.0000.0000.0000.000
182B186ASN0-0.043-0.03845.6930.3060.3060.0000.0000.0000.000
183B187TRP0-0.005-0.00144.4200.1110.1110.0000.0000.0000.000
184B188ASN0-0.010-0.00248.1760.1260.1260.0000.0000.0000.000
185B189ARG10.8070.89046.5546.8796.8790.0000.0000.0000.000
186B190LYS11.0210.99551.9595.5975.5970.0000.0000.0000.000
187B191GLY00.000-0.00355.2130.0200.0200.0000.0000.0000.000
188B192TYR0-0.028-0.02349.091-0.041-0.0410.0000.0000.0000.000
189B193SER00.0220.02047.8810.0900.0900.0000.0000.0000.000
190B194ALA00.0230.01046.648-0.059-0.0590.0000.0000.0000.000
191B195PRO0-0.052-0.01842.5560.0230.0230.0000.0000.0000.000
192B196ASP-1-0.899-0.93740.578-7.971-7.9710.0000.0000.0000.000
193B197VAL0-0.032-0.04336.099-0.115-0.1150.0000.0000.0000.000
194B198LEU00.0280.03733.074-0.109-0.1090.0000.0000.0000.000
195B199TYR00.0470.00029.637-0.183-0.1830.0000.0000.0000.000
196B200PHE00.0280.00427.6720.0330.0330.0000.0000.0000.000
197B201TRP00.0110.00724.804-0.357-0.3570.0000.0000.0000.000
198B202PRO00.0220.01223.6120.3200.3200.0000.0000.0000.000
199B203HIS10.8930.94423.98111.37511.3750.0000.0000.0000.000
200B204GLN0-0.002-0.01219.788-0.014-0.0140.0000.0000.0000.000
201B205SER00.0030.00823.150-0.344-0.3440.0000.0000.0000.000
202B206PRO00.0250.00224.2500.0670.0670.0000.0000.0000.000
203B207ARG10.8780.95326.1189.7959.7950.0000.0000.0000.000
204B208HIS0-0.048-0.03626.6500.2150.2150.0000.0000.0000.000
205B209GLU-1-0.772-0.86728.499-9.109-9.1090.0000.0000.0000.000
206B210PHE0-0.022-0.01229.309-0.449-0.4490.0000.0000.0000.000
207B211SER0-0.033-0.02830.3850.2480.2480.0000.0000.0000.000
208B212MET0-0.048-0.01931.086-0.398-0.3980.0000.0000.0000.000
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210B214TYR0-0.066-0.04835.904-0.099-0.0990.0000.0000.0000.000
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